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Selected Grantee Publications

2024 Publications



Macrophages Derived From Human Induced Pluripotent Stem Cells (iPSCs) Serve as a High-Fidelity Cellular Model for Investigating HIV-1, Dengue, and Influenza Viruses

Yang et al., Journal of Virology. 2024.

Macrophages can be weaponized by viruses to host viral reproduction and support long-term persistence. The most common way of studying these cells is by isolating their precursors from donor blood and differentiating the isolated cells into macrophages. This method is costly and technically challenging, and it produces varying results. In this study, researchers confirmed that macrophages derived from iPSC cell lines—a model that is inexpensive, consistent, and modifiable by genome editing—are a suitable model for experiments involving HIV and other viruses. Macrophages derived from iPSCs are as susceptible to infection as macrophages derived from blood, with similar infection kinetics and phenotypes. This new model offers researchers an unlimited source of cells for studying viral biology. Supported by ORIP (R01OD034046, S10OD021601), NIAID, NIDA, NIGMS, and NHLBI.



SHIV-C109p5 NHP Induces Rapid Disease Progression in Elderly Macaques With Extensive GI Viral Replication

Bose et al., Journal of Virology. 2024.

Researchers are interested in developing animal models infected with simian–human immunodeficiency virus (SHIV) to better understand prevention of HIV acquisition. Researchers generated pathogenic SHIV clade C transmitted/founder stock by in vivo passage using geriatric rhesus macaques of both sexes. They reported that the infection resulted in high sustained viral loads and induced rapid pathology and wasting, necessitating euthanasia between 3 and 12 weeks post-infection. The extensive viral replication in gut and lymphoid tissues indicated a fit viral stock. This work provides a new nonhuman primate model for HIV pathogenicity and cure studies. Supported by ORIP (R24OD010947) and NIDDK.



Potent Antibody-Dependent Cellular Cytotoxicity of a V2-Specific Antibody Is Not Sufficient for Protection of Macaques Against SIV Challenge

Grunst et al., PLOS Pathogens. 2024.

Antibody-dependent cellular cytotoxicity (ADCC) has been correlated with decreased risk of HIV acquisition. Researchers tested the ability of PGT145, an antibody that neutralizes genetically diverse HIV-1 isolates, to protect rhesus macaques against simian immunodeficiency virus (SIV) via ADCC activity. They found that a single amino acid substitution in the V2 core epitope of the SIV envelope increases PGT145 binding and confers sensitivity to neutralization. Peak and chronic phase viral loads were lower, and time to peak viremia was delayed. They concluded that ADCC is insufficient for protection by this antibody, but increasing the affinity of antibody binding could confer partial protection. Supported by ORIP (P51OD011106), NIAID, and NCI.



Consistent Survival in Consecutive Cases of Life-Supporting Porcine Kidney Xenotransplantation Using 10GE Source Pigs

Eiseson et al., Nature Communications. 2024.

Xenotransplantation offers potential for addressing organ donor shortages, and the U.S. Food and Drug Administration recently issued guidance on a regulatory path forward. Researchers have performed studies in this area, but concerns have been expressed about safe clinical translation of their results (e.g., survival, preclinical procurement, immunosuppression, clinical standards of care). In this study, the authors report consistent survival in consecutive cases of kidney xenotransplantation from pigs (male and female) to baboons (male and female). The authors propose that their findings serve as proof of concept for prevention of xenograft rejection in recipients of genetically modified porcine kidneys. This work offers insights for immunosuppression regimens for first-in-human clinical trials. Supported by ORIP (P40OD024628).



Identifying Potential Dietary Treatments for Inherited Metabolic Disorders Using Drosophila Nutrigenomics

Martelli et al., Cell Reports. 2024.

Inherited metabolic disorders are known to cause severe neurological impairment and child mortality and can sometimes respond to dietary treatment; however, a suitable paradigm for testing diets is lacking for developing effective dietary treatment. In this study, researchers found that 26 of 35 Drosophila amino acid disorder models screened for disease–diet interactions displayed diet-altered development and/or survival. Among these models, researchers showed that dietary cysteine depletion normalizes metabolic profile and rescues development, neurophysiology, behavior, and life span in a model for isolated sulfite oxidase deficiency. These findings demonstrate the value of using Drosophila in studying diet-sensitive metabolic disorders and developing potential dietary therapies. Supported by ORIP (R24OD031447) and NHGRI.



Cdk8/CDK19 Promotes Mitochondrial Fission Through Drp1 Phosphorylation and Can Phenotypically Suppress Pink1 Deficiency in Drosophila

Liao et al., Nature Communications. 2024.

Pink1 is a mitochondrial kinase implicated in Parkinson’s disease and is conserved among humans, rodents, and flies. In this study, researchers found that Cdk8 in Drosophila (i.e., the orthologue of vertebrate CDK8 and CDK19) promotes the phosphorylation of Drp1 (i.e., a protein required for mitochondrial fission) at the same residue as Pink1. Cdk8 is expressed in both the cytoplasm and nucleus, and neuronal loss of Cdk8 reduces fly life span and causes bang sensitivity and elongated mitochondria in both muscles and neurons. Overexpression of Cdk8 suppresses elevated levels of reactive oxygen species, mitochondrial dysmorphology, and behavioral defects in flies with low levels of Pink1. These findings suggest that Cdk8 regulates Drp1-mediated mitochondrial fission in a similar manner as Pink1 and may contribute to the development of Parkinson’s disease. Supported by ORIP (R24OD022005, R24OD031447, P40OD018537, P40OD010949), NICHD, and NINDS.



Obesity Causes Mitochondrial Fragmentation and Dysfunction in White Adipocytes Due to RalA Activation

Xia et al., Nature Metabolism. 2024.

This study presents a molecular mechanism for mitochondrial dysfunction as a characteristic trait of obesity. Chronic activation of the small GTPase RalA in inguinal white adipocytes (iWAT), in male mice fed a high-fat diet (HFD) represses energy expenditure by shifting mitochondrial dynamics toward excessive fission, contributing to weight gain and metabolic dysfunction. Targeted deletion of RalA in iWAT attenuated HFD-induced obesity due to increased energy expenditure and mitochondrial oxidative phosphorylation. Mechanistically, RalA dephosphorylates inhibitory Serine637 on fission protein Drp1, leading to excessive fission in adipocytes and mitochondrial fragmentation. Expression of a human homolog of Drp1—DNM1L—in adipose tissue is positively correlated with obesity and insulin resistance. These findings open avenues to investigate RalA-Drp1 axis in energy homeostasis. Supported by ORIP (S10OD023527), NCI, NHLBI, and NIDDK.



Proof-of-Concept Studies With a Computationally Designed Mpro Inhibitor as a Synergistic Combination Regimen Alternative to Paxlovid

Papini et al., PNAS. 2024.

As the spread and evolution of SARS-CoV-2 continues, it is important to continue to not only work to prevent transmission but to develop improved antiviral treatments as well. The SARS-CoV-2 main protease (Mpro) has been established as a prominent druggable target. In the current study, investigators evaluate Mpro61 as a lead compound, utilizing structural studies, in vitro pharmacological profiling to examine possible off-target effects and toxicity, cellular studies, and testing in a male and female mouse model for SARS-CoV-2 infection. Results indicate favorable pharmacological properties, efficacy, and drug synergy, as well as complete recovery from subsequent challenge by SARS-CoV-2, establishing Mpro61 as a promising potential preclinical candidate. Supported by ORIP (R24OD026440, S10OD021527), NIAID, and NIGMS.



Murine MHC-Deficient Nonobese Diabetic Mice Carrying Human HLA-DQ8 Develop Severe Myocarditis and Myositis in Response to Anti-PD-1 Immune Checkpoint Inhibitor Cancer Therapy

Racine et al., Journal of Immunology. 2024.

Myocarditis has emerged as a relatively rare but often lethal autoimmune complication of checkpoint inhibitor (ICI) cancer therapy, and significant mortality is associated with this phenomenon. Investigators developed a new mouse model system that spontaneously develops myocarditis. These mice are highly susceptible to myocarditis and acute heart failure following anti-PD-1 ICI-induced treatment. Additionally, the treatment accelerates skeletal muscle myositis. The team performed characterization of cardiac and skeletal muscle T cells using histology, flow cytometry, adoptive transfers, and RNA sequencing analyses. This study sheds light on underlying immunological mechanisms in ICI myocarditis and provides the basis for further detailed analyses of diagnostic and therapeutic strategies. Supported by ORIP (U54OD020351, U54OD030187), NCI, NIA, NIDDK, and NIGMS.



Potent HPIV3-Neutralizing IGHV5-51 Antibodies Identified From Multiple Individuals Show L Chain and CDRH3 Promiscuity

Abu-Shmais et al., Journal of Immunology. 2024.

Human parainfluenza virus 3 fusion glycoprotein (HPIV3 F), responsible for facilitating viral entry into host cells, is a major target of neutralizing antibodies that inhibit infection. More work is needed to understand these dynamics. Researchers characterized the genetic signatures, epitope specificity, neutralization potential, and publicness of HPIV3-specific antibodies identified across multiple individuals. From this work, they identified 12 potently neutralizing antibodies targeting three nonoverlapping epitopes on HPIV3 F. Six of the antibodies used immunoglobulin heavy variable gene, IGHV 5-51. These antibodies used different L chain variable genes (VL) and diverse H chain CDR 3 (CDRH3) sequences. These findings help elucidate the genetic and functional characteristics of HPIV3-neutralizing antibodies and indicate the existence of a reproducible H chain variable–dependent antibody response associated with VL and CDRH3 promiscuity. Supported by ORIP (K01OD036063), NCATS, NCI, NEI, NIAID, and NIDDK.



Ultrasoft Platelet-Like Particles Stop Bleeding in Rodent and Porcine Models of Trauma

Nellenbach et al., Science Translational Medicine. 2024.

Platelet transfusions are the current standard of care to control bleeding in patients following acute trauma, but their use is limited by short shelf life and limited supply. Immunogenicity and contamination risks also are a concern. Using ultrasoft and highly deformable nanogels coupled to fibrin-specific antibody fragments, researchers developed synthetic platelet-like particles (PLPs) as an alternative for immediate treatment of uncontrolled bleeding. They report that PLPs reduced bleeding and facilitated healing of injured tissue in mice, rat, and swine models (sex not specified) for traumatic injury. These findings can inform further translational studies of synthetic PLPs for the treatment of uncontrolled bleeding in a trauma setting. Supported by ORIP (T32OD011130) and NHLBI.



CDK4/6 Inhibition Sensitizes Intracranial Tumors to PD-1 Blockade in Preclinical Models of Brain Metastasis

Nayyer et al., Clinical Cancer Research. 2024.

Brain metastases are associated with high morbidity and are often resistant to immune checkpoint inhibitors. In this study, investigators evaluated the efficacy of combining CDKi (abemaciclib) and anti–PD-1 therapy (“combination therapy”) in mouse models for brain metastases, elucidated how combination therapy remodeled the tumor–immune microenvironment (TIME) and T-cell receptor (TCR) repertoires, and investigated the effects of CDKi on T-cell development and maintenance in NOD-scid Il2rgnull (NSG) mice engrafted with human immune systems (“humanized mice”). Results offer a strong rationale for the clinical evaluation of combination CDKi and PD-1 blockade in patients with brain metastases. Supported by ORIP (R24OD026440), NCI, and NIAID.



De Novo Variants in FRYL Are Associated With Developmental Delay, Intellectual Disability, and Dysmorphic Features

Pan et al., The American Journal of Human Genetics. 2024.

FRY-like transcription coactivator (FRYL) belongs to a Furry protein family that is evolutionarily conserved from yeast to humans, and its functions in mammals are largely unknown. Investigators report 13 individuals who have de novo heterozygous variants in FRYL and one individual with a heterozygous FRYL variant that is not confirmed to be de novo. The individuals present with developmental delay; intellectual disability; dysmorphic features; and other congenital anomalies in cardiovascular, skeletal, gastrointestinal, renal, and urogenital systems. Using fruit flies, investigators provide evidence that haploinsufficiency in FRYL likely underlies a disorder in humans with developmental and neurological symptoms. Supported by ORIP (U54OD030165), NHLBI, NICHD, and NCATS.



Epigenetic MLH1 Silencing Concurs With Mismatch Repair Deficiency in Sporadic, Naturally Occurring Colorectal Cancer in Rhesus Macaques

Deycmar et al., Journal of Translational Medicine. 2024.

Rhesus macaques serve as a useful model for colorectal cancer (CRC) in humans, but more data are needed to understand the molecular pathogenesis of these cancers. Using male and female rhesus macaques, researchers investigated mismatch repair status, microsatellite instability, genetic mutations, transcriptional differences, and epigenetic alterations associated with CRC. Their data indicate that epigenetic silencing suppresses MLH1 transcription, induces the loss of MLH1 protein, abrogates mismatch repair, and drives genomic instability in naturally occurring CRC in rhesus macaques. This work provides a uniquely informative model for human CRC. Supported by ORIP (P51OD011092, R24OD010947, R24OD021324, P40OD012217, U42OD010426, T35OD010946, T32OD010957), NCATS, and NCI.



Intestinal Epithelial Adaptations to Vertical Sleeve Gastrectomy Defined at Single-Cell Resolution

Koch-Laskowski et al., Genomics. 2024.

Perturbations in the intestinal epithelium have been linked to the pathogenesis of metabolic disease. Bariatric procedures, such as vertical sleeve gastrectomy (VSG), cause gut adaptations that induce robust metabolic improvements. Using a male mouse model, the authors assessed the effects of VSG on different cell lineages of the small intestinal epithelium. They show that Paneth cells display increased expression of the gut peptide Reg3g after VSG. Additionally, VSG restores pathways pertaining to mitochondrial respiration and cellular metabolism, especially within crypt-based cells. Overall, this work demonstrates how adaptations among specific cell types can affect gut epithelial homeostasis; these findings can help researchers develop targeted, less invasive treatment strategies for metabolic disease. Supported by ORIP (F30OD031914), NCI, and NIDDK.



Pathogenesis and Virulence of Coronavirus Disease: Comparative Pathology of Animal Models for COVID-19

Kirk et al., Virulence. 2024.

Researchers have used animal models that can replicate clinical and pathologic features of severe human coronavirus infections to develop novel vaccines and therapeutics in humans. The purpose of this review is to describe important animal models for COVID-19, with an emphasis on comparative pathology. The highlighted species included mice, ferrets, hamsters, and nonhuman primates. Knowledge gained from studying these animal models can help inform appropriate model selection for disease modeling, as well as for vaccine and therapeutic developments. Supported by ORIP (T32OD010993) and NIAID.



Pigs in Transplantation Research and Their Potential as Sources of Organs in Clinical Xenotransplantation

Raza et al., Comparative Medicine. 2024.

The pig has now gained importance as a potential source of organs for clinical xenotransplantation. When an organ from a wild-type (i.e., genetically unmodified) pig is transplanted into an immunosuppressed nonhuman primate, a vigorous host immune response causes hyperacute rejection (within minutes or hours). This response has been largely overcome by (1) extensive gene editing of the organ-source pig and (2) administration to the recipient of novel immunosuppressive therapy based on blockade of the CD40/CD154 T-cell costimulation pathway. The combination of gene editing and novel immunosuppressive therapy has extended life-supporting pig kidney graft survival to greater than 1 year and of pig heart survival to up to 9 months. This review briefly describes the techniques of gene editing, the potential risks of transfer of porcine endogenous retroviruses with the organ, and the need for breeding and housing of donor pigs under biosecure conditions. Supported by ORIP (P40OD024628) and NIAID.



TGF-β Blockade Drives a Transitional Effector Phenotype in T Cells Reversing SIV Latency and Decreasing SIV Reservoirs In Vivo

Kim et al., Nature Communications. 2024.

Interruption of antiretroviral therapy leads to rapid rebound of viremia due to the establishment of a persistent viral reservoir early after infection. Using a treatment regimen similar to the one tested in clinical trials, the authors show how galunisertib affects immune cell function, increases simian immunodeficiency virus (SIV) reactivation, and reduces the viral reservoir in female rhesus macaques. Their findings reveal a galunisertib-driven shift toward an effector phenotype in T and natural killer cells. Taken together, this work demonstrates that galunisertib, a clinical-stage TGF-β inhibitor, reverses SIV latency and decreases SIV reservoirs by driving T cells toward an effector phenotype, enhancing immune responses in vivo in the absence of toxicity. Supported by ORIP (R24OD010947), NIAID, and NCI.



Trade-Offs Shaping Transmission of Sylvatic Dengue and Zika Viruses in Monkey Hosts

Hanley et al., Nature Communications. 2024.

Mosquito-borne dengue (DENV) and Zika (ZIKV) viruses originated in Old World sylvatic (forest) cycles involving monkeys and canopy-living Aedes mosquitoes. Both viruses spilled over into human transmission and were translocated to the Americas, opening a path for spillback into neotropical sylvatic cycles. This article reports that the trade-offs that shape within-host dynamics and transmission of these viruses are lacking, hampering efforts to predict spillover and spillback. The data revealed evidence of an immunologically mediated trade‑off between duration and magnitude of virus replication, as higher-peak ZIKV titers are associated with shorter durations of viremia, and higher natural killer cell levels are associated with lower peak ZIKV titers and lower anti-DENV-2 antibody levels. Furthermore, patterns of transmission of each virus from a neotropical monkey suggest that ZIKV has greater potential than DENV-2 to establish a sylvatic transmission cycle in the Americas. Supported by ORIP (P40OD010938) and NIAID.



Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression

Hasselluhn et al., Cancer Discovery. 2024.

This study presents a key mechanism that prevents pancreatic ductal adenocarcinoma (PDAC) from undergoing neoangiogenesis, which affects its development, pathophysiology, metabolism, and treatment response. Using human and murine PDAC explants, which effectively retain the complex cellular interactions of native tumor tissues, and single-cell regulatory network analysis, the study identified a cascade of three paracrine pathways bridging between multiple cell types and acting sequentially, Hedgehog to WNT to VEGF, as a key suppressor of angiogenesis in KRAS-mutant PDAC cells. This study provides an experimental paradigm for dissecting higher-order cellular interactions in tissues and has implications for PDAC treatment strategies. Supported by ORIP (S10OD012351, S10OD021764), NCI, and NIDDK.



Induction of Durable Remission by Dual Immunotherapy in SHIV-Infected ART-Suppressed Macaques

Lim et al., Science. 2024.

The latent viral reservoir is established within the first few days of HIV infection and remains a barrier to a clinical cure. Researchers characterized the effects of a combined Anktiva (N-803) treatment with broadly neutralizing antibodies (bNAbs) using male and female rhesus macaques infected with simian–human immunodeficiency virus infection. Their data suggest that these agents synergize to enhance CD8+ T-cell function, particularly when multiple bNAbs are used. Taken together, this work indicates that immune-mediated control of viral rebound is not a prerequisite for sustained remission after discontinuation of antiretroviral therapy and that immune-mediated control of viral rebound is achievable, sufficient, and sustainable in this model. Supported by ORIP (P51OD011106, P40OD028116, R24OD011195) and NIAID.



Plasticity of Intragraft Alloreactive T Cell Clones in Human Gut Correlates With Transplant Outcomes

Fu et al., Journal of Experimental Medicine. 2024.

This study provides novel insights into tissue-resident memory T-cell (TRM) biology. The authors performed single-cell immune profiling to integrate clonotype, alloreactivity, and gene expression profiles of graft-repopulating recipient T cells in the intestinal mucosa after transplantation. They found that preexisting host-versus-graft (HvG)–reactive T cells were heterogenous and identified a trajectory from TRM to effector T/TRM profiles for rejection and dominant TRM profiles with tolerance in the quiescent allografts. Putative de novo HvG-reactive T cells showed a transcriptional profile skewed to cytotoxic effectors in rejecting grafts. Analysis of the inferred protein regulon network revealed upstream regulons for alloreactive T-cell tolerance and effector functions, opening opportunities for future translational studies to induce immune tolerance and overcome rejection. Supported by ORIP (S10OD020056) and NIAID.


 The Landscape of SETBP1 Gene Expression and Transcription Factor Activity Across Human Tissues

Whitlock et al., PLOS One. 2024.

The SET binding protein 1 (SETBP1) gene encodes a transcription factor (TF) involved in various cellular processes. Variants in SETBP1 can result in different diseases determined by the introduction (i.e., germline vs. somatic) and location of the variant. To better understand the tissue-specific mechanisms involving SETBP1, investigators analyzed publicly available RNA-sequencing data from the Genotype-Tissue Expression project. This study provides insight into the landscape of SETBP1 expression across 31 non-diseased human tissues and reveals tissue-specific expression and activity of SETBP1 and its targets. Supported by ORIP (U54OD030167) and NIGMS.


 Host Genetic Variation Impacts SARS-CoV-2 Vaccination Response in the Diversity Outbred Mouse Population

Cruz Cisneros et al., Vaccines. 2024.

The COVID-19 pandemic led to the rapid and worldwide development of highly effective vaccines against SARS-CoV-2. Although host genetic factors are known to affect vaccine efficacy for such respiratory pathogens as influenza and tuberculosis, the impact of host genetic variation on vaccine efficacy against COVID-19 is not well understood. Investigators used the diversity outbred mouse model to study the effects of genetic variation on vaccine efficiency. Data indicate that variations in vaccine response in mice are heritable, similar to that in human populations. Supported by ORIP (U42OD010924), NIAID, and NIGMS.


 The Monarch Initiative in 2024: An Analytic Platform Integrating Phenotypes, Genes and Diseases Across Species

Putman et al., Nucleic Acids Research. 2024.

The Monarch Initiative aims to bridge the gap between the genetic variations, environmental determinants, and phenotypic outcomes critical for translational research. The Monarch app provides researchers access to curated data sets with information on genes, phenotypes, and diseases across species and advanced analysis tools for such diverse applications as variant prioritization, deep phenotyping, and patient profile matching. Researchers describe upgrades to the app, including scalable cloud-based infrastructure, simplified data ingestion and knowledge graph integration systems, enhanced data mapping and integration standards, and a new user interface with novel search and graph navigation features. A customized plugin for OpenAI’s ChatGPT allows the use of large language models to interrogate knowledge in the Monarch graph and increase the reliability of the responses of Monarch’s analytic tools. These upgrades will enhance clinical diagnosis and the understanding of disease mechanisms. Supported by ORIP (R24OD011883), NLM, and NHGRI.


 Conduction-Dominated Cryomesh for Organism Vitrification

Guo et al., Advanced Science. 2024.

Vitrification-based cryopreservation via cryomesh is a promising approach for maintaining biodiversity, health care, and sustainable food production via long-term preservation of biological systems. Here, researchers conducted a series of experiments aimed at optimizing the cooling and rewarming rates of cryomesh to increase the viability of various cryopreserved biosystems. They found that vitrification was significantly improved by increasing thermal conductivity, reducing mesh wire diameter and pore size, and minimizing the nitrogen vapor barrier of the conduction-dominated cryomesh. Cooling rates increased twofold to tenfold in a variety of biosystems. The conduction-dominated cryomesh improved the cryopreservation outcomes of coral larvae, Drosophila embryos, and zebrafish embryos by vitrification. These findings suggest that the conduction-dominated cryomesh can improve vitrification in such biosystems for biorepositories, agriculture and aquaculture, and research. Supported by ORIP (R24OD028444, R21OD028758, R24OD034063, R21OD028214), NIDDK, and NIGMS.


 Newly Identified Roles for PIEZO1 Mechanosensor in Controlling Normal Megakaryocyte Development and in Primary Myelofibrosis

Abbonante et al., American Journal of Hematology. 2024.

Mechanisms through which mature megakaryocytes (Mks) and their progenitors sense the bone marrow extracellular matrix to promote lineage differentiation are only partially understood. The authors report that PIEZO1, a mechanosensitive cation channel, is expressed in mouse and human Mks, and activation of PIEZO1 increased the number of immature Mks in mice. Piezo1/2 knockout mice show an increase in Mk size and platelet count, both at basal state and upon marrow regeneration. Together, these data suggest that PIEZO1 places a brake on Mk maturation and platelet formation in physiology, and its upregulation might contribute to aggravating disease. Supported by ORIP (K01OD025290), NHGRI, NHLBI, and NCATS.


 The Gene Expression Profile and Cell of Origin of Canine Peripheral T-Cell Lymphoma

Owens et al., BMC Cancer. 2024.

Peripheral T-cell lymphoma (PTCL) refers to a heterogenous group of T-cell neoplasms with poor treatment responses and survival times. Canine PTCL clinically and immunophenotypically resembles the most common human subtype, PTCL-NOS (PTCL-not otherwise specified), and is a naturally occurring model for human PTCL. Gene expression profiling in human PTCL-NOS has helped characterize this ambiguous diagnosis into distinct subtypes, but similar gene expression profiling in canine PTCL is lacking. Canine CD4+ PTCL most closely resembles the GATA3-PTCL subtype of PTCL-NOS and may originate from an earlier stage of T-cell development than the more conventionally posited mature T-helper cell origin. Supported by ORIP (T32OD010437).


 Establishment of a Practical Sperm Cryopreservation Pathway for the Axolotl (Ambystoma mexicanum): A Community-Level Approach to Germplasm Repository Development

Coxe et al., Animals. 2024.

The axolotl (Ambystoma mexicanum) is an important biomedical research model for organ regeneration, but housing and maintaining live animals is expensive and risky as new transgenic lines are developed. The authors report an initial practical pathway for sperm cryopreservation to support germplasm repository development. They assembled a pathway through the investigation of axolotl sperm collection by stripping, refrigerated storage in various osmotic pressures, cryopreservation in various cryoprotectants, and in vitro fertilization using thawed sperm. This work is the first report of successful production of axolotl offspring with cryopreserved sperm and provides a general framework for pathway development to establish Ambystoma germplasm repositories for future research and applications. Supported by ORIP (R24OD010441, R24OD028443, P40OD019794).


 Cytomegalovirus Infection Facilitates the Costimulation of CD57+CD28- CD8 T Cells in HIV Infection and Atherosclerosis via the CD2–LFA-3 Axis

Winchester et al., Journal of Immunology. 2024.

People with HIV are at increased risk of developing atherosclerosis and other cardiovascular diseases, and HIV coinfection with cytomegalovirus (CMV) is associated with immune activation and inflammation. In this study, researchers explored the role of the CD2–LFA-3 axis in driving activation and proliferation of CD57+CD28- CD8 T cells using clinical samples from patients with or without HIV. They propose a model in which CMV infection is linked to enhanced CD2 expression on the T cells, enabling the activation via LFA-3 signals and potentially leading to cardiopathogenic interactions with vascular endothelial cells that express LFA-3. This work provides a potential therapeutic target in atherosclerosis development and progression, especially for people with HIV. Supported by ORIP (P51OD011132, U24OD011023) and NIAID.


 Validity of Xiphophorus Fish as Models for Human Disease

Schartl and Lu, Disease Models & Mechanisms. 2024.

Xiphophorus is the one of the oldest animal systems for studying melanoma. In this article, the authors summarize current Xiphophorus models for other human diseases. They review how Xiphophorus fishes and their interspecies hybrids can be used for studying human diseases and highlight research opportunities enabled by these unique models (both established and emerging). They identified several emerging Xiphophorus models, including for albinism, micromelanophore pigmentation, fin regeneration, and diet-induced obesity. The research on cancer and reproductive maturation discussed in this review substantiates the value of Xiphophorus as a model for human disease throughout all three phases of validation—face, construct, and predictive—and continues to provide important scientific insights. Supported by ORIP (R24OD031467, R21OD031910) and NCI.


 Identification of Constrained Sequence Elements Across 239 Primate Genomes

Kuderna et al., Nature. 2024.

Functional genomic elements that have acquired selective constraints specific to the primate order are prime candidates for understanding evolutionary changes in humans, but the selective constraints specific to the phylogenetic branch from which the human species ultimately emerged remain largely unidentified. Researchers constructed a genome-wide multiple sequence alignment of 239 primate species to better characterize constraint at noncoding regulatory sequences in the human genome. Their work reveals noncoding regulatory elements that are under selective constraint in primates but not in other placental mammals and are enriched for variants that affect human gene expression and complex traits in diseases. These findings highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals. Supported by ORIP (P40OD024628), NHGRI, NIA, and NICHD.


 Molecular Basis of Human Trace Amine-Associated Receptor 1 Activation

Zilberg et al., Nature Communications. 2024.

The authors reported the cryogenic electron microscopy structure of human trace amine-associated receptor 1 (hTAAR1, hTA1) signaling complex, a key modulator in monoaminergic neurotransmission, as well as its similarities and differences with other TAAR members and rodent TA1 receptors. This discovery has elucidated hTA1’s molecular mechanisms underlining the strongly divergent pharmacological properties of human and rodent TA1 and therefore will boost the translation of preclinical studies to clinical applications in treating disorders of dopaminergic dysfunction, metabolic disorders, cognitive impairment, and sleep-related dysfunction. Supported by ORIP (S10OD019994, S10OD026880, and S10OD030463), NIDA, NIGMS, NIMH, and NCATS.


 Targeting Pancreatic Cancer Metabolic Dependencies Through Glutamine Antagonism

Encarnación-Rosado et al., Nature Cancer. 2024.

Pancreatic ductal adenocarcinoma (PDAC) cells thrive in the austere, complex tumor microenvironment by reprogramming their metabolism and relying on scavenging pathways, but more work is needed to translate this knowledge into clinically relevant therapeutic interventions. Investigators demonstrated that treating PDAC cells with a Gln antagonist, 6‑diazo-5-oxo-l-norleucine (DON), caused a metabolic crisis by globally impairing Gln metabolism, resulting in a significant decrease in proliferation. They observed a profound decrease in tumor growth in several in vivo models using sirpiglenastat (DRP-104), a pro-drug version of DON that was designed to circumvent DON-associated toxicity. These proof-of-concept studies suggested that broadly targeting Gln metabolism could provide a therapeutic avenue for PDAC. Combining this therapeutic with an extracellular-signal-regulated kinase (or ERK) signaling pathway inhibitor could further improve it. Supported by ORIP (S10OD021747), NCI, and NIAID.


 Effect of Hormone Replacement Therapy on Amyloid Beta (Aβ) Plaque Density in the Rhesus Macaque Amygdala

Appleman et al., Frontiers in Aging Neuroscience. 2024.

Amyloid beta plaque density is associated with Alzheimer’s disease. In this study, the authors examined its concentration in aged female nonhuman primates’ cerebrospinal fluid, as well as in the amygdala, an area of the brain involved with emotion and memory. They set out to test the hypothesis that estrogen hormone replacement therapy can beneficially affect amygdala Aβ plaque density in “surgically menopausal” females (i.e., aged rhesus macaques that had undergone ovariectomy). Female rhesus macaques that received estrogen replacement therapy showed fewer amyloid plaques than those that did not receive the hormone. This effect was observed regardless of the type of diet that the animals consumed. These findings suggest that hormone replacement might be a helpful treatment to consider for Alzheimer’s disease. Supported by ORIP (P51OD011092, R24OD011895, S10OD025002) and NIA.


 GenomeMUSter Mouse Genetic Variation Service Enables Multitrait, Multipopulation Data Integration and Analysis

Ball et al., Genome Research. 2024.

Advances in genetics, including transcriptome-wide and phenome-wide association analysis methods, create compelling new opportunities for using fully reproducible and widely studied inbred mouse strains to characterize the polygenetic basis for individual differences in disease-related traits. Investigators developed an imputation approach and implemented data service to provide a broad and more comprehensive mouse variant resource. They evaluated the strain-specific imputation accuracy on a “held-out” test set that was not used in the imputation process. The authors present its application to multipopulation and multispecies analyses of complex trait variation in type 2 diabetes and substance use disorders and compare these results to human genetics studies. Supported by ORIP (U42OD010921, P40OD011102, R24OD035408), NCI, NIAAA, NIDA, and NIDCD.


 Antibiotic-Induced Gut Dysbiosis Elicits Gut–Brain–Axis Relevant Multi-Omic Signatures and Behavioral and Neuroendocrine Changes in a Nonhuman Primate Model

Hayer et al., Gut Microbes. 2024.

Gut microbiome–mammalian cell interactions influence the development of metabolic, immune-mediated, and neuropsychiatric disorders. Dysbiosis of the gut microbiome has been linked to behavioral characteristics in previous nonhuman primate (NHP) studies, but additional studies using NHPs are necessary to understand microbiota–gut–brain communication. The authors sought to evaluate whether antibiotic-induced gut dysbiosis can elicit changes in gut metabolites and behavior indicative of gut–brain axis disruption in common marmosets of both sexes. For the first time in an NHP model, this study demonstrated that antibiotics induce gut dysbiosis, alter gut metabolites relevant to gut–brain communication, affect neuroendocrine responses in response to stressful stimuli, and change social behavior. Supported by ORIP (K01OD030514), NCI, and NIGMS.


 Injury-Induced Cooperation of InhibinβA and JunB is Essential for Cell Proliferation in Xenopus Tadpole Tail Regeneration

Nakamura et al., Scientific Reports. 2024.

Certain animal species (e.g., amphibians) that can regenerate lost tissues and limbs after injury offer potential for applications in regenerative medicine. Cell proliferation is essential for the reconstruction of injured tissue, but the molecular mechanisms that regulate the transition from wound healing to regenerative cell proliferation remain unclear. Using Xenopus tropicalis, investigators examined the effects of injury on the expression of inhibin subunit beta A (inhba) and junb. Their findings shed light on the mechanisms underlying injury-induced cell proliferation in regenerative animals. Supported by ORIP (P40OD010997, R24OD030008).


 A Single-Cell Time-Lapse of Mouse Prenatal Development From Gastrula to Birth

Qiu et al., Nature. 2024.

In this study, investigators combined single-cell transcriptome profiling of male and female mouse embryos and newborn pups with previously published data to construct a tree of cell-type relationships tracing development from zygote to birth. They applied optimized single-cell combinatorial indexing to profile the transcriptional states of 12.4 million nuclei from 83 embryos, precisely staged at 2- to 6-hour intervals spanning late gastrulation to birth; establish a global framework for exploring mammalian development; and construct a rooted tree of cell-type relationships, from zygote to birth. Their analysis allowed them to systematically nominate genes that encode transcription factors and other proteins as candidate drivers of the in vivo differentiation of hundreds of cell types. Extending this framework to postnatal time points could yield a single-cell time-lapse of the entire mammalian life span, from conception to death. Supported by ORIP (UM1OD023222) and NHGRI.


Publications Archive



 De Novo Protein Fold Design Through Sequence-Independent Fragment Assembly Simulations

Pearce et al., PNAS. 2023 Jan;120(4):e2208275120.

Researchers developed an automated open-source program, FoldDesign, to create high-fidelity stable folds. Through sequence-independent replica-exchange Monte Carlo simulations and energy force field optimalization of secondary structure, FoldDesign can render novel areas of protein structure and function space that natural proteins have not reached through evolution. These completely different yet stable structures replicate natural proteins’ characteristics with closely matching buried residues and solvent-exposed areas. This work demonstrates a strong potential of creating desired protein structures with potential clinical and industrial applications. Supported by ORIP (S10OD026825), NIAID, NCI, NIEHS, and NIGMS.


 Duration of Antiretroviral Therapy Impacts the Degree of Residual SIV Infection in the Gut in Long‐Term Non‐Progressing Chinese Rhesus Macaques

Solis-Leal, Antonio et al., Journal of Medical Virology. 2023 Jan;95(1):e28185.

HIV and simian immunodeficiency virus (SIV) reservoirs have been shown to persist with antiretroviral therapy (ART), particularly in the gut‐associated lymphoid tissues in the intestine. The effects of ART on the reservoir size, however, had not been explored fully. In this study, researchers used male Chinese‐origin rhesus macaques to assess the effects of long- and short-term ART on gut infection—across segments of the small and large intestines—in long‐term non‐progressors (LTNPs). They reported that although ART does not eliminate SIV in LTNPs, a longer ART period dramatically reduces SIV infection and diversity in the gut. Further studies are needed to better understand the reduction of HIV gut reservoirs in this context. Supported by ORIP (P51OD011133, P51OD011104), NIAID, NIMH, and NINDS.


 The Ras GTPase‐Activating‐Like Protein IQGAP1 Bridges Gasdermin D to the ESCRT System to Promote IL‐1β Release via Exosomes

Liao, Yun et al., The EMBO Journal. 2023 Jan 4;42(1):e110780.

The investigators identified IQGAP1, a scaffold protein, as a gasdermin D (GSDMD)–interacting protein through a nonbiased proteomic analysis. Functional investigation indicated that the interaction is required for lipopolysaccharide (LPS)- and ATP-induced exosome release. Further analysis revealed that IQGAP1 serves as an adaptor that bridges GSDMD and the associated IL‐1β complex to Tsg101 and enables the packaging of GSDMD and IL‐1β into exosomes. This process is dependent on an LPS‐induced increase in GTP‐bound CDC42, a small GTPase known to activate IQGAP1. This study reveals IQGAP1 as a link between inflammasome activation and exosomal release of IL‐1β. Supported by ORIP (S10OD023436) and NIAID.


 Surrogate Biomarkers of Disease Progression in Human Pegivirus Seropositive Human Immunodeficiency Virus–Infected Individuals

Vimali, Jaisheela et al., Viral Immunology. 2023 Jan;36(1):55–62.

Researchers have previously observed that human pegivirus (HPgV) infection is associated with reduced progression of HIV. Investigators examined markers of HIV progression in male and female individuals with HIV and HPgV infection. They reported that HIV plasma viral load was lower in HPgV-seropositive individuals with HIV than in HPgV‑seronegative individuals with HIV. They also found that clinical markers of hepatic damage were significantly lower in HPgV-seropositive individuals with HIV. Future work could examine pathways through which HPgV influences HIV control, which might inform the development of new therapeutics. Supported by ORIP (P51OD011132) and NIAID.


 Elevated Transferrin Receptor Impairs T Cell Metabolism and Function in Systemic Lupus Erythematosus

Voss, Kelsey et al., Science Immunology. 2023 Jan 13;8(79):eabq0178.

Systemic lupus erythematosus (SLE) is an autoimmune disease in which dysfunctional T cells exhibit abnormalities in metabolism. Investigators performed a CRISPR screen to examine mechanisms associated with the role of excess iron in dysfunctional T cells. The transferrin receptor (CD71) was identified as differentially critical for Type 1 T helper cells and inhibitory for induced regulatory T cells. Activated T cells induced CD71 and iron uptake, which was exaggerated in SLE-prone T cells. Disease severity correlated with CD71 expression in cells from male and female patients with SLE, and blocking CD71 in vitro enhanced interleukin 10 secretion. These findings suggest that T cell iron uptake via CD71 contributes to T cell dysfunction and can be targeted to limit SLE-associated pathology. Supported by ORIP (S10OD030264), NIAID, NCI, and NIDDK.


 PGRN Deficiency Exacerbates, Whereas a Brain Penetrant PGRN Derivative Protects, GBA1 Mutation–Associated Pathologies and Diseases

Zhao, Xiangli et al., PNAS. 2023 Jan 3;120(1):e2210442120.

Mutations in GBA1 are associated with Gaucher disease (GD) and are also genetic risks in developing Parkinson’s disease (PD). Investigators created a mouse model and demonstrated that progranulin (PGRN) deficiency in Gba1 mutant mice caused early onset and exacerbated GD phenotypes, leading to substantial increases in substrate accumulation and inflammation in visceral organs and the central nervous system. These in vivo and ex vivo data demonstrated that PGRN plays a crucial role in the initiation and progression. In addition, the mouse model provides a clinically relevant system for testing therapeutic approaches for GD and PD. Supported by ORIP (R21OD033660), NIAMS, and NINDS.


 Impaired Placental Hemodynamics and Function in a Non-Human Primate Model of Gestational Protein Restriction

Lo, Jamie et al., Scientific Reports. 2023 Jan 16;13(1):841.

Maternal malnutrition is a global health epidemic that adversely affects fetal outcomes and results in long-term health complications in children. Investigators used a previously developed model in nonhuman primates for gestational protein restriction to study the impact of undernutrition, specifically protein deficiency, on placental function and pregnancy outcomes. The data demonstrate that a 50% protein-restricted diet reduces maternal placental perfusion, decreases fetal oxygen availability, and increases fetal mortality. These alterations in placental hemodynamics could partly explain human growth restriction and stillbirth seen with severe protein restriction in developing countries. Supported by ORIP (P51OD011092) and NICHD.


 Human Hematopoietic Stem Cell Engrafted IL-15 Transgenic NSG Mice Support Robust NK Cell Responses and Sustained HIV-1 Infection

Abeynaike, Shawn et al., Viruses. 2023 Jan 27;15(2):365.

A major obstacle to human natural killer (NK) cell reconstitution is the lack of human interleukin‑15 (IL-15) signaling, as murine IL-15 is a poor stimulator of the human IL-15 receptor. Researchers show that immunodeficient NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice expressing a transgene encoding human IL-15 (NSG-Tg(IL-15)) have physiological levels of human IL-15 and support long-term engraftment of human NK cells when transplanted with human umbilical cord blood–derived hematopoietic stem cells (HSCs). These mice demonstrate robust and long-term reconstitution with human immune cells but do not develop graft-versus-host disease, allowing long-term studies of human NK cells. The HSC-engrafted mice can sustain HIV-1 infection, resulting in human NK cell responses. This work provides a robust novel model to study NK cell responses to HIV-1. Supported by ORIP (R24OD026440), NIAID, NCI, and NIDDK.


 3D-Bioprinted Phantom with Human Skin Phototypes for Biomedical Optics

Yim, Wonjun et al., Advanced Materials. 2023 Jan;35(3):e2206385.

Human skin offers important physical and immunological protection based on its makeup with diverse cell types, including melanocytes, and variations in skin phototypes controlled by melanin concentration have negatively affected many optic technologies and wearable health-tracking electronic devices. To mimic the effects of melanosome variation, investigators studied optical properties and photoacoustic signal of synthetic melanin to create a 3D bioprinting rendition of the human epidermal thin layers. The effect of skin phototypes on thin-layer skin imaging at different wavelengths was quantified. These data could serve as a benchmark calibration tool of light-mediated diagnostics toward clinical use and further underpin development of biomedical optics. Supported by ORIP (S10OD023527, S10OD021821).


 A Deep Learning Platform to Assess Drug Proarrhythmia Risk

Serrano, Ricardo et al., Cell Stem Cell. 2023 Jan;30(1):86–95.e4.

Investigators trained a convolutional neural network (CNN) classifier to learn and ultimately identify features of in vitro action potential recordings of human induced pluripotent stem cell (iPSC)–derived cardiomyocytes (hiPSC-CMs) that are associated with lethal Torsade de Pointes arrhythmia. The CNN classifier accurately predicted the risk of drug-induced arrhythmia. The risk profiles of the test drugs were similar across hiPSC-CMs derived from different healthy donors. In addition, pathogenic mutations that cause arrhythmogenic cardiomyopathies in patients significantly increased the proarrhythmic propensity to certain intermediate and high‑risk drugs in the hiPSC-CMs. These data indicate that deep learning can identify in vitro arrhythmic features that correlate with clinical arrhythmia and discern the influence of patient genetics on the risk of drug-induced arrhythmia. Supported by ORIP (S10OD030264) and NHLBI.


 TMEM161B Modulates Radial Glial Scaffolding in Neocortical Development

Wang, Lu et al., Proc Natl Acad Sci USA. 2023 Jan;120(4):e2209983120.

Neocortical folding (i.e., gyrification) is a fundamental evolutionary mechanism allowing the expansion of cortical surface area and increased cognitive function. This study identifies TMEM161B in gyral spacing in humans, likely affecting radial glial cell polarity through effects on the actin cytoskeleton. Patients carrying TMEM161B mutations exhibit striking neocortical polymicrogyria and intellectual disability. TMEM161B knockout mice fail to develop midline hemispheric cleavage, whereas knock-in of patient mutations and patient-derived brain organoids show defects in apical cell polarity and radial glial scaffolding. The data implicating TMEM161B in murine holoprosencephaly may suggest shared mechanisms between the formation of the brain midline and cortical gyrification. Supported by ORIP (U54OD030187), NINDS, and NHGRI.


 Chronic TREM2 Activation Exacerbates Aβ-Associated Tau Seeding and Spreading

Jain, Nimansha et al., Journal of Experimental Medicine. 2023 Jan;220(1):e20220654.

Using a mouse model for amyloidosis in which Alzheimer’s Disease (AD)–associated tau is injected into the brain to induce amyloid β (Aβ)–dependent tau seeding/spreading, investigators found that chronic administration of an activating triggering receptor expressed on myeloid cells 2 (TREM2) antibody increases microglial activation of dystrophic neurites surrounding Aβ plaques (NP) but increases NP-tau pathology and neuritic dystrophy without altering Aβ plaque burden. These data suggest that sustained microglial activation through TREM2 that does not result in strong myeloid removal might exacerbate Aβ-induced tau pathology, which could have important clinical implications. Supported by ORIP (S10OD021629) and NIA.


 Multimodal Single-Cell and Whole-Genome Sequencing of Small, Frozen Clinical Specimens

Wang, Yiping et al., Nature Genetics. 2023 Jan;55(1):19–25.

Single-cell RNA sequencing has led to improved understanding of tumor heterogeneity to drug response, but the broad application of those methods remains challenging due to practical requirements that are incompatible with clinical care workflow, such as the need for large and fresh tissues. The researchers demonstrated that several single-cell genomics techniques are feasible from small, frozen tissues and provide biological data outputs similar to those collected from fresh tissue while reducing artifactual signals and compositional biases introduced by fresh-tissue processing. These results provide a new perspective for translating these methods to clinical studies. Supported by ORIP (S10OD020056), NIAID, and NCI.


 Production and Characterization of Monoclonal Antibodies to Xenopus Proteins

Horr et al., Development. 2023 Feb;150(4):dev201309.

Monoclonal antibodies are powerful and versatile tools that enable the study of proteins in diverse contexts. They are often utilized to assist with identification of subcellular localization and characterization of the function of target proteins of interest. However, because there can be considerable sequence diversity between orthologous proteins in Xenopus and mammals, antibodies produced against mouse or human proteins often do not recognize Xenopus counterparts. To address this issue, the authors refined existing mouse monoclonal antibody production protocols to generate antibodies against Xenopus proteins of interest. Here, they describe several approaches for the generation of useful mouse anti-Xenopus antibodies to multiple Xenopus proteins and their validation in various experimental approaches. Supported by ORIP (R24OD021485, S10OD010645) and NIDCR.


 CD8+ Lymphocytes Do Not Impact SIV Reservoir Establishment under ART

Statzu, Maura et al., Nature Microbiology. 2023 Feb;8(2):299–308.

The HIV-1 latent reservoir has been shown to persist following antiretroviral therapy (ART), but the mechanisms underlying the establishment and maintenance of the reservoir are not fully understood. Using rhesus macaques of both sexes, investigators examined the effects of CD8+ T cells on formation of the latent reservoir with simian immunodeficiency virus (SIV) infection. They found that CD8+ T cell depletion resulted in slower decline of viremia but did not change the frequency of infected CD4+ T cells in the blood or lymph nodes. Additionally, the size of the persistent reservoir was unchanged. These findings suggest that the viral reservoir is established largely independent of SIV-specific cytotoxic T lymphocyte control. Supported by ORIP (P51OD011132), NIAID, NCI, NIDDK, NIDA, NHLBI, and NINDS.


 Alterations in Abundance and Compartmentalization of miRNAs in Blood Plasma Extracellular Vesicles and Extracellular Condensates during HIV/SIV Infection and its Modulation by Antiretroviral Therapy (ART) and Delta-9-Tetrahydrocannabinol (Δ9-THC)

Kopcho, Steven et al., Viruses. 2023 Feb 24;15(3):623.

MicroRNAs (miRNAs) have been shown to regulate host response to HIV infection. Previously, investigators proposed that the assortment of extracellular miRNAs into distinct carriers could provide a new dimension to miRNA-based biomarkers. In this follow-up study, the investigators used particle purification liquid chromatography to determine the abundance and compartmentalization of blood plasma extracellular miRNAs into extracellular vesicles and extracellular condensates during simian immunodeficiency virus (SIV) infection in male rhesus macaques. They reported that different treatments—combination ART and Δ9‑THC—impart distinct effects on the enrichment and compartmentalization of extracellular miRNAs. These data suggest that the extracellular miRNA profile in blood plasma is altered following SIV infection. Supported by ORIP (P51OD011104, P51OD011133), NIAID, and NIDA.


 Genome Structures Resolve the Early Diversification of Teleost Fishes

Parey, Elise et al., Science. 2023 Feb 10;379(6632):572–575.

The early evolution of teleost fishes remains an unanswered question among evolutionary biologists. The three earliest branching clades of crown teleosts are Elopomorpha (e.g., tarpons, eels), Osteoglossomorpha (e.g., arapaima, elephantnose fish), and Clupeocephala (e.g., zebrafish, medaka). Building on recently described genome assemblies in Elopomorpha, the authors explored teleost phylogeny using independent gene sequencing and chromosomal rearrangement phylogenomic approaches. They found that Elopomorpha and Osteoglossomorpha comprise a monophyletic sister group to all other teleosts. This report highlights the value of combining different levels of genome-wide information to solve complex phylogenies and will serve as a basis for new investigations into the genomic and functional evolution of teleosts. Supported by ORIP (R01OD011116).


 Prolonged Experimental CD4+ T-Cell Depletion Does Not Cause Disease Progression In SIV-Infected African Green Monkeys

Le Hingrat, Quentin et al., Nature Communications. 2023 Feb 22;14(1):979.

Chronically simian immunodeficiency virus (SIV)–infected African green monkeys (AGMs) partially recover mucosal CD4+ T cells, maintain gut integrity, and do not progress to AIDS. Investigators assessed the impact of prolonged, antibody-mediated CD4+ T cell depletion on gut integrity and natural history of SIV infection in AGMs. All circulating CD4+ T cells and more than 90% of mucosal CD4+ T cells were depleted. Plasma viral loads and cell-associated viral RNA in tissues were lower in CD4+-cell-depleted animals. CD4+-cell-depleted AGMs maintained gut integrity, controlled immune activation, and did not progress to AIDS. Therefore, CD4+ T cell depletion is not a determinant of SIV-related gut dysfunction when gastrointestinal tract epithelial damage and inflammation are absent, suggesting that disease progression and resistance to AIDS are independent of CD4+ T cell restoration in SIV-infected AGMs. Supported by ORIP (P40OD028116), NIAID, NIDDK, and NHLBI.


 SIV Infection Regulates Compartmentalization of Circulating Blood Plasma miRNAs within Extracellular Vesicles (EVs) and Extracellular Condensates (ECs) and Decreases EV-Associated miRNA-128

Kopcho, Steven et al., Viruses. 2023 Feb 24;15(3):622.

MicroRNAs (miRNAs) are thought to be involved in HIV pathogenesis, but the effect of HIV on the compartmentalization of miRNAs within extracellular particles is unclear. Researchers sequenced the small RNA population of paired EVs and ECs from male rhesus macaques. They showed that extracellular miRNAs in blood plasma are not restricted to any type of extracellular particles but are associated with lipid‑based carriers, with a significant proportion associated with ECs. Further, simian immunodeficiency virus (SIV) infection altered the miRNAome profile of EVs and revealed miR‑128‑3p as a potential target of infection. This work suggests that EV‑ and EC‑associated miRNAs potentially could serve as biomarkers for various diseases. Supported by ORIP (P51OD011104, P51OD011133), NIAID, and NIDA.


 Assessment of Anti-CD20 Antibody Pre-Treatment for Augmentation of CAR-T Cell Therapy in SIV-Infected Rhesus Macaques

Pampusch, Mary et al., Frontiers in Immunology. 2023 Feb 7;14:1101446.

Chronic HIV replication occurs primarily within lymphoid follicles, and investigators hypothesized that temporary disruption of these follicles would create space for chimeric antigen receptor (CAR) T cell engraftment and lead to increased abundance and persistence of CAR T cells. They evaluated CAR T cell abundance and persistence in rhesus macaques of both sexes following simian immunodeficiency virus (SIV) infection and antiretroviral therapy suppression. Their results suggest that CAR T cells expanded to a greater extent in the depleted and CAR T cell–treated animals. Further studies are needed to evaluate strategies for engraftment and the persistence of HIV-specific CAR T cells. Supported by ORIP (P51OD011106, P51RR000167), NIAID, and NIDA.


 PIKFYVE Inhibition Mitigates Disease in Models of Diverse Forms of ALS

Hung, Shu-Ting et al., Cell. 2023 Feb 16;186(4):786–802.e28.

Investigators showed that pharmacological suppression of PIKFYVE activity reduces pathology and extends survival of animal models and patient-derived motor neurons representing diverse forms of amyotrophic lateral sclerosis (ALS). Upon PIKFYVE inhibition, exocytosis is activated to transport aggregation-prone proteins out of the cells, a process that does not require stimulating macroautophagy or the ubiquitin-proteosome system. These findings suggest therapeutic potential to manage multiple forms of ALS. Supported by ORIP (S10OD021553) and NINDS.


 Pancreatic Cancer Cells Upregulate LPAR4 in Response to Isolation Stress to Promote an ECM-Enriched Niche and Support Tumour Initiation

Wu, Chengsheng et al., Nature Cell Biology. 2023 Feb;25(2):309–322.

Understanding drivers of tumor initiation is critical for cancer therapy. Investigators found transient increase of lysophosphatidic acid receptor 4 (LPAR4) in pancreatic cancer cells exposed to environmental stress or chemotherapy. LPAR4 induced tumor initiation, stress tolerance, and drug resistance by downregulating miR-139-5p, a tumor suppressor, and upregulating fibronectin. These results indicate that LPAR4 enhances cell-autonomous production of a fibronectin-rich extracellular matrix (ECM), allowing cells to survive isolation stress and compensate for the absence of stromal-derived factors by creating their own tumor-initiating niche. Supported by ORIP (K01OD030513, T32OD017863), NCI, and NHLBI.


 A Class of Anti-Inflammatory Lipids Decrease with Aging in the Central Nervous System

Tan, Dan et al., Nature Chemical Biology. 2023 Feb;19(2):187–197.

Impaired lipid metabolism in the brain has been implicated in neurological disorders of aging, yet analyses of lipid pathway changes with age have been lacking. The researchers examined the brain lipidome of mice of both sexes across the lifespan using untargeted lipidomics. They found that 3-sulfogalactosyl diacylglycerols (SGDGs) are structural components of myelin and decline with age in the central nervous system. The researchers discovered that SGDGs also are present in male human and rhesus macaque brains, demonstrating their evolutionary conservation in mammals. The investigators showed that SGDGs possess anti-inflammatory activity, suggesting a potential role for this lipid class in age-related neurodegenerative diseases. Supported by ORIP (P51OD011092), NIA, NCI, NIDDK, and NINDS.


 Naturally Occurring Osteochondrosis Latens Lesions Identified by Quantitative and Morphological 10.5 T MRI in Pigs

Armstrong et al., Journal of Orthopaedic Research. 2023 Mar;41(3):663–673.

Juvenile osteochondritis dissecans (JOCD) is a pediatric orthopedic disorder that is associated with pain and gait deficits. JOCD lesions form in the knee, elbow, and ankle joints and can progress to early-onset osteoarthritis. In this study, researchers used a noninvasive magnetic resonance imaging (MRI) method to identify naturally occurring lesions in intact knee and elbow joints of juvenile pigs. This work can be applied to noninvasive identification and monitoring of early JOCD lesions and determination of risk factors that contribute to their progression in children. Supported by ORIP (K58OD021293, T32OD580993), NIAMS, and NIBIB.


 In-Depth Virological and Immunological Characterization of HIV-1 Cure after CCR5A32/A32 Allogeneic Hematopoietic Stem Cell Transplantation

Jensen, Björn-Erik et al., Nature Medicine. 2023 Mar;29(3):583–587.

Evidence suggests that CCR5Δ32/Δ32 hematopoietic stem cell transplantation (HSCT) can cure HIV-1, but the immunological and virological correlates are unknown. Investigators performed a longitudinal virological and immunological analysis of the peripheral blood and tissue compartments of a 53-year-old male patient more than 9 years after CCR5Δ32/Δ32 allogeneic HSCT and 48 months after analytical treatment interruption. Sporadic traces of HIV-1 DNA were detected in peripheral T cell subsets and tissue-derived samples, but repeated ex vivo quantitative and in vivo outgrowth assays in humanized mice of both sexes did not reveal replication-competent virus. This case provides new insights that could guide future cure strategies. Supported by ORIP (P51OD011092) and NIAID.


 Cannabinoids Modulate the Microbiota–Gut–Brain Axis in HIV/SIV Infection by Reducing Neuroinflammation and Dysbiosis while Concurrently Elevating Endocannabinoid and Indole-3-Propionate Levels

McDew-White, Marina et al., Journal of Neuroinflammation. 2023 Mar 8;20(1):62.

Chronic neuroinflammation is thought to be a significant contributor to HIV-associated neurocognitive disorders. Using rhesus macaques of both sexes, researchers investigated the effects of simian immunodeficiency virus (SIV) infection on the microbiota–gut–brain axis (MGBA), as well as the use of low-dose cannabinoids to reverse MGBA dysregulation. They reported that tetrahydrocannabinol reduced neuroinflammation and dysbiosis and increased plasma endocannabinoid, endocannabinoid-like, glycerophospholipid, and indole-3-propionate levels. This study offers a potential strategy to promote brain health in people with HIV. Supported by ORIP (P51OD011104, P51OD011103), NIAID, and NIDA.


 Characterizing a Photoacoustic and Fluorescence Imaging Platform for Preclinical Murine Longitudinal Studies

Thompson, Weylan et al., Journal of Biomedical Optics. 2023 Mar;28(3):036001.

Preclinical studies using animal models require medical imaging technology with sufficient resolution and sensitivity for anatomical, functional, and molecular assessments. Photoacoustic (PA) tomography provides high resolution and specificity, and fluorescence (FL) molecular tomography provides high sensitivity; the combination of these imaging modalities capitalizes on their strengths and mitigates disadvantages. In this publication, the authors describe TriTom, a preclinical imaging system that integrates PA and FL. They characterized the PA spatial resolution, PA sensitivity, PA spectral accuracy, optical spatial resolution, and FL sensitivity of the platform and demonstrated anatomical imaging in mice. This report demonstrates TriTom’s suitability for biomedical imaging applications. Supported by ORIP (R43OD023029) and NCI.


 Spike and Nsp6 Are Key Determinants of SARS-CoV-2 Omicron BA.1 Attenuation

Chen, Da-Yuan et al., Nature. 2023 Mar;615(7950):143–150.

The ability of the SARS-CoV-2 virus to mutate and create variants of concern demands new vaccines to control the COVID-19 pandemic. The SARS-CoV-2 Omicron variant was shown to be more immune evasive and less virulent than current major variants. The spike (S) protein in this variant carries many mutations that drive these phenotypes. Researchers generated a chimeric recombinant SARS-CoV-2 virus encoding the S gene of Omicron (BA.1 lineage) in an ancestral SARS-CoV-2 isolate and compared it with the naturally circulating Omicron variant. The Omicron S-bearing virus escaped vaccine-induced humoral immunity, owing to mutations in the receptor-binding motif. The recombinant virus replicated efficiently in distal lung cell lines and in K18-hACE2 mice. Moreover, mutations induced in non-structural protein 6 (nsp6) in addition to the S protein were sufficient to restate the attenuated phenotype of Omicron. These findings indicate that the pathogenicity of Omicron is determined by mutations both inside and outside of the S gene. Supported by ORIP (S10OD026983, S10OD030269).


 Chronic Immune Activation and Gut Barrier Dysfunction Is Associated with Neuroinflammation in ART-Suppressed SIV+ Rhesus Macaques

Byrnes, Sarah et al., PLOS Pathogens. 2023 Mar 29;19(3):e1011290.

About 40% of people with HIV develop neurocognitive disorders, potentially resulting from persistent infection in the brain and neuroinflammation. Investigators characterized the central nervous system reservoir and immune environment of simian immunodeficiency virus (SIV)–infected rhesus macaques of both sexes during acute, chronic, or antiretroviral therapy (ART)–suppressed infection. They reported that neuroinflammation and blood–brain barrier dysfunction correlated with viremia and immune activation in the gut. Their findings suggest that gastrointestinal tract damage can contribute to neuroimmune activation and inflammation, even in the absence of SIV or HIV infection. This work also has implications for other neurological disorders where chronic inflammation is associated with pathogenesis. Supported by ORIP (P51OD011132, P51OD011092, U42OD011023, R24OD010445), NIAID, NCI, and NIMH.


 Mechanism of STMN2 Cryptic Splice-Polyadenylation and its Correction for TDP-43 Proteinopathies

Baughn, Michael et al., Science. 2023 Mar 17;379(6637):1140–1149.

Loss of the RNA-binding protein TDP-43 from the nuclei of affected neurons is a hallmark of neurodegeneration in TDP-43 proteinopathies (e.g., amyotrophic lateral sclerosis, frontotemporal dementia). Loss of functional TDP-43 is accompanied by misprocessing of the stathmin-2 (STMN2) RNA precursor. Investigators determined the elements through which TDP‑43 regulates STMN2 pre‑mRNA processing and identified steric binding antisense oligonucleotides that are capable of restoring normal STMN2 protein and RNA levels. This approach is potentially applicable for human therapy. Supported by ORIP (U42OD010921), NIA, NCI, NIGMS, and NINDS.


 Late Gene Expression–Deficient Cytomegalovirus Vectors Elicit Conventional T Cells That Do Not Protect against SIV

Hansen, Scott et al., Journal of Clinical Investigation Insight. 2023 Mar 22;8(6):e164692.

Cytomegalovirus (CMV)–based vaccines aim to exploit unique immunological adaptations, including host manipulation and immune evasion strategies. Translating CMV-based vaccines from rhesus macaques to humans requires translating the immune factors responsible for efficacy, as well as vaccine vectors that are sufficiently safe for widespread use. Researchers examined the impact of a stringent attenuation strategy on vector-induced immune protection against simian immunodeficiency virus (SIV) in rhesus macaques of both sexes. They reported that elicited CD8+ T cells exclusively failed to protect against SIV challenge. These data suggest that late viral gene expression and/or residual in vivo spreading are required to induce protective CD8+ T cell responses. Supported by ORIP (P51OD011092, P51OD011107, S10OD016261), NCI, NIAID, and NCATS.


 Anti–Human Immunodeficiency Virus‑1 Activity of Momo30 Protein Isolated from the Traditional African Medicinal Plant Momordica balsamina

Khan, Mahfuz et al., Virology Journal. 2023 Mar 22;20(1):50.

Momordica balsamina has been reported to produce a ribosome-inactivating protein with anti‑HIV-1 activity and is commonly used by traditional African healers for treatment of HIV. Investigators characterized the mechanism of action of the MoMo30 protein, as well as the sequence of the protein-coding gene. They reported that MoMo30 functions as a lectin or carbohydrate-binding agent (CBA) and inhibits HIV-1 at nanomolar levels, with minimal cellular toxicity at inhibitory levels. CBAs can block the binding of envelope glycoproteins with their target receptors on cells. Thus, this protein could represent a potential new treatment strategy for HIV. Supported by ORIP (R24OD010947), NCI, NIGMS, and NIMHD.


 Antiretroviral Therapy Reveals Triphasic Decay of Intact SIV Genomes and Persistence of Ancestral Variants

Fray, Emily et al., Cell Host & Microbe. 2023 Mar 8;31(3):356–372.e5.

Antiretroviral therapy (ART) halts HIV-1 replication but is not curative; a pool of latently infected CD4+ T cells persists, and viremia rapidly rebounds if ART is stopped. Using an intact proviral DNA assay, researchers characterized quantitative and qualitative changes in CD4+ T cells for 4 years following ART initiation in rhesus macaques of both sexes. They found that viruses replicating at ART initiation had mutations conferring antibody escape, and sequences with large numbers of antibody escape mutations became less abundant at later time points. Together, these findings reveal that the population of simian immunodeficiency virus (SIV)–infected CD4+ T cells is dynamic and provide a framework for evaluating and interpreting intervention trials. Supported by ORIP (R01OD011095), NIAID, and NIDCR.


 A Live Dengue Virus Vaccine Carrying a Chimeric Envelope Glycoprotein Elicits Dual DENV2–DENV4 Serotype-Specific Immunity

Young, Ellen et al., Nature Communications. 2023 Mar 13;14(1):1371.

Dengue vaccine development is challenging because some virus-specific antibodies are protective, whereas others are implicated in enhanced viral replication and more severe disease. Current dengue tetravalent vaccines contain four live attenuated serotypes formulated to induce balanced protective immunity. To simplify live-virus vaccine design, investigators identified co-evolutionary constraints inherent in flavivirus virion assembly. They found that the chimeric virus replicated efficiently in vitro and in vivo and that a single inoculation induced type-specific neutralizing antibodies in male macaques. These findings can be applied to the development of bivalent live dengue vaccines that induce independent immunity to multiple serotypes. Supported by ORIP (P40OD012217) and NIAID.


 Fc-Mediated Pan-Sarbecovirus Protection after Alphavirus Vector Vaccination

Adams, Lily et al., Cell Reports. 2023 Mar 30;42(4):112326.

Group 2B β-coronaviruses (i.e., sarbecoviruses) have resulted in regional and global epidemics. Here, the authors evaluate the mechanisms of cross-sarbecovirus protective immunity using a panel of alphavirus-vectored vaccines covering bat to human strains. They reported that vaccination does not prevent virus replication, but it protects against lethal heterologous disease outcomes in SARS-CoV-2 and clade 2 bat sarbecovirus challenge models. Full-length spike vaccines elicited the broadest pan-sarbecovirus protection. Additionally, antibody-mediated cross-protection was lost in absence of FcR function, supporting a model for non-neutralizing, protective antibodies. Taken together, these findings highlight the value of universal sarbecovirus vaccine designs that couple FcR-mediated cross-protection with potent cross-neutralizing antibody responses. Supported by ORIP (K01OD026529), NIAID, and NCI.


 Infant Rhesus Macaques Immunized against SARS-CoV-2 Are Protected against Heterologous Virus Challenge 1 Year Later

Milligan, Emma et al., Science Translational Medicine. 2023 Mar;15(685):eadd6383.

The Moderna and Pfizer–BioNTech mRNA vaccines received emergency use authorization for infants 6 months and older in June 2022, but questions remain regarding the durability of vaccine efficacy against emerging variants in this age group. Using a two-dose vaccine regimen consisting of stabilized prefusion Washington-strain spike protein encoded by mRNA and encapsulated in lipid nanoparticles, the investigators immunized 2-month-old rhesus macaques of both sexes. They found that the immune responses persisted and protected from severe disease after heterologous challenge with the Delta variant 1 year later. The decay kinetics of vaccine-induced neutralizing antibody responses in the infant monkeys are comparable to those observed in adult humans and nonhuman primates. Supported by ORIP (P51OD011107), NIAID, and NCI.


 Cholera Toxin B Scaffolded, Focused SIV V2 Epitope Elicits Antibodies That Influence the Risk of SIVmac251 Acquisition in Macaques

Rahman et al., Frontiers in Immunology. 2023 Apr 21:14:1139402.

Previous work has indicated that the production of antibodies against epitopes in the V2 loop of gp120—a protein component of the viral spikes used to infiltrate host cells—correlates with protection from viral acquisition. Researchers assessed the efficacy of a simian immunodeficiency virus (SIV) vaccine consisting of a V2c epitope scaffolded onto cholera toxin B in rhesus macaques of both sexes. Immunized animals generated V2c-specific antibody responses, and differences in the functional antibody and immune cell responses were observed and compared with responses in a historically protective vaccine regimen. Different responses also were observed when varying adjuvants were administered with the vaccines. Thus, full protection against SIV infection might require vaccines against multiple spike epitopes. Supported by ORIP (P51OD011104, R24OD010976) and NIAID.


 Longitudinal Characterization of Circulating Extracellular Vesicles and Small RNA During Simian Immunodeficiency Virus Infection and Antiretroviral Therapy

Huang et al., AIDS. Apr;37(5):733–744.

Antiretroviral therapy is effective for controlling HIV infection but does not fully prevent early aging disorders or serious non-AIDS events among people with HIV. Using pigtail and rhesus macaques (sex not specified), researchers profiled extracellular vesicle small RNAs during different phases of simian immunodeficiency virus infection to explore the potential relationship between extracellular vesicle–associated small RNAs and the infection process. They reported that average particle counts correlated with infection, but the trend could not be explained fully by virions. These findings raise new questions about the distribution of extracellular vesicle RNAs in HIV latent infection. Supported by ORIP (U42OD583117), NIDA, NIMH, NIAID, NCI, and NINDS.


 Structural Insights Into the Broad Protection Against H1 Influenza Viruses by a Computationally Optimized Hemagglutinin Vaccine

Dzimianski et al., Communications Biology. 2023 Apr;6(1):454.

Influenza is an ongoing public health concern, and computationally optimized broadly reactive antigen (COBRA) hemagglutinin proteins represent a potential strategy for formulating broadly effective influenza vaccines. Researchers determined the crystal structure of COBRA P1, as well as its binding to 1F8, a broadly neutralizing antibody. This work provides valuable insights into the underlying molecular basis for the broad effectiveness of P1, and these insights can be applied to future vaccine designs. Supported by ORIP (K58OD026569), NIAID, and NIGMS.


 Pembrolizumab and Cabozantinib in Recurrent Metastatic Head and Neck Squamous Cell Carcinoma: A Phase 2 Trial

Saba et al., Nature Medicine. 2023 Apr;29(4):880–887.

A multicenter clinical trial was conducted in 33 evaluable (36 enrolled) patients with recurrent metastatic head and neck squamous cell carcinoma (RMHNSCC) on a regimen combining cabozantinib, a tyrosine kinase inhibitor, with the standard of care of anti–programmed cell death protein 1 agent pembrolizumab. Results showed that 17 patients (52%) exhibited partial response and 13 (39%) exhibited stable disease, with an overall clinical benefit rate of 91%. Median progression-free survival (PFS) was 14.6 months, and the 1-year PFS was 54%. The pembrolizumab and cabozantinib regimen was well tolerated in patients with RMHNSCC. The promising clinical benefit warrants further investigation. Supported by ORIP (S10OD021644), NCI, and NIDCR.


 Effect of the Snake Venom Component Crotamine on Lymphatic Endothelial Cell Responses and Lymph Transport

Si et al., Microcirculation. 2023 Apr;30(2-3):e12775.

The pathology of snake envenomation is closely tied to the severity of edema in the tissue surrounding the area of the bite. This study focused on one of the most abundant venom components in North American viper venom, crotamine, and the effects it has on the cells and function of the lymphatic system. The authors found that genes that encode targets of crotamine are highly present in lymphatic tissues and cells and that there is a differential distribution of those genes that correlates with phasic contractile activity. They found that crotamine potentiates calcium flux in human dermal lymphatic endothelial cells in response to stimulation with histamine and shear stress—but not alone—and that it alters the production of nitric oxide in response to shear, as well as changes the level of F-actin polymerization of those same cells. Crotamine alters lymphatic transport of large molecular weight tracers to local lymph nodes and is deposited within the node, mostly in the immediate subcapsular region. Results suggest that snake venom components may have an impact on the function of the lymphatic system and provide new targets for improved therapeutics to treat snakebites. Supported by ORIP (P40OD580960).


 Leukocyte Tyrosine Kinase (Ltk) Is the Mendelian Determinant of the Axolotl Melanoid Color Variant

Kabangu et al., Genes. 2023 Apr;14(4):904.

The diversity of color patterns among amphibians is largely explained by the differentiation of a few pigment cell types during development. Mexican axolotls have a variety of color phenotypes, from leucistic to highly melanistic. The melanoid axolotl is a Mendelian variant characterized by large numbers of melanophores, fewer xanthophores, and no iridophores. Studies of melanoid were influential in developing the single-origin hypothesis of pigment cell development, proposing that all three pigment cell types derive from a common progenitor cell, with pigment metabolites playing potential roles in directing the development of organelles that define different pigment cell types. Xanthine dehydrogenase (XDH) activity was identified as a mechanism for the permissive differentiation of melanophores at the expense of xanthophores and iridophores. The authors used bulked segregant RNA-Seq (including a region on chromosome 14q) to screen the axolotl genome for melanoid candidate genes and identify the associated locus. The region 14q contains gephyrin (Gphn), an enzyme that catalyzes the synthesis of the molybdenum cofactor that is required for XDH activity, and Ltk, a cell surface signaling receptor required for iridophore differentiation in zebrafish. Wild-type Ltk crispants present similar pigment phenotypes to melanoid, strongly implicating Ltk as the melanoid locus. The results support the idea of direct fate specification of pigment cells, as well as the single-origin hypothesis of pigment cell development. Supported by ORIP (P40OD589794, R24OD580435, R24OD021479).


 The Incompetence of Mosquitoes—Can Zika Virus Be Adapted to Infect Culex tarsalis Cells?

Gallichotte, Emily et al., mSphere. 2023 Apr 20;8(2):e0001523.

Zika virus (ZIKV) is transmitted between humans by Aedes aegypti mosquitoes. However, the 2015 to 2017 outbreak raised questions regarding the role of Culex species mosquitoes in transmission. Investigators attempted to adapt ZIKV to C. tarsalis by serially passaging the virus on cocultured A. aegypti and C. tarsalis cells to identify viral determinants of species specificity. Next-generation sequencing of cocultured virus passages revealed variants of interest that were engineered into nine recombinant viruses. None of these viruses showed increased infection of Culex cells or mosquitoes. Thus, although ZIKV might infect Culex mosquitoes occasionally, Aedes mosquitoes likely drive transmission and human risk. Supported by ORIP (T32OD010437) and NIAID.


 Hematopoietic Stem Cells Preferentially Traffic Misfolded Proteins to Aggresomes and Depend on Aggrephagy to Maintain Protein Homeostasis

Chua, Bernadette et al., Cell Stem Cell. 2023 Apr 6;30(4):460–472.e6.

Investigators studied the mechanism of hematopoietic stem cells (HSCs) being dependent on managing proteostasis. Their findings demonstrated that HSCs preferentially depend on aggrephagy, a form of autophagy, to maintain proteostasis. When aggrephagy is disabled, HSCs compensate by increasing proteasome activity, but proteostasis is ultimately disrupted as protein aggregates accumulate and HSC function is impaired. The investigators also showed that Bag3 deficiency blunts aggresome formation in HSCs, resulting in protein aggregate accumulation, myeloid-biased differentiation, and diminished self-renewal activity, thus demonstrating Bag3 as a regulator of HSC proteostasis. HSC aging is associated with loss of aggresomes and reduced autophagic flux. Protein degradation pathways are thus configured in young-adult HSCs to preserve proteostasis and fitness but become dysregulated during aging. Supported by ORIP (S10OD032316, S10OD021831), NCI, and NIDDK.


 Cerebrospinal Fluid Protein Markers Indicate Neuro-Damage in SARS-CoV-2-Infected Nonhuman Primates

Maity, Sudipa et al., Molecular & Cellular Proteomics. 2023 Apr;22(4):100523.

In this study, researchers examined the proteins expressed in cerebrospinal fluid (CSF) in nonhuman primates (NHPs) to better understand how COVID-19 infection can result in brain pathology, a common outcome. The study found that even in NHPs with minimal or mild COVID‑19, CSF proteins were significantly dysregulated compared with uninfected NHPs. Furthermore, the most affected proteins were enriched in the same brain regions that show lesions after COVID-19 infection, including the cerebral cortex, basal ganglia, and brain stem. Collectively, these regions have wide-ranging control over such crucial functions as cognition, motor control, and breathing, showing how even mild COVID-19 infection can result in significant neurological impairment. Supported by ORIP (P51OD011104, S10OD032453), NIGMS, NCI, and NICHD.


 Identification of a Heterogeneous and Dynamic Ciliome during Embryonic Development and Cell Differentiation

Elliott, Kelsey et al., Development. 2023 Apr 15;150(8):dev201237.

Ciliopathies are a class of diseases that arise when the structure or function of the cilium is compromised. To definitively determine the extent of heterogeneity within the ciliome, investigators compared the ciliomes of six distinct embryonic domains. The data comprehensively revealed that about 30% of the ciliome is differentially expressed across analyzed tissues in the developing embryo. Furthermore, upregulation of numerous ciliary genes correlated with osteogenic cell-fate decisions, suggesting that changes in the ciliome contribute to distinct functions of cell types in vertebrate species. Supported by ORIP (UM1OD023222), NIDCR, and NIGMS.


 Topologically Associating Domain Boundaries Are Required for Normal Genome Function

Rajderkar, Sudha et al., Communications Biology. 2023 Apr 20;6(1):435.

Eukaryotic genomes fold into topologically associating domains (TADs), sub-megabase-scale chromatin segments characterized by high intra-domain chromatin contact frequency. Investigators selected eight independent TAD boundaries in the vicinity of genes active during embryonic development, individually deleted these boundaries from the mouse genome, and systematically examined the consequences on survival, genome organization, gene expression, and development. Results of the studies demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to consider the potential pathogenicity of deletions affecting TAD boundaries in clinical genetics screening. Supported by ORIP (UM1OD023221), NIGMS, and NHGRI.


 Resolution of Structural Variation in Diverse Mouse Genomes Reveals Chromatin Remodeling due to Transposable Elements

Ferraj, Ardian et al., Cell Genomics. 2023 Apr 5;3(5):100291.

Diverse inbred mouse strains are important biomedical research models, yet genome characterization of many strains is fundamentally lacking in comparison with humans. Here, investigators used long-read whole genome sequencing to assemble the genomes of 20 diverse inbred laboratory strains of mice. From whole-genome comparisons, they generated a sequence-resolved callset of 413,758 structural variants. These data are presented as a comprehensive resource that can be used for future genomic studies, aid in modeling and studying the effects of genetic variation, and enhance genotype-to-phenotype research. Supported by ORIP (R24OD021325), NCI, NIGMS, and NHGRI.


 High-Resolution Genomes of Multiple Xiphophorus Species Provide New Insights into Microevolution, Hybrid Incompatibility, and Epistasis

Lu, Yuan et al., Genome Research. 2023 Apr;33(4):557–571.

Existing Xiphophorus genome assemblies are not at the chromosomal level and are prone to sequence gaps, hindering advancement of evolutionary, comparative, and translational biomedical studies. Investigators assembled high-quality chromosome-level genome assemblies for three distantly related Xiphophorus species. They found that expanded gene families and positively selected genes associated with live bearing. Positively selected gene families were enriched in nonpolymorphic transposable elements, suggesting that dispersal has accompanied the evolution of the genes, possibly by incorporating new regulatory elements. The investigators also characterized interspecific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related to specific disease states in humans. Supported by ORIP (R24OD011120, R24OD031467, R24OD011198) and NCI.


 An E1–E2 Fusion Protein Primes Antiviral Immune Signaling in Bacteria

Ledvina, Hannah et al., Nature. 2023 Apr;616(7956):319–325.

Investigators show that the cGAS/DncV–like nucleotidyltransferase (CD‑NTase)–associated protein 2 (Cap2) primes bacterial CD-NTases for activation through a ubiquitin transferase–like mechanism. A cryo-electron microscopy structure of the Cap2-CD-NTase complex reveals Cap2 as an all-in-one ubiquitin transferase–like protein, with distinct domains resembling eukaryotic E1 and E2 proteins. The structure captures a reactive-intermediate state with the CD-NTase C terminus positioned in the Cap2 E1 active site and conjugated to AMP. Cap2 conjugates the CD-NTase C terminus to a target molecule that primes the CD-NTase for increased cGAMP production. The investigators further demonstrate bacteria control immune signaling using an ancient, minimized ubiquitin transferase–like system and provide insight into the evolution of the E1 and E2 machinery across domains of life. Supported by ORIP (S10OD023498, S10OD021527, S10OD025267) and NIGMS.


 In Vivo MRI Is Sensitive to Remyelination in a Nonhuman Primate Model of Multiple Sclerosis

Donadieu, Maxime et al., eLife. 2023 Apr 21;12:e73786.

Experimental autoimmune encephalomyelitis (EAE) in the common marmoset is a model for studying inflammatory demyelination in multiple sclerosis (MS). Researchers investigated the feasibility and sensitivity of magnetic resonance imaging (MRI) in characterizing remyelination, a crucial step to recover from MS. Investigators demonstrated that multisequence 7T MRI could detect spontaneous remyelination in marmoset EAE at high statistical sensitivity and specificity in vivo. This study suggests that in vivo MR can be used for preclinical testing of therapeutic remyelinating agents for MS. Supported by ORIP (R21OD030163) and NINDS.


 Effect of Passive Administration of Monoclonal Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like Coil/Helical or β-Sheet Conformations on Time of SIVmac251 Acquisition

Stamos, James et al., Journal of Virology. 2023 Apr 27;97(4):e0186422.

Research suggests that the SIV variable region 2 (V2) is a region of virus vulnerability, likely because of its exposure on the apex of virions and on the surfaces of SIV-infected cells. Researchers examined the effects of two monoclonal antibodies, NCI05 and NCI09, on the acquisition of SIV using rhesus macaques (sex not specified). They found that NCI05, but not NCI09, delays SIV acquisition, highlighting the complexity of antibody responses to V2. Both antibodies were unable to decrease the risk of viral acquisition. This study demonstrates that such antibodies as NCI05 alone are insufficient to protect against SIV acquisition. Supported by ORIP (S10OD027000), NIAID, and NCI.


 Cannabinoid Enhancement of lncRNA MMP25-AS1/MMP25 Interaction Reduces Neutrophil Infiltration and Intestinal Epithelial Injury in HIV/SIV Infection

Premadasa, Lakmini et al., Journal of Clinical Investigation Insight. 2023 Apr 10;8(7):e167903.

Gastrointestinal CD4+ T cell depletion during acute simian immunodeficiency virus (SIV) and HIV infection causes significant structural and functional damage, disrupting intestinal immune homeostasis and leading to intestinal epithelial barrier dysfunction. Oral phytocannabinoids are safe and well tolerated in people with HIV, but more information is needed regarding the effects of long-term tetrahydrocannabinol (THC) use on the intestinal epithelial compartment. Investigators profiled gene expression in the colonic epithelium of SIV-infected rhesus macaques of both sexes that were administered THC. They reported that low-dose THC can reduce neutrophil infiltration and intestinal epithelial injury, potentially by downregulating MMP25 expression through modulation of a long noncoding RNA, MMP25-AS1. Supported by ORIP (P51OD011104, P51OD011103), NIAID, and NIDA.


 Effect of Viral Strain and Host Age on Clinical Disease and Viral Replication in Immunocompetent Mouse Models of Chikungunya Encephalomyelitis

Anderson et al., Viruses. 2023 May;15(5):1057.

Chikungunya virus (CHIKV) is associated with neurologic complications, but studies in the central nervous system are challenging to perform in humans. Using a mouse model of both sexes, researchers established the relative severity of neurological disease across multiple stages of neurodevelopment in three strains of CHIKV. The disease was found to be strain dependent, with differences in severity of neurological disease, viral titers in the brain and spinal cord, and proinflammatory gene expression and CD4+ T cell infiltration in the brain. This work provides a mouse model for future studies of CHIKV pathogenesis and the host immune response. Supported by ORIP (K58OD026529), NIAID, and NCI.


 CD8+ T Cells Promote HIV Latency by Remodeling CD4+ T Cell Metabolism to Enhance Their Survival, Quiescence, and Stemness

Mutascio et al., Immunity. 2023 May;56(5):1132–1147.e6.

An HIV reservoir persists following antiretroviral therapy, representing the main barrier to an HIV cure. Using a validated in vitro model, investigators explored the mechanism by which CD8+ T cells promote HIV latency and inhibit latency reversal in HIV-infected CD4+ T cells. They reported that CD8+ T cells favor the establishment of HIV latency by modulating metabolic, stemness, and survival pathways that correlate with the downregulation of HIV expression and promote HIV latency. In future studies, comparative analyses may provide insight into common molecular mechanisms in the silencing of HIV expression by CD8+ T cells and macrophages, which can be applied to new intervention strategies that target the HIV reservoir. Supported by ORIP (P51OD011132, S10OD026799), NIAID, NIDDK, NIDA, NHLBI, and NINDS.


 Exosome Cell Origin Affects In Vitro Markers of Tendon Repair in Ovine Macrophages and Tenocytes

von Stade et al., Tissue Engineering Part A. 2023 May;29(9-10):282–291.

The underlying pathogenesis of rotator cuff tendinopathy reflects a combination of intrinsic and extrinsic factors, and recent work suggests that cell-to-cell communication drives the severity of tendon changes. Researchers are interested in the role of extracellular vesicles in tendon mechanical resilience, tissue organization, and anti-inflammatory macrophage phenotype predominance in response to tendon injury. In this study, investigators demonstrated how exosomes differ functionally based on cell source. This work suggests that control of exosome composition could lead to more effective therapies for certain tissues. Supported by ORIP (K01OD022982) and NCATS.


 Ion Channel Function in Translational Bovine Gallbladder Cholangiocyte Organoids: Establishment and Characterization of a Novel Model System

Nagao and Ambrosini, Frontiers in Veterinary Science. 2023 May:10:1179836.

The study of biliary physiology and pathophysiology has long been hindered by the lack of in vitro models that accurately reflect the complex functions of the biliary system. Recent advancements in 3D organoid technology may offer a promising solution to this issue. Bovine gallbladder models have recently gained attention in the investigation of human diseases due to their remarkable similarities in physiology and pathophysiology to the human gallbladder. In this study, the investigators successfully established and characterized bovine gallbladder cholangiocyte organoids (GCOs) that retain key characteristics of the gallbladder in vivo, including stem cell properties and proliferative capacity. Notably, their findings demonstrate that these organoids exhibit specific and functional cystic fibrosis transmembrane conductance regulator activity. These bovine GCOs represent a valuable tool for studying the physiology and pathophysiology of the gallbladder with human significance. Supported by ORIP (K01OD030515, R21OD031903).


 Lipid Droplets and Peroxisomes Are Co-Regulated to Drive Lifespan Extension in Response to Mono-Unsaturated Fatty Acids

Papsdorf et al., Nature Cell Biology. 2023 May;25(5):672–684.

Investigators studied the mechanism by which mono-unsaturated fatty acids (MUFAs) extend longevity. They found that MUFAs upregulated the number of lipid droplets in fat storage tissues of Caenorhabditis elegans, and increased lipid droplets are necessary for MUFA-induced longevity and predicted remaining lifespan. Lipidomics data revealed that MUFAs modify the ratio of membrane lipids and ether lipids, which leads to decreased lipid oxidation in middle-aged individuals. MUFAs also upregulate peroxisome number. A targeted screen revealed that induction of both lipid droplets and peroxisomes is optimal for longevity. This study opens new interventive avenues to delay aging. Supported by ORIP (S10OD025004, S10OD028536, P40OD010440), NIA, NCCIH, NIDDK, and NHGRI.


 HIV, Asymptomatic STI, and the Rectal Mucosal Immune Environment Among Young Men Who Have Sex With Men

Van Doren et al., PLOS Pathogens. 2023 May;19(5):e1011219.

Young men who have sex with men (YMSM) are affected disproportionately by HIV and bacterial sexually transmitted infections (STIs) and therefore are likely to face an increased burden of associated chronic inflammation. Researchers studied the immunologic effects and interactions of HIV and bacterial STIs, as well as their effects on the rectal mucosal immune environment, among various populations of YMSM. Their findings suggest that asymptomatic bacterial STIs could contribute to inflammation, particularly among YMSM with HIV. This study provides insights into the immunopathogenesis of asymptomatic bacterial STIs and identifies a syndemic interaction between HIV and bacterial STIs in YMSM. Supported by ORIP (P51OD011132), NIAID, and NICHD.


 Probiotic Therapy During Vaccination Alters Antibody Response to Simian–Human Immunodeficiency Virus Infection But Not to Commensals

Wilson et al., AIDS Research and Human Retroviruses. 2023 May;39(5):222–231.

Strategies to boost vaccine-induced mucosal humoral responses are critical to developing an HIV-1 vaccine, and probiotic supplementation could help boost antibody responses. Researchers analyzed antibody titers to explore this topic in rhesus macaques (sex not specified) infected with simian–human immunodeficiency virus (SHIV). They reported that probiotic treatment during vaccination led to delayed kinetics in the circulating HIV-specific IgA response after breakthrough SHIV infection. These findings highlight the potential of probiotic supplementation for reducing IgA-specific HIV antibodies in the plasma, which could help reduce HIV acquisition in vaccinated individuals. Supported by ORIP (P51OD011104, R21OD031435) and NIAID.


 Association of Age at Menopause and Hormone Therapy Use With Tau and β-Amyloid Positron Emission Tomography

Coughlan et al., JAMA Neurology. 2023 May;80(5):462-473.

To understand the predominance (70%) of women among individuals with Alzheimer’s disease, the investigators studied regional tau and β-amyloid (Aβ) in relation to age at menopause and hormone therapy (HT) in postmenopausal women and age-matched men using positron emission tomography. The study demonstrated that females exhibited higher tau deposition compared with age-matched males, particularly in the setting of elevated Aβ; earlier age at menopause and late initiation of HT were associated with increased tau vulnerability. This study suggests female individuals with these conditions may be at higher risk of pathological burden. Supported by ORIP (S10OD025245), NIA, and NICHD.


 Cell-Type Memory in a Single-Cell Eukaryote Requires the Continuous Presence of a Specific Transcription Regulator

Lee, Chien-Der et al., PNAS. 2023 May 23;120(21):e2220568120.

Investigators studied the fundamental question and underlying mechanism of how a eukaryotic cell type can be stably maintained through many rounds of DNA replication and cell division in a fungal species where two different cell types (i.e., white and opaque) arise from the same genome. Investigators found that destruction of Wor1, the primary transcription activator of the opaque state, led opaque cells to irreversibly lose their memory and switch to the white-cell state within about 1 hour. This study demonstrates that the continuous presence of Wor1 is needed to maintain the opaque cell state. Data also suggested that a threshold concentration of Wor1 is needed to maintain the opaque state, indicating the importance of the transcription factor in maintaining cell-type memory. Supported by ORIP (S10OD028511), NIAID, and NIGMS.


 Giardia Hinders Growth by Disrupting Nutrient Metabolism Independent of Inflammatory Enteropathy

Giallourou, Natasa et al., Nature Communications. 2023 May 18;14(1):2840.

Giardia lamblia is one of the most common intestinal pathogens among children in low- and middle-income countries. Investigators performed translational investigations using the Malnutrition and Enteric Diseases (MAL-ED) male and female cohort, as well as mice of both sexes, to identify mechanistic pathways that might explain Giardia-induced effects on early childhood growth. They identified signatures in the urinary metabolome of young children, suggesting that host growth restriction during infection is mediated by dysregulated amino acid metabolism. Supported by ORIP (P40OD010995), NIAID, and NIDDK.


 Therapeutic Blocking of VEGF Binding to Neuropilin-2 Diminishes PD-L1 Expression to Activate Antitumor Immunity in Prostate Cancer

Wang, Mengdie et al., Science Translational Medicine. 2023 May 3;15(694):eade5855.

Prostate cancers often escape immune detection and destruction. Investigators report that neuropilin-2 (NRP2), which functions as a vascular endothelial growth factor (VEGF) receptor on tumor cells, is an attractive target to activate antitumor immunity in prostate cancer. They found that NRP2 depletion increased T cell activation in vitro. Additionally, inhibition of the binding of VEGF to NRP2 using a mouse-specific anti-NRP2 monoclonal antibody resulted in necrosis and tumor regression. These findings provide justification for the initiation of clinical trials using this function-blocking antibody in treatment of prostate cancer, especially for patients with aggressive disease. Supported by ORIP (R24OD026440) and NCI.


 Very-Long-Chain Fatty Acids Induce Glial-Derived Sphingosine-1-Phosphate Synthesis, Secretion, and Neuroinflammation

Chung, Hyung-Iok et al., Cell Metabolism. 2023 May 2;35(5):855–874.e5.

Very-long-chain fatty acids (VLCFAs) are the most abundant fatty acids in myelin. During age‑associated degeneration of myelin, glia are exposed to increased levels of VLCFAs. Investigators previously described a novel phenotype in patients that harbors a novel variant in the peroxisomal enzyme ACOX1. Here, they report that that glial loss of ACOX1 leads to an increase of VLCFAs, which results in a concomitant increase in sphingosine-1-phosphate (S1P). They found that suppressing S1P function attenuates the pathological phenotypes caused by excess VLCFAs. This work suggests that lowering of VLCFAs and S1P could be applied as a treatment avenue for multiple sclerosis. Supported by ORIP (R24OD022005, R24OD031447, P40OD018537), NINDS, and NICHD


 Using Mass Spectrometry Imaging to Map Fluxes Quantitatively in the Tumor Ecosystem

Schwaiger-Haber, Michaela et al., Nature Communications. 2023 May 19;14(1):2876.

Mass spectrometry imaging (MSI) can be used to identify metabolic patterns within different microenvironments of tumors but has not been fully integrated into metabolomics workflows. Investigators developed an integrated approach by combining MSI, stable isotope labeling, and a spatial variant of Isotopologue Spectral Analysis to study metabolic pathways across the brains of mice harboring GL261 glioma, a mouse model for glioblastoma. This study reveals the importance of multiple anabolic pathways, including fatty acid elongation flux, in glioma. Supported by ORIP (R24OD024624).


 Complement Contributes to Antibody-Mediated Protection against Repeated SHIV Challenge

Goldberg, Benjamin et al., PNAS. 2023 May 16;120(20):e2221247120.

The first clinical efficacy trials of a broadly neutralizing antibody (bNAb) resulted in less benefit than expected and suggested that improvements are needed to prevent HIV infection. Using rhesus macaques of both sexes, investigators sought to further investigate the contribution of antibody-mediated activation of complement to the protective potency of an HIV bNAb in passive transfer and simian–human immunodeficiency virus (SHIV) challenge experiments. They observed that fewer bNAbs were required to protect animals from plasma viremia when complement activity was enhanced, suggesting that complement-mediated effector functions contribute to in vivo antiviral activity and might contribute to further improvements in the efficacy of antibody-mediated prevention strategies. Supported by ORIP (P51OD011092, U42OD023038) and NIAID.


 Efficient Ex Vivo Expansion of Conserved Element Vaccine-Specific CD8+ T Cells from SHIV-Infected, ART-Suppressed Nonhuman Primates

Dross, Sandra et al., Frontiers in Immunology. 2023 May 3;14:1188018.

HIV-specific T cells are necessary for control of HIV-1 replication but are largely insufficient for viral clearance. Using male rhesus macaques, investigators sought to increase the frequency of specific T cell responses in vivo using an ex vivo cell manufacturing approach. The resulting products contained high frequencies of specific, polyfunctional T cells, but no significant differences in T cell persistence were observed, nor was acquisition of simian–human immunodeficiency virus (SHIV). This work underscores this animal model as an important approach to optimize the manufacturing of antigen-specific immune effectors that can prevent virus acquisition and control viral rebound after discontinuing antiretroviral therapy (ART). Supported by ORIP (P51OD010425, U42OD011123), NIAID, and NCI.


 Antibody-Dependent Cellular Cytotoxicity, Infected Cell Binding and Neutralization by Antibodies to the SIV Envelope Glycoprotein

Grunst, Michael et al., PLOS Pathogens. 2023 May 30;19(5):e1011407.

Antibodies that bind to the envelope glycoprotein (Env) on the surface of virus-infected cells can recruit cells from the immune system to kill infected cells by antibody-dependent cellular cytotoxicity (ADCC). Researchers characterized ADCC, Env binding, and neutralization in rhesus macaque antibodies that were specific for diverse epitopes of the simian immunodeficiency virus (SIV) envelope glycoprotein. They found that most antibodies that inhibit SIV infectivity also bind to Env on infected cells and mediate ADCC, but this trend was not observed in select instances. Based on these findings, the authors suggest that some antibody–Env interactions can uncouple antiviral activities. Supported by ORIP (P51OD011106) and NIAID.


 Infection of the Maternal–Fetal Interface and Vertical Transmission following Low-Dose Inoculation of Pregnant Rhesus Macaques (Macaca mulatta) with an African-Lineage Zika Virus

Koenig, Michelle et al., PLOS ONE. 2023 May 4;18(5):e0284964.

Researchers examined transmission of Zika virus to nonhuman primate fetuses during pregnancy. Even with a low dosage of inoculation of the dams, the investigators found that the Zika virus infected fetuses, despite the presence of a “placental fortress,” which normally protects fetuses during gestation. This transmission illustrates the high level of infectivity threat that Zika poses, which may increase if mosquitoes expand their global habitats. Understanding how Zika breaches the placental barrier will help researchers develop strategies to prevent fetal infection during pregnancy and thereby prevent adverse outcomes, such as brain malformation defects. Supported by ORIP (P51OD011106, S10OD023526), NIAID, NCI, and NIGMS.


 Innate Lymphoid Cells and Interferons Limit Neurologic and Articular Complications of Brucellosis

Moley, Charles et al., The American Journal of Pathology. 2023 May 30;S0002-9440(23)00198-0.

Brucellosis is a globally significant zoonotic disease. The current study investigated the role of innate lymphoid cells (ILCs) in the pathogenesis of focal brucellosis caused by Brucella melitensis. Following pulmonary infection with B. melitensis, mice lacking adaptive immune cells and ILCs developed arthritis, neurologic complications, and meningitis. Transcriptional analysis of Brucella-infected brains revealed marked upregulation of genes associated with inflammation and interferon responses. Collectively, these findings indicate that ILCs and interferons play an important role in prevention of focal complications during Brucella infection and that mice with deficiencies in ILCs or interferons can be used to study pathogenesis of neurobrucellosis. Supported by ORIP (T32OD011126) and NIAID.


 Effects of Acute Femoral Head Ischemia on the Growth Plate and Metaphysis in a Piglet Model of Legg-Calvé-Perthes Disease

Armstrong et al., Osteoarthritis and Cartilage. 2023 Jun;31(6):766–774.

Legg-Calvé-Perthes disease (LCPD) can lead to permanent deformity of the femoral head and premature osteoarthritis, but the underlying cause remains unknown. More work is needed to determine optimal treatment methods for LCPD. Using a piglet model for LCPD, researchers assessed the effects of acute femoral head ischemia on the proximal femoral growth plate and metaphysis. They reported that alterations to the growth plate zones and metaphysis occurred by 2 days post-ischemia and persisted at 7 days post-ischemia. These findings suggest that growth disruption may occur sooner after the onset of ischemia than researchers had hypothesized previously. Supported by ORIP (T32OD580993, K58OD021293), NIAMS, and NCATS.


 Lymph-Node-Based CD3+ CD20+ Cells Emerge From Membrane Exchange Between T Follicular Helper Cells and B Cells and Increase Their Frequency Following Simian Immunodeficiency Virus Infection

Samer et al., Journal of Virology. 2023 Jun;97(6):e5876022.

CD4+ T follicular helper cells are known to persist during antiretroviral therapy (ART) and have been identified as key targets for viral replication and persistence. Researchers identified a lymphocyte population that expresses CD3 (i.e., T cell lineage marker) and CD20 (i.e., B cell lineage marker) on the cellular surface in lymphoid tissues from rhesus macaques of both sexes and humans of male and female sexes. In macaques, the cells increased following simian immunodeficiency virus infection, were reduced with ART, and increased in frequency after ART interruption. These cells represent a potential area for future therapeutic strategies. Supported by ORIP (P51OD581132, U42OD581023), NIAID, NCI, NIDDK, NIDA, NHLBI, and NINDS.


 Brain Microglia Serve as a Persistent HIV Reservoir Despite Durable Antiretroviral Therapy

Tang et al., The Journal of Clinical Investigation. 2023 Jun;133(12):e167417.

Brain microglia are likely to play a role in rebound viremia following the cessation of antiretroviral therapy, but more work is needed to fully understand HIV persistence in the central nervous system (CNS). The investigators developed a protocol to isolate highly pure populations of brain myeloid cells and microglia from the tissues of male rhesus macaques, as well as from rapid autopsies of men and women with HIV. Their observations support the concept that brain microglia are a stable reservoir of quiescent infection. Thus, this work provides a physiologically relevant platform for studies of the biology of CNS reservoirs. Supported by ORIP (P51OD581132), NIAID, and NIMH.


 Early Detection of Pseudocapillaria tomentosa by qPCR in Four Lines of Zebrafish, Danio rerio (Hamilton 1882)

Schuster et al., Journal of Fish Diseases. 2023 Jun;46(6):619–627.

The intestinal nematode Pseudocapillaria tomentosa in zebrafish (Danio rerio) causes profound intestinal lesions, emaciation, and death and is a promoter of a common intestinal cancer in zebrafish. This nematode has been detected in an estimated 15% of zebrafish laboratories. Adult worms are readily detected about 3 weeks after exposure by either histology or wet mount preparations of the intestine, and larval worms are inconsistently observed in fish before this time. A quantitative PCR (qPCR) test was recently developed to detect the worm in fish and water, and here the authors determined that the test on zebrafish intestines was effective for earlier detection. Supported by ORIP (R24OD580998, P40OD581021).


 A LGR5 Reporter Pig Model Closely Resembles Human Intestine for Improved Study of Stem Cells in Disease

Schaaf, Cecilia et al., The FASEB Journal. 2023 Jun;37(6):e22975.

The constant epithelial regeneration in the intestine is the sole responsibility of intestinal epithelial stem cells (ISCs), which reside deep in the intestinal crypt structures. To effectively study ISCs, tools to identify this cell population are necessary. This study validates ISC isolation in a new porcine Leucine Rich Repeat Containing G Protein–Coupled Receptor 5 (LGR5) reporter line and demonstrates the use of these pigs as a novel colorectal cancer model. Overall, this novel porcine model provides critical advancement to the field of translational gastrointestinal research. Supported by ORIP (R21OD019738, K01OD019911), NCI, and NIDDK.


 Simultaneous Evaluation of Treatment Efficacy and Toxicity for Bispecific T-Cell Engager Therapeutics in a Humanized Mouse Model

Yang, Jiwon et al., The FASEB Journal. 2023 Jun;37(6):e22995.

Immuno-oncology-based therapies are an evolving powerful treatment strategy that targets the immune system and harness it to kill tumor cells directly. Investigators describe the novel application of a humanized mouse model that can simultaneously evaluate the efficacy of bispecific T cell engagers to control tumor burden and the development of cytokine release syndrome. The model also captures variability in responses for individual patients. Supported by ORIP (R24OD026440), NIAID, NCI, and NIDDK.


  p38MAPKα Stromal Reprogramming Sensitizes Metastatic Breast Cancer to Immunotherapy

Faget et al., Cancer Discovery. 2023 Jun 2;13(6):1454–1477. 

This study emphasizes the importance of the metastatic tumor microenvironment in metastatic breast cancer growth and the identification of effective antimetastatic therapies. Using a stromal labeling approach and single-cell RNA sequencing, the authors showed that a combination of p38MAPK inhibition (p38i) and anti-OX40 synergistically reduced metastatic tumor growth and increased overall survival. Further engagement of cytotoxic T cells cured all metastatic disease in mice and produced durable immunologic memory. The Cancer Genome Atlas data analysis revealed that patients with p38i metastatic stromal signature and a high tumor mutational burden (TMB) had increased overall survival. These findings suggest that patients with high TMB would benefit the most from the p38i plus anti-OX40 approach. Supported by ORIP (S10OD028483), NIA, NCI, and NIGMS.


 The Drosophila Chemokine-Like Orion Bridges Phosphatidylserine and Draper in Phagocytosis of Neurons

Ji, Hui et al., PNAS. 2023 Jun 13;120(24):e2303392120.

Degenerating neurons can be cleared by phagocytosis triggered by “eat-me” signal phosphatidylserine (PS) and mediated by the engulfment receptor Draper (Drpr), yet the process is poorly understood. Investigators used several Drosophila models to study dendrite degeneration and demonstrated that the fly chemokine-like protein Orion binds to PS and mediates interactions between PS and Drpr to enable phagocytosis. This study identifies a link between immunomodulatory proteins and phagocytosis of neurons and reveals conserved mechanisms of clearing degenerating neurons. Supported by ORIP (R24OD031953, R21OD023824, S10OD018516) and NINDS.


 A Global Catalog of Whole-Genome Diversity from 233 Primate Species

Kuderna, Lukas et al., Science. 2023 Jun 2;380(6648):906–913.

Researchers are interested in studying the remarkable diversity of morphology and behavior across primates to answer long‑standing questions in evolutionary and conservation biology. Using whole-genome sequencing, the investigators created a nuclear DNA phylogeny and reassessed evolutionary divergence times among primate clades. They found that intraspecies genetic diversity across families and geographic regions was associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differed among species, potentially influenced by effective population sizes. Lastly, they identified extensive recurrence of missense mutations that previously were thought to be human specific. Supported by ORIP (P40OD024628).


 The Landscape of Tolerated Genetic Variation in Humans and Primates

Gao, Hong et al., Science. 2023 Jun 2;380(6648):eabn8153.

Investigators created a whole-genome sequence database from 809 nonhuman primates (NHPs) of 233 species to test the hypothesis that gene variants that do not cause disease in NHPs would likely be benign also in humans. They found that 99% of the genetic variants that were benign in NHPs also were classified as benign in the human ClinVar database. In contrast, only 71% to 87% of genomic variants classified as benign in non-primate animals were benign in humans. Building on this approach, the authors reclassified more than 4 million human genetic variants of unknown health impact as likely being benign based on effects in NHPs. This work illustrates the power of comparative medicine approaches between NHPs and humans. Supported by ORIP (P40OD024628, P51OD011106) and NIGMS.


 Sequential Intrahost Evolution and Onward Transmission of SARS-CoV-2 Variants

Gonzalez-Reiche, Ana et al., Nature Communications. 2023 Jun 3;14(1):3235.

Most patients with COVID-19 clear the virus upon resolution of acute infection, but a subset of immunocompromised individuals develop persistent SARS-CoV-2 infections. In this study, investigators describe sequential persistent SARS-CoV-2 infections in three individuals that led to the emergence, forward transmission, and continued evolution of the Omicron BA.1 variant Omicron BA.1.23. The study demonstrated that in the presence of suboptimal immune responses, persistent viral replication is an important driver of SARS-CoV-2 diversification. This and other studies also highlight that strategies to prevent virus persistence and shedding and more effective therapies are needed to limit the spread of newly emerging, neutralization-resistant variants in vulnerable patients. Supported by ORIP (S10OD026880, S10OD030463), NIAID, and NCATS.


 Whole Genome Analysis for 163 gRNAs in Cas9-Edited Mice Reveals Minimal Off-Target Activity

Peterson, Kevin et al., Communications Biology. 2023 Jun 10;6(1):626.

CRISPR/Cas9 genome editing offers potential as a treatment for genetic diseases in humans. Using whole-genome sequencing, investigators assessed the occurrence of Streptococcus pyogenes Cas9–induced off-target mutagenesis in Cas9-edited founder mice. Sequencing and computational analysis indicate that the risk of Cas9 cutting at predicted off-target sites is lower than random genetic variation introduced into the genomes of inbred mice through mating. These findings will inform future design and use of Cas9-edited animal models and can provide context for evaluating off-target potential in genetically diverse patient populations. Supported by ORIP (UM1OD023221, UM1OD023222) and NHGRI.


 Phytochemical Compound PB125 Attenuates Skeletal Muscle Mitochondrial Dysfunction and Impaired Proteostasis in a Model of Musculoskeletal Decline

Musci, Robert et al., Journal of Physiology. 2023 Jun;601(11):2189–2216.

Age-related musculoskeletal decline contributes to disability and cardiometabolic diseases and is linked to impaired mitochondrial function and disrupted proteostasis. Using male and female Hartley guinea pigs, investigators tested a purported phytochemical activator of nuclear factor erythroid 2-related factor 2, which helps promote redox homeostasis, proteome maintenance, and mitochondrial energetics. They reported that the activator, PB125, improved mitochondrial respiration and attenuated disease- and age-related declines in skeletal muscle protein synthesis. This study provides insights for the development of interventions in humans. Supported by ORIP (T32OD010437) and NIA.


 GluN2B Inhibition Confers Resilience against Long-Term Cocaine-Induced Neurocognitive Sequelae

Li, Dan et al., Neuropsychopharmacology. 2023 Jun;48(7):1108–1117.

Cocaine self-administration can disrupt the capacity of humans and rodents to flexibly modify familiar behavioral routines, but effects on mechanistic factors—particularly those driving long-term behavioral changes—have not been characterized fully. Researchers used mice to examine the flexibility of decision-making behavior with oral cocaine self-administration. They found that GluN2B inhibition prevented cocaine-induced dysregulation of neuronal structure and function in the orbitofrontal cortex (OFC), preserving mature, mushroom-shaped dendritic spine densities on deep-layer pyramidal neurons. These findings suggest that cocaine potentiates GluN2B-dependent signaling, which triggers a series of durable adaptations that result in the dysregulation of post-synaptic neuronal structure in the OFC, ultimately weakening the capacity for flexible choice. Supported by ORIP (P51OD011132) and NINDS.


 Epigenetic Dysregulation From Chromosomal Transit in Micronuclei

Agustinus et al., Nature. 2023 Jul;619(7968):176–183.

The authors reported a mechanistic link between epigenetic alterations and chromosomal instability induced during their transit in micronuclei, both being hallmarks of advanced and metastatic cancers. It was demonstrated that the landscape of histone post-translational modifications was profoundly changed due to missegregation of mitotic chromosomes, their sequestration in micronuclei and subsequent rupture of the micronuclear envelope. The transcriptional redistribution was attributed to micronuclei’s strong positional bias with increased promoter accessibility. The continuous formation and reincorporation of micronuclei promotes epigenetic reprogramming and heterogeneity in cancer. Supported by ORIP (S10OD030286) and others.


 Osteopontin Is an Integral Mediator of Cardiac Interstitial Fibrosis in Models of Human Immunodeficiency Virus Infection

Robinson et al., The Journal of Infectious Diseases. 2023 Jul;228(2):122–132.

HIV infection is associated with increased risk of cardiovascular disease. Plasma osteopontin (Opn) is correlated with cardiac pathology, but more work is needed to understand the underlying mechanisms driving cardiac fibrosis. Researchers explored this topic using mouse embryonic fibroblasts, male macaques, and humanized mice of both sexes. They reported the accumulation of Opn in the heart with simian immunodeficiency virus infection. Systemic inhibition of Opn can prevent HIV-associated interstitial fibrosis in the left ventricle. These findings suggest that Opn could be a potential target for adjunctive therapies to reduce cardiac fibrosis in people with HIV. Supported by ORIP (P51OD581104), NIAID, NHLBI, NIMH, and NINDS.


 Allogeneic Immunity Clears Latent Virus Following Allogeneic Stem Cell Transplantation in SIV-Infected ART-Suppressed Macaques

Wu et al., Immunity. 2023 Jul;56(7):1649-1663.e5.

Allogeneic hematopoietic stem cell transplantation (alloHSCT) has been documented as curative for HIV, but the mechanisms are not yet known. Using Mauritian cynomolgus macaques of both sexes, researchers performed reduced-intensity alloHSCT experiments to define the individual contributions of allogeneic immunity and CCR5 deficiency to an alloHSCT-mediated HIV cure. They reported that allogeneic immunity was the major driver of reservoir clearance, mediating graft-versus-reservoir effects in HIV infection. Their results also point to a protective mechanism for CCR5 deficiency early during engraftment. Future efforts could focus on harnessing the beneficial effects of allogeneic immunity while avoiding graft-versus-host disease. Supported by ORIP (P51OD581092) and NIAID.


 Photoreceptor Disc Incisures Form as an Adaptive Mechanism Ensuring the Completion of Disc Enclosure

Lewis et al., eLife. 2023 Jul;12:e89160.

The first steps of vision take place within a stack of tightly packed disc-shaped membranes, or discs, located in the outer segment compartment of photoreceptor cells. In rod photoreceptors, discs are enclosed inside the outer segment and contain deep indentations in their rims called incisures. This presence of incisures has been documented in several species, yet their role remains elusive. This study demonstrated that incisures are formed only after discs become completely enclosed. At the earliest stage of their formation, discs are not round but rather are highly irregular in shape and resemble expanding lamellipodia. In genetically modified mice and frogs, researchers measuring outer segment protein abundances found that incisure size is determined by the molar ratio between peripherin-2, a disc rim protein critical for the process of disc enclosure, and rhodopsin, the major structural component of disc membranes. High perpherin-2-to-rhodopsin ratio causes an increase in incisure size and structural complexity; low ratio precludes incisure formation. They propose a model whereby normal rods express a modest excess of peripherin-2 over the amount required for complete disc enclosure to ensure that this important step of disc formation is accomplished. Once the disc is enclosed, the excess peripherin-2 incorporates into the rim to form an incisure. Supported by ORIP (P40OD580997, R24OD030008).


 Proteomic Profiling of Extracellular Vesicles Isolated From Plasma and Peritoneal Exudate in Mice Induced by Crotalus scutulatus scutulatus Crude Venom and Its Purified Cysteine-Rich Secretory Protein (Css-CRiSP)

Reyes et al., Toxins (Basel). 2023 Jul;15(7):434.

Toxins in viperid snakes can induce clinically heterogeneous effects, but most viper venoms are composed of only 10 main protein families. Researchers investigated the proteome expression profile of extracellular vesicles isolated from biofluid samples from male and female mice after injection with crude venom and cysteine-rich secretory proteins. They reported changes in the expression of proteins involved in cell adhesion, cytoskeleton rearrangement, signal transduction, immune responses, and vesicle-mediated transports. This work could be applied in future efforts for early detection and assessment of local effects. Supported by ORIP (P40OD580960), NIGMS, and NHLBI.


 A Comprehensive Drosophila Resource to Identify Key Functional Interactions Between SARS-CoV-2 Factors and Host Proteins

Guichard, Annabel et al., Cell Reports. 2023 Jul 20;42(8):112842.

To address how interactions between SARS-CoV-2 factors and host proteins affect COVID-19 symptoms, including long COVID, and facilitate developing effective therapies against SARS-CoV-2 infections, researchers reported the generation of a comprehensive set of resources, mainly genetic stocks and a human cDNA library, for studying viral–host interactions in Drosophila. Researchers further demonstrated the utility of these resources and showed that the interaction between NSP8, a SARS-CoV-2 factor, and ATE1 arginyltransferase, a host factor, causes actin arginylation and cytoskeleton disorganization, which may be relevant to several pathogenesis processes (e.g., coagulation, cardiac inflammation, fibrosis, neural damage). Supported by ORIP (R24OD028242, R24OD022005, R24OD031447), NIAID, NICHD, NIGMS, and NINDS.


 SALL1 Enforces Microglia-Specific DNA Binding and Function of SMADs to Establish Microglia Identity

Fixsen, Bethany et al., Nature Immunology. 2023 Jul;24(7):1188–1199.

Microglia function is thought to play a role in neurodevelopmental, psychiatric, and neurodegenerative diseases. Using knockout mice, investigators explored functional interactions between spalt-like transcription factor 1 (SALL1) and SMAD4, which demonstrated that interactions are mediated by a conserved microglia-specific SALL1 super-enhancer and result in direct activation of regulatory elements. The concerted interactions induce a microglia lineage determining program of gene expression. These findings indicate that expression of SALL1 and associated genes could contribute to phenotypes of aging and neurodegenerative diseases. Supported by ORIP (S10OD026929), NIA, NIMH, and NINDS.


 Diverse Targets of SMN2-Directed Splicing-Modulating Small Molecule Therapeutics for Spinal Muscular Atrophy

Ottesen, Eric et al., Nucleic Acids Research. 2023 Jul 7;51(12):5948–5980.

Spinal muscular atrophy (SMA) results from deletions or mutations of the SMN1 gene. SMN2 is a nearly identical copy of SMN1 but cannot compensate for its loss. Manipulation of splicing to restore SMN2 exon 7 inclusion provides a promising therapeutic avenue for SMA, and two small-molecule agents—risdiplam and branaplam—restore body-wide inclusion of the SMN2 exon 7 upon oral administration. In this study, researchers demonstrate the advantages of combined treatments with low doses of risdiplam and branaplam. These findings can be applied to develop the next generation of small‑molecule therapeutics, with a focus on better efficacies and fewer off-target effects. Supported by ORIP (T35OD027967) and NINDS.


 Canine Models of Charcot-Marie-Tooth: MTMR2, MPZ, and SH3TC2 Variants in Golden Retrievers With Congenital Hypomyelinating Polyneuropathy

Cook et al., Neuromuscular Disorders. 2023 Aug;33(8):677–691.

Both demyelination and hypomyelination of the nervous system are associated with various clinical diseases. Using whole-genome sequencing, researchers determined the genetic underpinnings of congenital hypomyelinating polyneuropathy in canines of both sexes. These variants genetically describe the first peripheral nervous system–exclusive hypomyelinating polyneuropathies in dogs. By testing for these mutations, breeders can prevent the production of affected offspring. Supported by ORIP (K58OD027051, K58OD027058).


 Focused Ultrasound–Mediated Brain Genome Editing

Lao et al., PNAS. 2023 Aug;120(34):e2302915820.

Gene editing in the brain has been challenging because of the restricted transport imposed by the blood–brain barrier (BBB). In this study, investigators described a safe and effective gene‑editing technique by using focused ultrasound (FUS) to transiently open the BBB for the transport of intravenously delivered CRISPR machinery to the brain. By combining FUS with adeno-associated virus–mediated gene delivery, researchers can achieve more than 25% editing efficiency of particular cell types. This method has the potential to expand toolkit options for CRISPR delivery and opens opportunities for treating diseases of the brain, such as neurodegenerative disorders, with somatic genome editing. Supported by ORIP (U42OD026635) and NINDS.


 A Germ-Free Humanized Mouse Model Shows the Contribution of Resident Microbiota to Human-Specific Pathogen Infection

Wahl et al., Nature Biotechnology. 2023 Aug;10.1038/s41587-023-58906-5.

Germ-free (GF) mice are of limited value in the study of human-specific pathogens because they do not support their replication. In this report, investigators developed a GF humanized mouse model using the bone marrow–liver–thymus platform to provide a robust and flexible in vivo model that can be used to study the role of resident microbiota in human health and disease. They demonstrated that resident microbiota promote viral acquisition and pathogenesis by using two human-specific pathogens, Epstein–Barr virus and HIV. Supported by ORIP (P40OD580995), FIC, NIAID, NCI, and NIDDK.


 Disentangling the Link Between Zebrafish Diet, Gut Microbiome Succession, and Mycobacterium chelonae Infection

Sieler et al., Animal Microbiome. 2023 Aug;5(1):38.

Despite the long-established importance of zebrafish (Danio rerio) as a model organism and their increasing use in microbiome-targeted studies, relatively little is known about how husbandry practices involving diet impact the zebrafish gut microbiome. Given the microbiome's important role in mediating host physiology and the potential for diet to drive variation in microbiome composition, the authors sought to clarify how three different dietary formulations that are commonly used in zebrafish facilities impact the gut microbiome. They report that diet drives the successional development of the gut microbiome, as well as its sensitivity to exogenous exposure. Consequently, investigators should carefully consider the role of diet in their microbiome zebrafish investigations, especially when integrating results across studies that vary by diet. Supported by ORIP (R24OD580998) and NIEHS.


 Preclinical Safety and Biodistribution of CRISPR Targeting SIV in Non-Human Primates

Burdo et al., Gene Therapy. 2023 Aug;10.1038/s41434-023-00410-4.

Nonhuman primates have served as a valuable resource to evaluate novel eradication and cure strategies for HIV infection. Using a male rhesus macaque model, researchers demonstrated the safety and utility of CRISPR gene-editing technology for targeting integrated simian immunodeficiency virus (SIV). Their work suggests that a single intravenous inoculation for HIV gene editing can be utilized to reach viral reservoirs throughout the body. Additionally, no off-target effects or abnormal pathology were observed. Taken together, these findings support the continued development of HIV eradicative cure strategies using CRISPR technology in humans. Supported by ORIP (P40OD582217, U42OD021458).


 The Contribution of Maternal Oral, Vaginal, and Gut Microbiota to the Developing Offspring Gut

Russell et al., Scientific Reports. 2023 Aug;13(1):13660.

The maturation process of the gut microbiota (GM) is an essential process for life-long health that is defined by the acquisition and colonization of microorganisms in the gut and the subsequent immune system induction that occurs during early life. To address significant knowledge gaps in this area, investigators characterized the neonatal fecal and ileal microbiota of entire litters of mice at multiple pre-weaning time-points. Results indicated that specific-pathogen-free mouse microbiotas undergo a dynamic and somewhat characteristic maturation process, culminating by roughly two to three weeks of age. Prior to that, the neonatal GM is more similar in composition to the maternal oral microbiota, as opposed to the vaginal and fecal microbiotas. Further studies are needed to expand our knowledge regarding the effect of these developmental exposures on host development. Supported by ORIP (U42OD580918, R03OD028259).


 Antiretroviral Therapy Ameliorates Simian Immunodeficiency Virus–Associated Myocardial Inflammation by Dampening Interferon Signaling and Pathogen Response in the Heart

Robinson et al., The Journal of Infectious Diseases. 2023 Aug;228(3):276–280.

HIV is associated with increased risk of cardiovascular disease, but the underlying mechanisms are not fully understood. Using RNA sequencing, investigators characterized the effects of simian immunodeficiency virus (SIV) infection on the hearts of male rhesus macaques. They demonstrated that SIV infection drives a canonical antiviral response in the heart, as well as dysregulation of genes involved in fatty acid shuttling and metabolism. Their findings suggest that antiretroviral therapy helps mitigate immune activation during viremic conditions and plays a cardioprotective role. Future studies are needed to assess the long-term effects of these dynamics. Supported by ORIP (P51OD581104), NIAID, NIMH, and NINDS.


 Downregulation of CCR5 on Brain Perivascular Macrophages in Simian Immunodeficiency Virus–Infected Rhesus Macaques

Hattler et al., Brain and Behavior. 2023 Aug;13(8):e3126.

C‐C chemokine receptor 5 (CCR5) is the major coreceptor for HIV entry into cells, but its specific expression and importance in brain pathogenesis have not been explored fully. Investigators characterized the number and distribution of CCR5‐positive cells in formalin-fixed brain tissue from male and female rhesus macaques with and without simian immunodeficiency virus, as well as men and women with and without HIV. They reported an increase in total CCR5‐positive cells in the brain with progression to AIDS and encephalitis. These findings support the potential value of combination therapy targeting CCR5‐low cells while simultaneously blocking spread to CCR5‐positive cells. Supported by ORIP (P51OD581104) and NIMH.


 Intradermal but Not Intramuscular Modified Vaccinia Ankara Immunizations Protect Against Intravaginal Tier2 Simian–Human Immunodeficiency Virus Challenges in Female Macaques

Bollimpelli et al., Nature Communications. 2023 Aug;14:4789.

Researchers have been exploring multiple strategies to develop an HIV vaccine. In this study, the investigators determined the immunogenicity and efficacy of intradermal and intramuscular routes of modified vaccinia Ankara (MVA) vaccination in female rhesus macaques. They found that both routes of MVA vaccination enabled control of viral replication, but only the intradermal vaccination was effective in protection against viral acquisition. Their findings suggest that the intradermal MVA vaccinations provide protection by modulating the innate and T helper responses. Taken together, this work underscores the importance of testing the influence of the route of immunization for HIV vaccines in humans. Supported by ORIP (P51OD581132, R24OD580976) and NIAID.


 Identification of an Anergic BND Cell–Derived Activated B Cell Population (BND2) in Young-Onset Type 1 Diabetes Patients

Stensland et al., The Journal of Experimental Medicine. 2023 Aug;220(8):e20221604.

B cells have been shown to play a role in the pathogenesis of type 1 diabetes (T1D), but the specificity, phenotype, and function of B cells in young-onset T1D is not understood fully. The investigators performed a cross-sectional analysis comparing insulin-reactive to tetanus-reactive B cells in the blood of male and female T1D patients and control participants using mass cytometry. They found elevated insulin-reactive BND2 cells in the blood and pancreatic lymph nodes of young-onset T1D donors. This work suggests that an antigen-specific B cell subset could contribute to the rapid progression of young-onset T1D. Supported by ORIP (K58OD028759) and NIDDK.


 A Gut-Restricted Glutamate Carboxypeptidase II Inhibitor Reduces Monocytic Inflammation and Improves Preclinical Colitis

Peters et al., Science Translational Medicine. 2023 Aug;15(708):eabn7491.

Many patients with moderate-to-severe inflammatory bowel disease (IBD) do not have adequate disease control, and glutamate carboxypeptidase II (GCPII) offers a promising target for therapeutic development. Researchers generated a class of GCPII inhibitors. They demonstrated that the inhibitor reduced monocytic inflammation in mice and protected against the loss of barrier integrity in primary human colon epithelial air–liquid interface monolayers. Their findings suggest that local inhibition of GCPII could be applied for the development of IBD therapeutics. Supported by ORIP (K58OD030517, T32OD581089), NIGMS, and NCCIH.


 Assessment of Various Standard Fish Diets on Gut Microbiome of Platyfish Xiphophorus maculatus

Soria et al., Journal of Experimental Zoology Part B. 2023 Aug;10.1002/jez.b.23218.

Diet is an important factor affecting experimental reproducibility and data integration across studies. Reference diets for nontraditional animal models are needed to control diet-induced variation. In a study of the dietary impacts on gut microbiome, researchers found that switching from a custom diet to zebrafish diets altered the Xiphophorus gut microbiome. Their findings suggest that diets developed specifically for zebrafish can affect the gut microbiome composition and might not be optimal for Xiphophorus. Supported by ORIP (R24OD581120, R24OD031467, P40OD581021) and NCI.


 Intestinal Microbiota Controls Graft-Versus-Host Disease Independent of Donor–Host Genetic Disparity

Koyama et al., Immunity. 2023 Aug;56(8):1876-1893.e8.

Allogeneic hematopoietic stem cell transplantation is a curative therapy for hematopoietic malignancies and non-malignant diseases, but acute graft-versus-host disease (GVHD) remains a serious complication. Specifically, severe gut GVHD is the major cause of transplant-related mortality. Here, the authors show that genetically identical mice, sourced from different vendors, had distinct commensal bacterial compositions, which resulted in significantly discordant severity in GVHD. These studies highlight the importance of pre-transplant microbiota composition for the initiation and suppression of immune-mediated pathology in the gastrointestinal tract, demonstrating the impact of non-genetic environmental determinants to transplant outcome. Supported by ORIP (S10OD028685), NIA, NCI, and NHLBI.


 Baseline Tumor Gene Expression Signatures Correlate With Chemoimmunotherapy Treatment Responsiveness in Canine B Cell Lymphoma

Dittrich et al., PLoS One. 2023 Aug;18(8):e0290428.

Pet dogs develop spontaneous diffuse large B cell lymphoma (DLBCL), and veterinary clinical trials have been employed to treat canine DLBCL and to inform clinical trials for their human companions. Investigators evaluated gene expression in lymph node aspirates from 18 trial dogs and defined good responders as those who relapsed after 90 days, and poor responders as those who relapsed prior to 90 days. They found increased CCND3 correlated with poor prognosis and increased CD36 correlated with good prognosis, as is observed in humans. These findings identify biomarkers that may help guide the choice of chemoimmunotherapy treatment in dogs. Supported by ORIP (K58OD028268) and NCI.


 A Novel Auxin-Inducible Degron System for Rapid, Cell Cycle–Specific Targeted Proteolysis

Capece et al., Cell Death & Differentiation. 2023 Sep;30(9):2078–2091.

The discrimination of protein biological functions in different phases of the cell cycle is limited by the lack of experimental approaches that do not require pre-treatment with compounds affecting the cell-cycle progression. Therefore, potential cycle-specific biological functions of a protein of interest could be biased by the effects of cell treatments. The OsTIR1/auxin-inducible degron (AID) system allows “on-demand” selective and reversible protein degradation upon exposure to the phytohormone auxin. However, this technology does not allow researchers to study the effect of acute protein depletion selectively in one phase of the cell cycle, as auxin similarly affects all the treated cells irrespective of their proliferation status. Therefore, the AID system requires coupling with cell synchronization techniques, which can alter the basal biological status of the studied cell population, as with previously available approaches. Here, the investigators introduce the Regulate OsTIR1 Levels based on the Cell Cycle Status (ROLECCS) system, which induces proteolysis of both exogenously transfected and endogenous gene-edited targets in specific phases of the cell cycle. They propose the use of the ROLECCS system as a new and improved way of studying the differential roles that target proteins may have in specific phases of the cell cycle. Supported by ORIP (K58OD031811) and NCI.


 Large-Scale Production of Human Blastoids Amenable to Modeling Blastocyst Development and Maternal-Fetal Crosstalk

Yu et al., Cell Stem Cell. 2023 Sep;30(9):1246-1261.e9.

Human blastoids provide a valuable model to study early human development and implantation with reduced genetic heterogeneity between samples. Investigators reported a protocol for efficient generation of high-fidelity human blastoids from naïve pluripotent stem cells. The similarities between blastoids and blastocysts in signaling activities—demonstrated using single-cell RNA sequencing—support the use of blastoids to model lineage differentiation and cavity formation. Additionally, endometrial stromal effects in promoting trophoblast cell survival, proliferation, and syncytialization during co-culture with blastoids demonstrated the capability to model maternal–fetal crosstalk. The protocol will facilitate broader use of human blastoids as an ethical model for human blastocysts. Supported by ORIP (S10OD028630) and others.


 Long-Acting Lenacapavir Protects Macaques Against Intravenous Challenge With Simian-Tropic HIV

Swanstrom et al., eBioMedicine. 2023 Sep;95:104764.

Pre-exposure prophylaxis (PrEP) is effective in preventing new HIV infections, but regimen adherence remains a challenge. Antiretrovirals with long-acting pharmacokinetic properties could help overcome this limitation. Researchers examined the protective efficacy of lenacapavir, a first-in-class HIV capsid inhibitor, using male pigtail macaques. They reported that a single administration of the drug provided protection from simian-tropic HIV infection. These data demonstrate the value of this nonhuman primate model and support the clinical development of long-acting lenacapavir for PrEP in humans. Future studies could further explore and refine the drug exposure–efficacy relationship. Supported by ORIP (P40OD028116), NIAID, and NCI.


 The Latent Reservoir of Inducible, Infectious HIV-1 Does Not Decrease Despite Decades of Antiretroviral Therapy

McMyn et al., The Journal of Clinical Investigation. 2023 Sep;133(17):e171554.

Antiretroviral therapy (ART) does not eliminate the latent HIV reservoir, but it is unknown whether sustained reservoir decay occurs with long-term ART. Researchers used a quantitative viral outgrowth assay, an intact proviral DNA assay, and proviral sequencing to characterize the latent reservoir in men and women with HIV who had maintained suppression of viral replication on ART for 14 to 27 years. They found that the reservoir decay did not continue with long-term ART. Further studies could provide insight into the mechanism underlying these findings. These results reinforce the need for lifelong ART and indicate that the reservoir remains a major barrier to an HIV-1 cure. Supported by ORIP (R58OD581095), NIAID, and NIDCR.


 Host-Derived Growth Factors Drive ERK Phosphorylation and MCL1 Expression to Promote Osteosarcoma Cell Survival During Metastatic Lung Colonization

McAloney et al., Cell Oncology. 2023 Sep;10.1007/s13402-023-00867-w.

Mortality from osteosarcoma is closely linked to lung metastasis, even though the lung appears to be a hostile environment for tumor cells. Using female mice, researchers assessed changes in both host and tumor cells during colonization. Their findings suggest that the mitogen-activated protein kinase (MAPK) pathway is significantly elevated in early and established metastases, which correlates with expression of anti-apoptotic genes (e.g., MCL1). The authors conclude that niche-derived growth factors drive increased MAPK activity and MCL1 expression in osteosarcoma, promoting metastatic colonization. This gene is a promising target for future therapeutic development. Supported by ORIP (K58OD031811), NCI, and NCATS.


 CD8+ Cells and Small Viral Reservoirs Facilitate Post-ART Control of SIV Replication in M3+ Mauritian Cynomolgus Macaques Initiated on ART Two Weeks Post-Infection

Harwood et al., PLOS Pathogens. 2023 Sep;19(9):e1581676.

A rare group of people infected with HIV can achieve sustainable HIV remission after antiretroviral therapy (ART) withdrawal, but the underlying mechanisms are not understood fully. A team of investigators observed post-treatment control in a cohort of male cynomolgus macaques that were initiated on ART 2 weeks post-infection. Additionally, they reported that the cynomolgus macaques had smaller acute reservoirs than similarly infected rhesus macaques. Collectively, these data suggest that a combination of small reservoirs and immune-mediated virus suppression contributes to post-treatment control in cynomolgus macaques. This model could be used in future studies to develop therapeutic interventions. Supported by ORIP (P51OD581106, P40OD028116), NIAID, and NCI.


 Spontaneous HIV Expression During Suppressive ART Is Associated With the Magnitude and Function of HIV-Specific CD4+ and CD8+ T Cells

Dubé et al., Cell Host Microbe. 2023 Sep;31(9):1507–1522.e5.

CD4+ and CD8+ T cells are essential in the control of simian immunodeficiency virus and HIV infections, but the mechanisms are not understood fully. Using multiplexed single-cell RNAflow-fluorescence in situ hybridization, researchers quantified and phenotyped viral reservoirs spontaneously expressing viral RNA and the p24 protein in primary clinical samples from men. They reported associations between active reservoirs and HIV-specific CD4+ and CD8+ T cells, and the active reservoirs were largely dominated by defective proviruses. Their findings suggest that viral reservoirs maintain HIV-specific responses during suppressive antiretroviral therapy (ART), and low-level viral gene expression by spontaneous reservoirs is sufficient to maintain anti-HIV adaptive immunity. Supported by ORIP (P51OD581092) and NIAID.


 Enhanced IL-17 Producing and Maintained Cytolytic Effector Functions of Gut Mucosal CD161+CD8+ T Cells in SIV-Infected Rhesus Macaques

Thirugnanam et al., Viruses. 2023 Sep;15(9):1944.

HIV infection is associated with the depletion of CD161-expressing CD4+ Th17 cells, but the effects on other IL-17–producing T cell subsets are not understood fully. Researchers characterized the functions of non-invariant CD161-expressing CD8+ T cell subpopulations in peripheral blood and mucosal tissues of rhesus macaques (sex not specified) during chronic simian immunodeficiency virus (SIV) infection. They demonstrated that cell frequencies and function were unaffected by infection, but enhanced IL-17 production capacity and sustained Th1-type and cytolytic functions were observed. This work suggests that CD161-expressing CD8+ T cells might have important functions in gut mucosal immunity during chronic HIV infection. Supported by ORIP (P51OD581104, S10OD026800), NIAID, NIDDK, and NIMH.


 A Defect in Mitochondrial Fatty Acid Synthesis Impairs Iron Metabolism and Causes Elevated Ceramide Levels

Dutta et al., Nature Metabolism. 2023 Sep;5(9):1595–1614.

Human mitochondrial enoyl coenzyme A reductase (Mecr), required for the last step of mitochondrial fatty acid synthesis (mtFAS), is linked to pediatric-onset neurodegeneration, but with unknown mechanisms. Researchers investigated phenotypes of mecr mutants in Drosophila and human-derived fibroblasts. They found that loss of function of Mecr in the whole body resulted in a defect in Fe-S cluster biogenesis and increased iron levels, leading to elevated ceramide levels and lethality in flies. Similar elevated ceramide levels and impaired iron homeostasis were observed human-derived fibroblasts with Mecr deficiency. Neuronal loss of Mecr led to progressive neurodegeneration in flies. This study pointed out a mechanistic link between mtFAS and neurodegeneration through Mecr. Supported by ORIP (R24OD022005, R24OD031447), NICHD, and NINDS.


 Body Stiffness Is a Mechanical Property That Facilitates Contact-Mediated Mate Recognition in Caenorhabditis elegans

Weng et al., Current Biology. 2023 Sep;33(17):3585-3596.e5.

Body stiffness is a mechanical property that facilitates contact-mediated mate recognition in Caenorhabditis elegans. Chemical cues have been extensively studied as sensory cures of mate recognition, whereas the role of mechanical cues is largely unknown. Investigators studied the link of the hypodermis and body stiffness with mate recognition and mating efficiency in the worm C. elegans. They found that worm males assess attractiveness of potential mates though contact-mediated cues determined by species, sex, and developmental stages of the hypodermis. Body stiffness maintained by a group of cuticular collagens is critical for mate recognition and mating efficiency. This study suggests the important role of mechanosensory cues in mate recognition and provides a platform for mechanistically studying social behavior. Supported by ORIP (R24OD023041, P40OD580440) and NINDS.


 The Eotaxin-1/CCR3 Axis and Matrix Metalloproteinase-9 Are Critical in Anti-NC16A IgE-Induced Bullous Pemphigoid

Jordan et al., The Journal of Immunology. 2023 Oct;211(8):1216–1223.

Bullous pemphigoid is associated with eosinophilic inflammation and circulating and tissue-bound IgG and IgE autoantibodies. Researchers previously established the pathogenicity of anti-NC16A IgE through passive transfer of patient-derived autoantibodies to double-humanized mice. In this study, they characterized the molecular and cellular events that underlie eosinophil recruitment and eosinophil-dependent tissue injury. Their work establishes the eotaxin-1/CCR3 axis and matrix metalloproteinase-9 as key players in the disease and as candidate therapeutic targets for drug development and testing. Supported by ORIP (T32OD581130) and NIAMS.


 Effects of Pulsatile Intravenous Follicle-Stimulating Hormone Treatment on Ovarian Function in Women With Obesity

Luu et al., Fertility and Sterility. 2023 Oct;120(4):890–898.

By performing intravenous (IV) administration of pulsatile recombinant follicle-stimulating hormone (FSH), researchers established conditions for effective hypothalamic suppression in women with normal and high body mass index (BMI). In women with obesity, the treatment resulted in E2 and inhibin B levels comparable to those in normal-weight women. This work offers a potential strategy to mitigate some of the adverse effects of high BMI on fertility, assisted reproduction, and pregnancy outcomes. Supported by ORIP (K58OD026526), NIA, and NICHD.


 Zebrafish as a High Throughput Model for Organ Preservation and Transplantation Research

Da Silveira Cavalcante et al., The FASEB Journal. 2023 Oct;37(10):e23187.

Organ transplantation increases the quality of life and life expectancy of patients with chronic end-stage diseases, but the preservation of organs for transplantation remains a significant barrier. In the current study, researchers demonstrate the value of zebrafish as a high-throughput model organism in the fields of solid-organ preservation and transplantation, with a focus on heart preservation via partial freezing. Their techniques have the potential to advance research in the fields of cryobiology and solid-organ transplantation. Supported by ORIP (R24OD031955) and NHLBI.


 First-in-Human ImmunoPET Imaging of COVID-19 Convalescent Patients Using Dynamic Total-Body PET and a CD8-Targeted Minibody

Omidvari et al., Science Advances. 2023 Oct;9(41):eadh7968.

Developing noninvasive methods for in vivo quantification of T cell distribution and kinetics is important because most T cells reside in the tissue. Investigators presented the first use of dynamic positron emission tomography (PET) and kinetic modeling for in vivo measurement of CD8+ T cell distribution in healthy individuals and COVID-19 patients. Kinetic modeling results aligned with the expected T cell trafficking effects. Tissue-to-blood ratios were consistent with modeled net influx rates and flow cytometry analysis. These results provide a promising platform for using dynamic PET to study the total-body immune response and memory. Supported by ORIP (S10OD588223) and NCI.


 Increased Collective Migration Correlates With Germline Stem Cell Competition in a Basal Chordate

Fentress and De Tomaso, PLOS One. 2023 Oct;18(10):e0291104.

Cell competition is a process that compares the relative fitness of progenitor cells and results in healthier cells, contributing a higher proportion to the final tissue composition. Investigators are studying cell competition in a novel model organism, the colonial ascidian, Botryllus schlosseri. They demonstrated that winner germline stem cells show enhanced migratory ability to chemotactic cues ex vivo and that enhanced migration correlates with both expression of the Notch ligand, Jagged, and cluster size. The ability to study conserved aspects of cell migration makes Botryllus an excellent model for future studies on competition, chemotaxis, and collective cell migration. Supported by ORIP (R21OD030520) and NIGMS.


 Biphasic Decay of Intact SHIV Genomes Following Initiation of Antiretroviral Therapy Complicates Analysis of Interventions Targeting the Reservoir

Kumar et al., PNAS. 2023 Oct;120(43):e2313209120.

The latent HIV-1 reservoir persists with antiretroviral therapy (ART), and assays for quantifying intact proviruses in nonhuman primate models are needed. Researchers used a simian–human immunodeficiency virus (SHIV) intact proviral DNA assay to describe viral decay during the first year of ART in female rhesus macaques. Their results suggest that intact SHIV genomes in circulating CD4+ T cells undergo biphasic decay during the first year of ART, with a rapid first phase and a slower second phase. These findings can provide insight for future studies using SHIV models, as well as new cure interventions. Supported by ORIP (R58OD581095) and NIAID.


 AZD5582 Plus SIV-Specific Antibodies Reduce Lymph Node Viral Reservoirs in Antiretroviral Therapy–Suppressed Macaques

Dashti et al., Nature Medicine. 2023 Oct;29(10):2535–2546.

Researchers are interested in targeting the HIV reservoir via a latency reversal and clearance approach. Previously, investigators demonstrated that AZD5582 induces systemic latency reversal in rhesus macaques and humanized mice, but a consistent reduction in the viral reservoir was not observed. In the current study, they combined AZD5582 with four simian immunodeficiency virus (SIV)–specific rhesus monoclonal antibodies using rhesus macaques of both sexes. They reported a reduction in total and replication-competent SIV DNA in lymph node–derived CD4+ T cells in the treated macaques. These findings provide proof of concept for the potential of the latency reversal and clearance HIV cure strategy. Supported by ORIP (P51OD581132, R58OD581095), NIAID, NCI, and NHLBI.


 Timing of Initiation of Anti-Retroviral Therapy Predicts Post-Treatment Control of SIV Replication

Pinkevych et al., PLOS Pathogens. 2023 Oct;19(10):e1581660.

Researchers are interested in approaches to reducing viral rebound following interruption of antiretroviral therapy, but more work is needed to understand major factors that determine the viral “setpoint” level. Researchers previously assessed how timing of treatment can affect the frequency of rebound from latency. In the current study, the authors analyzed data from multiple studies of simian immunodeficiency virus (SIV) infection in rhesus macaques to further explore the dynamics and predictors of post-treatment viral control. They determined that the timing of treatment initiation was a major predictor of both the level and the duration of post-rebound SIV control. These findings could help inform future treatments. Supported by ORIP (U42OD581023, P51OD581132, P51OD581092), NIAID, NCI, NIDA, NIDDK, NHLBI, NIMH, and NINDS.


 CD8+ T Cells Control SIV Infection Using Both Cytolytic Effects and Non-Cytolytic Suppression of Virus Production

Policicchio et al., Nature Communications. 2023 Oct;14(1):6657.

HIV continuously evades and subdues the host immune responses through multiple strategies, and an understanding of these strategies can help inform research efforts. Using a mathematical model, investigators assessed whether CD8+ cells from male rhesus macaques exert a cytolytic response against infected cells prior to viral production. Their goal was to elucidate the possible mode of action of CD8+ cells on simian immunodeficiency virus (SIV)–infected cells. Models that included non‑cytolytic reduction of viral production best explained the viral profiles across all macaques, but some of the best models also included cytolytic mechanisms. These results suggest that viral control is best explained by the combination of cytolytic and non-cytolytic effects. Supported by ORIP (P40OD028116, R58OD581095), NIAID, NIDDK, and NHLBI.


 Interferon Regulatory Factor 7 Modulates Virus Clearance and Immune Responses to Alphavirus Encephalomyelitis

Troisi et al., Journal of Virology. 2023 Oct;97(10):e0095923.

Interferon regulatory factor 7 (IRF7)–deficient mice develop fatal paralysis after CNS infection with Sindbis virus, while wild-type mice recover. Irf7-/- mice produce low levels of IFN-α but high levels of IFN-β with induction of IFN-stimulated genes, so the reason for this difference is not understood. The current study shows that Irf7-/- mice developed inflammation earlier but failed to clear virus from motor neuron–rich regions of the brainstem and spinal cord. Therefore, IRF7 is either necessary for the neuronal response to currently identified mediators of clearance or enables the production of additional antiviral factor(s) needed for clearance. Supported by ORIP (T32OD581089, K58OD026529) NINDS, and NIAID.


 Allelic Strengths of Encephalopathy-Associated UBA5 Variants Correlate Between In Vivo and In Vitro Assays

Pan et al., eLife. 2023 Oct;10.1158/2023.07.17.23292782.

The UBA5 gene is associated with developmental and epileptic encephalopathy 44 (DEE44), an autosomal recessive disorder, in humans. The link between UBA5 variants and severity of DEE44, however, is not established. Investigators developed humanized fly models carrying a series of patient UBA5 variants. These flies showed differences in survival rates, developmental progress, life span, and neurological well-being. The severity of these defects correlated strongly with functional defects of UBA5 variants, allowing the classification of UBA5 loss-of-function variants into mild, intermediate, and severe allelic strengths in patients. This study provides resources for systematic investigation of the mechanistic link between UBA5 variants and DEE44 and for developing diagnostic approaches. Supported by ORIP (R24OD022005, R24OD031447, U54OD035865) and NCATS.


 High Throughput Analysis of B Cell Dynamics and Neutralizing Antibody Development During Immunization With a Novel Clade C HIV-1 Envelope

Mopuri et al., PLoS Pathogens. 2023 Oct 25;19(10):e1011717.

Broadly neutralizing antibodies from chronic infection are an area of interest for HIV-1 vaccine development. Using male and female rhesus macaques, a team of researchers conducted a high-throughput longitudinal study to determine how B cells respond to vaccines expressing different HIV-1 Env immunogens. In most animals, the B cells failed to achieve neutralizing activity. One animal, however, developed neutralizing antibodies against the vaccine strain. These data suggest that early elicitation might favor the induction of neutralizing antibodies against HIV-1 Env. This work offers new insights for autologous neutralizing antibody lineages. Supported by ORIP (P51OD011132, S10OD026799) and NIAID.


 Vpr Attenuates Antiviral Immune Responses and Is Critical for Full Pathogenicity of SIVmac239 in Rhesus Macaques

Laliberté et al., iScience. 2023 Oct 26;26(12):108351.

The accessory viral protein R (Vpr) exhibits multilayered functions, and more work is needed to understand its roles in viral replication, immune evasion, and pathogenicity in vivo. Using male and female rhesus macaques, researchers examined how deletion of vpr affects simian immunodeficiency virus (SIV) replication kinetics, innate immune activation, B- and T-cell responses, and neutralizing activity. They found that lack of Vpr delays and attenuates viral replication during acute infection, allowing most animals to mount efficient and persisting immune responses and higher levels of neutralizing antibodies. Overall, these results suggest that Vpr promotes viral replication and innate immune evasion during acute SIV infection. Supported by ORIP (P51OD011133, P51OD011132, S10OD026799).


 HIV-1 Remission: Accelerating the Path to Permanent HIV-1 Silencing

Lyons et al., Viruses. 2023 Oct 28;15(11):2171.

Current HIV treatment strategies are focused on forced proviral reactivation and elimination of reactivated cells with immunological or toxin-based technologies. Researchers have proposed the use of a novel “block-lock-stop” approach, which entails the long-term durable silencing of viral expression and permanent transcriptional deactivation of the latent provirus. In the present study, the authors present this approach and its rationale. More research is needed to understand the (1) epigenetic architecture of integrated provirus, (2) cell types and epigenetic cell states that favor viral rebound, (3) molecular functions of Tat (a protein that controls transcription of HIV) and host factors that prevent permanent silencing, (4) human endogenous retrovirus silencing in the genome, and (5) approaches to generate defective proviruses. Additionally, community engagement is crucial for this effort. Supported by ORIP (K01OD031900), NIAID, NCI, NIDA, NIDDK, NHLBI, NIMH, and NINDS.


 Simian Immunodeficiency Virus and Storage Buffer: Field-Friendly Preservation Methods for RNA Viral Detection in Primate Feces

Wilde et al., mSphere. 2023 Nov;8(6):e00484-23.

Simian immunodeficiency virus (SIV) infects more than 40 nonhuman primate (NHP) species in sub-Saharan Africa, but testing in wild NHP populations can be challenging. Researchers compared methods for SIV RNA preservation and recovery from NHP fecal samples stored in four different buffers. The goal of this work was to identify a robust “field-friendly” method (i.e., without freezing or refrigeration) for this effort, and the samples were collected from a mantled guereza colobus housed at the Columbus Zoo and Aquarium. The authors reported that the DNA/RNA shield is an optimal buffer for preserving SIV RNA in fecal samples in the field. Their findings will inform future fieldwork and facilitate improved approaches for studies of SIV and other RNA viruses. Supported by ORIP (P51OD011132) and NIAID.


 IL-21-IgFc Immunotherapy Alters Transcriptional Landscape of Lymph Node Cells Leading to Enhanced Flu Vaccine Response in Aging and SIV Infection

Pallikkuth et al., Aging Cell. 2023 Nov;22(11):e13984.

Aging is associated with increased risk of seasonal flu disease burden and serious flu-related complications, particularly for people with HIV. In this study, investigators aimed to elucidate the immunomodulation following flu vaccination in aging male and female rhesus macaques infected with simian immunodeficiency virus (SIV). Their results suggest that IL-21 treatment at the time of flu vaccination modulates the inductive lymph node germinal center activity to reverse SIV-associated immune dysfunction. The authors identified IL-21 as a potential candidate molecule for immunotherapy to enhance flu vaccine responses in affected populations. Further studies could examine the overall benefit of IL-21 immunotherapy on mucosal lung immunity and protection against infection. Supported by ORIP (R24OD010947), NIA, and NIAID.


 A SACS Deletion Variant in Great Pyrenees Dogs Causes Autosomal Recessive Neuronal Degeneration

Ekenstedt et al., Human Genetics. 2023 Nov;142(11):1587–1658.

ARSACS (autosomal recessive spastic ataxia of Charlevoix-Saguenay) is an early-onset, slowly progressive neurodegenerative disorder. To date, no naturally occurring large animal model has been reported for ARSACS. In this study, the authors describe a novel spontaneous genetic model for SACS-associated neuronal degeneration using Great Pyrenees dogs of both sexes. The canine models described in this study fit closely with the typical early‑onset ARSACS phenotype in humans, and molecular genetic studies demonstrated that these dogs exhibit a deleterious SACS mutation. The clinical and histopathological descriptions of this canine disorder contribute to the description of human ARSACS. Supported by ORIP (K58OD027051).


 Global Frequency Analyses of Canine Progressive Rod-Cone Degeneration-Progressive Retinal Atrophy and Collie Eye Anomaly Using Commercial Genetic Testing Data

Clark et al., Genes (Basel). 2023 Nov;14(11):2093.

Hundreds of genetic variants associated with canine traits and disorders have been identified; however, the geographic distributions and changes in allele and genotype frequencies over prolonged, continuous periods of time are lacking. This study utilized a large set of genotypes from dogs tested for progressive rod-cone degeneration-progressive retinal atrophy (prcd‑PRA) and collie eye anomaly (CEA). Both diseases exhibited significant differences in genotype frequencies (p=2.7 × 10-152 for prcd-PRA and 0.023 for CEA) with opposing graphical trends. This study shows that genetic testing informed breeding decisions to produce fewer affected dogs. Supported by ORIP (K58OD027051).


 The Power of the Heterogeneous Stock Rat Founder Strains in Modeling Metabolic Disease

Wagner et al., Endocrinology. 2023 Nov;164(12):bqad157.

Metabolic diseases are a host of complex conditions, including obesity, diabetes mellitus, and metabolic syndrome. Endocrine control systems (e.g., adrenals, thyroid, gonads) are causally linked to metabolic health outcomes. In this study, investigators determined novel metabolic and endocrine health characteristics in both sexes of six available substrains similar to the N/NIH Heterogeneous Stock (HS) rat founders. This deep-phenotyping protocol provides new insight into the exceptional potential of the HS rat population to model complex metabolic health states. The following hypothesis was tested: The genetic diversity in the HS rat founder strains represents a range of endocrine health conditions contributing to the diversity of cardiometabolic disease risks exhibited in the HS rat population. Supported by ORIP (R24OD024617), NHLBI, NIGMS and NIDDK.


 DAZL Knockout Pigs as Recipients for Spermatogonial Stem Cell Transplantation

Lara et al., Cells. 2023 Nov;12(21):2582.

Spermatogonial stem cell (SSC) transplantation is a technique that holds potential for addressing male infertility, as well as generation of genetically modified animal models. DAZL (Deleted in Azoospermia–Like) is a conserved RNA-binding protein important for germ cell development, and DAZL knockout (KO) causes defects in germ cell commitment and differentiation. Investigators characterized DAZL-KO pigs as SSC transplantation recipients. DAZL-KO pigs support donor-derived spermatogenesis following SSC transplantation, but low spermatogenic efficiency currently limits their use for the production of offspring. Supported by ORIP (R58OD586575) and NIGMS.


 Broad Receptor Tropism and Immunogenicity of a Clade 3 Sarbecovirus

Lee et al., Cell Host and Microbe. 2023 Nov;31(12):1961–1973.

Investigators showed that the S glycoprotein of the clade 3 sarbecovirus PRD-0038 in the African Rhinolophus bat has a broad angiotensin-converting enzyme 2 (ACE2) usage and that receptor-binding domain (RBD) mutations further expand receptor promiscuity and enable human ACE2 utilization. They generated a cryogenic electron microscopy structure of the RBD bound to ACE2, explaining receptor tropism and highlighting differences between SARS-CoV-1 and SARS-CoV-2. PRD‑0038 S vaccination elicits greater titers of antibodies cross-reacting with vaccine-mismatched clade 2 and clade 1a sarbecoviruses, compared with SARS-CoV-2. These findings underline a potential molecular pathway for zoonotic spillover of a clade 3 sarbecovirus, as well as the need to develop pan-sarbecovirus vaccines and countermeasures. Supported by ORIP (S10OD032290, S10OD026959, S10OD021644), NIAID, NCI, and NIGMS.


 Intravenous Bacille Calmette–Guérin Vaccination Protects Simian Immunodeficiency Virus–Infected Macaques From Tuberculosis

Larson et al., Nature Microbiology. 2023 Nov;8(11):2080–2092.

People with HIV are susceptible to developing tuberculosis and experiencing associated complications. Researchers assessed the safety, immunogenicity, and efficacy of intravenous Bacille Calmette–Guérin vaccination in male and female cynomolgus macaques coinfected with simian immunodeficiency virus (SIV) and Mycobacterium tuberculosis. The vaccine conferred protection in all vaccinated SIV-naive animals and in 9 of 12 vaccinated SIV-infected animals. These data suggest that the vaccine is immunogenic and efficacious in SIV-infected animals. Overall, this work establishes a model to identify correlates of protection, and these findings can be applied in future studies to develop effective vaccine regimens for people with HIV. Supported by ORIP (P51OD581106, K58OD033539) and NIAID.


 A Combined Adjuvant Approach Primes Robust Germinal Center Responses and Humoral Immunity in Non-Human Primates

Phung et al., Nature Communications. 2023 Nov;14(1):7107.

Protein antigens require adjuvants for high immunogenicity, and delivery kinetics are a critical component of rational HIV vaccine design. Investigators employed a combined adjuvant approach (i.e., short phosphoserine peptide linkers that promote tight binding to aluminum hydroxide, plus saponin/MPLA nanoparticles) with slow antigen delivery and potent immune-stimulating complexes in rhesus macaques of both sexes. They reported that pSer-modified antigen shifts immunodominance to allow subdominant epitope-targeting of rare B cells. These findings indicate that a combined adjuvant approach can augment humoral immunity by modulating immunodominance, and this work can be applied for the development of clinical therapeutics. Supported by ORIP (P51OD581104) and NIAID.


 Prime Editing–Mediated Correction of the CFTR W1282X Mutation in iPSCs and Derived Airway Epithelial Cells

Li et al., PLOS One. 2023 Nov;18(11):e0295009.

Cystic fibrosis (CF) is caused by recessive mutations in the CF transmembrane conductance regulator (CFTR) gene. Correction of nonsense CFTR mutations, which affects 10% of CF patients, via genomic editing represents a promising therapeutic approach. In this study, investigators tested whether prime editing can be applied as a potential therapeutic modality. Induced pluripotent stem cells (iPSCs) from a CF patient homozygous for the CFTR W1282X mutation were used. Studies demonstrated that prime editing corrected mutant allele in iPSCs, which effectively restored CFTR function in iPSC-derived airway epithelial cells and organoids. Supported by ORIP (R58OD026594).


 The Impact of SIV-Induced Immunodeficiency on Clinical Manifestation, Immune Response, and Viral Dynamics in SARS-CoV-2 Coinfection

Melton et al., bioRxiv. 2023 Nov 16:2023.11.15.567132.

The effects of immunodeficiency caused by chronic HIV infection on COVID-19 have not been directly addressed in a controlled setting. Investigators conducted a pilot study in which two pigtail macaques (PTMs) chronically infected with SIVmac239 were exposed to SARS-CoV-2 and compared with SIV-naive PTMs infected with SARS-CoV-2. Despite the marked decrease in CD4+ T cells in the SIV-positive animals prior to exposure to SARS-CoV-2, investigators found that disease progression, viral persistence, and evolution of SARS-CoV-2 were comparable to the control group. These findings suggest that SIV-induced immunodeficiency alters the immune response to SARS-CoV-2 infection, leading to impaired cellular and humoral immunity. However, this impairment does not significantly alter the course of infection. Supported by ORIP (P51OD011104, U42OD013117, S10OD026800, S10OD030347) and NIAID.


 Conjugation of HIV-1 Envelope to Hepatitis B Surface Antigen Alters Vaccine Responses in Rhesus Macaques

Nettere et al., NPJ Vaccines. 2023 Nov 24;8(1):183.

Researchers are interested in developing an HIV-1 vaccine that improves upon the regimen used in the RV144 clinical trial. The authors tested the hypothesis that a conjugate vaccine based on the learned response to immunization with hepatitis B virus could be utilized to expand T-cell help and improve antibody production against HIV-1. Using juvenile rhesus macaques of both sexes, they evaluated the immunogenicity of their conjugate regimen. Their findings suggest that conjugate vaccination can engage both HIV-1 Env– and hepatitis B surface antigen–specific T­cell help and modify antibody responses at early time points. This work may help inform future efforts to improve the durability and efficacy of next-generation HIV vaccines. Supported by ORIP (P51OD011107, K01OD024877) and NIAID.


 Host Immunity Associated With Spontaneous Suppression of Viremia in Therapy-Naive Young Rhesus Macaques Following Neonatal SHIV Infection

Evangelous et al., Journal of Virology. 2023 Nov 30;97(11):e0109423.

Previously, investigators developed a pediatric rhesus macaque model for simian–human immunodeficiency virus infection that can be exploited to identify host immunity associated with viremia suppression. In the present study, they used the model (with male and female animals) to characterize humoral and cellular immunity and plasma biomarkers associated with spontaneous viremia suppression. They identified CD8-expressing cells and varied T-cell subsets that were associated with viremia suppression. Additionally, the authors observed intermediate monocytes with upregulation of inhibitory genes that previously had been reported only in cytotoxic cells. These findings suggest a complex immunologic milieu of viremia suppression in pediatric populations. Supported by ORIP (P51OD011092, U42OD010426) and NIAID.



 Lymphoid Tissues Contribute to Plasma Viral Clonotypes Early After Antiretroviral Therapy Interruption in SIV-Infected Rhesus Macaques

Solis-Leal et al., Science Translational Medicine. 2023 Dec;15(726):eadi9867.

Researchers are interested in better understanding the sources, timing, and mechanisms of HIV rebound that occurs after interruption of antiretroviral therapy (ART). Using rhesus macaques (sex not specified), investigators tracked barcoded simian immunodeficiency virus (SIV) clonotypes over time and among tissues. Among the tissues studied, mesenteric lymph nodes, inguinal lymph nodes, and spleen contained viral barcodes detected in plasma. Additionally, the authors reported that CD4+ T cells harbored the most viral RNA after ART interruption. These tissues are likely to contribute to viral reactivation and rebound after ART interruption, but further studies are needed to evaluate the relative potential contributions from other tissues and organs. Supported by ORIP (P51OD011104, P51OD011133, S10OD028732, S10OD028653), NCI, NIMH, and NINDS.


 Age-Associated DNA Methylation Changes in Xenopus Frogs

Morselli et al., Epigenetics. 2023 Dec;18(1):2258517.

Age-associated changes in DNA methylation have not been characterized yet in amphibians, which include widely studied model organisms. Here the authors present clear evidence that the aquatic vertebrate species Xenopus tropicalis displays patterns of age-associated changes in DNA methylation. Whole-genome bisulfite sequencing profiles from skin samples of frogs representing young, mature, and old adults demonstrated that many of the methylation features and changes they observed are consistent with what is known in mammalian species, suggesting that the mechanism of age-related changes is conserved. The results of this study will allow researchers to leverage the unique resources available for Xenopus to study how DNA methylation relates to other hallmarks of aging. Supported by ORIP (R24OD031956, P40OD580997, R24OD030008) and NICHD.


 Tenth Aquatic Models of Human Disease Conference 2022 Workshop Report: Aquatics Nutrition and Reference Diet Development

Sharpton et al., Zebrafish. 2023 Dec;20(6):243–249.

Standard reference diets (SRDs) for aquatic model organisms, vital for supporting scientific rigor and reproducibility, are yet to be adopted. At this workshop, the authors presented findings from a 7-month diet test study conducted across three aquatic research facilities: Zebrafish International Resource Center (University of Oregon), Kent and Sharpton laboratories (Oregon State University), and Xiphophorus Genetic Stock Center (Texas State University). They compared the effects of two commercial diets and a suggested zebrafish SRD on general fish husbandry, microbiome composition, and health in three fish species (zebrafish, Xiphophorus, and medaka), and three zebrafish wild-type strains. They reported outcomes, gathered community feedback, and addressed the aquatic research community's need for SRD development. Discussions underscored the influence of diet on aquatic research variability, emphasizing the need for SRDs to control cross-experiment and cross-laboratory reproducibility. Supported by ORIP (P40OD581021, R24OD581120, and R24OD580998) and NICHD.


 Investigation of Monoclonal Antibody CSX-1004 for Fentanyl Overdose

Bremer et al., Nature Communications. 2023 Dec 5;14(1):7700.

The opioid crisis in the United States is primarily driven by the highly potent synthetic opioid fentanyl and has led to more than 70,000 overdose deaths annually; thus, new therapies for fentanyl overdose are urgently needed. Here, the authors present the first clinic-ready, fully human monoclonal antibody CSX-1004 with picomolar affinity for fentanyl and related analogs. In mice, CSX-1004 reverses fentanyl antinociception and the intractable respiratory depression caused by the ultrapotent opioid carfentanil. Using a highly translational nonhuman primate model for respiratory depression, they demonstrate CSX-1004-mediated protection from repeated fentanyl challenges for 3–4 weeks. These data establish the feasibility of CSX-1004 as a promising candidate medication for preventing and reversing fentanyl-induced overdose. Supported by ORIP (P40OD010938) and NIDA.


 Deep Analysis of CD4 T Cells in the Rhesus CNS During SIV Infection

Elizaldi et al., PLOS Pathogens. 2023 Dec 7;19(12):e1011844.

Systemic HIV infection results in chronic inflammation that causes lasting damage to the central nervous system (CNS), despite long-term antiretroviral therapy (ART). Researchers studied neurocognitive outcomes in male and female rhesus macaques infected with simian immunodeficiency virus (SIV) using an ART regimen simulating suboptimal adherence; one group received no ART, and the other received ART with periodic interruptions. Using single-cell transcriptomic profiling, the researchers also identified molecular programs induced in the brain upon infection. They found that acute infection led to marked imbalance in the CNS CD4/CD8 T‑cell ratio, which persisted into the chronic phase. The studies provide insight into the role of CD4 T cells in the CNS during HIV infection. Supported by ORIP (P51OD011107, K01OD023034), NIA, NIAID, and NCI.




 Complement Blockade in Recipients Prevents Delayed Graft Function and Delays Antibody-mediated Rejection in a Nonhuman Primate Model of Kidney Transplantation

Eerhart et al. in Transplantation.

Investigators evaluated the efficacy of a high-dose recombinant human C1 esterase inhibitor (rhC1INH) in preventing delayed graft function (DGF) in a rhesus macaque (RM) model of kidney transplantation after brain death and prolonged cold ischemia. The majority (4 of 5) of vehicle-treated recipients developed DGF, whereas DGF was observed in only 1 of 8 rhC1INH-treated recipients. RM treated with rhC1INH also had faster creatine recovery, superior urinary output, and reduced biomarkers of allograft injury for the first week. The results suggest high-dose C1INH treatment in transplant recipients is an effective strategy to reduce kidney injury and inflammation, prevent DGF, delay antibody-mediated rejection development, and improve transplant outcomes. Supported by ORIP (P51OD011106) NIAID, and NIDDK.


 Immune Correlates Analysis of the mRNA-1273 COVID-19 Vaccine Efficacy Clinical Trial

Gilbert et al. in Science.

Investigators determined that antibodies are the correlate of protection in vaccinated individuals enrolled in the Moderna coronavirus efficacy phase 3 clinical trial. Vaccine recipients were assessed for neutralizing and binding antibodies as correlates of risk for COVID-19 disease and as correlates of protection. All markers were inversely associated with COVID-19 risk and directly associated with vaccine efficacy. These results help define immune marker correlates of protection and may guide approval decisions for messenger RNA (mRNA) COVID-19 vaccines and other COVID-19 vaccines. Supported by ORIP (S10OD028685).


 Protection from SARS-CoV-2 Delta One Year after mRNA-1273 Vaccination in Rhesus Macaques Coincides with Anamnestic Antibody Response in the Lung

Gagne et al. in Cell.

Efficacy of the vaccine mRNA-1273 against SARS-CoV-2 Delta decreases with time, yet there are limited data on how durability of immune responses affects protection. Researchers immunized male rhesus macaques with mRNA-1273 and challenged them with Delta one year later. Serum neutralizing antibody responses to Delta and protection in upper airway were low one year after mRNA-1273 vaccination. However, mRNA-1273 provided durable protection against Delta in the lower airway and against severe lung disease one year after vaccination, likely through anamnestic induction of antibody responses in the lung. These findings highlight the importance of booster shots for sustained upper and lower airway protection. Supported by ORIP (P51OD011132), NIAID, Emory Executive Vice President for Health Affairs Synergy Fund, Woodruff Health Sciences Center, and Pediatric Research Alliance Center for Childhood Infections and Vaccines.


 Neuroinflammatory Profiling in SIV-Infected Chinese-Origin Rhesus Macaques on Antiretroviral Therapy

Solis-Leal, Antonio et al., Viruses. 2022 Jan;14(1):139.

The central nervous system (CNS) HIV reservoir contributes to residual neuroimmune activation, which can lead to HIV-associated neurocognitive disorder. Researchers characterized the expression of signaling molecules associated with inflammation in plasma, cerebrospinal fluid, and basal ganglia of Chinese-origin rhesus macaques (sex not specified) with simian immunodeficiency virus (SIV). They reported a correlation between levels of CCL2 in plasma and cerebrospinal fluid, suggesting that researchers could infer the degree of CNS inflammation by testing CCL2 levels in peripheral blood. Overall, these findings provide insight into neuroinflammation and signaling associated with HIV persistence in the CNS. Supported by ORIP (P51OD011104, P51OD011133), NIMH, and NINDS.


 Reduced Infant Rhesus Macaque Growth Rates due to Environmental Enteric Dysfunction and Association with Histopathology in the Large Intestine

Hendrickson, Sara et al., Nature Communications. 2022 Jan;13(1):234.

Researchers characterized environmental enteric (relating to the intestines) dysfunction (EED) among infant rhesus macaques (n=80, both sexes) naturally exposed to enteric pathogens commonly linked to human growth stunting. Despite atrophy and abnormalities observed in the small intestine, poor growth trajectories and low serum tryptophan (an amino acid needed for protein and enzymes) levels were correlated with increased histopathology (microscopic tissue examination for disease manifestation) in the large intestine. This study provides insight into the mechanisms underlying EED and indicates that the large intestine may be an important target for therapeutic intervention. Supported by ORIP (P51OD011092, P51OD011107) and NIGMS.


 Estimation of the In Vivo Neutralization Potency of eCD4Ig and Conditions for AAV-Mediated Production for SHIV Long-Term Remission

Goyal, Ashish et al., Science Advances. 2022 Jan;8(2):eabj5666.

The engineered protein eCD4Ig, a synthetic antibody-like inhibitor designed to limit HIV entry into cells, shows promise as an approach to achieve HIV remission without antiretroviral therapy. Researchers used mathematical modeling to characterize in vivo antiviral neutralization of eCD4Ig, as well as possible antibody-dependent cell-mediated cytotoxicity effects, in rhesus macaques infected with simian–human immunodeficiency virus (SHIV) (sex not specified). The research team modeled SHIV and pharmacokinetics dynamics and projected the levels of eCD4Ig needed with a viral vector production approach to suppress SHIV viremia. The data suggest that endogenous, continuous expression of eCD4Ig could overcome the diminishing effects of antidrug antibodies and allow long-term remission of SHIV viremia in nonhuman primates. Supported by ORIP (P51OD011132) and NIAID.


 Expression, Activity, and Regulation of Phosphorylating Enzymes in Tissues and Cells Relevant to HIV-1 Sexual Transmission

Hu, Minlu et al., AIDS Research and Human Retroviruses. 2022 Jan;38(1):22–32.

Phosphorylating enzymes (PEs) are critical for activating nucleoside/nucleotide reverse transcriptase inhibitors (e.g., tenofovir [TFV]), but limited information is available about the expression of PEs in the female genital tract and colon tissue. Investigators compared the mRNA expression of seven PEs involved in metabolism of TFV in cervicovaginal and colon tissues. This work involved human, pigtailed macaque, and rabbit tissues; human cervicovaginal epithelial cell lines; T cell lines; and primary CD4+ T cells. Taken together, this study suggests that TFV activation differs among immune cells and local tissues under varying conditions. Additionally, the variability of PE expression levels found across species provides critical information to assist with the interpretation of data obtained using these animal models. Supported by ORIP (P51OD010425) and NIAID.


 AAV5 Delivery of CRISPR-Cas9 Supports Effective Genome Editing in Mouse Lung Airway

Liang, Shun-Qing et al., Molecular Therapy (Journal of the American Society of Gene Therapy). 2022 January 5;30(1):238-243. doi: 10.1016/j.ymthe.2021.10.023. Epub 2021 October 23. PMID: 34695545; PMCID: PMC8753568.

Genome editing in the lung has the potential to provide long-term expression of therapeutic protein to treat lung genetic diseases. Liang et al. illustrated that AAV5 can efficiently deliver CRISPR-Cas9 to mouse lung airways and was the first to achieve ∼20% editing efficiency in those airways. Results were confirmed through independent experiments at two different institutes. This highly efficient dual AAV platform will facilitate the study of genome editing in the lung and other tissue types. Supported by ORIP U42OD026645 and awarded to Drs. Jason D. Heaney, Mary E. Dickinson and William R. Lagor at Baylor College of Medicine, Houston, TX, USA.


 Heritability of Social Behavioral Phenotypes and Preliminary Associations with Autism Spectrum Disorder Risk Genes in Rhesus Macaques: A Whole Exome Sequencing Study

Gunter, Chris et al., Autism Research (official journal of the International Society for Autism Research). 2022 January 29. doi: 10.1002/aur.2675. Epub ahead of print. PMID: 35092647.

Investigators quantified individual variation in social interactions among juvenile rhesus macaques (n= 212, both sexes) using both a standard macaque ethogram (a catalogue of animal behavior over time) and a macaque-relevant modification of the human Social Responsiveness Scale to study genetic influences on key aspects of social behavior and interactions. The analyses demonstrate that various aspects of juvenile social behavior exhibit significant genetic heritability, with quantitative genetic effects similar to the autism spectrum disorder (ASD) in human children. The significant genetic and sequencing data may be used to examine potential genetic associations with human ASD. Supported by ORIP (P51OD011132), NIGRI and NIMH. 


 Functional and Ultrastructural Analysis of Reafferent Mechanosensation in Larval Zebrafish

Odstrcil, Iris, et al., Current Biology. 2022 January 10;32(1):176-189.e5. PMC8752774

All animals need to differentiate between exafferent stimuli (caused by the environment) and reafferent stimuli (caused by their own movement). Researchers characterized how hair cells in zebrafish larvae discriminate between reafferent and exafferent signals. Dye labeling of the lateral line nerve and functional imaging was combined with ultra-structural EM circuit reconstruction to show that cholinergic signals originating from the hindbrain transmit efference copies and dopaminergic signals from the hypothalamus may affect threshold modulation. Findings suggest that this circuit is the core implementation of mechanosensory reafferent suppression in these young animals. Supported by ORIP Small Business grants (R43OD024879, R44OD024879) and NINDS.


 Simian Immunodeficiency Virus Infection Mediated Changes in Jejunum and Peripheral SARS-CoV-2 Receptor ACE2 and Associated Proteins or Genes in Rhesus Macaques

Boby, Nongthombam et al., Frontiers in Immunology. 2022 Feb;13:835686.

Recent studies suggest that people with HIV—particularly those not receiving antiretroviral therapy or those with low CD4 cell counts—are at increased risk of severe illness from SARS‑CoV-2 coinfection. Angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, is likely to play an important role in modulating physiological and pathological events during HIV infection. In this study, the researchers used a rhesus macaque model to characterize the expression profiles of ACE2, other renin-angiotensin system (RAS)–associated genes (AGTR1/2, ADAM17, and TMPRSS2), and inflammatory cytokines (IL-1β, IL-6, and TNF‑α) in the jejunum and lung during simian immunodeficiency virus (SIV) infection. SIV infection was associated with multiple changes in gene expression, including downregulation of ACE2, which could lead to loss of gut homeostasis. Further studies could provide insight on the role of RAS-associated proteins during HIV and SARS-CoV-2 co-infection. Supported by ORIP (P51OD011104) and NIDDK.


 Characterization of Near Full-Length Transmitted/Founder HIV-1 Subtype D and A/D Recombinant Genomes in a Heterosexual Ugandan Population (2006–2011)

Balinda, Sheila et al., Viruses. 2022 Feb;14(2):334.

About 80 percent of heterosexual HIV-1 transmission events are thought to be attributable to a single transmitted/founder (T/F) virus. Studies of HIV T/F viruses could yield valuable insights on transmission and help inform the design of vaccines and therapeutics. To date, most T/F studies have focused on subtype B and C viruses; few studies have focused on subtype D. In this study, the researchers characterized near full-length T/F viral genomes to identify subtype D and A/D recombinants from heterosexual mucosal transmissions in humans. They reported high viral diversity and high pathogenicity, underscoring the importance of matching vaccine designs to the predominant subtypes within populations. Further studies of the full genome sequence could provide additional information for subtyping. Supported by ORIP (P51OD011132) and NIAID.


 CAR/CXCR5–T Cell Immunotherapy Is Safe and Potentially Efficacious in Promoting Sustained Remission of SIV Infection

Pampusch, Mary et al., PLOS Pathogens. 2022 Feb;18(2):e1009831.

HIV and simian immunodeficiency virus (SIV) replication are concentrated within the B cell follicles of secondary lymphoid tissues. In this study, the researchers developed immunotherapeutic chimeric antigen receptor (CAR) T cells that home to follicles and clear SIV-infected cells in a rhesus macaque model. The CAR T cells localized to the follicle, replicated, and interacted directly with infected cells. Most of the treated animals maintained lower viral loads in the blood and follicles, compared to control animals. These findings demonstrate the safety and potential efficacy of this immunotherapy approach for long-term remission of HIV without requiring the lifelong use of antiretroviral therapy. Supported by ORIP (P51OD011106), NIAID, and NHLBI.


 Vaccine-Induced, High-Magnitude HIV Env-Specific Antibodies with Fc-Mediated Effector Functions Are Insufficient to Protect Infant Rhesus Macaques against Oral SHIV Infection

Curtis, Alan et al., mSphere. 2022 Feb;7(1):e0083921.

A tailored, effective HIV vaccine is needed to prevent mother-to-child viral transmission. In nonhuman primate models, infection with simian–human immunodeficiency virus (SHIV) can be prevented by administering broadly neutralizing HIV envelope (Env)–specific antibodies. Investigators tested the efficacy of an intramuscular vaccine regimen against SHIV infection in male and female infant rhesus macaques. The vaccine induced Env-specific antibodies in plasma, with antibody-dependent cellular cytotoxicity and phagocytic function. These antibodies, however, were insufficient for protection against infection. Future studies could focus on improving the breadth of antibody response and improving cell-mediated immunity. Supported by ORIP (P51OD011107), NCI, NIAID, and NIDCR.


 The Early Life Microbiota Mediates Maternal Effects on Offspring Growth in a Nonhuman Primate

Petrullo, Lauren et al., iScience. 2022 Feb;25(3):103948.

Mammalian mothers influence offspring development by providing nutrients and other bioactive compounds through the placenta or milk. A relatively unexplored mechanism for maternal effects is vertical transmission of bacteria through milk to the infant gut. Infants that receive more glycan-utilizing bacteria from milk might better exploit oligosaccharides, which could improve nutrition and accelerate growth. Researchers found that first-time vervet mothers harbored a milk bacterial community that was less diverse due to the dominance of Bacteroides fragilis, a glycan-utilizing bacteria. These low-parity females had infants that grew faster, suggesting that vertical transmission of bacteria via milk can mediate maternal effects on growth. These results indicate non-nutritive milk constituents play important roles in development. Commercial milk formula might need to be improved or supplemented to better support infant health. Supported by ORIP (P40OD010965) and NCATS.


 Progression and Resolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Golden Syrian Hamsters

Mulka, Kathleen et al., The American Journal of Pathology. 2022 Feb;192(2):195–207.

To catalyze SARS-CoV-2 research, disease progression was characterized in a robust model. Male and female golden Syrian hamsters were inoculated intranasally with SARS-CoV-2 to track clinical, pathology, virology, and immunology outcomes. Inoculated animals lost body weight during the first week of infection, had higher lung weights at terminal time points, and developed lung consolidation. At day 7, when the presence of infectious virus was rare, interstitial and alveolar macrophage infiltrates and marked reparative epithelial responses dominated in the lung. These lesions resolved over time. The use of quantitative approaches to measure cellular and morphologic alterations in the lung provides valuable outcome measures for developing therapeutic and preventive interventions for COVID-19. Supported by ORIP (T32OD011089).


 Natural Disaster and Immunological Aging in a Nonhuman Primate

Watowich, Marina M., et al., Proceedings of the National Academy of Sciences of the United States of America. 2022 February 22;119(8):e2121663119. PMC8872742

Weather-related disasters can exacerbate existing morbidities and increase mortality risk. Researchers examined Hurricane Maria’s impact on immune cell gene expression in large, age-matched, cross-sectional samples from free-ranging rhesus macaques (Macaca mulatta) living on an isolated island. Hurricane Maria was significantly associated with differential expression of 4% of immune-cell-expressed genes and were correlated with age-associated alterations in gene expression in addition to expression of key immune genes, dysregulated proteostasis networks, and greater expression of inflammatory immune cell-specific marker genes. These findings illuminate that natural disasters might become biologically embedded and contribute to earlier onset of disease and death. Supported by ORIP (P40 OD012217), NIA, NIMH.


 Complex Decay Dynamics of HIV Virions, Intact and Defective Proviruses, and 2LTR Circles Following Initiation of Antiretroviral Therapy

White, Jennifer A. et al., Proc Natl Acad Sci USA. 2022 Feb 8;119(6):e2120326119. 

In people living with HIV-1 (PLWH) who start antiretroviral therapy (ART), virus in blood decreases rapidly to below detection, but remaining infected cells may become part of the latent reservoir. Researchers investigated viral decay dynamics and identified decay processes with pronounced differences between intact and defective proviruses. Infected cells that survive second-phase decay may down-regulate HIV-1 gene expression and enter the stable latent reservoir. This research provides insight into meaningful latent reservoir markers and mechanisms for elimination of cells with intact viral genomes. Supported by ORIP (R01OD011095), NIAID, U.S. Department of Energy, Bill and Melinda Gates Foundation, and Howard Hughes Medical Institute.


 Phagocytosis by an HIV Antibody Is Associated with Reduced Viremia Irrespective of Enhanced Complement Lysis

Spencer, David A. et al., Nature Communications. 2022 Feb 3;13(1):662. 

Researchers used the bNAb 10E8v4 targeting the HIV Env protein to examine the role of antibody-mediated effector and complement (C’) activity when 10E8v4 was administered prophylactically to rhesus monkeys challenged with simian-human immunodeficiency virus (SHIV). With sub-protective dosing, the researchers found a 78–88% reduction in post-acute viremia that was associated with 10E8v4-mediated phagocytosis. These results suggest that effector functions inherent to unmodified 10E8v4 contribute to therapeutic efficacy against SHIV, while C’ functions do not contribute to efficacy in this context. This research informs the design of bNAb modifications for improving the protective efficacy of this therapeutic approach against HIV. Supported by ORIP (P51OD011092, U42OD023038) and NIAID.


 A novel wireless ECG system for prolonged monitoring of multiple zebrafish for heart disease and drug screening studies

Le T et al. Biosens Bioelectron. 2022 Feb 1;197:113808. doi: 10.1016/j.bios.2021.113808. Epub 2021 Nov 16.

Zebrafish and their mutant lines have been extensively used in cardiovascular studies. In the current study, the novel system, Zebra II, is presented for prolonged electrocardiogram (ECG) acquisition and analysis for multiple zebrafish within controllable working environments. The Zebra II is composed of a perfusion system, apparatuses, sensors, and an in-house electronic system. First, the Zebra II is validated in comparison with a benchmark system, namely iWORX, through various experiments. The validation displayed comparable results in terms of data quality and ECG changes in response to drug treatment. The effects of anesthetic drugs and temperature variation on zebrafish ECG were subsequently investigated in experiments that need real-time data assessment. The Zebra II's capability of continuous anesthetic administration enabled prolonged ECG acquisition up to 1 h compared to that of 5 min in existing systems. The novel, cloud-based, automated analysis with data obtained from four fish further provided a useful solution for combinatorial experiments and helped save significant time and effort. The system showed robust ECG acquisition and analytics for various applications including arrhythmia in sodium induced sinus arrest, temperature-induced heart rate variation, and drug-induced arrhythmia in Tg(SCN5A-D1275N) mutant and wildtype fish. The multiple channel acquisition also enabled the implementation of randomized controlled trials on zebrafish models. The developed ECG system holds promise and solves current drawbacks in order to greatly accelerate drug screening applications and other cardiovascular studies using zebrafish. Supported by ORIP (R44 OD024874), NHLBI, NSF


 Using the Autofluorescence Finder on the Sony ID7000TM Spectral Cell Analyzer to Identify and Unmix Multiple Highly Autofluorescent Murine Lung Populations

Wanner, Nicholas et al., Frontiers in Bioengineering and Biotechnology. 2022 Mar;10:827987.

The investigators explored a new imaging approach to detect faint fluorescent signals that are masked in the background of cell types that emit high‑intensity autofluorescence (AF) signals in a flow cytometry panel. Using a novel AF finder tool on the Sony ID7000™ spectral cell analyzer, the investigators studied multiple AF subsets in complex and heterogeneous murine lung single-cell suspensions. Major immune and lung tissue resident cells in a murine model of asthma were easily identified in a multi-color panel using AF subtraction. The findings demonstrate the practicality of the AF finder tool, particularly when analyzing samples with multiple AF populations of varying intensities, to reduce fluorescence background and increase signal resolution in spectral flow cytometry. Supported by ORIP (S10OD025207) and NHLBI.


 Presence of Natural Killer B Cells in Simian Immunodeficiency Virus–Infected Colon That Have Properties and Functions Similar to Those of Natural Killer Cells and B Cells but Are a Distinct Cell Population

Cogswell, Andrew et al., Journal of Virology. 2022 March;96(7):e0023522.

HIV infection of the gut is associated with increased mucosal inflammation, and the role of natural killer B (NKB) cells in this process requires further investigation. In this study, the researchers used rhesus and cynomolgus macaque models to characterize the function and characteristics of NKB cells in response to simian immunodeficiency virus (SIV) infection. They reported that NKB cells can kill target cells, proliferate, and express several inflammatory cytokines. The properties of NKB cells could provide insight into the inflammation observed in the gut during SIV infection, and the individual contributions of each cytokine and receptor–ligand interaction could be explored in a future study. Supported by ORIP (P51OD011106), NIAID, and NIGMS.


 American Alligators Are Capable of West Nile Virus Amplification, Mosquito Infection and Transmission

Byas, Alex et al., Virology. 2022 Mar;568:49–55.

West Nile virus (WNV) overwintering is poorly understood and likely multifactorial. Interest in alligators as a potential amplifying host arose when it was shown that they develop viremias theoretically sufficient to infect mosquitoes. Researchers examined potential ways in which alligators may contribute to the natural ecology of WNV. They experimentally demonstrated that alligators are capable of WNV amplification with subsequent mosquito infection and transmission capability, that WNV-infected mosquitoes readily infect alligators, and that water can serve as a source of infection for alligators but does not easily serve as an intermediate means for transmission between birds and alligators. These findings indicate potential mechanisms for maintenance of WNV outside of the primary bird–mosquito transmission cycle. Supported by ORIP (T32OD010437) and NIAID.


 Inflammatory Blockade Prevents Injury to the Developing Pulmonary Gas Exchange Surface in Preterm Primates

Toth, Andrea et al., Science Translational Medicine. 2022 Mar 30;14(638):eabl8574.

Chorioamnionitis, an inflammatory condition affecting the placenta and fluid surrounding the developing fetus, affects 25 to 40% of preterm births. Investigators used a prenatal rhesus macaque model to assess how fetal inflammation could affect lung development. They found that inflammatory injury directly disrupted the developing gas exchange surface of the primate lung, with extensive damage to alveolar structure. Blockade of the inflammatory cytokines IL-1β and TNFα ameliorated LPS-induced inflammatory lung injury by blunting stromal responses to inflammation and modulating innate immune activation in myeloid cells. These data provide new insight into key mechanisms of developmental lung injury and highlight targeted inflammatory blockade as a potential therapeutic approach to ameliorate lung injury in the neonatal population. Supported by ORIP (P51OD011107), NIAID, NHLBI, NICHD, and NIEHS.


 Antibody-peptide epitope conjugates for personalized cancer therapy

Zhang et al. in Cancer Res.

Antibody-peptide epitope conjugates (APEC) are a new class of modified antibody-drug conjugates that redirect T cell viral immunity against tumor cells. Investigators developed an experimental pipeline to create patient-specific APECs and identified new preclinical therapies for ovarian carcinoma. Using functional assessment of viral peptide antigen responses to common viruses like cytomegalovirus in ovarian cancer patients, a library of 192 APECs with distinct protease cleavage sequences was created using the anti-epithelial cell adhesion molecule (EpCAM) antibody. The streamlined and systemic approach includes assessing APEC function in vivo using a new zebrafish xenograft platform that facilitates high-resolution single cell imaging to assess therapy responses and then validating top candidates using traditional mouse xenograft studies and primary patient samples. This study develops a high-throughput preclinical platform to identify patient-specific antibody-peptide epitope conjugates that target cancer cells and demonstrates the potential of this immunotherapy approach for treating ovarian carcinoma. Supported by ORIP (R24OD016761).


 A Potent Myeloid Response Is Rapidly Activated in the Lungs of Premature Rhesus Macaques Exposed to Intra-Uterine Inflammation

Jackson, Courtney et al., Mucosal Immunology. 2022 Apr;15(4):730–744.

Up to 25 to 40% of preterm births are associated with histological chorioamnionitis (HCA), which can lead to neonatal mortality, sepsis, respiratory disease, and neurodevelopmental problem. Researchers used rhesus macaques to comprehensively describe HCA-induced fetal mucosal immune responses and delineate the individual roles of IL-1β and TNFα in HCA-induced fetal pathology. Their data indicate that the fetal innate immune system can mount a rapid, multi-faceted pulmonary immune response to in utero exposure to inflammation. Taken together, this work provides mechanistic insights into the association between HCA and the postnatal lung morbidities of the premature infant and highlights therapeutic potential of inflammatory blockade in the fetus. Supported by ORIP (P51OD011107), NIEHS, NIDDK, NHLBI, and NICHD.


 Common and Divergent Features of T Cells from Blood, Gut, and Genital Tract of Antiretroviral Therapy–Treated HIV+ Women

Xie, Guorui et al., Journal of Immunology. 2022 Apr;208(7):1790–1801.

T cells residing in mucosal tissues play important roles in homeostasis and defense against microbial pathogens, but how organ system environments affect the properties of resident T cells is relatively unknown. Researchers phenotyped T cells in the gut and reproductive tract using blood and tissue samples from women with HIV who have achieved viral suppression via antiretroviral therapy. The T cells exhibited differing expression of CD69 and CD103 markers, whereas resident memory CD8+ T cells from the female reproductive tract expressed PD1 preferentially. Additionally, CXCR4+ T inflammatory mucosal cells expressed multiple chemokine receptors differentially. These results suggest that T cells take on distinct properties in different mucosal sites, which allows them to tailor activities to their surrounding milieu. This study offers important insights for reproductive medicine in women. Supported by ORIP (S10OD018040), NHLBI, NIAID, and NIDDK.


 Obesity Alters Pathology and Treatment Response in Inflammatory Disease

Bapat, Sagar et al., Nature. 2022 Apr;604(7905):337–342.

Obesity and metabolic disease have been shown to affect immunotherapeutic outcomes. By studying classical type 2 T helper cells (TH2) in lean and obese male mouse models for atopic dermatitis, investigators found that the biologic therapies protected lean mice but exacerbated disease in obese mice. RNA sequencing and genome analyses revealed decreased activity of nuclear receptor peroxisome proliferator-activated receptor-γ (PPARγ) in TH2 cells in obese mice when compared to lean mice, indicating that PPARγ is required to prevent aberrant non-TH2 inflammation. Understanding the effects of obesity on immunological disease could inform a potential precision medicine approach to target obesity-induced immune dysregulation. Supported by ORIP (S10OD023689), NIAID, NCI, NIDDK, and NIGMS.


 Early Post-Vaccination Gene Signatures Correlate with the Magnitude and Function of Vaccine-Induced HIV Envelope–Specific Plasma Antibodies in Infant Rhesus Macaques

Vijayan, KK Vidya et al., Frontiers in Immunology. 2022 Apr;13:840976.

An effective vaccine is needed to reduce HIV infections, particularly among younger people. The initiation of an HIV vaccine regimen in early life could allow the development of mature HIV‑specific antibody responses that protect against infection. The investigators compared the effects of two vaccine regimens in infant rhesus macaques (sex not specified). Both vaccines induced a rapid innate response, indicated by elevated inflammatory plasma cytokines and altered gene expression. By performing a network analysis, the investigators identified differentially expressed genes associated with B cell activation. These findings suggest that vaccine-induced immunity can be optimized by modulating specific antibody and T cell responses. Supported by ORIP (P51OD011107), NCI, NIAID, and NIDCR.


 Antimicrobial Prophylaxis Does Not Improve Post-Surgical Outcomes in SIV/SHIV–Uninfected or SIV/SHIV–Infected Macaques (Macaca mulatta and Macaca fascicularis) Based on a Retrospective Analysis

Moats, Cassandra et al., PLOS One. 2022 Apr;17(4):e0266616.

Some institutions routinely administer antimicrobial prophylaxis to nonhuman primates prior to surgery to prevent surgical site infections. In this study, the investigators assessed the influence of antimicrobial prophylaxis on complication rates in macaques of both sexes receiving peripheral lymph node (PLN) and laparoscopic biopsies. After PLN biopsies, no significant differences were observed between animals that received antimicrobial prophylaxis and those that did not. After laparoscopic biopsies, complication rates were greater in animals that received antimicrobial prophylaxis. Because of these findings, the authors recommend eliminating the use of unnecessary antibiotics in research animals. Supported by ORIP (U42OD023038, P51OD011092).


 Adverse Biobehavioral Effects in Infants Resulting from Pregnant Rhesus Macaques’ Exposure to Wildfire Smoke

Capitanio, John et al., Nature Communications. 2022 Apr;13(1):1774.

Exposure to wildfire smoke (WFS) is a growing health concern as wildfires increase in number and size due to climate change. Researchers found that developing rhesus monkeys exposed to WFS from the Camp Fire in California (November 2018) during the first third of gestation exhibited greater inflammation, blunted cortisol, more passive behavior, and memory impairment compared to animals conceived after smoke had dissipated. Analysis of a historical control cohort did not support the alternative hypothesis that conception timing alone explained the results. These findings suggest that WFS may have a teratogenic effect on neural development in the primate fetus. Supported by ORIP (P51OD011107, R24OD010962) and NIEHS.


 Generation of SIV-Resistant T Cells and Macrophages from Nonhuman Primate Induced Pluripotent Stem Cells with Edited CCR5 Locus

D’Souza, Saritha et al., Stem Cell Reports. 2022 Apr;17(4):953–963.

Genetically modified T cells have shown promise as a potential therapy for HIV. A renewable source of T cells from induced pluripotent stem cells (iPSCs) could help to further research progress in this area. The researchers used Mauritian cynomolgus macaques to generate simian immunodeficiency virus (SIV)–resistant T cells and macrophages from iPSCs. These engineered cells demonstrated impaired capacity for differentiation into CD4+CD8+ T cells. T cells and macrophages from the edited iPSCs did not support SIV replication. These findings could be applied to the development of new HIV therapies. Supported by ORIP (R24OD021322, P51OD011106) and NHLBI.


 Altered Expression of ACE2 and Co-Receptors of SARS-CoV-2 in the Gut Mucosa of the SIV Model of HIV/AIDS

Hu, Shuang et al., Frontiers in Microbiology. 2022 Apr;13:879152.

The investigators assessed the influence of pre-existing HIV infection—which is known to target the gut mucosal immune system—on the vulnerability to SARS-CoV-2 infection and disease. Using a rhesus macaque model (sex not specified), they investigated changes in the expression of ACE2 and other SARS-CoV-2 receptors and related pathways. Simian immunodeficiency virus (SIV) infection resulted in sustained or increased ACE2 expression in an inflamed and immune-impaired gut mucosal microenvironment. These changes are likely to increase susceptibility to SARS-CoV-2 infection and disease severity. Taken together, these results demonstrate the utility of SIV models to fill knowledge gaps related to HIV infection and coinfections. Supported by ORIP (P51OD011107) and NIAID.


 Cannabinoid Receptor 1 Antagonist Genistein Attenuates Marijuana-Induced Vascular Inflammation

Wei, Tzu-Tang et al., Cell. 2022 May;185(10):1676–1693.e23.

Marijuana use is increasing and is associated with increased risk of cardiovascular disease (CVD); however, the link between marijuana and CVD remains largely unknown. Investigators demonstrated that a psychoactive component of marijuana, Δ9-tetrahydrocannabinol (Δ9‑THC), activates cannabinoid receptor 1 (CB1), causing vascular inflammation, oxidative stress, endothelial dysfunction, and atherosclerosis. This in silico virtual screening study suggested that genistein, a soybean isoflavone, would be a putative CB1 antagonist. Their validation study showed that in male mice, genistein blocked Δ9-THC-induced endothelial dysfunction in wire myograph, reduced atherosclerotic plaque, and had minimal penetration of the central nervous system. This study for the first time revealed that genistein is a CB1 antagonist that attenuates Δ9-THC-induced atherosclerosis while preserving clinically useful effects. Supported by ORIP (S10OD030452).


 The Ex Vivo Pharmacology of HIV-1 Antiretrovirals Differs between Macaques and Humans

Herrera, Carolina et al., iScience. 2022 May;25(6):104409.

Nonhuman primates (NHPs) are used widely for studies of antiretroviral (ARV)–based pre‑exposure prophylaxis (PrEP), but more work is needed to address dose–efficacy discrepancies between NHP studies and human clinical trials of PrEP candidates. Investigators explored the use of colorectal and cervicovaginal ex vivo mucosal tissue explants as a bridging model between NHPs and humans. They reported differences in inhibitory potency of drug combinations between NHP and human mucosal tissue explants. These findings suggest that tissue explants can help researchers refine and interpret NHP ARV studies. Supported by ORIP (P51OD011104) and NIAID.


 Large Comparative Analyses of Primate Body Site Microbiomes Indicate That the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates

Asangba, Abigail et al., Microbiol Spectrum. 2022 Jun;10(3):e0164321.

Microbiomes are critical to host health and disease, but large gaps remain in the understanding of the determinants, coevolution, and variation of microbiomes across body sites and host species. Thus, researchers conducted the largest comparative study of primate microbiomes to date by investigating microbiome community composition at eight distinct body sites in 17 host species. They found that the oral microbiome is unique in exhibiting notable similarity across primate species while being distinct from the microbiomes of all other body sites and host species. This finding suggests conserved oral microbial niche specialization, despite substantial dietary and phylogenetic differences among primates. Supported by ORIP (P51OD010425, P51OD011107, P40OD010965, R01OD010980), NIA, NIAID, and NICHD.


 A Cellular Trafficking Signal in the SIV Envelope Protein Cytoplasmic Domain Is Strongly Selected for in Pathogenic Infection

Lawrence, Scott et al., PLOS Pathogens. 2022 Jun;18(6):e1010507.

Envelope glycoproteins within the cytoplasmic domain of HIV and simian immunodeficiency virus (SIV) include a tyrosine-based motif that mediates endocytosis and polarized sorting in infected cells. Mutation of this tracking signal has been shown to lead to suppressed viral replication and failed systemic immune activation, but the mechanism has not been explored fully. Using rhesus and pigtail macaque models, the researchers demonstrated that molecular clones containing the mutations reconstitute signals for both endocytosis and polarized sorting. Their findings suggest strong selection pressure for these processes during pathogenic HIV and SIV infection. Supported by ORIP (P51OD011104), NCI, and NIAID.


 Myeloid Cell Tropism Enables MHC-E–Restricted CD8+ T Cell Priming and Vaccine Efficacy by the RhCMV/SIV Vaccine

Hansen, Scott et al., Science Immunology. 2022 Jun;7(72):eabn9301.

Simian immunodeficiency virus (SIV) vaccines based on strain 68-1 rhesus cytomegalovirus vectors have been shown to arrest viral replication early in primary infection. The specific characteristics underlying this effect are not understood fully. In this study, the researchers used host microRNA–mediated vector tropism restriction to demonstrate that the targeted responses are dependent on vector infection of distinct cell types in a rhesus macaque model. Only vectors programmed to elicit major histocompatibility complex E–restricted CD8+ T cell responses provided protection against SIV challenge. These findings could be applied in the development of other vaccines for cancers and infectious diseases. Supported by ORIP (P51OD011092), NCI, and NIAID.


 Substitutions in Nef That Uncouple Tetherin and SERINC5 Antagonism Impair Simian Immunodeficiency Virus Replication in Primary Rhesus Macaque Lymphocytes

Janaka, Sanath et al., Journal of Virology. 2022 Jun;96(11):e00176-22.

Tetherin inhibits the release of certain enveloped viruses from infected host cells. Most simian immunodeficiency viruses (SIVs) use Nef, a nonenzymatic accessory protein, to overcome this restriction. Nef also has been shown to enhance viral infectivity by preventing the incorporation of SERINC5 into virions. Researchers demonstrated previously that tetherin antagonism is necessary for efficient SIV replication in rhesus macaques. They explored this effect by defining substitutions within Nef that distinguish tetherin and SERINC5 antagonism. The researchers engineered an SIV molecular clone with substitutions that uncouple relevant Nef functions. This clone can be used to further study the effects of tetherin and adaptive immune responses. Supported by ORIP (P51OD011106) and NIAID.


 Safety and Antiviral Activity of Triple Combination Broadly Neutralizing Monoclonal Antibody Therapy against HIV-1: A Phase 1 Clinical Trial

Julg, Boris et al., Nature Medicine. 2022 Jun;28(6):1288–1296.

Previous evidence suggests that at least three broadly neutralizing antibodies (bNAbs) targeting different epitope regions are needed for robust treatment and control of HIV. The investigators evaluated the safety, tolerability, and pharmacokinetics of PGDM1400, an HIV-1 V2-glycan–specific antibody, in a first-in-human trial. The primary endpoints were safety, tolerability, pharmacokinetics, and antiviral activity. The trial met the prespecified endpoints in male and female adults. These data will help advance understanding of the capabilities, limitations, and future role of bNAb combinations in HIV prevention and care. Supported by ORIP (R01OD024917), NIAID, and NCATS.


 Effects of Ex Vivo Blood Anticoagulation and Preanalytical Processing Time on the Proteome Content of Platelets

Yunga, Samuel et al., Journal of Thrombosis and Haemostasis. 2022 Jun;20(6):1437–1450.

The investigators studied how various blood anticoagulation options and processing times affect platelet function and protein content ex vivo. Using platelet proteome quantification and triple quadrupole mass spectrometry, they found that anticoagulant-specific effects on platelet proteomes included increased complement system and decreased α-granule proteins in platelets from EDTA-anticoagulated blood. Heparinized blood had higher levels of histone and neutrophil-associated proteins, as well as formation of platelet–neutrophil extracellular trap interactions in whole blood ex vivo. The study indicates that different anticoagulants and preanalytical processing times affect platelet function and platelet protein content ex vivo, suggesting more rigorous phenotyping strategies for platelet omics studies. Supported by ORIP (S10OD012246), NHLBI, NCI and NEI.


 Innate Immune Regulation in HIV Latency Models

Olson, Rebecca et al., Retrovirology. 2022 Jul;19(1):15.

Researchers are interested in developing therapeutic approaches to target latent HIV reservoirs, which are unaffected by antiretroviral therapy. Previous studies suggest that HIV latency might be related to viral RNA sensing, interferon (IFN) signaling, and IFN-stimulated gene (ISG) activation. In this study, the researchers evaluated responses to stimulation by retinoic acid–inducible gene I agonists and IFN in multiple CD4+ T cell line models for HIV latency. The models represented various aspects of latent infection and viral control. Several of the cell lines demonstrated reduced ISG induction, suggesting that long-term latency might be related to dysregulation of the downstream IFN response. These effects likely reflect transcriptional changes occurring within a core set of ISGs and altering IFN responses. Additional studies could provide insight into the functions of these ISGs in HIV latency. Supported by ORIP (P51OD010425), NCATS, and NIAID.


 Allogeneic MHC‑Matched T‑Cell Receptor Α/Β‑Depleted Bone Marrow Transplants in SHIV‑Infected, ART‑Suppressed Mauritian Cynomolgus Macaques

Weinfurter, Jason et al., Scientific Reports. 2022 Jul;12(1):12345.

Allogeneic hematopoietic stem cell transplants are effective in reducing HIV reservoirs following antiretroviral therapy (ART). A better understanding of this mechanism could enable the development of safer and more efficacious HIV treatment regimens. In this study, the researchers used a Mauritian cynomolgus macaque model to study the effects of allogeneic major histocompatibility complex–matched α/β T cell–depleted bone marrow cell transplantation following infection with simian–human immunodeficiency virus (SHIV). The macaques began ART 6 to 16 weeks post-infection. In three of the four macaques, SHIV DNA was undetectable in blood but persisted in other tissues. These results suggest that extended ART likely is needed to eradicate the HIV reservoir following transplantation. In future studies, full donor engraftment should be balanced with suppression of graft-versus-host disease. Supported by ORIP (OD011106, R24OD021322), and NCI.


 A Clade C HIV-1 Vaccine Protects against Heterologous SHIV Infection by Modulating IgG Glycosylation and T Helper Response in Macaques

Sahoo, Anusmita et al., Science Immunology. 2022 Jul;7(73):eabl4102.

Vaccines for HIV-1 capable of generating a broadly cross-reactive neutralizing antibody response are needed urgently. The researchers tested the protective efficacy of a clade C HIV-1 vaccination regimen in male rhesus macaques. The vaccine was administered either orally using a needle-free injector or via parenteral injection. Significant protection was observed for both vaccination routes following the simian–human immunodeficiency virus (SHIV) challenge, with an estimated efficacy of 68% per exposure. The glycosylation profile of IgG and HIV-resistant helper T cell response contributes to the protection. Supported by ORIP (P51OD011132), NIAID, and NIDCR.


 A Novel DPH5-Related Diphthamide-Deficiency Syndrome Causing Embryonic Lethality or Profound Neurodevelopmental Disorder

Shankar, Suma et al., Genetics in Medicine. 2022 Jul;24(7):1567–1582.

Neurodevelopmental disorders (NDDs) affect more than 3% of the pediatric population and often have associated neurologic or multisystem involvement. The underlying genetic etiology of NDDs remains unknown in many individuals. Investigators characterized the molecular basis of NDDs in children of both sexes with nonverbal NDDs from three unrelated families with distinct overlapping craniofacial features. The investigators also used a mouse model of both sexes to determine the pathogenicity of variants of uncertain significance, as well as genes of uncertain significance, to advance translational genomics and provide precision health care. They identified several variants in DPH5 as a potential cause of profound NDD. Their findings provide strong clinical, biochemical, and functional evidence for DPH5 variants as a novel cause of embryonic lethality or profound NDD with multisystem involvement. Based on these findings, the authors propose that “DPH5-related diphthamide deficiency syndrome” is a novel autosomal-recessive Mendelian disorder. Supported by ORIP (K01OD026608, U42OD012210) and NHGRI.


 Sunitinib Inhibits STAT3 Phosphorylation in Cardiac Muscle and Prevents Cardiomyopathy in the mdx Mouse Model of Duchenne Muscular Dystrophy

Oliveira-Santos, Ariany et al., Human Molecular Genetics. 2022 Jul;31(14):2358–2369.

Duchenne muscular dystrophy (DMD) is the most common form of muscular dystrophy, affecting about 1 in 5,000 boys worldwide. DMD is a fatal X-linked genetic disorder that results from mutations in the dystrophin gene and leads to progressive muscular degeneration. Individuals with DMD often die at a young age from respiratory or heart failure. To date, few studies have examined the basis of cardiac failure associated with DMD, and no effective U.S. Food and Drug Administration (FDA)–approved treatment options are available. Using a mouse model of both sexes, researchers characterized the effectiveness of sunitinib, an FDA-approved small-molecule drug, in preventing DMD-related cardiomyopathy. The treatment reduced STAT3 activation in cardiac muscle and prevented cardiomyopathy disease progression. Inhibition of STAT3 activation in cardiac muscle can reduce inflammation and fibrosis and prevent heart failure. These findings demonstrate sunitinib’s potential as a novel treatment option for skeletal and cardiac muscle dysfunction in patients with DMD. Supported by ORIP (R42OD030543).


 Infection Order Outweighs the Role of CD4+ T Cells in Tertiary Flavivirus Exposure

Marzan-Rivera, Nicole et al., iScience. 2022 Jul;25(8):104764.

The link between CD4+ T and B cells in immune responses to Dengue virus (DENV) and Zika virus (ZIKV) and their roles in cross-protection during heterologous infection are poorly known. The authors used CD4+ lymphocyte depletions to dissect the impact of cellular immunity on humoral responses during tertiary flavivirus infection in male macaques. CD4+ depletion in DENV/ZIKV–primed animals, followed by DENV, resulted in dysregulated adaptive immune responses. They show a delay in DENV-specific antibody titers and binding and neutralization in the DENV/ZIKV–primed, CD4-depleted animals but not in ZIKV/DENV–primed, CD4-depleted animals. This study confirms the role of CD4+ cells in priming an early humoral response during sequential flavivirus infections and suggests that the order of exposure affects the outcome of a tertiary infection. Supported by ORIP (P40OD012217), NIAID, and NIGMS.


 Recreating thRecreatinge Heart’s Helical Structure–Function Relationship with Focused Rotary Jet Spinning

Chang, Huibin et al., Science. 2022 Jul;377(6602):180–185.

The investigators developed a tissue engineering approach that enables rapid deposition of cardiomyocyte microfibers with programmable alignments in 3D geometries. Using this focused rotary jet spinning (FRJS) method, they reproduced tissue scaffolds with contractile cells’ helical alignments, resembling complex structures of the musculature and properties of a natural heart. This work represents an important advance towards biofabrication of tissue models for healthy and diseased hearts by manipulating orientation of specific fibers. With the technological advancement over other competing methods, FRJS might provide a pathway towards fabricating other tissues and organs with diverse cell populations. Supported by ORIP (S10OD023519) and NCATS.


 Neuroprotective Effects of Electrical Stimulation Following Ischemic Stroke in Non‑Human Primates

Zhou, Jasmine et al., Institute of Electrical and Electronics Engineers. 2022 Jul;2022:3085–3088.

Using rhesus macaques of both sexes, researchers identified a novel treatment for ischemic stroke, which occurs when brain cells die due to lack of oxygen. The treatment consisted of applying 60 minutes of electrical brain stimulation shortly after the stroke. The animals that received electrical stimulation had less brain damage, fewer cell deaths, and more protective neural activity patterns than the monkeys that did not receive electrical stimulation. Future work can determine whether this stimulation can be applied noninvasively, as well as how to improve the electrical stimulation patterns to optimize health outcomes for stroke patients. Supported by ORIP (P51OD010425) and NINDS.


 Mosaic RBD Nanoparticles Protect against Challenge by Diverse Sarbecoviruses in Animal Models

Cohen, Alexander at al., Science. 2022 Aug;377(6606):eabq0839.

Two animal coronaviruses from the SARS-like betacoronavirus (sarbecovirus) lineage—SARS-CoV and SARS-CoV-2—have caused epidemics or pandemics in humans during the past 20 years. New SARS-CoV-2 variants have prolonged the COVID-19 pandemic, and the discovery of diverse sarbecoviruses in bats raises the possibility of another coronavirus pandemic. Vaccines and therapeutics are needed to protect against both SARS-CoV-2 variants and zoonotic sarbecoviruses with the potential to infect humans. The authors designed mosaic-8 nanoparticles (SARS-CoV-2 and seven animal sarbecoviruses) that present randomly arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against epitopes that are conserved and relatively occluded rather than variable, immunodominant, and exposed. Their results of immune responses elicited by mosaic-8 RBD nanoparticles in mice and macaques suggest that mosaic nanoparticles could protect against both SARS-CoV-2 variants and zoonotic sarbecoviruses with the potential to infect humans. Supported by ORIP (P40OD012217, U42OD021458, S10OD028685) and NIAID.


 Durable Protection against the SARS-CoV-2 Omicron Variant Is Induced by an Adjuvanted Subunit Vaccine

Arunachalam, Prabhu et al., Science Translational Medicine. 2022 Aug;14(658):eabq4130.

Additional SARS-CoV-2 vaccines are needed, owing to waning immunity to the original vaccines and the emergence of variants of concern. A recent study in male rhesus macaques demonstrated durable protection against the Omicron BA.1 variant induced by a subunit SARS-CoV-2 vaccine comprising the receptor binding domain of the ancestral strain (RBD-Wu) on the I53-50 nanoparticle adjuvanted with AS03, an oil-in-water emulsion containing α‑tocopherol. Two immunizations with the vaccine resulted in durable immunity, without cross-reactivity. Further boosting with a version of the vaccine containing the Beta variant or the ancestral RBD elicited cross-reactive immune responses that conferred protection against Omicron challenge. Supported by ORIP (P51OD011104), NCI, and NIAID.


 Parallel Processing, Hierarchical Transformations, and Sensorimotor Associations along the “Where” Pathway

Doudlah, Raymond et al., eLife. 2022 Aug;11:e78712.

Visually guided behaviors require the brain to transform ambiguous retinal images into object-level spatial representations and map those representations to motor responses. These capabilities are supported by the dorsal “where” pathway in the brain, but the specific contributions of areas along this pathway have remained elusive. Using a rhesus macaque model, researchers compared neuronal activity in two areas along the “where” pathway that bridge the parieto-occipital junction: intermediate visual area V3A and the caudal intraparietal (CIP) area. Neuronal activity was recorded while the animals made perceptual decisions based on judging the tilt of 3D visual patterns. The investigators found that CIP shows higher-order spatial representations and more choice-correlated responses, which support a V3A-to-CIP hierarchy. The researchers also discovered modulation of V3A activity by extraretinal factors, suggesting that V3A might be better characterized as contributing to higher-order behavioral functions rather than low-level visual feature processing. Supported by ORIP (P51OD011106), NEI, NICHD, and NINDS.


 Stromal P53 Regulates Breast Cancer Development, the Immune Landscape, and Survival in an Oncogene-Specific Manner

Wu, Jinghai et al., Molecular Cancer Research. 2022 Aug;20(8):1233–1246.

Loss of stromal p53 function drives tumor progression in breast cancer, but the exact mechanisms have been relatively unexplored. Using mouse models, researchers demonstrated that loss of cancer-associated fibroblast (CAF) p53 enhances carcinoma formation driven by oncogenic KRAS G12D, but not ERBB2, in mammary epithelia. These results corresponded with increased tumor cell proliferation and DNA damage, as well as decreased apoptosis, in the KRAS G12D model. Furthermore, a gene cluster associated with CAF p53 deficiency was found to associate negatively with survival in microarray and heat map analyses. These data indicate that stromal p53 loss promotes mammary tumorigenesis in an oncogene-specific manner, influences the tumor immune landscape, and ultimately affects patient survival. Supported by ORIP (K01OD026527) and NCI.


 Targeted Suppression of Human IBD-Associated Gut Microbiota Commensals by Phage Consortia for Treatment of Intestinal Inflammation

Federici, Sara et al., Cell. 2022 Aug;185(16):2879–2898.e24

Human gut commensals increasingly are suggested to affect noncommunicable diseases, such as inflammatory bowel disease (IBD), yet their targeted suppression remains an unmet challenge. In this report, investigators identified a clade of Klebsiella pneumoniae (Kp) strains—featuring a unique antibiotic resistance and mobilome signature—that is associated strongly with disease exacerbation and severity. Transfer of clinical IBD-associated Kp strains into colitis-prone, germ-free, and colonized mice of both sexes enhances intestinal inflammation. An orally administered combination phage therapy targeting sensitive and resistant IBD-associated Kp clade members enables effective Kp suppression, suggesting the feasibility of avoiding antibiotic resistance while effectively inhibiting noncommunicable disease–contributing pathobionts. Supported by ORIP (P40OD010995) and NIDDK.


 Distinct Sensitivities to SARS-CoV-2 Variants in Vaccinated Humans and Mice

Walls, Alexandra et al., Cell Reports. 2022 Aug;40(9):111299.

Emergence of SARS-CoV-2 variants necessitates real-time evaluation of their impact on serum neutralizing activity, as a proxy for vaccine efficacy, to inform public health policies and guide vaccine development. The investigators report that vaccinated female BALB/c mice do not recapitulate faithfully the breadth and potency of neutralizing antibody responses toward the SARS-CoV-2 Beta and Gamma variants of concern, compared with humans of both sexes and male nonhuman primates (i.e., rhesus and pigtail macaques). This finding was consistent across several vaccine modalities, doses, antigens, and assays, suggesting caution should be exercised when interpreting serum neutralizing data obtained from mice. Supported by ORIP (P51OD010425, U42OD011123) and NIAID.


 Early Treatment Regimens Achieve Sustained Virologic Remission in Infant Macaques Infected with SIV at Birth

Wang, Xiaolei et al., Nature Communications. 2022 Aug;13(1):4823.

About 150,000 children are infected postnatally with HIV each year. Early antiretroviral therapy (ART) in infants with HIV can reduce viral reservoir size, but ART-free virologic remission has not been achieved. The researchers hypothesized that proviral reservoir seeding in infants exposed to HIV might differ from that in adults. They characterized viral reservoirs in neonatal rhesus macaques of both sexes inoculated with simian immunodeficiency virus (SIV) at birth and given combination ART. The researchers reported that 9 months of treatment initiated at day 3 resulted in a sustained virologic remission, suggesting that early intervention with proper treatment regimens could be an effective strategy. Supported by ORIP (P51OD011104), NIAID, NICHD, and NIDCR.


 Evolution of the Nitric Oxide Synthase Family in Vertebrates and Novel Insights in Gill Development

Annona, Giovanni et al., Proceedings: Biological Sciences. 2022 Aug;289(1980):2022.0667

Nitric oxide (NO) plays essential roles in biological systems, including cardiovascular homeostasis, neurotransmission, and immunity. Knowledge of NO synthases (NOS) is substantial, but the origin of nos gene orthologues in fishes, with respect to tetrapods, remains largely unknown. The recent identification of nos3 in the spotted gar, considered lost in this lineage, prompted the authors to explore nos gene evolution. Here, they report that nos2 experienced several lineage-specific gene duplications and losses. Additionally, nos3 was found to be lost independently in two teleost lineages, Elopomorpha and Clupeocephala. Further, the expression of at least one nos paralogue in gills of developing shark, bichir, sturgeon, and gar, but not in gills of lamprey, suggests nos expression in the gill might have arisen in the last common ancestor of gnathostomes. These results provide a framework for further research on the role of nos genes. Supported by ORIP (P40OD019794, R01OD011116).


 A Multidimensional Metabolomics Workflow to Image Biodistribution and Evaluate Pharmacodynamics in Adult Zebrafish

Jackstadt, Madelyn et al., Disease Models & Mechanisms. 2022 Aug;15(8):dmm049550.

The evaluation of tissue distribution and pharmacodynamic properties of a drug is essential but often expensive in clinical research. The investigators developed a multidimensional metabolomics platform to evaluate drug activity that integrates mass spectrometry–based imaging, absolute drug quantitation, in vivo isotope tracing, and global metabolome analysis in zebrafish. They validated this platform by evaluating whole-body distribution of the anti-rheumatic agent hydroxychloroquine sulfate and its impact on the systemic metabolism of adult zebrafish. This work suggests that the multidimensional metabolomics platform is a cost-effective method for evaluating on- and off-target effects of drugs. Supported by ORIP (R24OD024624) and NIEHS.


 Rbbp4 Loss Disrupts Neural Progenitor Cell Cycle Regulation Independent of Rb and Leads to Tp53 Acetylation and Apoptosis

Schultz-Rogers, Laura et al., Developmental Dynamics. 2022 Aug;251(8):1267–1290.

Retinoblastoma binding protein 4 (Rbbp4) is a component of transcription regulatory complexes that control cell cycle gene expression by cooperating with the Rb tumor suppressor to block cell cycle entry. The authors used genetic analysis to examine the interactions of Rbbp4, Rb, and Tp53 in zebrafish neural progenitor cell cycle regulation and survival. Rbbp4 is upregulated across the spectrum of human embryonal and glial brain cancers, and it is essential for zebrafish neurogenesis. Rbbp4 loss leads to apoptosis and γ-H2AX in the developing brain that is suppressed by tp53 knockdown or maternal zygotic deletion. Mutant retinal neural precursors accumulate in M phase and fail to initiate G0 gene expression. Rbbp4; Rb1 double mutants show an additive effect on the number of M phase cells. The study demonstrates that Rbbp4 is necessary for neural progenitor cell cycle progression and initiation of G0, independent of Rb, and suggests that Rbbp4 is required for cell cycle exit and contributes to neural progenitor survival. Supported by ORIP (R24OD020166) and NIGMS.


 Metabolic Transitions Define Spermatogonial Stem Cell Maturation

Voigt, A et al., Human Reproduction. 2022 Aug;37(9):2095–2112.

The spermatogonial stem cell (SSC) is the basis of male fertility. One potential option to preserve fertility in patients treated with anti-cancer therapy is isolation and laboratory culture of the juvenile SSC pool with subsequent transplantation to restore spermatogenesis. However, efficient culture of undifferentiated spermatogonia, including SSCs, in mammals other than rodents remains challenging. Investigators reported that the metabolic phenotype of prepubertal human spermatogonia is distinct from that of adult spermatogonia and that SSC development is characterized by specific metabolic transitions from oxidative phosphorylation to anaerobic metabolism. Supported by ORIP (R01OD016575) and NICHD.


 A Molecularly Integrated Amygdalo-Fronto-Striatal Network Coordinates Flexible Learning and Memory

Li, Dan et al., Nature Neuroscience. 2022 Sep;25(9):1213–1224.

Behavioral flexibility is critical for navigating dynamic environments and requires the durable encoding and retrieval of new memories to guide future choice. The orbitofrontal cortex (OFC) supports outcome-guided behaviors, but the coordinated neural circuitry and cellular mechanisms by which OFC connections sustain flexible learning and memory are not understood fully. Using a mouse model, researchers demonstrated that the OFC neuronal ensembles store a memory trace for newly learned information. They describe the directional transmission of information within an integrated amygdalo-fronto-striatal circuit across time. Supported by ORIP (P51OD011132), NIDA, NIMH, and NINDS.


  Sequencing Reveals Early Cryptic SARS-CoV-2 Variant Transmission

Karthikeyan, Smruthi et al., Nature. 2022 Sep;609(7925):101–108.

The investigators explored the use of SARS-CoV-2 RNA concentration in wastewater as a practical approach to estimate community prevalence of COVID-19, detect emerging variants, and track regional infection dynamics. Two obstacles must be overcome to leverage wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. The investigators developed and deployed improved virus concentration protocols and deconvolution software to fully resolve multiple virus strains from wastewater. Results indicate that emerging variants of concern were detected up to 14 days earlier in wastewater samples, and multiple instances of virus spread that were not captured by clinical genomic surveillance were identified by wastewater-based genomic surveillance. The study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission. The work suggests a critical, urgently needed methodology for early detection of emerging variants and early public health interventions. Supported by ORIP (S10OD026929), and NIAID.


 X Chromosome Agents of Sexual Differentiation

Arnold, Arthur, Nature Reviews Endocrinology. 2022 Sep;18(9):574–583.

Many diseases affect one sex disproportionately. A major goal of biomedical research is to understand which sex-biasing factors influence disease severity and to develop therapeutic strategies to target these factors. Two groups of such agents are sex chromosome genes and gonadal hormones. Researchers use the “four core genotypes” model to enable comparisons among animals with different sex chromosomes but the same type of sex hormones, which allows investigators to distinguish disease mechanisms influenced by the sex chromosomes. Supported by ORIP (R01OD030496, R21OD026560), NICHD, NIDDK, and NHLBI.


 Isoniazid and Rifapentine Treatment Effectively Reduces Persistent M. tuberculosis Infection in Macaque Lungs

Sharan, Riti et al., Journal of Clinical Investigation. 2022 Sep;132(18):e161564.

People with HIV and asymptomatic latent tuberculosis (TB) coinfection are at risk of developing active TB symptoms. The Centers for Disease Control and Prevention recommends a weekly dose of isoniazid and rifapentine for 3 months (3HP) for treatment of latent TB infection, but the sterilizing efficacy of the regimen has not been demonstrated previously. Using rhesus macaques of both sexes, researchers evaluated the efficacy of the 3HP regimen in eradicating persistent Mycobacterium tuberculosis infection. They found that treatment reduced the risk of developing active TB but did not establish complete sterilization. This work establishes a new animal model for evaluating the efficacy of different drug regimens. Supported by ORIP (P51OD011133, S10OD028732).


 Molecular and Cellular Evolution of the Primate Dorsolateral Prefrontal Cortex

Ma, Shaojie et al., Science. 2022 Sep;377(6614):eabo7257.

The dorsolateral prefrontal cortex (dlPFC) exists only in primates, lies at the center of high-order cognition, and is a locus of pathology underlying many neuropsychiatric diseases. The investigators generated single-nucleus transcriptome data profiling more than 600,000 nuclei from the dlPFC of adult humans, chimpanzees, rhesus macaques, and common marmosets of both sexes. Postmortem human samples were obtained from tissue donors. The investigators’ analyses delineated dlPFC cell-type homology and transcriptomic conservation across species and identified species divergence at the molecular and cellular levels, as well as potential epigenomic mechanisms underlying these differences. Expression patterns of more than 900 genes associated with brain disorders revealed a variety of conserved, divergent, and group-specific patterns. The resulting data resource will help to vertically integrate marmoset and macaque models with human-focused efforts to develop treatments for neuropsychiatric conditions. Supported by ORIP (P51OD011133), NIA, NICHD, NIDA, NIGMS, NHGRI, NIMH, and NINDS.


  Profiling Development of Abdominal Organs in the Pig

Gabriel, George et al., Scientific Reports. 2022 Sep;12(1):16245.

The pig is a model system for studying human development and disease due to its similarities to human anatomy, physiology, size, and genome. Moreover, advances in CRISPR gene editing have made genetically engineered pigs a viable model for the study of human pathologies and congenital anomalies. However, a detailed atlas illustrating pig development is necessary for identifying and modeling developmental defects. Here, the authors describe normal development of the pig abdominal system (i.e., kidney, liver, pancreas, spleen, adrenal glands, bowel, gonads) and compare them with congenital defects that can arise in gene-edited SAP130 mutant pigs. This atlas and the methods described here can be used as tools for identifying developmental pathologies of the abdominal organs in the pig at different stages of development. Supported by ORIP (U42OD011140), NHLBI, NIAID, NIBIB, NICHD, and NINDS.


 Distinct Metabolic States Guide Maturation of Inflammatory and Tolerogenic Dendritic Cells

Adamik, Juraj et al., Nature Communications. 2022 Sep;13(1):5184.

The investigators mapped single-cell metabolic states and immune profiles of inflammatory and tolerogenic monocytic dendritic cells using recently developed multiparametric approaches. Activation scores revealed simultaneous engagement of multiple metabolic pathways in distinct monocytic dendritic cell differentiation stages (e.g., rapid reprogramming of glycolytic monocytes and transient co-activation of mitochondrial pathways followed by maturation of dendritic cells). This data set provides insights into metabolic pathways that affect the immune profiles of human dendritic cells. Supported by ORIP (S10OD026940) and NIDDK.


 Lesion Environments Direct Transplanted Neural Progenitors Towards a Wound Repair Astroglial Phenotype in Mice

O’Shea, T et al., Nature Communications. 2022 Sep;13(1):5702.

Neural progenitor cells (NPCs) are potential cell transplantation therapies for central nervous system (CNS) injuries. Investigators derived NPCs expressing a ribosomal protein-hemagglutinin tag (RiboTag) for transcriptional profiling. Their findings reveal similarities between the transcriptional profiles, cellular morphologies, and functional features of cells transplanted into subacute CNS lesions and host astroglia. The astroglia are stimulated by injuries to proliferate and adopt a naturally occurring, border-forming wound repair phenotype in mice of both sexes. Understanding the autonomous cues instructing NPCs transplanted in CNS host tissue will be fundamental to therapeutic NPC transplantation. Supported by ORIP (U42OD010921, UM1OD023222, U42OD011174) and NINDS.


 Pharmacogenetic Gene–Drug Associations in Pediatric Burn and Surgery Patients

Grimsrud, Kristin et al., Journal of Burn Care & Research. 2022 Sep;43(5):987–996.

Simultaneous administration of many medications is common in management of critically ill patients. The researchers investigated drug–drug interactions in these treatments during hospitalization, which might decrease drug efficacy or increase adverse reactions. Genetic and medication data from 30 pediatric burn and surgery patients were analyzed to identify pharmacogene–drug associations. Nineteen patients were identified with predicted altered gene functions. Approximately one-third of the patients tested had functionally impactful genotypes in each of the primary drug metabolizing pathways. This study suggests that the vast variability in drug efficacy is partly due to genetic variants and that pharmacogenetic analysis may help optimize dosing regimens. Supported by ORIP (K01OD026608) and NCI.


Molecular Insights into Antibody-Mediated Protection against the Prototypic Simian Immunodeficiency Virus

Zhao, Fangzhu et al., Nature Communications. 2022 Sep;13(1):5236.

Most simian immunodeficiency virus (SIV) vaccines have focused on inducing T cell responses alone or in combination with non-neutralizing antibody responses. To date, studies investigating neutralizing antibody (nAb) responses to protect against SIV have been limited. In this study, researchers isolated 12 potent monoclonal nAbs from chronically infected rhesus macaques of both sexes and mapped their binding specificities on the envelope trimer structure. They further characterized the structures using cryogenic electron microscopy, mass spectrometry, and computational modeling. Their findings indicate that, in the case of humoral immunity, nAb activity is necessary and sufficient for protection against SIV challenge. This work provides structural insights for future vaccine design. Supported by ORIP (P51OD011106), NIAID, and NCI.


 Promoting Validation and Cross-Phylogenetic Integration in Model Organism Research

Cheng, Keith et al., Disease Models & Mechanisms. 2022 Sep;15(9):dmm049600.

Model organisms are essential for biomedical research and therapeutic development, but translation of such research to the clinic is low. The authors summarized discussions from an NIH virtual workshop series, titled “Validation of Animal Models and Tools for Biomedical Research,” held from 2020 to 2021. They described challenges and opportunities for developing and integrating tools and resources and provided suggestions for improving the rigor, validation, reproducibility, and translatability of model organism research. Supported by ORIP (R01OD011116, R24OD031447, R03OD030597, R24OD018559, R24OD017870, R24OD026591, R24OD022005, U42OD026645, U42OD012210, U54OD030165, UM1OD023221, P51OD011107), NIAMS, NIDDK, NIGMS, NHGRI, and NINDS.


 De Novo Variants in EMC1 Lead to Neurodevelopmental Delay and Cerebellar Degeneration and Affect Glial Function in Drosophila

Chung, Hyung-Lok et al., Human Molecular Genetics. 2022 Sep;31(19):3231–3244.

Variants in EMC1, which encodes a subunit of the endoplasmic reticulum (ER)–membrane protein complex (EMC), are associated with developmental delay in children. Functional consequences of these variants are poorly understood. The investigators identified de novo variants in EMC1 in three children affected by global developmental delay, hypotonia, seizures, visual impairment, and cerebellar atrophy. They demonstrated in Drosophila that these variants are loss-of-function alleles and lead to lethality when expressed in glia but not in neurons. This work suggests the causality of EMC variants in disease. Supported by ORIP (R24OD022005, R24OD031447), NINDS, and NICHD.


 Canine Reference Genome Accuracy Impacts Variant Calling: Lessons Learned from Investigating Embryonic Lethal Variant

Kinsey, Nathan et al., 2022 Oct;53(5):706–708.

With increasingly affordable whole-genome sequencing, hundreds of canine genomes now can be analyzed for embryonic lethal mutations. Investigators examined whole-genome sequence data from 675 dogs of both sexes to investigate for variants with missing homozygosity and high predicted impact. They identified 45 likely embryonic lethal mutations in 32 genes but found that all but one of those were labeled incorrectly and were artifacts associated with a widely utilized canine reference genome. This effect is a major obstacle to studies focusing on loci with high heterozygosity. The investigators propose that by using newer, multiple reference genomes, researchers could reduce artifacts and identify variants more accurately. Supported by ORIP (K01OD027051, K01OD019912).


 Maternal Western-Style Diet Reduces Social Engagement and Increases Idiosyncratic Behavior in Japanese Macaque Offspring

Mitchell, AJ et al., Brain, Behavior, and Immunity. 2022 Oct;105:109–121.

Evidence points to an association between maternal obesity and risk of early-emerging neurodevelopmental disorders in offspring, yet few preclinical studies have tested for associations between maternal Western-style diet (mWSD) and offspring behavior. Using Japanese macaques, researchers found that mWSD offspring exhibited less proximity to peers and initiated fewer affiliative social behaviors. These outcomes appear to be mediated by increased maternal interleukin-12 during the third trimester of pregnancy. Additionally, mWSD offspring displayed increased idiosyncratic behavior, which was related to alterations in maternal adiposity and leptin. These findings suggest specific prevention and intervention targets for early-emerging neurodevelopmental disorder in humans. Supported by ORIP (P51OD011092), NIMH, and NICHD.


 Mendelian Gene Identification through Mouse Embryo Viability Screening

Cacheiro, Pilar et al., Genome Medicine. 2022 Oct;14(1):119.

The investigators dissected phenotypic similarities between patients and model organisms by assessing the embryonic stage at which homozygous loss of function results in lethality in mice of both sexes obtained from the International Mouse Phenotyping Consortium. Information on knockout mouse embryo lethality can be used to prioritize candidate genes associated with certain disorders. Access to unsolved cases from rare-disease genome sequencing programs allows for the screening of those genes for potentially pathogenic variants, which could lead to a diagnosis and new potential treatment options to inform the management of human disease. Supported by ORIP (UM1OD023221, UM1OD023222, U42OD011174) and NHGRI.


 Neuroinflammatory Transcriptional Programs Induced in Rhesus Pre‑Frontal Cortex White Matter During Acute SHIV Infection

Hawes, Chase et al., Journal of Neuroinflammation. 2022 Oct;19(1):250.

Neuroinflammation has evolved as a protective immune response within the central nervous system (CNS), but chronic neuroinflammation leads to oxidative stress, cellular damage, and neurodegeneration. People living with HIV are at increased risk for age-related neurodegenerative diseases. Using rhesus macaques of both sexes, the researchers characterized the molecular underpinnings of acute neuroinflammation following simian–human immunodeficiency virus (SHIV) infection. Viral entry and integration within the CNS demonstrated vulnerabilities of key cognitive and motor function brain regions during the acute phase of infection. SHIV-induced transcriptional alterations also were observed. These findings indicate the presence of pervasive immune surveillance at homeostasis and reveal key perturbations during infection. Supported by ORIP (S10OD010786, K01OD023034) and NIAID.


 Reduced Alcohol Preference and Intake after Fecal Transplant in Patients with Alcohol Use Disorder Is Transmissible to Germ-Free Mice

Wolstenholme, Jennifer et al., Nature Communications. 2022 Oct;13(1):6198.

Alcohol use disorder is a major cause of reduced life expectancy worldwide, and this misuse has increased exponentially during the COVID-19 pandemic. Fecal microbiota transplant has been shown previously to reduce alcohol craving in humans with cirrhosis. Here, the investigators report that the reduction in craving and alcohol preference is transmissible to male germ-free mice only when live bacteria—and not germ-free supernatants—are used for colonization. This differential colonization was associated with alterations in the gut immune–inflammatory response through short-chain fatty acids. Supported by ORIP (P40OD010995), NIAAA, NIDDK, and NIMH.


 Control of Simian Immunodeficiency Virus Infection in Prophylactically Vaccinated, Antiretroviral Treatment–Naive Macaques Is Required for the Most Efficacious CD8 T Cell Response during Treatment with the Interleukin-15 Superagonist N-803

Ellis-Connell, Amy et al., Journal of Virology. 2022 Oct;96(20):e0118522.

Recent evidence suggests that immunotherapeutic agents, such as N-803, could improve the ability of CD8+ T cells to target and destroy cells infected with HIV. In this study, investigators defined the features that are associated with N-803-mediated suppression of simian immunodeficiency virus (SIV) replication in rhesus macaques of both sexes. They hypothesized that preexisting vaccine-elicited CD8+ T cells were required for suppressing replication. Their results indicate that N-803 is most effective in animals with preexisting immunological ability to control SIV replication. These findings support further exploration of N-803 as an immunotherapeutic agent for HIV. Supported by ORIP (P51OD011106) and NIAID.


 Rapid Joule Heating Improves Vitrification Based Cryopreservation

Zhan, Li et al., 2022 Oct;13(1):6017.

Cryopreservation by vitrification is an effective approach for long-term preservation of biosystems, but effective vitrification often requires high concentrations of cryoprotective agent (CPA), which can be toxic. The investigators described a joule heating–based platform technology for rapid rewarming of biosystems, which allows the use of low concentrations of CPA. They demonstrated the success of this platform in cryopreservation of three model systems: adherent cells, Drosophila melanogaster embryos, and rat kidney slices with low CPA concentrations. This work provides a general solution to cryopreserve a broad spectrum of cells, tissues, organs, and organisms. Supported by ORIP (R21OD028758), NIDDK, NHLBI, and NIGMS.


 Orthotopic Transplantation of the Full-Length Porcine Intestine after Normothermic Machine Perfusion

Abraham, Nader et al., Transplantation Direct. 2022 Oct;8(11):e1390.

Successful intestinal transplantation currently is hindered by graft injury that occurs during procurement and storage, which contributes to postoperative sepsis and allograft rejection. Improved graft preservation could expand transplantable graft numbers and enhance post-transplant outcomes. Superior transplant outcomes recently have been demonstrated in clinical trials using machine perfusion to preserve the liver. The investigators report the development and optimization of machine perfusion preservation of small intestine and successful transplantation of intestinal allografts in a porcine model. Supported by ORIP (K01OD019911), NIAID, and NIDDK.


 System-Wide Identification of Myeloid Markers of TB Disease and HIV-Induced Reactivation in the Macaque Model of Mtb Infection and Mtb/SIV Co-Infection

Gough, Maya et al., Frontiers in Immunology. 2022 Oct;13:777733.

HIV is known to catalyze the reactivation of latent tuberculosis (TB) infection. The investigators characterized Mycobacterium tuberculosis (Mtb) and simian immunodeficiency virus (SIV) coinfection using a rhesus macaque model of both sexes, with a focus on pathways relevant to myeloid origin cells (e.g., macrophages). They identified gene signatures of host disease state and progression, as well as clustering algorithms for differentiation between host disease states and relationships among genes. The gene signatures were associated with pathways relevant to apoptosis, adenosine triphosphate production, phagocytosis, cell migration, and type I interferon, which are related to macrophage function. Collectively, these findings suggest that novel macrophage functions influence Mtb infection both with and without SIV coinfection. Supported by ORIP (P51OD011104, P51OD011103, U42OD010442) and NIAID.


 Effect of Single Housing on Innate Immune Activation in Immunodeficiency Virus–Infected Pigtail Macaques (Macaca nemestrina) as a Model of Psychosocial Stress in Acute HIV Infection

Castell, Natalie et al., Psychosomatic Medicine. 2022 Oct;84(8):966–975.

Psychosocial stress is associated with immune system dysregulation and worsened clinical outcomes in people with HIV. Investigators performed a retrospective analysis of acute simian immunodeficiency virus (SIV) infection of male pigtail macaques to compare the innate immune responses of social and single housing. The singly housed macaques showed reduced expansion of classical and intermediate monocytes, prolonged thrombocytopenia, and suppression of platelet activation during the first 2 weeks after inoculation. These findings indicate that psychosocial stress might induce clinically significant immunomodulatory effects in the innate immune system during acute SIV infection. Supported by ORIP (P40OD013117, K01OD018244, T32OD011089, U42OD013117), NIAID, NIMH, and NINDS.


 Long-Term Evolutionary Adaptation of SIVcpz toward HIV-1 Using a Humanized Mouse Model

Schmitt, Kimberly et al., Journal of Medical Primatology. 2022 Oct;51(5):288–291.

Chimpanzee-derived simian immunodeficiency viruses (SIVcpz) are thought to have evolved into the highly pathogenic HIV-1 Group M, but the genetic adaptations required for SIV progenitor viruses to become pathogenic and established as HIVs in the human population have remained unclear. Using humanized mice of both sexes, researchers mimicked the evolution of SIVcpz into HIV-1 Group M through serial passaging. After four generations, the researchers observed increased initial viral load, increased CD4+ T cell decline, and nonsynonymous substitutions. Overall, these data indicate increased viral fitness and pathogenicity. This work also demonstrates the utility of humanized mice in recreating the adaptive pressures necessary for the evolution of SIVcpz into HIV-1. Supported by ORIP (P51OD011104, P51OD011106), NCATS, and NIAID.


 Cell-Specific Regulation of Gene Expression Using Splicing-Dependent Frameshifting

Ling, Jonathan et al., Nature Communications. 2022 Oct;13(1):5773.

Precise and reliable cell-specific gene delivery remains technically challenging. Investigators report a splicing-based approach for controlling gene expression whereby separate translational reading frames are coupled to the inclusion or exclusion of mutated, frameshifting cell-specific alternative exons. Candidate exons are identified by analyzing thousands of publicly available RNA sequencing datasets and filtering by cell specificity, conservation, and local intron length. This method, which they denote as splicing-linked expression design (SLED), can be combined in a Boolean manner with such existing techniques as minipromoters and viral capsids. SLED can use strong constitutive promoters, without sacrificing precision, by decoupling the tradeoff between promoter strength and selectivity. AAV-packaged SLED vectors can selectively deliver fluorescent reporters and calcium indicators to various neuronal subtypes in vivo. The authors also demonstrate gene therapy utility by creating SLED vectors that can target PRPH2 and SF3B1 mutations. The flexibility of SLED technology enables creative avenues for basic and translational research. Supported by ORIP (T32OD011089, S10OD026859), NEI, and NIMH.


 SARS-CoV-2 Infects Neurons and Induces Neuroinflammation in a Non-Human Primate Model of COVID-19

Beckman, Danielle et al., Cell Reports. 2022 Nov;41(5):111573.

SARS-CoV-2 causes brain fog and other neurological complications in some patients. It has been unclear whether SARS-CoV-2 infects the brain directly or whether central nervous system sequelae result from systemic inflammatory responses triggered in the periphery. Using a rhesus macaque model, researchers detected SARS-CoV-2 in the olfactory cortex and interconnected regions 7 days after infection, demonstrating that the virus enters the brain through the olfactory nerve. Neuroinflammation and neuronal damage were more severe in elderly monkeys with type 2 diabetes. The researchers found that in aged monkeys, SARS-CoV-2 traveled farther along nerve pathways to regions associated with Alzheimer's disease. Supported by ORIP (P51OD011107) and NIA.


 Sociability in a Non-Captive Macaque Population Is Associated with Beneficial Gut Bacteria

Johnson, Katerina et al., Frontiers in Microbiology. 2022 Nov;13:1032495.

Social connections are essential for good health and well-being in social animals, such as humans and other primates. Increasingly, evidence suggests that the gut microbiome—through the so-called “gut–brain axis”—plays a key role in physical and mental health and that bacteria can be transmitted socially (e.g., through touch). Here, the authors explore behavioral variation in non‑captive rhesus macaques of both sexes with respect to the abundance of specific bacterial genera. Their results indicate that microorganisms whose abundance varies with individual social behavior also have functional links to host immune status. Overall, these findings highlight the connections between social behavior, microbiome composition, and health in an animal population. Supported by ORIP (P40OD012217) and NIMH.


 Transfer Efficiency and Impact on Disease Phenotype of Differing Methods of Gut Microbiota Transfer

Zhang, Chunye et al., Scientific Reports. 2022 Nov;12(1):19621.

To test causal relationships between complex gut microbiota (GM) and host outcomes, researchers frequently transfer GM between donor and recipient mice via embryo transfer (ET) rederivation, cross-fostering (CF), and co‑housing. In this study, the investigators assessed the influence of transfer method and differences in baseline donor and recipient microbiota richness on transfer efficiency in mice of both sexes. Their results demonstrate that both transfer method and transfer direction influence experimental GM transfer efficiency. ET showed the highest transfer efficiency, whereas the CF method—with the advantage of lower cost and complexity compared to ET—provided a possible viable alternative option for GM transfer studies where high efficiency is desired. Supported by ORIP (U42OD010918).


 Transient T Cell Expansion, Activation, and Proliferation in Therapeutically Vaccinated Simian Immunodeficiency Virus–Positive Macaques Treated with N-803

Harwood, Olivia et al., Journal of Virology. 2022 Nov;e0142422.

Many HIV vaccine strategies induce neutralizing antibodies and CD8+ T cells, but more information on these protective immune responses is needed. Researchers hypothesized that CD8+ T cells elicited by vaccination during antiretroviral therapy (ART) would be recalled and boosted by treatment with N-803 after ART discontinuation. They tested this approach in male Mauritian cynomolgus macaques infected with simian immunodeficiency virus. The regimen enhanced the frequency of Gag-specific lymphocytes with phenotypes associated with activation, proliferation, and memory in the peripheral blood and lymph nodes of vaccinated animals. These results help demonstrate N-803’s potential as an immunomodulatory agent for treatment of HIV. Supported by ORIP (P51OD011106) and NIAID.


 Gut Microbiome Dysbiosis in Antibiotic-Treated COVID-19 Patients Is Associated with Microbial Translocation and Bacteremia

Bernard-Raichon, Lucie et al., Nature Communications. 2022 Nov 1;13(1):5926.

The investigators demonstrated that SARS-CoV-2 infection induced gut microbiome dysbiosis in male mice. Samples collected from human COVID-19 patients of both sexes also revealed substantial gut microbiome dysbiosis. Analysis of blood culture results testing for secondary microbial bloodstream infections with paired microbiome data indicated that bacteria might translocate from the gut into the systemic circulation of COVID-19 patients. These results were consistent with a direct role for gut microbiome dysbiosis in enabling dangerous secondary infections during COVID-19. Supported by ORIP (S10OD021747), NCI, NHLBI, NIAID, and NIDDK.


 Two Neuronal Peptides Encoded from a Single Transcript Regulate Mitochondrial Complex III in Drosophila

Bosch, Justin et al., eLife. 2022 Nov 8;11:e82709.

Transcripts with small open-reading frames (smORFs) are underrepresented in genome annotations. Functions of peptides encoded by smORFs are poorly understood. The investigators systematically characterized human-conserved smORF genes in Drosophila and found two peptides, Sloth1 and Sloth2, that are highly expressed in neurons. They showed that Sloth1 and Sloth2 are paralogs with high sequence similarity but are not functionally redundant. Loss of either peptide resulted in lethality, impaired mitochondrial function, and neurodegeneration. This work suggests the value of phenotypic analysis of smORFs using Drosophila as a model. Supported by ORIP (R24OD019847), NHGRI, and NIGMS.


 Recombinant Simian Varicella Virus–Simian Immunodeficiency Virus Vaccine Induces T and B Cell Functions and Provides Partial Protection against Repeated Mucosal SIV Challenges in Rhesus Macaques

Pahar, Bapi et al., Viruses. 2022 Dec;14(12):2819.

An effective vaccine is needed urgently to control the global HIV epidemic completely by 2030. Recombinant simian varicella virus (rSVV) vaccines expressing SIV antigens offer a potential new approach in the evaluation of HIV vaccine candidates. Building on their previous findings, the investigators induced systemic and mucosal immune responses with live, attenuated rSVV vaccinations followed by SIV group–specific antigen and SIV envelope protein boosts in female rhesus macaques treated with repeated intravaginal SIV challenges. Their findings demonstrate that the vaccination with protein boosts induces a 37.5% efficacy rate against pathogenic SIV challenge by generating mucosal memory, virus‑specific neutralizing antibodies, binding antibodies, and polyfunctional T cell responses. Supported by ORIP (P51OD011104) and NIAID.


 Gigapixel Imaging with a Novel Multi-Camera Array Microscope

Thomson, Eric et al., eLife. 2022 Dec;11:e74988.

The dynamics of living organisms are organized across many spatial scales. The investigators created assembled a scalable multi-camera array microscope (MCAM) that enables comprehensive high-resolution, large field-of-view recording from multiple spatial scales simultaneously, ranging from structures that approach the cellular scale to large-group behavioral dynamics. By collecting data from up to 96 cameras, they computationally generated gigapixel-scale images and movies with a field of view over hundreds of square centimeters at an optical resolution of 18 µm. This system allows the team to observe the behavior and fine anatomical features of numerous freely moving model organisms on multiple spatial scales (e.g., larval zebrafish, fruit flies, slime mold). Overall, by removing the bottlenecks imposed by single-camera image acquisition systems, the MCAM provides a powerful platform for investigating detailed biological features and behavioral processes of small model organisms. Supported by ORIP (R44OD024879), NIEHS, NCI, and NIBIB.


 Genetic Control of the Pluripotency Epigenome Determines Differentiation Bias in Mouse Embryonic Stem Cells

Byers, Candice et al., EMBO J. 2022 December 17;41(2): e109445. doi: 10.15252/embj.2021109445. Epub 2021 Dec 21. PMID: 34931323; PMCID: PMC8762565.

Investigators used derivation of mouse embryonic stem cells (ESC) to identify points or places regulating cell state transitions. This work demonstrated that ESCs derived from genetically diverse strains do not share equal developmental potential in vitro. Recent experiments have shown that differences in cell-fate choice during development may be critical in predisposing individuals to complex diseases due to underlying differences in cell-type composition. The BXD Resource at the Jackson Laboratory is supported by ORIP P40 OD011102 and awarded to Dr. Cathleen M. Lutz.




 Lung Expression of Human Angiotensin-Converting Enzyme 2 Sensitizes the Mouse to SARS-CoV-2 Infection

Han, Kun et al., American Journal of Respiratory Cell and Molecular Biology. 2021 Jan; 64(1):79-88.

A rapidly deployable mouse model that recapitulates a disease caused by a novel pathogen would be a valuable research tool during a pandemic. Researchers were able to produce C57BL/6J mice with lung expression of human angiotensin-converting enzyme 2 (hACE2), the receptor for SARS-CoV-2. They did so by oropharyngeal delivery of a recombinant human adenovirus type 5 expressing hACE2. The transduced mice were then infected with SARS-CoV-2. Thereafter, the mice developed interstitial pneumonia with perivascular inflammation, exhibited higher viral load in lungs compared to controls, and displayed a gene expression phenotype resembling the clinical response in lungs of humans with COVID-19. Supported by ORIP (P51OD011104, R21OD024931), NHLBI, and NIGMS.


 Antibody-Mediated Depletion of Viral Reservoirs is Limited in SIV-Infected Macaques Treated Early With Antiretroviral Therapy

Swanstrom, Adrienne E. et al., Journal of Clinical Investigation. 2021 Jan; Epub ahead of print.

Virus-specific strategies to target the latent HIV reservoir in individuals on combination antiretroviral therapy (cART) have been limited by inefficient induction of viral protein expression. Researchers used rhesus macaques to investigate an antibody-mediated reservoir targeting strategy, targeting the CD4 molecule rather than a viral protein, to deplete potential viral target cells irrespective of infection status. Despite profound CD4+ T cell depletion in blood and lymph nodes, time to viral rebound following cART cessation was not delayed in anti-CD4 treated animals compared with controls, likely due to the limited antibody-mediated cell depletion that occurred in rectal tissue and lymphoid follicles. Supported by ORIP (R24OD010976), NCI, and NIAID.


 Increased Proviral DNA in Circulating Cells Correlates with Plasma Viral Rebound in SIV-Infected Rhesus Macaques after Antiretroviral Therapy Interruption

Ziani et al., J Virol. 2021 Jan 6;JVI.02064-20

Investigators longitudinally tracked dynamic decay of cell-associated viral RNA/DNA in systemic and lymphoid tissues in SIV-infected rhesus macaques on prolonged combined antiretroviral therapy (cART) to evaluate predictors of viral rebound after treatment cessation. Suppressive cART substantially reduced plasma SIV RNA, cell-associated unspliced, and multiply spliced SIV RNA to undetectable levels, yet viral DNA remained detectable in systemic tissues and lymphoid compartments throughout cART. A rapid increase of integrated proviral DNA in peripheral mononuclear cells was detected once cART was withdrawn, accompanied by the emergence of detectable plasma viral load. The increase of peripheral proviral DNA post cART interruption correlated with the emergence and degree of viral rebound. These results suggest that measuring total viral DNA in SIV infection may be a relatively simple surrogate marker of reservoir size, and may predict viral rebound after treatment interruption, and inform treatment strategies. Supported by ORIP (P51OD011104), NIAID and NICHD.


 Deploying MMEJ using MENdel in Precision Gene Editing Applications for Gene Therapy and Functional Genomics

Martínez-Gálvez G. et al. Nucleic Acids Research. 2021 January 11;49(1):67-78 (PMC7797032)

Gene-editing experiments commonly elicit the error-prone non-homologous end joining for DNA double-strand break (DSB) repair. Martinez-Galvez et al. compared three DSB repair prediction algorithms - MENTHU, inDelphi, and Lindel. MENTHU correctly identified 46% of all PreMAs available, a ∼2- and ∼60-fold sensitivity increase compared to inDelphi and Lindel, respectively. The investigators report the new algorithm MENdel, a combination of MENTHU and Lindel, that achieves the most predictive coverage of homogeneous out-of-frame mutations. They suggest that the use of MENdel helps researchers use MMEJ at scale for reverse genetics screenings to be viable for nearly all loss-of-function based gene editing therapeutic applications. Supported by ORIP (R24 OD020166), NIGMS.


 Thresholds for Post-Rebound SHIV Control after CCR5 Gene-Edited Autologous Hematopoietic Cell Transplantation

Cardozo-Ojeda et al., Elife. 2021 Jan 12;10:e57646

Investigators developed a mathematical model to project the minimum threshold of C-C chemokine receptor type 5 (CCR5) gene-edited cells necessary for a functional cure from HIV. This was based on blood T cell reconstitution and plasma simian-HIV (SHIV) dynamics from SHIV-1157ipd3N4-infected juvenile pig-tailed macaques that underwent autologous transplantation with CCR5 gene editing. The model predicts that viral control can be obtained following analytical treatment interruption (ATI) when: (1) transplanted hematopoietic stem and progenitor cells (HSPCs) are at least fivefold higher than residual endogenous HSPCs after total body irradiation and (2) the fraction of protected HSPCs in the transplant achieves a threshold (76–94%) sufficient to overcome transplantation-dependent loss of SHIV immunity. Under these conditions, if ATI is withheld until transplanted gene-modified cells engraft and reconstitute to a steady state, spontaneous viral control is projected to occur. Supported by ORIP (P51OD010425), NCATS and NIAID.


 Myelin‐specific T Cells in Animals with Japanese Macaque Encephalomyelitis

Govindan, Aparna N. et al., Annals of Clinical and Translational Neurology, first published 13 January 2021, Vol. 8, Issue 2.

Investigators characterized the CD4+ and CD8+ T cells in demyelinating Japanese macaque encephalomyelitis (JME) lesions in age‐ and sex‐matched macaques and discovered differences in expression of myelin antigen sequences in the T cell. Mapping myelin epitopes revealed a heterogeneity in T cell responses among JME animals, which are associated with a proinflammatory pathogenic role in multiple sclerosis (MS). These findings draw further parallels between JME and MS and support the hypothesis that JME and possibly MS are triggered by mechanisms involving myelin damage and not myelin epitope mimicry. Supported by ORIP (P51OD011092) and NINDS.


 Endogenous Zebrafish Neural Cre Drivers Generated by CRISPR/Cas9 Short Homology Directed Targeted Integration

Almeida, M.P. et al., Scientific Reports. 2021 January 18;11(1):1732 (PMC7813866)

Almeida et al. previously reported precision targeted integration of reporter DNA in zebrafish using CRISPR/Cas9. Here, they isolated zebrafish Cre recombinase drivers. A 2A-Cre recombinase transgene with 48 bp homology arms was targeted into proneural genes ascl1bolig2 and neurod1. They observed high rates of germline transmission from 10 to 100% (10% olig2; 20% neurod1; 100% ascl1b). The lines Tg(ascl1b-2A-Cre)is75Tg(olig2-2A-Cre)is76, and Tg(neurod1-2A-Cre)is77 expressed functional Cre recombinase in the cell populations. Results demonstrate Cre recombinase expression is driven by the native promoter and regulatory elements of targeted genes. This approach is a cost-effective method to generate cell type specific zebrafish Cre and CreERT2 drivers. Supported by ORIP (R24 OD020166).


 A Modular Master Regulator Landscape Controls Cancer Transcriptional Identity

Paul et al., Cell. 2021 Jan 21;184(2):334-351.e20

The mechanisms linking genomic alterations to transcriptional identity of cancer cells remain elusive. Integrative genomic analysis, using a network-based approach, identified 407 master regulator (MR) proteins responsible for canalizing the genetics of individual samples from 20 cohorts in The Cancer Genome Atlas into 112 transcriptionally distinct tumor subtypes. MR proteins could be further organized into 24 pan-cancer, MR block modules (MRBs), each regulating key cancer hallmarks and predictive of patient outcome in multiple cohorts. Of all somatic alterations detected in each individual sample, >50% were predicted to induce aberrant MR activity, yielding insight into mechanisms linking tumor genetics and transcriptional identity and establishing non-oncogene dependencies. Genetic and pharmacological validation assays confirmed the predicted effect of upstream mutations and MR activity on downstream cellular identity and phenotype. Thus, co-analysis of mutational and gene expression profiles identified elusive subtypes and provided testable hypothesis for mechanisms mediating the effect of genetic alterations. Supported by ORIP (S10OD012351 and S10OD021764), NCI, and other sources.


 Severely Ill COVID-19 Patients Display Impaired Exhaustion Features in SARS-CoV-2-Reactive CD8+ T Cells

Kusnadi1 et al., Sci Immunol. 2021 Jan 21;6(55):eabe4782

How CD8+ T cells respond to SARS-CoV-2 infection is not fully known. Investigators reported on the single-cell transcriptomes of >80,000 virus-reactive CD8+ T cells, obtained using a modified Antigen-Reactive T cell Enrichment assay, from 39 COVID-19 patients and 10 healthy subjects. COVID-19 patient cells were segregated into two groups based on whether the dominant CD8+ T cell response to SARS-CoV-2 was “exhausted” or not. SARS-CoV-2-reactive cells in the exhausted subset were increased in frequency and displayed less cytotoxicity and inflammatory features in COVID-19 patients with mild compared to severe illness. In contrast, SARS-CoV-2-reactive cells in the dominant non-exhausted subset from patients with severe disease showed enrichment of transcripts linked to co-stimulation, pro-survival Nuclear Factor κB signaling, and anti-apoptotic pathways, suggesting the generation of robust CD8+ T cell memory responses in patients with severe COVID-19 illness. Overall, this single-cell analysis revealed substantial diversity in the nature of CD8+ T cells responding to SARS-CoV-2. Supported by ORIP (S10RR027366 and S10OD025052), NIAID, NHLBI, NIGMS, and other sources.


 SARS-CoV-2 Induces Robust Germinal Center CD4 T Follicular Helper Cell Responses in Rhesus Macaques

Lakshmanappa, Yashavanth Shaan et al., Nature Communications. 22 January 2021, Article 541.

SARS-CoV-2 infection in both sexes of rhesus macaques, either infused with convalescent plasma, normal plasma, or receiving no infusion, resulted in transient accumulation of pro-inflammatory monocytes and proliferating CD4 T follicular helper (Tfh) cells, which are critical for persistent antibody responses. CD4 helper cell responses skewed predominantly toward a Th1 response in blood, lung, and lymph nodes. This skewing is important to note, as weak interferon responses observed in COVID patients could hamper effective antiviral antibody and CD8 T-cell responses. Collectively, the data show induction of GC responses in a rhesus model of mild COVID-19. Supported by ORIP (P51OD011107 and P40OD010976) and NIAID.


 Modified Vaccinia Ankara Vector-Based Vaccine Protects Macaques from SARS-CoV-2 Infection, Immune Pathology and Dysfunction in the Lung

Routhu, Nanda Kishore et al., Immunity. 2021 Feb; Epub ahead of print.

Any SARS-CoV-2 vaccine may have limitations such as need for ultracold storage, poor induction of CD8+ T cell response, or lack of cross-reactivity with emerging strains. Thus, multiple vaccines may be needed to bring COVID-19 under control. Using rhesus macaques, researchers showed that a modified vaccinia Ankara (MVA) vector-based SARS-CoV-2 vaccine expressing prefusion-stabilized spike protein induced strong neutralizing antibody and CD8+ T cell responses. The vaccine protected macaques from SARS-CoV-2 infection as well as infection-induced inflammation and B cell abnormalities in the lung. These results are promising considering the excellent safety and performance of MVA vector-based vaccines for other pathogens. Supported by ORIP (P51OD011132, S10OD026799) and NIAID.


 Germline Transmission of Donor, Maternal and Paternal mtDNA in Primates

Ma, Hong et al, Human Reproduction. 2021 February;36(2)

Mitochondrial gene mutations contribute to incurable human disorders. The possibility of using mitochondrial replacement therapy (MRT) to prevent transmission of pathogenic mitochondrial (mt)DNA was explored in rhesus macaques. Development of spindle MRT transfer in oocytes in 5 female rhesus macaques resulted in healthy and fertile offspring. These results demonstrate that MRT is compatible with normal postnatal development including overall health and reproductive fitness in nonhuman primates with no detected adverse effects. Additional research is needed to more fully explore the use of MRT to prevent disorders as this study had a limited number of animals with only one female offspring. Supported by ORIP (P51OD0092) and NIA.


 Trim-Away Mediated Knock Down Uncovers a New Function for Lbh During Gastrulation of Xenopus laevis

Weir, Emma et al. Dev Biol. 2021 Feb; 470:74-83 (PMC7855437)

The protein Lbh was identified as necessary for cranial neural crest cell migration in Xenopus. To investigate its role in embryonic events, the authors employed the technique "Trim-Away" to degrade this maternally deposited protein. Trim-Away utilizes the E3 ubiquitin ligase trim21 to degrade proteins targeted with an antibody. Early knockdown of Lbh in Xenopus results in defects in gastrulation that present with a decrease in fibronectin matrix assembly, an increase in mesodermal cell migration and decrease in endodermal cell cohesion. The technique is also effective on a second abundant maternal Protein Kinase C And Casein Kinase Substrate In Neurons 2. Supported by ORIP (R24 OD021485), NIDCR.


 Natural Killer Cells Activated through NKG2D Mediate Lung Ischemia-Reperfusion Injury

Calabrese et al., J Clin Invest. 2021 Feb 1;131(3):e137047

Pulmonary ischemia-reperfusion injury (IRI) causes early mortality and has no effective therapies. While natural killer (NK) cells are innate lymphocytes capable of recognizing injured cells, their roles in acute lung injury are incompletely understood. Here, investigators demonstrated that NK cells were increased in frequency and cytotoxicity in 2 different IRI mouse models. They showed that NK cells trafficked to the lung tissue from peripheral reservoirs and were more mature within lung tissue. Acute lung ischemia-reperfusion injury was blunted in a NK cell–deficient mouse strain but restored with adoptive transfer of NK cells. In human lung tissue, NK cells were increased at sites of ischemia-reperfusion injury and activated NK cells were increased in prospectively-collected human bronchoalveolar lavage in subjects with severe IRI. These data support a causal role for recipient peripheral NK cells in pulmonary IRI via NK cell NKG2D receptor ligation. Therapies targeting NK cells may hold promise in acute lung injury. Supported by ORIP (1S10OD026940), NHLBI, NIDDK, and other sources.


 BNT162b Vaccines Protect Rhesus Macaques from SARS-CoV-2

Vogel et al., Nature. 2021 Feb 1. Online ahead of print

The preclinical development of two BNT162b vaccine candidates, which contain lipid-nanoparticle formulated nucleoside-modified mRNA encoding SARS-CoV-2 spike glycoprotein-derived immunogens, was performed in rhesus macaques at the Southwest National Primate Research Center (SNPRC). BNT162b1 encodes a soluble, secreted, trimerised receptor-binding domain. BNT162b2 encodes the full-length transmembrane spike glycoprotein, locked in its prefusion conformation. Prime/boost vaccination of rhesus macaques with BNT162b candidates elicits SARS-CoV-2 neutralizing antibody titers that are 8.2 to 18.2 times that of a SARS-CoV-2 convalescent human serum panel. The vaccine candidates protected macaques from SARS-CoV-2 challenge, with BNT162b2 protecting the lower respiratory tract from the presence of viral RNA and with no evidence of disease enhancement. The BNT162b2 vaccine recently received emergency use authorization from FDA and is being administered within the United States. The SNPRC is supported by ORIP P51OD011103.


 Evaluating a New Class of AKT/mTOR Activators for HIV Latency-Reversing Activity Ex Vivo and In Vivo

Gramatica, Andrea et al., Journal of Virology. 2021 Feb 3; Epub ahead of print.

Activation of latent HIV-1 expression could benefit many HIV cure strategies. Researchers evaluated two AKT/mTOR activators, SB-216763 and tideglusib, as a potential new class of LRAs. The drugs reactivated latent HIV-1 present in blood samples from aviremic individuals on antiretroviral therapy without causing T cell activation or impaired effector function of cytotoxic T lymphocytes or NK cells. When tested in vivo in monkeys, tideglusib showed unfavorable pharmacodynamic properties and did not reverse SIV latency. The discordance between the ex vivo and in vivo results underscores the importance of developing novel LRAs that allow systemic drug delivery to relevant anatomical compartments. Supported by ORIP (P51OD011092), NIAID, NIGMS, NIMH, NCI, amfAR Institute for HIV Cure Research, University of California San Francisco-Gladstone Institute of Virology & Immunology Center for AIDS Research, and James B. Pendleton Charitable Trust.


 Modified Adenovirus Prime–Protein Boost Clade C HIV Vaccine Strategy Results in Reduced Viral DNA in Blood and Tissues Following Tier 2 SHIV Challenge

Malherbe, Delphine C. et al., Frontiers in Immunology, 2021 Feb 15;11:626464

Researchers conducted a comparative vaccine challenge study in rhesus macaques. One group of monkeys was vaccinated using co-immunization with DNA Gag and Env expression plasmids and trimeric Env gp140 glycoprotein. The other group was primed with two replicating simian adenovirus-vectored vaccines expressing Gag and boosted with trimeric Env gp140. Both strategies elicited antigen-specific humoral and cellular immune responses, but neither approach provided significant protection from viral acquisition upon repeated mucosal challenges with a heterologous Tier 2 SHIV. Nevertheless, both regimens significantly lowered cell-associated viral DNA in multiple tissues, thus potentially dampening the infection and providing clues for further vaccine development. Supported by ORIP (U42OD023038, P51OD011092) and NIAID.


 Acoustofluidic Rotational Tweezing Enables High-speed Contactless Morphological Phenotyping of Zebrafish Larvae

Chen, Chuyi et al. Nature Communications. 18 February 2021;12(1):1118. PMC7892888

These authors demonstrate an acoustofluidic rotational tweezing platform that enables contactless, high-speed, 3D multispectral imaging and digital reconstruction of zebrafish larvae for quantitative phenotypic analysis. The acoustic-induced polarized vortex streaming achieves contactless and rapid (~1 s/rotation) rotation of zebrafish larvae enabling multispectral imaging of the zebrafish body and internal organs. They developed a 3D reconstruction pipeline that yields accurate 3D models based on the multi-view images for quantitative evaluation. With its contactless nature and advantages in speed and automation, the acoustofluidic rotational tweezing system has the potential to be a valuable asset for developmental biology and pre-clinical drug development in pharmacology. Supported by ORIP (R43 OD024963), NCI, NIGMS.


 Larval Zebrafish Use Olfactory Detection of Sodium and Chloride to Avoid Salt Water

Herrera, Kristian J. et al. Current Biology. 22 February 2021;31(4):782-793.e3. PMC7904661.

Zebrafish are freshwater fish unable to tolerate high-salt environments and would benefit from neural mechanisms that enable the navigation of salt gradients to avoid high salinity. Yet zebrafish lack epithelial sodium channels, the primary conduit land animals use to taste sodium. This suggests fish may possess novel, undescribed mechanisms for salt detection. In the present study, the authors show that zebrafish indeed respond to small temporal increases in salt by reorienting more frequently. In summary, this study establishes that zebrafish larvae can navigate and thus detect salinity gradients and that this is achieved through previously undescribed sensory mechanisms for salt detection. Supported by ORIP (R43 OD024879, R44 OD024879), NINDS.


 Polyfunctional Tier 2–Neutralizing Antibodies Cloned Following HIV-1 Env Macaque Immunization Mirror Native Antibodies in a Human Donor

Spencer, David A. et al., Journal of Immunology. 2021 Mar; 206(5):999-1012.

HIV vaccine efforts are limited by viral strain diversity and the shielding of neutralization epitopes on the viral envelope, yet isolation of broadly neutralizing antibodies from infected individuals suggests the potential for eliciting protective antibodies through vaccination. Researchers cloned 58 monoclonal antibodies (mAbs) from a rhesus monkey immunized with envelope glycoprotein immunogens from an HIV-1 clade C–infected volunteer. Twenty mAbs exhibited some neutralizing activity. Cloned mAbs targeting the V3 region and CD4 binding site were capable of tier 2 (i.e., moderate) neutralization. This study demonstrates partial recapitulation of the human donor’s humoral immune response through nonhuman primate vaccination. Supported by ORIP (P51OD011092) and NIAID.


 Immune Variations Throughout the Course of Tuberculosis Treatment and its Relationship with Adrenal Hormone Changes in HIV-1 Patients Co-Infected with Mycobacterium tuberculosis

Vecchione, María Belén et al., Tuberculosis. 2021 Mar; 127:102045.

The probability of developing tuberculosis (TB) is 19 times higher in people infected with human immunodeficiency virus (HIV) compared to the general population. As host immune response defines the course of infection, researchers aimed to identify immuno-endocrine changes over six months of anti-TB chemotherapy in HIV+ people. Throughout the course of anti-TB/HIV treatment, plasma dehydroepiandrosterone (DHEA) and DHEA-sulfate levels increased while cortisol decreased. The balance between cortisol and DHEA, together with clinical assessment, served as a predictor of clinical outcome after anti-TB treatment. This research suggests that combined anti-HIV/TB therapies may partially restore both immune function and adrenal hormone levels. Supported by ORIP (P51OD011133), Argentina’s National Agency for the Promotion of Research, Technological Development, and Argentine Innovation, and the University of Buenos Aires.


 Autologous Transplant Therapy Alleviates Motor and Depressive Behaviors in Parkinsonian Monkeys

Tao, Yunlong et al., Nature Medicine, 1 March 2021.

Generation of induced pluripotent stem cells (iPSCs) enables standardized of dopamine (DA) neurons for autologous transplantation therapy to improve motor functions in Parkinson disease (PD). Adult male rhesus PD monkeys receiving autologous, but not allogenic, transplantation exhibited recovery from motor and depressive signs of PD over a 2-year period without immunosuppressive therapy. Mathematical modeling showed correlations between surviving DA neurons with PET signal intensity and behavior recovery regardless of autologous or allogeneic transplant, suggesting a predictive power of PET and motor behaviors for surviving DA neuron number. The results demonstrate favorable efficacy of the autologous transplant approach to treat PD. Supported by ORIP (P51OD011106) NINDS, and NICHD.


 New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention, and Cure

Li, Hui et al., Journal of Virology, 3 March 2021;95(11):e00071-21

Researchers knew that substitution of HIV-1 Env residue 375-serine by aromatic residues enhances binding to rhesus CD4 enabling primary HIV-1 Envs to support replication as simian-human immunodeficiency virus (SHIV) chimeras in rhesus monkeys. The investigators constructed SHIVs containing 10 primary Envs corresponding to HIV-1 subtypes A, B, C, AE, and AG. Only one with histidine at Env375 replicated efficiently in rhesus cells. Replacement of wildtype Env375 residues by tryptophan, tyrosine, phenylalanine, or histidine in the other 9 SHIVs led to efficient replication. These new SHIVs transmit via mucosal routes like HIV-1 and have use for vaccine testing in nonhuman primates. Supported by ORIP (U42OD021458, P40OD012217), NIAID, NCI, and Bill & Melinda Gates Foundation.


 A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution

Warren WC et al. Nat Commun. 2021 Mar 4;12(1):1447 (PMC7933363)

Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. Cave-dwelling Astyanax mexicanus populations are well adapted to subterranean life and many populations appear to have evolved troglomorphic (morphological adaptation of an animal to living in the constant darkness of caves) traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Warren et al. present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, they performed quantitative trait locus (QTL) mapping analyses and found new candidate genes for eye loss (dusp26). They also generated the first genome-wide evaluation of deletion variability across cavefish populations to gain insight into this potential source of cave adaptation. The surface fish genome reference now provides a more complete resource for comparative, functional and genetic studies of drastic trait differences within a species. Supported by ORIP (R24 OD011198), NIA, NICHD, NIGMS, NIDCR.


 Persistence of Viral RNA in Lymph Nodes in ART-suppressed SIV/SHIV-infected Rhesus Macaques

Cadena, Anthony M. et al., Nature Communications. 2021 March 5;12(1):1474 

The long-lived viral reservoir is a key obstacle to curing HIV/AIDS, yet the features of that reservoir during antiretroviral therapy (ART) remain poorly understood. Researchers undertook a comprehensive analysis of the SIV/SHIV reservoir in multiple lymphoid and non-lymphoid tissues from SIV/SHIV-infected rhesus macaques suppressed with ART for one year. Their findings support a model in which the tissue viral reservoir is rapidly and broadly seeded early during acute infection. Viral RNA persists lymphoid tissues despite a long period of suppressive ART. Therefore, viral latency does not appear to be universally transcriptionally silent; the reservoir may include a spectrum of latency depths. Supported by ORIP (R01OD024917), NIAID, and Ragon Institute.


 Creb5 Establishes the Competence for Prg4 Expression in Articular Cartilage

Zhang, Cheng-Hai et al., Communications Biology. 2021 Mar 12; 4(1):332

Cells comprising the superficial zone of articular cartilage express lubricin, encoded by the Prg4 gene, that lubricates joints. Researchers identified Creb5 as a transcription factor that is required for TGF-β and EGFR signaling to induce Prg4 expression. Forced expression of Creb5 in deep-zone chondrocytes of articular cartilage confers competence for TGF-β and EGFR signals to induce Prg4 expression. The researchers showed that Creb5 directly binds to two Prg4 promoter-proximal regulatory elements, which work together with a more distal regulatory element to drive induction of Prg4 by TGF-β. Thus, Creb5 is a critical regulator of Prg4/lubricin expression in the articular cartilage. Supported by ORIP (U42OD11158), NIAMS, NIDDK, and Arthritis National Research Foundation.


 Virus Control in Vaccinated Rhesus Macaques Is Associated with Neutralizing and Capturing Antibodies against the SHIV Challenge Virus but Not with V1V2 Vaccine–Induced Anti-V2 Antibodies Alone

Hessell, Ann J. et al., Journal of Immunology. 2021 Mar 15; 206(6):1266-1283.

In the RV144 human immunodeficiency virus (HIV) vaccine trial, the only immune response associated with reduced infection was a high level of antibodies (Abs) targeting the second variable (V2) loop of the HIV envelope protein (Env). The mechanism underlying this suggested contribution of V2 Abs to protection remains unknown. Researchers tested the role of vaccine-induced anti-V2 Abs in rhesus macaques. Three vaccines strategies were designed to induce only V1V2 Abs before simian-human immunodeficiency virus (SHIV) challenge. Vaccine-induced V2 Abs did not independently control SHIV infection. However, neutralizing and virus capture anti-Env Abs were found to correlate with SHIV control. Supported by ORIP (P51OD011092) and NIAID.


 A pulsatile release platform based on photo-induced imine-crosslinking hydrogel promotes scarless wound healing

Jian Zhang, et al., Nat Commun. 2021 Mar 15;12(1):1670

Skin wound healing is a dynamic and interactive process involving the collaborative efforts of growth factors, extracellular matrix (ECM), and different tissue and cell lineages. Although accumulating studies with a range of different model systems have increased our understanding of the cellular and molecular basis underlying skin scar formation, they have not been effectively translated to therapy. Development of effective therapeutic approaches for skin scar management is urgently needed. In this study, team of investigators devise a water-oil-water double emulsion strategy to encapsulate proteins within a photo-crosslinkable poly-lactic-co-glycolic acid (PLGA) shell, which can produce microcapsules with pulsatile drug release kinetics after administration. The results show that pulsatile release of the TGF-β inhibitor can accelerate skin wound closure while suppressing scarring in murine skin wounds and large animal preclinical models, suggesting that it could be an effective approach to achieve scarless wound healing in skin. ORIP support grant: R01OD023700.


 A Platform for Experimental Precision Medicine: The Extended BXD Mouse Family

Ashbrook, David G. et al., Cell Systems, 17 March 2021; Volume 12, Issue 3, Pages 235-247

Systems genetics using rodent models has recently been revitalized thanks to several resources: the BXD family, the Hybrid Mouse Diversity Panel, and the Collaborative Cross. The main limitation has been modest mapping power and precision due to small strain numbers. Investigators expanded the BXD family of mice to 140 fully isogenic strains. Heritable traits can be mapped with precision. Current BXD phenomes include much omics data and thousands of quantitative traits. BXDs can be extended by a single-generation cross up to 19,460 isogenic F1 progeny. This extended BXD family is an effective platform for testing causal modeling and predictive validation. The BXD Resource at the Jackson Laboratory is supported by ORIP P40 OD011102 awarded to Dr. Cathleen M. Lutz.


 A Novel Tau-Based Rhesus Monkey Model of Alzheimer’s Pathogenesis

Beckman, Danielle et al., Alzheimer’s & Dementia. 2021 Mar 18; Epub ahead of print.

Alzheimer’s disease (AD) is becoming more prevalent as the population ages, but there are no effective treatments for this devastating condition. Researchers developed a rhesus monkey model of AD by targeting the entorhinal cortex with an adeno-associated virus expressing mutant tau protein. Within 3 months they observed evidence of misfolded tau propagation, similar to what is hypothesized for AD patients. Treated monkeys developed robust alterations in AD core biomarkers in cerebrospinal fluid and blood. These results highlight the initial stages of tau seeding and propagation in rhesus macaques, a potentially powerful translational model with which to test new AD therapies. Supported by ORIP (P51OD 011107) and NIA.


 Resident Memory T Cells Form during Persistent Antigen Exposure Leading to Allograft Rejection

Abou-Daya et al., Sci Immunol., 2021 Mar 19;6(57):eabc8122.

It is not clear whether Tissue-resident memory T cells (TRM) function in organ transplants where cognate antigen persists. This is a key question in transplantation as T cells are detected long term in allografts. Investigators showed that antigen-specific and polyclonal effector T cells differentiated in the graft into TRM and subsequently caused allograft rejection. Graft TRM proliferated locally, produced interferon-γ upon restimulation, and their in vivo depletion attenuated rejection. The vast majority of antigen-specific and polyclonal TRM lacked phenotypic and transcriptional exhaustion markers. Single-cell analysis of graft T cells early and late after transplantation identified a transcriptional program associated with transition to the tissue-resident state that could serve as a platform for the discovery of therapeutic targets. Thus, recipient effector T cells differentiate into functional graft TRM that maintain rejection locally. Targeting these TRM could improve renal transplant outcomes. ORIP grant support: 1S10OD011925-01 and 1S10OD019942-01.


 Metabolomics analysis of follicular fluid coupled with oocyte aspiration reveals importance of glucocorticoids in primate periovulatory follicle competency

Ravisankar et al., Sci Rep. 22 March 2021

Assisted reproductive therapy in primates requires ovarian stimulation protocols, which result in multiple heterogeneous oocytes with variable capacity for fertilization, cleavage, and blastocyst formation. Recovered oocytes from rhesus macaque follicles (n=74 follicles) were fertilized in vitro and classified as failed to cleave, cleaved but arrested, or able to form blastocysts. Metabolomics analysis of the follicular fluid identified 60 metabolites that were different among embryo classifications; key was an increase in the intrafollicular ratio of cortisol to cortisone in the blastocyst group, which was associated with translocation of the glucocorticoid receptor, NR3C1. The data suggest a role for NR3C1 in the regulation of follicular processes, such as expansion of cumulus granulosa cells, via paracrine signaling. Supported by ORIP (P51OD011092) and NICHD.


 The SARS-CoV-2 Receptor and Other Key Components of the Renin-Angiotensin-Aldosterone System Related to COVID-19 are Expressed in Enterocytes in Larval Zebrafish

Postlethwait, John H. et al. Biology Open (23 March 2021) 10, bio058172. doi:10.1242/bio.058172

Hypertension and respiratory inflammation are exacerbated by the Renin-Angiotensin-Aldosterone System (RAAS), which normally protects from dropping blood pressure via Angiotensin II (Ang II) produced by the enzyme Ace. The Ace paralog Ace2 degrades Ang II and serves as the SARS-CoV-2 receptor. To exploit zebrafish to understand the relationship of RAAS to COVID-19, the group conducted genomic and phylogenetic analyses. Results identified a type of enterocyte as the expression site of zebrafish orthologs of key RAAS components, including the SARSCoV-2 co-receptor. Results identified vascular cell subtypes expressing Ang II receptors and identified cell types to exploit zebrafish as a model for understanding COVID-19 mechanisms. Supported by ORIP (R24 OD026591, R01 OD011116), NIGMS, NICHD.


 Cytomegaloviral Determinants of CD8+ T Cell Programming and RhCMV/SIV Vaccine Efficacy

Malouli et al., Science Immunology. 2021 Mar 25; 6(57):eabg5413

Cytomegalovirus (CMV)-based vaccine vectors were developed to leverage the ability of CMVs to elicit sustained CD4+ and CD8+ T cell responses with broad tissue distribution. The 68-1 rhesus cytomegalovirus (RhCMV) vectors that express simian immunodeficiency virus (SIV) inserts induce major histocompatibility complex E (MHC-E)- and MHC-II-restricted, SIV-specific CD8+ T cell responses. The contribution of this unconventional MHC restriction to RhCMV/SIV vaccine efficacy are poorly understood. Researchers demonstrated that these responses result from genetic rearrangements in 68-1 RhCMV that disrupt the function of eight immunomodulatory proteins encoded by the virus. Repair of each of these genes with either RhCMV or human CMV counterparts shifted responses to MHC-Ia-restricted, or MHC-Ia- and MHC-II-restricted, CD8 T cell responses, but repairing the RhCMV genes did not protect against SIV. These findings suggest that MHC-E-restricted CD8+ T cell responses may be critical to protection against SIV. ORIP grant support: U42 OD023038 and P51 OD011092.


 Best Practices for Correctly Identifying Coronavirus by Transmission Electron Microscopy

Bullock et al., Kidney Int. 2021 Apr;99(4):824-827

This paper provides strategies for identifying coronaviruses by transmission electron microscopy in ultrathin sections of tissues or tissue cultures. As illustrated by results in the literature, organ damage may be incorrectly attributed to the presence of virus, since images of coronavirus may resemble subcellular organelles. The paper also references numerous biochemical and imaging techniques to aid an investigator in avoiding pseudo positive identifications. ORIP grant support: S10OD026776.


 Sensitive Tracking of Circulating Viral RNA Through All Stages of SARS-CoV-2 Infection

Huang et al., Journal of Clinical Investigation. 2021 Apr 1; 131(7):e146031

Circulating SARS-CoV-2 RNA could represent a more reliable indicator of infection than nasal RNA, but quantitative reverse transcription PCR (RT-qPCR) lacks diagnostic sensitivity for blood samples. Researchers developed a CRISPR-amplified, blood-based COVID-19 (CRISPR-ABC) assay to detect SARSCoV-2 in plasma. They evaluated the assay using samples from SARS-CoV-2-infected African green monkeys and rhesus macaques as well as from COVID-19 patients. CRISPR-ABC consistently detected viral RNA in the plasma of the experimentally infected primates from 1 to 28 days after infection. The increases in plasma SARS-CoV-2 RNA in the monkeys preceded rectal swab viral RNA increases. In the patient cohort, the new assay demonstrated 91.2% sensitivity and 99.2% specificity versus RT-qPCR nasopharyngeal testing, and it also detected COVID-19 cases with transient or negative nasal swab RT-qPCR results. These findings suggest that detection of SARS-CoV-2 RNA in blood by CRISPR-augmented RT-PCR could improve COVID-19 diagnosis, facilitate the evaluation of SARS-CoV-2 infection clearance, and help predict the severity of infection. ORIP grant support: P51 OD011104.


 Interneuron Origins in the Embryonic Porcine Medial Ganglionic Eminence

Casalia, Mariana L. et al, Journal of Neuroscience, 7 April 2021, Volume 41, Issue 14, Pages 3105-3119

The authors report that transcription factor expression patterns in porcine embryonic subpallium are similar to rodents. Their findings reveal that porcine embryonic MGE progenitors could serve as a valuable source for interneuron-based xenotransplantation therapies. They demonstrate that porcine medial ganglionic eminence exhibits a distinct transcriptional and interneuron-specific antibody profile, in vitro migratory capacity, and are amenable to xenotransplantation. This is the first comprehensive examination of embryonic interneuron origins in the pig; because a rich neurodevelopmental literature on embryonic mouse medial ganglionic eminence exists (with some additional characterizations in monkeys and humans), their work allows direct neurodevelopmental comparisons with this literature. Supported by ORIP (U42 OD011140), NINDS.


 Establishing an Immunocompromised Porcine Model of Human Cancer for Novel Therapy Development with Pancreatic Adenocarcinoma and Irreversible Electroporation

Hendricks-Wenger, Alissa et al., Scientific Reports. 07 April 2021; 11(1):7584 (PMC8027815).

Efficacious interventions to treat pancreatic cancer lack a preclinical model to recapitulate patients' anatomy and physiology. The authors developed RAG2/IL2RG deficient pigs using CRISPR/Cas9 with the novel application of cancer xenograft studies of human pancreatic adenocarcinoma. These pigs were successfully generated using on-demand genetic modifications in embryos. Human Panc01 cells injected into the ears of RAG2/IL2RG deficient pigs demonstrated 100% engraftment. The electrical properties and response to irreversible electroporation of the tumor tissue were found to be similar to excised human pancreatic cancer tumors. This model will be useful to bridge the gap of translating therapies from the bench to clinical application. Supported by ORIP (R21OD027062), NIBIB, NCI.


 Rhesus Macaques Build New Social Connections After a Natural Disaster

Testard, Camille et al. Current Biology. 2021 April 8; S0960-9822(21)00368-7

Climate change has increased the frequency and intensity of weather-related disasters such as hurricanes and floods. In 2017, Puerto Rico suffered its worst natural disaster, Hurricane Maria, leaving 3,000 dead and provoking a mental health crisis. Cayo Santiago Island, home to a population of rhesus macaques (Macaca mulatta), was devastated by this storm. Testard et al. compared social networks of two groups of macaques before and after the hurricane and found an increase in affiliative social connections, driven largely by monkeys most socially isolated before Hurricane Maria. Further analysis revealed monkeys invested in building new relationships rather than strengthening existing ones. Supported by ORIP (P40 OD012217), NIA, NIMH.


 Bilateral Visual Projections Exist in Non-teleost Bony Fish and Predate the Emergence of Tetrapods

Vigouroux, Robin J., et al. Science. 09 April 2021; 372(6538):150-156.

In most vertebrates, camera-style eyes contain retinal ganglion cell neurons that project to visual centers on both sides of the brain. However, in fish, ganglion cells were thought to innervate only the contralateral side, suggesting that bilateral visual projections appeared in tetrapods. Here, Vigouroux et al., showed that bilateral visual projections exist in non-teleost fishes and that the appearance of ipsilateral projections does not correlate with terrestrial transition or predatory behavior. However, overexpression of human ZIC2 induces ipsilateral visual projections in zebrafish. Therefore, the existence of bilateral visual projections likely preceded the emergence of binocular vision in tetrapods. Supported by ORIP (R01 OD011116).


 The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci

Schloissnig S. et al. Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2017176118.

Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with genome expansion is unclear, and how acute changes in gene regulation, as during axolotl limb regeneration, occur in the context of a vast genome has remained a riddle. Here, Schloissnig et al. describe the chromosome-scale assembly of the giant, 32 Gb axolotl genome. Hi-C contact data revealed the scaling properties of interphase and mitotic chromosome organization. Analysis of the assembly yielded understanding of the evolution of large, syntenic multigene clusters, including the Major Histocompatibility Complex (MHC) and the functional regulatory landscape of the Fibroblast Growth Factor 8 (Axfgf8) region. The axolotl serves as a primary model for studying successful regeneration. Supported by ORIP (R24 OD010435, P40 OD019794).


 Functional Convergence of a Germline-Encoded Neutralizing Antibody Response in Rhesus Macaques Immunized with HCV Envelope Glycoproteins

Chen, Fang et al., Immunity. 2021 Apr 13; 54(4):781-796

 Immunoglobulin heavy chain variable gene IGHV1-69-encoded broadly neutralizing antibodies (bnAbs) targeting the hepatitis C virus (HCV) envelope glycoprotein (Env) E2 are important for protection against HCV infection in humans. An IGHV1-69 ortholog, VH1.36, is preferentially used for bnAbs isolated from rhesus macaques immunized against HCV Env. Researchers investigated the genetic, structural, and functional properties of VH1.36-encoded bnAbs generated by HCV Env vaccination of macaques and compared their findings to IGHV1-69-encoded bnAbs from HCV patients. The investigators found that macaque VH1.36- and human IGHV1-69-encoded bnAbs share many common features, which provides an excellent framework for rational HCV vaccine design and testing. Supported by ORIP (P51OD011133, U42OD010442), NIAID, NCI, NIGMS, Dept. of Energy, Independent Research Fund Denmark, Novo Nordisk Foundation, Candys Foundation, and Lundbeck Foundation


 Characterization of Axolotl Lampbrush Chromosomes by Fluorescence in Situ Hybridization and Immunostaining

Keinath, Melissa C., et al., Experimental Cell Research, 15 April 2021;401(2):112523

The lampbrush chromosomes (LBCs) in oocytes of the Mexican axolotl (Ambystoma mexicanum) were identified by their relative lengths and predicted centromeres; they have never been associated completely with the mitotic karyotype, linkage maps, or genome assembly. The authors identified nine of the axolotl LBCs using RNAseq to identify actively transcribed genes and thirteen BAC (bacterial artificial clone) probes containing pieces of active genes. This study presents a simple and reliable way to identify each axolotl LBC cytologically and to anchor chromosome-length sequences to the LBCs by immunostaining and fluorescence in situ hybridization. This data will facilitate a more detailed analysis of LBC loops. Supported by ORIP (P40 OD019794, R24 OD010435), NIGMS.


 The High Affinity Dopamine D2 Receptor Agonist MCL-536: A New Tool for Studying Dopaminergic Contribution to Neurological Disorders

Subburaju, Sivan et al. ACS Chemical Neuroscience. 2021 April 21;12(8):1428-1437 (PMC8426090)

The dopamine D2 receptor exists in two different states, D2high and D2low; the former is the functional form of the D2 receptor and associates with intracellular G-proteins. The D2 agonist [3H]MCL-536 has high affinity for the D2 receptor (Kd 0.8 nM) and potently displaces the binding of (R-(-)-N-n-propylnorapomorphine (NPA; Ki 0.16 nM) and raclopride (Ki 0.9 nM) in competition binding assays. The authors characterized [3H]MCL-536. [3H]MCL-536 as metabolically stable. In vitro autoradiography on transaxial and coronal brain sections showed specific binding of [3H]MCL-536. [3H]MCL-536's unique properties make it a valuable tool for research on neurological disorders like Parkinson's disease or schizophrenia. Supported by ORIP (R43 OD020186, R44 OD024615), NIMH.


 Cryopreservation Method for Drosophila Melanogaster Embryos

Zhan, Li. et al., Nature Communications, 2021 April 23;12(1):2412

D. melanogaster is a premier model for biomedical research. However, preservation of Drosophila stocks is labor intensive and costly to pass live cultures monthly to fresh food. Researchers at University of Minnesota reported an efficient method for cryopreservation by optimizing key steps including embryo permeabilization and cryoprotectant agent loading. This method resulted in >10% of embryos developing into fertile adults after cryopreservation for 25 distinct strains from different sources. The further optimization and wide adoption of this protocol will solve the long-standing issue in reliably preserving Drosophila stocks and will significantly impact Drosophila as a model organism for biomedical research. Supported by ORIP (1R21OD028758), NIGMS, NSF, and other sources.


 Evidence in Primates Supporting the Use of Chemogenetics for the Treatment of Human Refractory Neuropsychiatric Disorders

Roseboom, Patrick H. et al., Molecular Therapy, 2021 April 23;S1525-0016(21)00209-4

A rhesus macaque model of pathological anxiety was used to investigate the feasibility of decreasing anxiety using chemogenetics, known as DREADDs (designer receptors exclusively activated by designer drugs), to reduce amygdala neuronal activity. A low-dose clozapine administration strategy was developed to induce DREADD-mediated amygdala inhibition. Compared to controls, clozapine selectively decreased anxiety-related freezing behavior in the human intruder paradigm in the chemogentic monkeys, while coo vocalizations and locomotion were unaffected. These results are an important step in establishing chemogenetic strategies for patients with refractory neuropsychiatric disorders in which amygdala alterations are central to disease pathophysiology. Supported by ORIP (P51OD011106), NIMH, and NICHD. 


 Modulation of MHC-E Transport by Viral Decoy Ligands Is Required for RhCMV/SIV Vaccine Efficacy

Verweij, Marieke C. et al., Science. 30 April 2021;372(6541):eabe9233.

Rhesus cytomegalovirus (RhCMV) strain 68-1-vectored simian immunodeficiency virus (SIV) vaccines elicit strong CD8+ T cell responses that can clear SIV infections. Peptides targeted by these T cells are presented on major histocompatibility complex (MHC) II and MHC-E rather than MHC-Ia. Researchers showed that VL9 drives intracellular transport of MHC-E and recognition of RhCMV-infected targets by MHC-E-restricted CD8+ T cells. Specific pathogen-free (SPF) rhesus macaques vaccinated with a mutant 68-1 RhCMV lacking VL9 showed no priming of MHC-E-restricted CD8+ T cells and no protection against SIV, suggesting that future effective CMV-based HIV vaccines will require MHC-E-restricted CD8+ T cell priming. Supported by ORIP (U42OD023038, P51OD011092), NIAID, NCI, and Bill & Melinda Gates Foundation.


 Identification of Basp1 as a Novel Angiogenesis-regulating Gene by Multi-model System Studies

Khajavi, Mehrdad et al. Federation of American Societies for Experimental Biology (FASEB). 2021 May;35(5):e21404. PMC8218237

The authors previously used genetic diversity in inbred mouse strains to identify quantitative trait loci (QTLs) responsible for differences in angiogenic response. Employing a mouse genome-wide association study (GWAS) approach, the region on chromosome 15 containing Basp1 was identified as being significantly associated with angiogenesis in inbred strains. To investigate its role in vivo, they knocked out basp1 in transgenic kdrl:zsGreen zebrafish embryos using a widely adopted CRISPR-Cas9 system. They further showed that basp1 promotes angiogenesis by upregulating β-catenin gene and the Dll4/Notch1 signaling pathway. These results provide the first in vivo evidence to indicate the role of Basp1 as an angiogenesis-regulating gene. Supported by ORIP (R24 OD017870), NEI, HHMI. 


 MRI Characteristics of Japanese Macaque Encephalomyelitis (JME): Comparison to Human Diseases

Tagge, Ian J. et al., 2021; Journal of Neuroimaging, 2021 May;31(3):480-492

MRI data were obtained from 114 Japanese macaques including 30 animals of both sexes that presented with neurological signs of JME. Quantitative estimates of blood-brain-barrier permeability to gadolinium-based-contrast agent (GBCA) were obtained in acute, GBCA-enhancing lesions, and longitudinal imaging data were acquired for 15 JME animals. Intense, focal neuroinflammation was a key MRI finding in JME. Several features of JME compare directly to human inflammatory demyelinating diseases. The development and validation of noninvasive imaging biomarkers in JME provides the potential to improve diagnostic specificity and contribute to the understanding of human demyelinating diseases. Supported by ORIP (P51OD011092, S10OD018224), NINDS, and NIBIB.


 Combining In Vivo Corneal Confocal Microscopy With Deep Learning-Based Analysis Reveals Sensory Nerve Fiber Loss in Acute Simian Immunodeficiency Virus Infection

McCarron, Megan E. et al., Cornea, 2021 May 1;40(5):635-642

Researchers characterized corneal subbasal nerve plexus features of normal and simian immunodeficiency virus (SIV)-infected pigtail and rhesus macaques using in vivo confocal microscopy and a deep learning approach for automated assessments. Corneal nerve fiber length and fractal dimension measurements did not differ between species, but pigtail macaques had significantly higher baseline corneal nerve fiber tortuosity than rhesus macaques. Acute SIV infection induced decreased corneal nerve fiber length and fractal dimension in the pigtail macaque model of HIV. Adapting deep learning analyses to clinical corneal nerve assessments will improve monitoring of small sensory nerve fiber damage in numerous clinical contexts, including HIV. Supported by ORIP (U42OD013117), NINDS, Johns Hopkins University School of Medicine, and Fulbright New Zealand.


 'Enhancing' Red Cell Fate through Epigenetic Mechanisms

Rossmann, Marlies P. and Zon, Leonard I., Current Opinion in Hematology, 1 May 2021; Volume 28, Issue 3, Pages 129-137

Transcription of erythroid-specific genes is regulated by the three-dimensional (3D) structure and composition of chromatin, which changes during erythroid differentiation. These authors address recent developments delineating the interface of chromatin regulation and erythroid-specific lineage transcription. They survey the erythroid chromatin landscape, erythroid enhancer-promotor interactions, super-enhancer functionality, the role of chromatin modifiers and epigenetic crosstalk, as well as the progress in mapping red blood cell (RBC) trait-associated genetic variants within cis-regulatory elements (CREs) identified in genome-wide association study (GWAS) efforts. New emerging technologies allow investigation of small cell numbers have advanced our understanding of chromatin dynamics during erythroid differentiation in vivo. Supported by ORIP (R24 OD017870), NHLBI.


 Postpubertal Spermatogonial Stem Cell Transplantation Restores Functional Sperm Production in Rhesus Monkeys Irradiated Before and After Puberty

Shetty, Gunapala et al., Andrology. 6 May 2021.

Cancer treatment of prepubertal patients impacts future fertility due to the abolition of spermatogonial stem cells (SSCs). Prepubertal rhesus monkeys (n=6) were unilaterally castrated, and the remaining testes irradiated twice to insure loss of SSCs; the animals were treated with a vehicle or GnRH antagonist for 8 weeks (n=3/treatment). The cryopreserved prepubertal testicular tissue was allergenically transplanted into the intact testes of the monkeys after puberty. Recovery of viable donor epididymal sperm was observed in half the monkeys. These results illustrate that sperm production can be restored in primates by transplantation of testicular cells from cryopreserved untreated prepubertal testes into seminiferous tubules of the remaining testes. Supported by ORIP (P51OD011092), NICHD, and NCI.


 Psychosocial Stress Alters the Immune Response and Results in Higher Viral Load During Acute SIV Infection in a Pigtailed Macaque Model of HIV

Guerrero-Martin, Selena et al., Journal of Infectious Diseases. 2021 May 10; Online ahead of print.

Social distancing is an important countermeasure for a pandemic, but social isolation may also have adverse health outcomes in the context of infectious diseases, such as HIV. Researchers compared commonly measured parameters of HIV progression between singly and socially housed simian immunodeficiency virus (SIV)-infected pigtailed macaques. Throughout acute SIV infection, singly housed pigtailed macaques had a higher viral load in the plasma and cerebrospinal fluid and demonstrated greater CD4+ T cell declines and more CD4+ and CD8+ T cell activation compared to socially housed macaques. These findings suggest that psychosocial stress could augment the progression of HIV infection. Supported by ORIP (U42OD013117, P40OD013117, K01OD018244), NIAID, NINDS, NIMH, AALAS Grants for Laboratory Animal Science, and Blaustein Pain Foundation.


 Tract Pathogen-Mediated Inflammation Through Development of Multimodal Treatment Regimen and Its Impact on SIV Acquisition in Rhesus Macaques

Bochart, Rachele M. et al., PLOS Pathogens. 10 May 2021;17(5):e1009565.

In addition to being premier HIV models, rhesus macaques are models for other infectious diseases and colitis, where background colon health and inflammation may confound results. Starting with the standard SPF model, researchers established a gastrointestinal pathogen-free (GPF) colony via multimodal therapy (enrofloxacin, azithromycin, fenbendazole, and paromomycin) to eliminate common endemic pathogens (EPs). This treatment combined with continued pathogen exclusion eliminated common EPs, improved mucosal barriers, and reduced mucosal and systemic inflammation without microbiota disruption. GPF animals challenged with SIV intrarectally demonstrated a more controlled and consistent rate of SIV acquisition, suggesting the value of this model for HIV studies. Supported by ORIP (U42OD023038, P51OD011092), NCI, and NIAID.


 Cell-specific Transcriptional Control of Mitochondrial Metabolism by TIF1γ Drives Erythropoiesis

Rossmann, Marlies P. et al. Science. 14 May 2021;372(6543):716-721. PMC8177078

Transcription and metabolism both influence cell function but dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. The authors discovered that inhibition of the pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase (DHODH) rescues erythroid differentiation in bloodless zebrafish moonshine (mon) mutant embryos defective for transcriptional intermediary factor 1 gamma (tif1γ). Upon tif1γ loss, CoQ levels are reduced, and a high succinate/α-ketoglutarate ratio leads to increased histone methylation. A CoQ analog rescues mon's bloodless phenotype. These results demonstrate that mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage. Supported by ORIP (R24 OD017870), NIGMS, NHLBI, NCI.


 A Participant-Derived Xenograft Model of HIV Enables Long-Term Evaluation of Autologous Immunotherapies

McCann, Chase D. et al., Journal of Experimental Medicine. 14 May 2021;218(7):e20201908.

HIV-specific CD8+ T cells partially control viral replication but rarely provide lasting protection due to immune escape. Investigators showed that engrafting NSG mice with memory CD4+ T cells from HIV+ donors enables evaluation of autologous T cell responses while avoiding graft-versus-host disease. Treating HIV-infected mice with clinically relevant T cell products reduced viremia. In vivo activity was significantly enhanced when T cells were engineered with surface-conjugated nanogels carrying an Interleukin-15 superagonist but was ultimately limited by the pervasive selection of escape mutations, recapitulating human patterns. This “participant-derived xenograft” model provides a powerful tool for developing T cell-based therapies for HIV.
Supported by ORIP (R01OD011095), NIAID, NIDA, NIMH, NINDS, NCATS, Canadian Institutes of Health Research, and Michael Smith Foundation for Health Research.


 IL-21 and IFNα Therapy Rescues Terminally Differentiated NK Cells and Limits SIV Reservoir in ART-Treated Macaques

Harper, Justin et al., Nature Communications. 2021 May 17; 12:2866.

Nonpathogenic simian immunodeficiency virus (SIV) infections in natural hosts, such as vervet monkeys, are characterized by a lack of gut microbial translocation, robust secondary lymphoid natural killer cell responses, and limited SIV dissemination in lymph node B-cell follicles. Using antiretroviral therapy-treated, SIV-infected rhesus monkeys—a pathogenic model—researchers showed that interleukin-21 and interferon alpha therapy generate terminally differentiated blood natural killer cells with potent human leukocyte antigen-E-restricted activity in response to SIV envelope peptides. The correlated reduction of replication-competent SIV in lymph node demonstrates that vervet-like natural killer cell differentiation can be rescued in rhesus monkeys to promote viral clearance. Supported by ORIP (P51OD011132, R24OD010947), NIAID, NCI, French National Agency for Research on AIDS and Viral Hepatitis, and Fondation J. Beytout.


 Mineralocorticoid Receptor Blockade Normalizes Coronary Resistance in Obese Swine Independent of Functional Alterations in Kv Channels

Goodwill, Adam G. et al., Basic Research in Cardiology, 20 May 2021; Volume 116, Article 35

Impaired coronary microvascular function (e.g., reduced dilation and coronary flow reserve) predicts cardiac mortality in obesity. Mineralocorticoid receptor (MR) antagonism improves coronary microvascular function in obese humans and animals. Inhibition of Kv channels reduced coronary blood flow and augmented coronary resistance under baseline conditions in lean but not obese swine and had no impact on hypoxemic coronary vasodilation. MR blockade prevented obesity-associated coronary arteriolar stiffening independent of cardiac capillary density and changes in cardiac function. These data indicate that chronic MR inhibition prevents increased coronary resistance in obesity independent of Kv channel function and is associated with mitigation of obesity-mediated coronary arteriolar stiffening. Supported by ORIP (U42 OD011140, S10 OD023438), NHLBI, NIBIB.


 Cryopreservation and Preparation of Thawed Spermatozoa from Rhesus Macaques (Macaca mulatta) for In Vitro Fertilization

De Carvalho, Fernanda M. et al., Journal of the American Association for Laboratory Animal Science. 23 May 2021.

Optimizing procedures for cryopreservation and subsequent thawing for rhesus macaques is required to prevent cryodamage that negatively impacts artificial insemination and in vitro fertilization rates. Investigators systematically assessed two cryopreservation methods and four recovery methods in three interdependent experiments. Results demonstrated that slow-freezing, coupled with density gradient centrifugation provided the highest efficacy in functional sperm for in vitro use. Additional studies are required to further optimize sperm cryopreservation in rhesus macaques. Supported by ORIP (P51OD011092).


 Nonhuman Primate Models for SARS-CoV-2 Research: Cryopreservation as a Means to Maintain Critical Models and Enhance the Genetic Diversity of Colonies

Arnegard, Matthew and Hild, Sheri. Lab Animal. 2021 May 24. Online ahead of print.

This commentary, written by ORIP staff, addresses the need for improved cryopreservation methods and resources for nonhuman primate (NHP) gametes and embryos to safeguard newly developed NHP models and enhance the genetic diversity of NHP colonies without reliance on animal importations. Cryopreservation also plays critical roles in medical approaches to preserve the fertility of patients who must undergo potentially gonadotoxic treatments, as well as nascent genome editing efforts to develop new NHP models for human diseases. Given these diverse benefits to research progress, ORIP continues to fund the development of cryopreservation tools and approaches for NHPs and other animal models.


 Algorithms Underlying Flexible Phototaxis in Larval Zebrafish

Chen, Alex B. et al. Journal of Experimental Biology. 24 May 2021;224(10):jeb238386. PMC8180250.

Given that physiological and environmental variables undergo constant fluctuations over time, how do biological control systems maintain control over these values? The authors demonstrate that larval zebrafish use phototaxis to maintain environmental luminance at a set point, that the value of this set point fluctuates on a time scale of seconds when environmental luminance changes, and it is determined by calculating the mean input across both sides of the visual field. Feedback from the surroundings drives allostatic changes to the luminance set point. The authors describe a novel behavioral algorithm with which larval zebrafish exert control over a sensory variable. Supported by ORIP (R43 OD024879, R44 OD024879), NINDS.


 Single-cell Protein Activity Analysis Identifies Recurrence-associated Renal Tumor Macrophages

Obradovic, Aleksandar et al., Cell, 27 May 2021;184(11),P2988-3005.e16.

Post-surgery course of clear cell renal carcinoma (ccRCC) is mixed because of the heterogeneity of the disease. Using high-performance computing cluster and storage systems funded by the NIH Shared Instrumentation Programs, investigators established an inclusive ccRCC tumor microenvironment (TME) map by using single-cell RNA sequencing data of subpopulations of tumor and tumor-adjacent tissues. Analysis of the data identified key TME subpopulations as well as their master regulators and candidate cell-cell interactions, revealing clinically relevant cell populations. Specifically, the study uncovered a tumor-specific macrophage subpopulation, validated by spatially resolved, quantitative multispectral immunofluorescence. In a large clinical validation cohort, markers of this subpopulation were significantly enriched in tumors from patients who recurred following surgery. Supported by ORIP (S10 OD012351, S10 OD021764).


 Neutralizing Antibody Vaccine for Pandemic and Pre-Emergent Coronaviruses

Saunders, Kevin O. et al., Nature, 2021 June;594(7864):553-559

SARS-CoV-2 is a new member of the betacoronavirus (beta-CoV) genus, which also includes two common mild beta-CoVs and the life-threatening SARS-CoV-1 and MERS-CoV. Vaccines that elicit protective immunity against SARS-CoV-2 and beta-CoVs that circulate in animals could prevent future pandemics. Researchers designed a novel 24-mer SARS-CoV-2 receptor binding domain-sortase A conjugated nanoparticle vaccine (RBD-scNP). Investigators demonstrated that the immunization of macaques with RBD-scNP, and adjuvanted with 3M-052 and alum, elicits cross-neutralizing antibody responses against bat coronaviruses, SARS-CoV, and multiple SARS-CoV-2 variants of concern. This pioneering approach serves as a multimeric protein platform for the further development of generalized anti-beta-CoV vaccines. Supported by ORIP (U42OD021458), NIAID, and NCI.


 Loss of Gap Junction Delta-2 (GJD2) Gene Orthologs Leads to Refractive Error in Zebrafish

Quint, Wim H. et al., Communications Biology, 2021 June 3, Volume 4, Pages 1-14

Myopia is the most common developmental disorder of juvenile eyes. Although little is known about the functional role of GJD2 in refractive error development, the authors find that depletion of gjd2a (Cx35.5) or gjd2b (Cx35.1) orthologs in zebrafish cause changes in eye biometry and refractive status. Their immunohistological and scRNA sequencing studies show that Cx35.5 (gjd2a) is a retinal connexin; its depletion leads to hyperopia and electrophysiological retina changes. They found a lenticular role; lack of Cx35.1 (gjd2b) led to a nuclear cataract that triggered axial elongation. The results provide functional evidence of a link between gjd2 and refractive error. Supported by ORIP (R24 OD026591), NIGMS, NINDS. 


 Antibody-Based CCR5 Blockade Protects Macaques from Mucosal SHIV Transmission

Chang, Xiao L. et al., Nature Communications. 2021 Jun 7; 12:3343.

The efficacy of antiretroviral therapy (ART) as pre-exposure prophylaxis against HIV is hindered by incomplete patient adherence and ART-resistant variants. Researchers found that competitive inhibition of HIV Env-CCR5 binding via the CCR5-specific antibody Leronlimab protects rhesus macaques against infection following repeated intrarectal challenges with a CCR5-tropic simian-human immunodeficiency virus (SHIVSF162P3). Biweekly injection of Leronlimab at 50 mg/kg provided complete protection from SHIV infection. Tissue biopsies from protected macaques post-challenge revealed complete CCR5 receptor occupancy and an absence of viral DNA. After Leronlimab washout, transfer of hematologic cells into naïve monkeys did not transmit infection, supporting the initiation of clinical trials. Supported by ORIP (P51OD011092, K01OD026561, P40OD028116) and NIAID.


 Thioesterase Superfamily Member 1 Undergoes Stimulus-coupled Conformational Reorganization to Regulate Metabolism in Mice

Li, Yue et al., Nature Communications, 9 June 2021;12(3493).

Thermogenesis is suppressed in brown adipose tissue by thioesterase superfamily member 1 (Them1), a long chain fatty acyl-CoA thioesterase. Them1 is highly upregulated by cold ambient temperature, where it reduces fatty acid availability and limits thermogenesis. Investigators show that Them1 regulates metabolism by undergoing conformational changes in response to β-adrenergic stimulation that alter Them1 intracellular distribution. Them1 forms metabolically active puncta near lipid droplets and mitochondria. Upon stimulation, Them1 is phosphorylated at the N-terminus, inhibiting puncta formation and activity, and resulting in a diffuse intracellular localization. Investigators show that Them1 puncta are biomolecular condensates that are inhibited by phosphorylation. Them1 forms intracellular biomolecular condensates that limit fatty acid oxidation and suppress thermogenesis. When energy is demanded, the condensates are disrupted by phosphorylation to allow for maximal thermogenesis. The stimulus-coupled reorganization of Them1 provides fine-tuning of thermogenesis and energy expenditure. Supported by ORIP (S10 OD019988).


 SARS-CoV-2 Vaccines Elicit Durable Immune Responses in Infant Rhesus Macaques

Garrido, Carolina et al., Science Immunology, 15 June 2021; Vol. 6, Issue 60.

The immunogenicity of two SARS-CoV-2 vaccines was evaluated in both sexes of infant rhesus macaques (n=8/group). Neither vaccine, stabilized prefusion SARS-CoV-2 S-2P spike (S) protein encoded by mRNA encapsulated in lipid nanoparticles or the purified S protein mixed with 3M-052, a synthetic TLR7/8 agonist in a squalene emulsion, induced adverse effects. Both elicited high magnitude neutralizing antibody titers peaking at week 6. S-specific T cell responses were dominated by IL-17, IFN-γ, or TNF-α. Antibody and cellular responses were stable through week 22. These data provide proof-of concept for a pediatric SARS-CoV-2 vaccine with the potential for durable immunity to decrease transmission of COVID-19. Supported by ORIP (P51OD011107), NIAID, and NCI.


 In Vitro and in Vivo Functions of SARS-CoV-2 Infection-Enhancing and Neutralizing Antibodies

Li, Dapeng et al., Cell. 18 June 2021;S0092-8674(21)00756-X.

Antibody-dependent enhancement of infection is a concern for clinical use of antibodies. Researchers isolated neutralizing antibodies against the receptor-binding domain (RBD) or N-terminal domain (NTD) of SARS-CoV-2 spike from COVID-19 patients. Cryo-electron microscopy of RBD and NTD antibodies demonstrated function-specific binding modes. RBD and NTD antibodies mediated both neutralization and infection enhancement in vitro. However, infusion of these antibodies into mice or macaques resulted in suppression of virus replication, demonstrating that antibody-enhanced infection in vitro does not necessarily predict enhanced infection in vivo. RBD-neutralizing antibodies having cross-reactivity against coronaviruses were protective against SARS-CoV-2, the most potent of which was DH1047. Supported by ORIP (P40OD012217, U42OD021458, S10OD018164), NIAID, NCI, NIGMS, NIH Common Fund, Defense Advanced Research Projects Agency, State of North Carolina, New York State, Burroughs Wellcome Fund, Simons Foundation, and Ting Tsung & Wei Fong Chao Foundation


 Western-style Diet Consumption Impairs Maternal Insulin Sensitivity and Glucose Metabolism During Pregnancy in a Japanese Macaque Model

Elsakr, Joseph M. et al., Scientific Reports, 21 June 2021; Volume 11, Issue 12977

Using a Japanese macaque model, investigators assessed the metabolic effects of obesity and a calorically dense, Western-style diet (WSD; 36.3% fat), either alone or together, on maternal glucose tolerance and insulin levels in dams during pregnancy (n = 95 females followed over multiple pregnancies [n = 273]). With prolonged WSD feeding, multiple diet switches, and/or increasing age and parity, WSD was associated with increasingly higher insulin levels during glucose tolerance testing, indicative of insulin resistance. The results suggest that prolonged or recurrent calorically dense WSD and/or increased parity, rather than obesity per se, drive excess insulin resistance and metabolic dysfunction. Supported by ORIP (P51OD011092), NIDDK and NIMH.


 Gut Germinal Center Regeneration and Enhanced Antiviral Immunity by Mesenchymal Stem/Stromal Cells

Weber, Marina G. et al., JCI Insight. 2021 June 22;6(12):e149033 

Researchers investigated the effects of mesenchymal stem/stromal cell (MSC) infusions on gut mucosal recovery, antiviral immunity, and viral suppression in SIV-infected rhesus macaques. MSC treatment heightened virus-specific responses and reduced viral load. Clearance of SIV-positive cells from gut mucosal effector sites was correlated with regeneration of germinal centers, restoration of follicular B cells and T follicular helper cells, and enhanced antigen presentation by viral trapping within the follicular dendritic cell network. These changes were associated with enhanced gene expression for type I/II interferon signaling, B cell proliferation, and interleukin 7. MSC treatment also activated metabolic pathways associated with enhanced immunity and viral reduction. Supported by ORIP (P51OD011107), NIAID, and Brazil National Council for Scientific and Technological Development.


 Immune Inactivation of Anti-Simian Immunodeficiency Virus Chimeric Antigen Receptor T Cells in Rhesus Macaques

Haeseleer, Françoise et al., Molecular Therapy–Methods & Clinical Development. 2021 Jun 24;22:304-319. 

Chimeric antigen receptor (CAR) T cell therapies are under development as potential HIV cures. Researchers found that CAR T cells expressing a single-chain variable fragment (scFv) that recognizes V1 or V3 of the SIV envelope eliminated SIV-infected T cells in vitro. However, in vivo infusion of these CAR T cells in rhesus macaques resulted in no detectable antiviral activity. Anti-SIV IgG antibodies in the SIV-infected animals were associated with inhibited CAR T cell effector functions. Thus, lack of in vivo efficacy of CAR T cells might be due to antibodies blocking the interaction between the CAR scFv and its epitope. Supported by ORIP (P51OD011092), NIAID, Gilead Sciences HIV Cure Grant Program, and Juno Therapeutics.


 Tissue-specific Transcriptional Profiling of Plasmacytoid Dendritic Cells Reveals a Hyperactivated State in Chronic SIV Infection

Lee, Michelle Y.-H. et al., PLOS Pathogens. 2021 June 28;17(6):e1009674

Persistent immune activation is an obstacle to optimal health for people living with HIV. Using RNA-Seq, researchers investigated the immunostimulatory potential of plasmacytoid dendritic cells (pDCs) in chronic SIV infection in rhesus macaques. They observed that pDCs have highly activated profiles in these animals. In contrast, pDCs from SIV-infected sooty mangabeys (natural hosts for SIV) had expression profiles similar to uninfected animals. In chronically infected rhesus macaques, interferon alpha transcripts were readily detected in lymph node-homing pDCs, but not those from blood. Therefore, pDCs are a major producer of type-I interferon in chronic SIV infection and could be a useful immunotherapy target. Supported by ORIP (R24OD010445, P51OD 011132, P51OD011092, S10OD026799) and NIAID.


 Protection of Newborn Macaques by Plant-Derived HIV Broadly Neutralizing Antibodies: A Model for Passive Immunotherapy During Breastfeeding

Rosenberg, Yvonne J. et al., Journal of Virology. 30 June 2021;JVI0026821; Online ahead of print.

Preventing vertical transmission of HIV to newborns is an unmet medical need in resource poor countries. Using a breastfeeding macaque model with multiple simian-human immunodeficiency virus challenge, researchers assessed the protective efficacy of two human broadly neutralizing antibodies (bnAbs) against HIV, PGT121 and VRC07-523, which are produced by a plant expression system. Despite the transient presence of plasma viral RNA, the bnAbs prevented productive infection in all newborns with no sustained plasma viremia, compared to viral loads ranging from 103 to 5x108 in four untreated controls. Thus, plant-expressed antibodies show promise as passive immunoprophylaxis in a breastfeeding model in newborns. Supported by ORIP (U42OD023038, P51OD011092) and NIAID.


 Phase Separation Drives Aberrant Chromatin Looping and Cancer Development

Ahn, Jeong Hyun et al., Nature, 2021 Jul;595(7868):591-595.

How unstructured intrinsically disordered regions (IDRs) contribute to oncogenesis is elusive. Using an ORIP-supported Orbitrap Fusion Tribrid Mass Spectrometer, investigators show that IDRs contained within NUP98–HOXA9, a homeodomain-containing transcription factor chimera recurrently detected in leukaemias, are essential for establishing liquid–liquid phase separation (LLPS) puncta of chimera and for inducing leukaemic transformation. LLPS of NUP98–HOXA9 not only promotes chromatin occupancy of chimera transcription factors, but also is required for the formation of a broad “super-enhancer”-like binding pattern typically seen at leukaemogenic genes, which potentiates transcriptional activation. An artificial HOX chimera, created by replacing the phenylalanine and glycine repeats of NUP98 with an unrelated LLPS-forming IDR of the FUS protein, had similar enhancing effects on the genome-wide binding and target gene activation of the chimera. This report describes a proof-of-principle example in which cancer acquires mutation to establish oncogenic transcription factor condensates via phase separation, which simultaneously enhances their genomic targeting and induces organization of aberrant three-dimensional chromatin structure during tumor transformation. Supported by ORIP (S10 OD018445).


 A Symphony of Destruction: Dynamic Differential Fibrinogenolytic Toxicity by Rattlesnake (Crotalus and Sistrurus) Venoms

Seneci, Lorenzo et al., Comparative Biochemistry and Physiology Part C: Toxicology and Pharmacology, 2021 July, Volume 245, 109034

This study adopts rattlesnakes as a model group to investigate the evolutionary history of venom coagulotoxicity in the context of phylogenetics, natural history, and biology. Venom-induced clotting of human plasma and fibrinogen was determined and mapped onto the rattlesnake phylogenetic tree to reconstruct the evolution of coagulotoxicity across the group. Results indicate that venom phenotype is often independent of phylogenetic relationships in rattlesnakes, suggesting the importance of diet and/or other environmental variables. This study is the most comprehensive effort to date to characterize the evolutionary and biological aspects of coagulotoxins in rattlesnake venom. Further research at finer taxonomic levels is recommended. Supported by ORIP (P40 OD010960).


 Innate Immunity Stimulation via CpG Oligodeoxynucleotides Ameliorates Alzheimer’s Disease Pathology in Aged Squirrel Monkeys

Patel, Akash G., et al., Brain, A Journal of Neurology, July 2021, Volume 144, Issue 7

Alzheimer's disease is the only illness among the top 10 causes of death for which there is no disease-modifying therapy. The authors have shown in transgenic Alzheimer's disease mouse models that harnessing innate immunity via TLR9 agonist CpG oligodeoxynucleotides (ODNs) modulates age-related defects associated with immune cells and safely reduces amyloid plaques, oligomeric amyloid-β, tau pathology, and cerebral amyloid angiopathy (CAA). They used a non-human primate model of sporadic Alzheimer's disease pathology that develops extensive CAA-elderly squirrel monkeys. They demonstrate that long-term use of Class B CpG ODN 2006 induces a favorable degree of innate immunity stimulation. CpG ODN 2006 has been well established in numerous human trials for a variety of diseases. This evidence together with their earlier research validates the beneficial therapeutic outcomes and safety of this innovative immunomodulatory approach. Supported by ORIP (P40 OD010938), NINDS, NIA, NCI.


 Recrudescence of Natural Coccidioidomycosis During Combination Antiretroviral Therapy in a Pigtail Macaque Experimentally Infected with Simian Immunodeficiency Virus

Guerriero, Kathryn A. et al., AIDS Research and Human Retroviruses. July 2021;37(7):505-509.

Coccidioidomycosis is a common fungal infection in people living with HIV, particularly in regions where Coccidioides is endemic, such as the US Southwest. Researchers diagnosed a recrudescent case of previously treated, naturally occurring coccidioidomycosis in a pigtail macaque experimentally infected with simian immunodeficiency virus (SIV) and virally suppressed on combination antiretroviral therapy (cART). Coccidioides IgG antibody titer became detectable before discontinuation of cART, but symptomatic coccidioidomycosis developed after cART withdrawal. This animal was screened and treated in accordance with the guidelines for coccidioidomycosis prevention and treatment. The researchers conclude that macaques with coccidioidomycosis history should be excluded from HIV studies. Supported by ORIP (P51OD010425), NIAID, and NIMH.


 Interleukin-15 Response Signature Predicts RhCMV/SIV Vaccine Efficacy

Barrenäs, Fredrik et al., PLOS Pathogens, 2021 Jul 6;17(7):e1009278

Standard immunogenicity measures do not predict efficacy of a vaccine based on strain 68-1 rhesus cytomegalovirus (RhCMV) vectors expressing SIV proteins (RhCMV/SIV). This vaccine robustly protects just over half of immunized monkeys. Using functional genomics, researchers found that RhCMV/SIV efficacy is correlated with a vaccine-induced response to interleukin-15 (IL-15) that includes modulation of immune cell, inflammation, toll-like receptor signaling, and cell death programming pathways. RhCMV/SIV imparts a coordinated and persistent induction of innate and adaptive immune pathways featuring IL-15, a known regulator of CD8+ T cell function, that support the ability of vaccine-elicited CD8+ T cells to mediate protection against SIV. Supported by ORIP (P51OD010425, P51OD011092), NIAID, and NCI.


 Early Treatment with a Combination of Two Potent Neutralizing Antibodies Improves Clinical Outcomes and Reduces Virus Replication and Lung Inflammation in SARS CoV-2 Infected Macaques

Van Rompay, Koen K. A. et al., PLOS Pathogens, 6 July 2021; Volume 17, Issue 7

The therapeutic efficacy of a combination of two SARS-CoV-2 monoclonal antibodies (mAbs), C135-LS and C144-LS, were investigated in young adult macaques (3 groups of 4 animals; equal sex distribution). Animals were treated intravenously with low or high doses of C135-LS and C144-LS mAbs or control mAb 24 hours post-infection with SARS-CoV-2. Compared to controls, animals treated with either dose of the anti-SARS-CoV-2 mAbs showed improved clinical scores, lower levels of virus replication in upper and lower respiratory tract, and reduced interstitial pneumonia, as measured by lung histology. The study provides proof-of-concept for development of these mAbs for treatment of COVID-19 during early infection. Supported by ORIP (P51OD011107) and NIAID.


 Systems Vaccinology of the BNT162b2 mRNA Vaccine in Humans

Arunachalam, Prabhu S. et al., Nature, 2021 Jul 12;596(7872):410-416

It was poorly understood how mRNA vaccines against SARS-CoV-2 stimulate protective immune responses. To address this, researchers comprehensively profiled innate and adaptive immune responses of healthy volunteers vaccinated with the Pfizer-BioNTech mRNA vaccine (BNT162b2). Vaccination resulted in robust production of neutralizing antibodies against wild-type SARS-CoV-2, to a lesser extent, the beta variant, as well as significant increases in antigen-specific polyfunctional CD4+ and CD8+ T cells after the second dose. Booster vaccination stimulated an enhanced innate immune response compared to primary vaccination, demonstrating the capacity of BNT162b2 to prime the innate immune system to mount a more potent response after booster immunization. Supported by ORIP (P51OD 011132, S10OD026799), NIAID, Open Philanthropy, Sean Parker Cancer Institute, Soffer endowment, Violetta Horton endowment, Stanford University, Henry Gustav Floren Trust, Parker Foundation, and Crown Foundation.


 A Yeast Expressed RBD-based SARS-CoV-2 Vaccine Formulated with 3M-052-alum Adjuvant Promotes Protective Efficacy in Non-human Primates

Pino, Maria et al., Science Immunology, 15 July 2021; Volume 6, Issue 61

Using a rhesus macaque model (n=5 males per group), investigators tested a receptor binding domain (RBD) recombinant protein formulation COVID vaccine candidate combined with an aluminum-based formulation of 3M’s Toll-like receptor 7 and 8 agonist 3M-052 (3M-052/Alum) and found the RBD+3M-052/Alum formulation produced a superior overall immune response than RBD+alum alone as demonstrated by higher SARS-CoV-2 neutralizing antibodies, improved Th1 biased CD4+T cell reactions, and increased CD8+ T cell responses. Collectively, these data suggest that the RBD+3M-052-alum formulation provides robust immune responses against SARS-CoV-2 and supports the development of this potential effective and easy to scale COVID vaccine candidate. Supported by ORIP (P51OD011132) and NIAID.


 Factor XII Plays a Pathogenic Role in Organ Failure and Death in Baboons Challenged with Staphylococcus aureus

Silasi, Robert et al., Blood, 15 July 2021;138(2):178-189 (article was featured on the journal’s cover; article’s editorial commentary

Activation of coagulation factor (F) XI promotes multiorgan failure in rodent models of sepsis and in a baboon model of lethal systemic inflammation induced by infusion of heat-inactivated Staphylococcus aureus. The authors used the anticoagulant FXII-neutralizing antibody 5C12 to verify the mechanistic role of FXII. Inhibition of FXII prevented fever, terminal hypotension, respiratory distress, and multiorgan failure. All animals receiving 5C12 had milder and transient clinical symptoms; untreated control animals suffered irreversible multiorgan failure. This study confirms their previous finding that at least two enzymes of FXIa and FXIIa play critical roles in the development of an acute and terminal inflammatory response. Supported by ORIP (P40 OD024628), NIAID, NHLBI, NIGMS.


 Advancing Human Disease Research with Fish Evolutionary Mutant Models

Beck, Emily A., et al., Trends in Genetics, 29 July 2021;S0168-9525(21)00191-8 (article acknowledges ORIP workshop session “Validation of Non-Zebrafish Aquatic Models for Preclinical Research)

Model organism research is essential to understand disease mechanisms. However, laboratory-induced genetic models can lack genetic variation and often fail to mimic disease severity. Evolutionary mutant models (EMMs) are species with evolved phenotypes that mimic human disease. They have improved our understanding of cancer, diabetes, and aging. Fish are the most diverse group of vertebrates, exhibiting a kaleidoscope of specialized phenotypes, many that would be pathogenic in humans but are adaptive in the species' specialized habitat. Evolved compensations can suggest avenues for novel disease therapies. This review summarizes current research using fish EMMs to advance our understanding of human disease. Supported by ORIP (R01 OD011116), NIA, NIDA, NIGMS, NSF.


 Previous Exposure to Dengue Virus is Associated with Increased Zika Virus Burden at the Maternal-fetal Interface in Rhesus Macaques

Crooks, Chelsea M. et al., PLOS Neglected Tropical Diseases, 30 July 2021

Pre-existing immunity to dengue virus (DENV) results in antibody-dependent enhancement (ADE) among DENV serotypes; Zika virus (ZIKV) has homology with DENV suggesting pre-existing DENV immunity may have an impact on ZIKV pathogenesis during pregnancy. In a rhesus macaque model, prior DENV-2 exposure resulted in a higher burden of ZIKV viral RNA in maternal-fetal interface tissues as compared to DENV-naive macaques. However, pre-existing DENV immunity had no detectable impact on ZIKV replication kinetics in maternal plasma; all pregnancies progressed to term without adverse outcomes at delivery. Investigating potential ADE in pregnant women is important as vaccines against DENV and ZIKV are developed. Supported by ORIP (P51OD011106) and NIAID.


 Deep Learning-based Framework for Cardiac Function Assessment in Embryonic Zebrafish from Heart Beating Videos 

Naderi, Amir Mohammad et al., Computers in Biology and Medicine, 2021 August, Vol. 135, p. 104565

Zebrafish is a powerful model system for a host of biological investigations, cardiovascular studies, and genetic screening. However, the current methods for quantifying and monitoring Zebrafish cardiac functions involve tedious manual work and inconsistent estimations. Naderi et al. developed a Zebrafish Automatic Cardiovascular Assessment Framework (ZACAF) based on a U-net deep learning model for automated assessment of cardiovascular indices, such as ejection fraction (EF) and fractional shortening (FS) from microscopic videos of wildtype and cardiomyopathy mutant zebrafish embryos. The framework could be widely applicable with any laboratory resources, and the automatic feature holds promise to enable efficient, consistent, and reliable processing and analysis capacity. Supported by ORIP (R44 OD024874)


 Sexual Dimorphic Impact of Adult-Onset Somatopause on Life Span and Age-Induced Osteoarthritis

Poudel et. al. Aging Cell.

Osteoarthritis (OA) is a major cause of disability worldwide. In humans, the age-associated decline in growth hormone (GH) levels was hypothesized to play a role in the etiology of OA. Investigators studied the impact of adult-onset isolated GH deficiency (AOiGHD) on the life span and skeletal integrity in aged mice. Reductions in GH during adulthood were associated with extended life span and reductions in body temperature in female mice only. However, end-of-life pathology revealed high levels of lymphomas in both sexes, independent of GH status. Skeletal characterization revealed increases in OA severity in AOiGHD mice. In conclusion, while their life span increased, AOiGHD female mice’s health span was compromised by high-grade lymphomas and the development of severe OA. In contrast, AOiGHD males, which did not show extended life span, showed an overall low grade of lymphomas but exhibited significantly decreased health span, evidenced by increased OA severity. Supported by ORIP (S10 OD010751), which contributed to purchasing the MicroComputed Tomography System used in the study.


 Cytomegalovirus Mediates Expansion of IL-15-Responsive Innate-Memory Cells with SIV Killing Function

Méndez-Lagares, Gema et al., Journal of Clinical Investigation. 2021 Aug 2 ;131(15):e148542. 

Researchers investigated the effects of rhesus cytomegalovirus (RhCMV) on the immune system in young rhesus macaques to determine if it could modulate the protection mediated by RhCMV-vectored vaccines. RhCMV was associated with dramatic changes in antigen presenting cells, T cells, and NK cells and marked expansion of innate-memory CD8+ T cells via host interleukin-15 (IL-15) production. The researchers also investigated immune changes following administration of RhCMV 68-1–vectored SIV vaccines, which led to expansion of CD8+ T cells with capacity to inhibit SIV replication ex vivo. These results suggest that innate-memory expansion could be achieved by other vaccine platforms expressing IL-15. Supported by ORIP (P51OD011107), NIAID, and California HIV/AIDS Research Foundation.


 Effects of Early Daily Alcohol Exposure on Placental Function and Fetal Growth in a Rhesus Macaque Model

Lo, Jamie O. et al., American Journal of Obstetrics and Gynecology, 5 August 2021

In a rhesus macaque model of chronic prenatal alcohol exposure, daily consumption during early pregnancy significantly diminished placental perfusion at mid to late gestation and significantly decreased the oxygen supply to the fetal vasculature throughout pregnancy. These findings were associated with the presence of microscopic placental infarctions. Although placental adaptations may compensate for early environmental perturbations to fetal growth, placental blood flow and oxygenation were reduced, consistent with the evidence of placental ischemic injury that persisted throughout pregnancy. Supported by ORIP (P51OD011092), NICHD, and NIAAA.


 TGF-β1 Signaling is Essential for Tissue Regeneration in the Xenopus Tadpole Tail

Nakamura, Makoto et al., Biochemical and Biophysical Research Communications, 2021 August 6, Vol. 565, Pages 91-96

Amphibians such as Xenopus tropicalis exhibit a remarkable capacity for tissue regeneration after traumatic injury. Nakamura et al. show that inhibition of TGF-β1 function prevents tail regeneration in Xenopus tropicalis tadpoles. CRISPR-mediated knock-out (KO) of tgfb1 retards tail regeneration; the phenotype of tgfb1 KO tadpoles can be rescued by injection of tgfb1 mRNA. Cell proliferation, critical for tissue regeneration, is downregulated in tgfb1 KO tadpoles; tgfb1 KO reduces the expression of phosphorylated Smad2/3 (pSmad2/3). These results show that TGF-β1 regulates cell proliferation through the activation of Smad2/3. They propose that TGF-β1 plays a critical role in TGF-β receptor-dependent tadpole tail regeneration in Xenopus. Supported by ORIP (P40 OD010997, R24 OD030008).


 A noncoding RNA modulator potentiates phenylalanine metabolism in mice.

Li, et al. Science.

The role of long noncoding RNAs (lncRNAs) in phenylketonuria (PKU), i.e., an inherited disorder causing build-up of an amino acid causing brain problems, is unknown. Investigators demonstrated that the mouse lncRNA Pair and human lncRNA HULC associate with phenylalanine hydroxylase (PAH). Pair-knockout mice exhibited phenotypes that faithfully models human PKU, such as excessive blood phenylalanine (Phe), growth retardation, and progressive neurological symptoms. HULC depletion led to reduced PAH enzymatic activities in human induced pluripotent stem cell-differentiated hepatocytes, i.e., that have the capacity to self-renew by dividing. To develop a strategy for restoring liver lncRNAs, these investigators designed lncRNA mimics that exhibit liver enrichment. Treatment with these mimics reduced excessive Phe in Pair -/- and PAH R408W/R408W mice and improved the Phe tolerance of these mice. Supported by ORIP (S10OD012304) which contributed to purchasing the Orbitrap Elite High-Resolution Mass Spectrometer for Proteomics and Metabolomics.


 Blocking α4β7 Integrin Delays Viral Rebound in SHIVSF162P3-Infected Macaques Treated with Anti-HIV Broadly Neutralizing Antibodies

Frank, Ines et al., Science Translational Medicine, 18 August 2021, Volume 13, Issue 607:eabf7201

To explore therapeutic potentials of combining anti-HIV broadly neutralizing antibodies (bNAbs) with α4β7 integrin blockade using the monoclonal antibody Rh-α4β7, investigators treated SHIVSF162P3-infected, viremic macaques with bNAbs only or bNAbs and Rh-α4β7. Treatment with bNAbs alone decreased viremia below 200 copies/ml in eight out of eight macaques, but seven of the monkeys rebounded within 3 weeks. In contrast, three of six macaques treated with both Rh-α4β7 and bNAbs maintained viremia below 200 copies/ml for 21 weeks, whereas three of those monkeys rebounded after six weeks. These findings suggest that α4β7 integrin blockade may prolong virologic control by bNAbs in SHIVSF162P3-infected macaques. Supported by ORIP (P51OD011104, U42OD010568, U42OD024282, P40OD028116), NIAID, and NCI.


 Neuropeptide S Receptor 1 is a Nonhormonal Treatment Target in Endometriosis

Tapmeier, Thomas T. et al., Science Translational Medicine, 25 August 2021; Volume 13, Issue 608

Investigators analyzed genetic sequences of humans (n=32 families) and pedigree rhesus macaques (n=849) with spontaneous endometriosis to uncover potential targets for treatment. Target associations indicated a common insertion/deletion variant in NPSR1, the gene encoding neuropeptide S receptor 1. Immunocytochemistry, RT-PCR, and flow cytometry experiments indicated NPSR1 was expressed in the glandular epithelium of eutopic and ectopic endometrium. In a mouse model of endometriosis, an inhibitor of NPSR1-mediated signaling blocked proinflammatory TNFα release, monocyte chemotaxis, and inflammatory cell infiltrate. Further studies in nonhuman primates are needed; however, these results provide support for a nonhormonal treatment of endometriosis. Supported by ORIP (R24OD011173 and P51OD011106).


 The Bowfin Genome Illuminates the Developmental Evolution of Ray-finned Fishes

Thompson, Andrew W., et al., Nature Genetics, 2021 September, Vol. 53, Issue 9, Pages 1373-1384.

The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here the authors present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era. Supported by ORIP (R01 OD011116).


 MIC-Drop: A Platform for Large-scale in Vivo CRISPR Screens

Parvez, Saba et al., Science, 3 September 2021;373(6559):1146-1151

CRISPR screens in animals are challenging because generating, validating, and keeping track of large numbers of mutant animals is prohibitive. These authors introduce Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform combining droplet microfluidics, single-needle en masse CRISPR ribonucleoprotein injections, and DNA barcoding to enable large-scale functional genetic screens in zebrafish. In one application, they showed that MIC-Drop could identify small-molecule targets. Furthermore, in a MIC-Drop screen of 188 poorly characterized genes, they discovered several genes important for cardiac development and function. With the potential to scale to thousands of genes, MIC-Drop enables genome-scale reverse genetic screens in model organisms. Supported by ORIP (R24 OD017870), NIGMS, NHLBI.


 PD-1 Blockade and Vaccination Provide Therapeutic Benefit Against SIV by Inducing Broad and Functional CD8+ T Cells in Lymphoid Tissue

Rahman, Sheikh Abdul et al., Science Immunology, 3 September 2021, Volume 6, Issue 63:eabh3034.

Effective HIV therapies must induce functional CD8+ T cells and clear latent viral reservoirs during antiretroviral therapy (ART). Using a rhesus macaque model, researchers showed that therapeutic vaccination under ART using a CD40L plus TLR7 agonist-adjuvanted DNA/modified vaccinia Ankara vaccine regimen induced robust SIV-specific CD4+ and CD8+ T cell responses. Addition of an anti-PD-1 antibody to the SIV vaccine increased cytotoxic CD8+ T cells in lymph nodes after ART interruption, correlating to the control of virus and prolonged survival compared with the vaccine alone. Thus, combining immune checkpoint blockade with vaccination may be a promising avenue toward an HIV cure. Supported by ORIP (P51OD011132), NIAID, and Emory University Integrated Cellular Imaging Microscopy Core. 


 Circulating Integrin α4β7+ CD4 T Cells Are Enriched for Proliferative Transcriptional Programs in HIV Infection

Lakshmanappa, Yashavanth S. et al., FEBS (Federation of European Biochemical Societies) Letters, 5 September 2021;595(17):2257-2270

HIV preferentially infects α4β7+ CD4 T cells, forming latent reservoirs that contribute to HIV persistence, yet the properties of α4β7+ CD4 T cells are poorly understood. Investigating HIV-infected humans and SHIV-infected rhesus macaques, investigators demonstrated that α4β7+ CD4 T cells in blood are enriched for genes regulating cell cycle progression and cellular metabolism. In contrast, rectal α4β7+ CD4 T cells exhibited a core tissue-residency gene expression program. These features were conserved across primate species, suggesting that the tissue environment influences memory T-cell transcriptional networks. These findings provide an important foundation for understanding the role of α4β7 in HIV infection. Supported by ORIP (K01OD023034, R24OD010976) and NIAID.


 IL-21 Enhances Influenza Vaccine Responses in Aged Macaques with Suppressed SIV Infection

Kvistad, Daniel et al., JCI Insight, 7 September 2021, online ahead of print.

Aging with HIV is associated with low-grade systemic inflammation, immune senescence, and impaired antibody (Ab) responses to vaccines such as influenza (flu). Researchers investigated the role of Interleukin (IL)-21, a CD4 T follicular helper cell regulator, on flu vaccine Ab response in rhesus macaques in the context of age and controlled simian immunodeficiency virus (SIV) mac239 infection. They found that IL-21 enhanced flu vaccine-induced Ab responses in SIV+ (anti-retroviral therapy-suppressed) aged rhesus macaques, adjuvanting the flu vaccine by modulating lymph node germinal center activity. Thus, strategies to supplement IL-21 in aging might improve vaccine responses in people aging with HIV. Supported by ORIP (R24OD010947) and NIAID.


 Multiplexed Drug-based Selection and Counterselection Genetic Manipulations in Drosophila

Matinyan, Nick, et al., Cell Reports, 36, 109700, 14 September 2021

Many highly efficient methods exist which enable transgenic flies to contribute to diagnostics and therapeutics for human diseases. A recent publication, “Multiplexed drug-based selection and counterselection genetic manipulations in Drosophila”, brings the transgenic efficiency up to a new level. Researchers described a drug-based genetic platform with four selection and two counterselection markers increasing transgenic efficiency by > 10-fold compared to established methods in flies. Researchers also developed a plasmid library to adapt this technology to other model organisms. This highly efficient transgenic approach significantly increases the power of not only D. melanogaster but many other model organisms for biomedical research.


 A large repertoire of B cell lineages targeting one cluster of epitopes in a vaccinated rhesus macaque

Li et al., Vaccine. 2021 Sep 15;39(39):5607-5614.

A rhesus macaque that was serially immunized six times with the 8-mer epitope for human monoclonal antibody (mAb) 447-52D—specific to the V3 region of gp120 HIV-1—provided a rare opportunity to study the repertoire of antibodies produced upon vaccination against a particular antigenic site. From a blood sample taken 3 weeks after the last immunization, researchers produced 41 V3-specific recombinant mAbs by single B cell isolation and cloning. Sequence analysis revealed 21 B cell lineages (single and clonally related). The broad repertoire of Abs directed to a small antigenic site shows the targeting potency of a vaccine-elicited immune response in rhesus macaques. Supported by ORIP (P51OD011092, U42OD010246) and NIAID. 


 Whole-organism 3D Quantitative Characterization of Zebrafish Melanin by Silver Deposition Micro-CT

Katz, Spencer R., et al, Elife, 16 September 2021;10:e68920. PMC8445617

This research team combined micro-CT with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. The resulting images enabled whole-body, computational analyses of regional melanin content and morphology. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy and allowed direct quantitative comparisons of melanin content. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, 3D computational phenomic analysis of a specific cell type at cellular resolution. Advances such as this in whole-organism, high-resolution phenotyping provide superior context for studying the phenotypic effects of genetic, disease, and environmental variables. Supported by ORIP (R24 OD018559).


 Improving Rigor and Reproducibility in Nonhuman Primate Research 

Bliss-Moreau, Eliza et al., American Journal of Primatology, 2021 September 20, Vol. 83, Issue 12

Investigators across interdisciplinary fields consider approaches to enhance rigor and producibility in nonhuman primate (NHP) research. Given their similarity to humans, NHPs are often the animal model of choice for translational/preclinical biomedical research. However, availability of NHPs is limited. Hence, increased rigor is required to maximize the information gained from NHP studies. The co-authors consider approaches, such as, normative protocols, preregistration, data sharing, and how more extensive training in biostatics can enhance rigorous research in NHPs across biomedical disciplines. Supported by ORIP (P51OD011107, P51OD011106, P51OD011132, P51OD010425, P51OD011104, P51OD011092, and P51OD011133).


 Prior Infection With SARS-CoV-2 WA1/2020 Partially Protects Rhesus Macaques Against Re-infection With B.1.1.7 and B.1.351 Variants

Chandrashekar, Abishek et al., Science Translational Medicine. 2021 September 21;eabj2641 Online ahead of print 

Using the rhesus macaque model, researchers addressed whether natural immunity induced by the original SARS-CoV-2 WA1/2020 strain protects against re-challenge with B.1.1.7 and B.1.351, known as the alpha and beta variants of concern, respectively. The investigators infected rhesus macaques with WA1/2020 and re-challenged them on day 35 with WA1/2020 or with the alpha or beta variants. Natural immunity to WA1/2020 led to robust protection against re-challenge with WA1/2020, partial protection against beta, and an intermediate degree of protection against alpha. These findings have important implications for vaccination and public health strategies in the context of emerging SARS-CoV-2 variants of concern. Supported by ORIP (P51OD011106), NCI, Bill & Melinda Gates Foundation, Janssen Vaccines & Prevention BV, Ragon Institute, Musk Foundation, and Massachusetts Consortium on Pathogen Readiness.


 Genetic Basis For an Evolutionary Shift From Ancestral Preaxial to Postaxial Limb Polarity in Non-urodele Vertebrates

Trofka, Anna et al. Current Biology. 2021 September 28;S0960-9822(21)01250-1

In most tetrapod vertebrates, limb skeletal progenitors condense with postaxial dominance. Posterior elements (ulna and fibula) appear prior to their anterior counterparts (radius and tibia), followed by digit-appearance order with continuing postaxial polarity. Recent fossil evidence suggests that preaxial polarity represents an ancestral rather than derived state. These authors report that 5'Hoxd (Hoxd11-d13) gene deletion in mouse is atavistic and uncovers an underlying preaxial polarity in mammalian limb formation. Evolutionary changes in Gli3R activity level - key in the fin-to-limb transition - appear to be fundamental to the shift from preaxial to postaxial polarity in formation of the tetrapod limb skeleton. Supported by ORIP (P40 OD01979), NCI, OHSU Medical Research Foundation and Shriners Hospitals for Children.


 A Novel Non-human Primate Model of Pelizaeus-Merzbacher Disease

Sherman, Larry S. et al., Neurobiology of Disease, October 2021; Volume 158

Pelizaeus-Merzbacher (PMD) disease in humans is a severe hypomyelinating disorder of the central nervous system (CNS) linked to mutations in the proteolipid protein-1 (PLP1) gene. Investigators report on three spontaneous cases of male neonatal rhesus macaques (RMs) with clinical symptoms of hypomyelinating disease. Genetic analysis revealed that the parents of these related RMs carried a rare, hemizygous missense variant in exon 5 of the PLP1 gene. These RMs represent the first reported NHP model of PMD, providing an opportunity for studies to promote myelination in pediatric hypomyelinating diseases as other animal models of PMD do not fully mimic human disorders. Supported by ORIP (R24OD021324, P51OD011092, and S10OD025002) and NINDS.


 Safety, Pharmacokinetics and Antiviral Activity of PGT121, a Broadly Neutralizing Monoclonal Antibody Against HIV-1: A Randomized, Placebo-Controlled, Phase 1 Clinical Trial

Stephenson, Kathryn et al., Nature Medicine. 2021 Oct;27(10):1718-1724. 

Researchers carried out a double-blind trial of one administration of the HIV-1 V3-glycan-specific antibody (Ab) PGT121 in HIV-uninfected and HIV-infected adults on antiretroviral therapy (ART), as well as an open-label trial of one infusion of PGT121 in viremic HIV-infected adults not on ART. The investigators observed no treatment-related serious adverse events among the 48 participants, and neutralizing anti-drug Abs were not elicited. PGT121 reduced plasma HIV RNA by a median of 1.77 log in viremic participants. Two individuals experienced ART-free viral suppression for ≥168 days following Ab infusion. These findings motivate further investigation of Ab-based therapeutic strategies for long-term HIV suppression. Supported by ORIP (R01OD024917, R01OD011095), NIAID, NCATS, and Bill and Melinda Gates Foundation.


 Comparative Cellular Analysis of Motor Cortex in Human, Marmoset and Mouse

Bakken, Trygve E., et al., Nature, 2021 October 6;(598):111-119

Investigators used high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmosets, and mice, to characterize the cellular makeup of the primary motor cortex (M1), which exhibits similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. Despite the overall conservation, many species-dependent specializations are apparent. These results demonstrate the robust molecular foundations of cell-type diversity in M1 across mammals and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations. Supported by ORIP (P51OD010425), NIMH, NCATS, NINDS, and NIDA.


 Limited Expansion of Human Hepatocytes in FAH/ RAG2-Deficient Swine

Nelson, Erek David, et al., Tissue Engineering – Part A, 2021 October 7, Online ahead of print.

The mammalian liver's regenerative ability has led researchers to engineer animals as incubators for expansion of human hepatocytes. Nelson et al. engineered immunodeficient swine to support expansion of human hepatocytes and identify barriers to their clinical application. Immunodeficient swine were engineered by knockout of the recombinase-activating gene 2 (RAG2) and fumarylacetoacetate hydrolase (FAH). Immature human hepatocytes (ihHCs) were injected into fetal swine by intrauterine cell transplantation (IUCT) at day 40 of gestation. They identified the mechanism of the eventual graft rejection by the intact NK cell population. They confirmed the presence of residual adaptive immunity in this model of immunodeficiency. Supported by ORIP (U42 OD011140).


 Collective Behavior Emerges from Genetically Controlled Simple Behavioral Motifs in Zebrafish

Harpaz, Roy, et al. Science Advances, 2021 October 8, Vol. 8, Issue 41;eabi7460.

Harpaz et al. report that zebrafish regulate their proximity and alignment with each other at early larval stages. Two visual responses (one measuring relative visual field occupancy and one accounting for global visual motion, account for emerging group behavior). Mutations in genes known to affect social behavior in humans perturb these reflexes in individual larval zebrafish and change their emergent collective behaviors. Model simulations show that changes in these two responses in individual mutant animals predict well the distinctive collective patterns that emerge in a group. Hence, group behaviors reflect in part genetically defined primitive sensorimotor “motifs” evident in young larvae. Supported by ORIP (R43 OD024879, R44 OD024879), NINDS, NSF.


 Integrated spatial multiomics reveals fibroblast fate during tissue repair

Foster et. al. Proc Natl Acad Sci U S A.

The function of regenerative medicine in wound healing remains elusive, partially because of how fibroblasts program and respond to injury remains unclear. Investigators presented a multimodal -omics platform for the comprehensive study of cell populations in complex tissue, which allowed characterization of cells involved in wound healing across time and space. Through integrated analysis of single cell chromatin landscapes and gene expression states, coupled with spatial transcriptomic profiling, fibroblast epigenomes were imputed with temporospatial resolution. This allowed revelation of potential mechanisms controlling fibroblast fate during migration, proliferation, and differentiation following skin injury, and reexamination of the canonical phases of wound healing. Supported by ORIP S10OD018220 which supported upgrading a High Throughput DNA Sequencer and S10OD010580 which contributed to purchasing a Nikon A1Rsi resonant spectral confocal microscope.


 Challenges and Considerations during In Vitro Production of Porcine Embryos

Chen PR et al. Cells. 2021 Oct 15;10(10):2770. PMC8535139.

Genetically modified pigs have become valuable tools for generating advances in animal agriculture and human medicine. Importantly, in vitro production and manipulation of embryos is an essential step in the process of creating porcine models. As the in vitro environment is still suboptimal, it is imperative to examine the porcine embryo culture system from several angles to identify methods for improvement. Understanding metabolic characteristics of porcine embryos and considering comparisons with other mammalian species is useful for optimizing culture media formulations. Furthermore, stressors arising from the environment and maternal or paternal factors must be taken into consideration to produce healthy embryos in vitro. In this review, Chen et al progress stepwise through in vitro oocyte maturation, fertilization, and embryo culture in pigs to assess the status of current culture systems and address points where improvements can be made. Supported by ORIP (U42 OD011140), USDA.


 CD4+ T Cells Are Dispensable for Induction of Broad Heterologous HIV Neutralizing Antibodies in Rhesus Macaques

Sarkar, Sanghita et al., Frontiers in Immunology. 20 October 2021;12:757811.

Researchers investigated the humoral response in vaccinated rhesus macaques with CD4+ T cell depletion, using the VC10014 DNA protein co-immunization vaccine platform (with gp160 plasmids and gp140 trimeric proteins derived from an HIV-1 infected subject). Both CD4+-depleted and non-depleted animals developed comparable Tier 1 and 2 heterologous HIV-1 neutralizing plasma antibody titers. Thus, primates generate HIV neutralizing antibodies in the absence of robust CD4+ T cell help, which has important implications for vaccine development.


 Negative Inotropic Mechanisms of β-cardiotoxin in Cardiomyocytes by Depression of Myofilament ATPase Activity without Activation of the Classical β-adrenergic Pathway

Lertwanakarn, Tuchakorn, et al., Scientific Reports, 2021 October 27, Issue 11, Page 21154

Beta-cardiotoxin (β-CTX) from the king cobra venom (Ophiophagus hannah) was previously proposed as a novel β-adrenergic blocker. However, the involvement of β-adrenergic signaling by this compound has never been elucidated. The objectives of this study were to investigate the underlying mechanisms of β-CTX as a β-blocker and its association with the β-adrenergic pathway. Healthy Sprague Dawley rats were used for cardiomyocytes isolation. In summary, the negative inotropic mechanism of β-CTX was discovered. β-CTX exhibits an atypical β-blocker mechanism. These properties of β-CTX may benefit in developing a novel agent aid to treat hypertrophic cardiomyopathy. Supported by ORIP (P40 OD010960), NHLBI.


 Selective G protein signaling driven by substance P–neurokinin receptor dynamics

Harris et al. Nature Chemical Biology.

Investigators determined the cryogenic-electron microscopy structures of active neurokinin-1 receptor (NK1R) bound to neuropeptide substance P (SP) or the G protein q (Gq)-biased peptide SP6–11. Peptide interactions deep within NK1R are critical for receptor activation. Conversely, interactions between SP and NK1R extracellular loops are required for potent Gs-signaling but not Gq-signaling. Molecular dynamics simulations showed that these superficial contacts restrict SP flexibility. SP6–11, which lacks these interactions, is dynamic while bound to NK1R. Structural dynamics of NK1R agonists therefore depend on interactions with the receptor extracellular loops and regulate G protein signaling selectivity. This data unveils the molecular mechanism of how two stimuli (SP and Neurokinin A) yield distinct G protein signaling at the same G protein-coupled receptor. ORIP grant support: S10OD021741 (Talos Arctica 200kV cryogenic transmission electron microscope) and S10OD020054 (high performance Linux cluster for near atomic resolution single particle cryo-EM).


 Deciphering the role of mucosal immune responses and the cervicovaginal microbiome in resistance to HIV infection in HIV-exposed seronegative women

Ponnan et al., Microbiology Spectrum. 2021 Oct 31;9(2):e0047021.

Identifying correlates of protection in HIV-exposed seronegative (HESN) individuals requires identification of HIV-specific local immune responses. Researchers performed a comprehensive investigation of the vaginal mucosa and cervicovaginal microbiome in HESN women. They found elevated antiviral cytokines, soluble immunoglobulins, activated NK cells, CXCR5+ CD8+ T cells, and T follicular helper cells in HESN women compared to HIV-unexposed healthy women. They also found greater bacterial diversity and increased abundance of Gardnerella species in the mucosa of HESN women. These findings suggest that the genital tract of HESN women contains innate immune factors, antiviral mediators, and T cell subsets that protect against HIV. Supported by ORIP (P51OD011132), NIAID, Indian Department of Health Research, Indian Council of Medical Research, and Swedish Research Council.


 Blastocyst Development after Fertilization with in Vitro Spermatids Derived from Nonhuman Primate Embryonic Stem Cells

Khampang, Sujittra et al., F & Science. Volume 2, Issue, 4, 2021 November, Pages 365-375. 

Rhesus macaque pluripotent stem cells were differentiated into spermatogenic germ cell linages and matured in vitro to form spermatids that were capable of fertilizing oocytes (female or germ cells involved in reproduction) by intracytoplasmic spermatid injection, i.e., the egg is fertilized outside the body and the sperm is injected through a needle into the egg. Successful in vitro preimplantation embryo development was observed in approximately 12% of zygotes. The data suggest potential mechanisms to address male infertility. Supported by ORIP (R21OD020182, R01OD028223, and P51OD011092).


 Monoclonal Antibodies Protect Aged Rhesus Macaques from SARS-CoV-2-induced Immune Activation and Neuroinflammation

Verma, Anil et al., Cell Reports, 2021 November 5, Vol. 37, Issue 5 

In aged diabetic female rhesus macaques, prophylactic administration of neutralizing monoclonal antibodies (mAbs) effectively limits SARS-CoV-2 replication in both the upper and lower respiratory tract, and decreases immune activation, including reducing interferon-induced chemokines and limiting effector CD4 T cell influx into the cerebrospinal fluid. These protective mechanisms took place in the areas of the body targeted by the virus and may prevent adverse inflammatory consequences of SARS-CoV-2 infection in high-risk populations. Supported by ORIP (P51OD011107), NIAID, and NIA. 


 Deep Learning is Widely Applicable to Phenotyping Embryonic Development and Disease

Naert, Thomas et al., Development. 05 November 2021;148(21):dev199664. PMC8602947

Genome editing simplifies the generation of new animal models for congenital disorders. The authors illustrate how deep learning (U-Net) automates segmentation tasks in various imaging modalities. They demonstrate this approach in embryos with polycystic kidneys (pkd1 and pkd2) and craniofacial dysmorphia (six1). They provide a library of pre-trained networks and detailed instructions for applying deep learning to datasets and demonstrate the versatility, precision, and scalability of deep neural network phenotyping on embryonic disease models.


 Precise Visuomotor Transformations Underlying Collective Behavior in Larval Zebrafish

Harpaz, Roy et al., Nature Communications. 12 November 2021;12(1):6578. PMC8590009

Sensory signals from neighbors, analyzed in the visuomotor stream of animals, is poorly understood. The authors studied aggregation behavior in larval zebrafish and found that over development larvae transition from over dispersed groups to tight shoals. Young larvae turn away from virtual neighbors by integrating and averaging retina-wide visual occupancy within each eye, and by using a winner-take-all strategy for binocular integration. Observed algorithms accurately predict group structure over development. These findings allow testable predictions regarding the neuronal circuits underlying collective behavior in zebrafish.


 An NR2F1-specific agonist suppresses metastasis by inducing cancer cell dormancy

Khalil BD et al. The Journal of Experimental Medicine.

Researchers described the discovery of a nuclear receptor NR2F1 antagonist that specifically activates dormancy programs in malignant cells. Agonist treatment resulted in a self-regulated increase in NR2F1 mRNA and protein and downstream transcription of a novel dormancy program. This program led to growth arrest in multiple human cell lines as well as patient-derived organoids. This effect was lost when NR2F1 was knocked out. In mice, agonist treatment resulted in inhibition of lung metastasis of head and neck squamous cell carcinomas, even after cessation of the treatment. This work provides proof of principle supporting the use of NR2F1 agonists to induce dormancy as a therapeutic strategy to prevent metastasis. Supported by ORIP (S10OD018522 and S10OD026880).


 Antiretroviral Therapy Timing Impacts Latent Tuberculosis Infection Reactivation in a Tuberculosis/Simian Immunodeficiency Virus Coinfection Model

Sharan, Riti et al., Journal of Clinical Investigation. 2 December 2021;e153090.

In the rhesus macaque model of Mycobacterium tuberculosis + simian immunodeficiency virus (SIV) co-infection, chronic immune activation rather than depletion of CD4+ T cells correlates with reactivation of latent tuberculosis infection (LTBI). Researchers administered combined antiretroviral therapy (cART) at 2 weeks post-SIV co-infection to study if restoration of CD4+ T cell immunity occurred more broadly, and if this prevented LTBI compared to cART initiated at 4 weeks post-SIV. Earlier initiation of cART enhanced survival led to better control of viral replication and reduced immune activation in the periphery and lung vasculature, thereby reducing the rate of SIV-induced reactivation. Supported by ORIP (K01OD031898, P51OD011133, P51OD011132, S10OD028653) and NIAID.


 Dynamics and Origin of Rebound Viremia in SHIV-Infected Infant Macaques Following Interruption of Long-Term ART

Obregon-Perko, Veronica et al., JCI Insight. 8 December 2021;6(23):e152526.

Researchers investigated viral rebound after analytical treatment interruption (ATI) in infant rhesus macaques infected with simian-human immunodeficiency virus (SHIV.C.CH505) and treated with long-term antiretroviral therapy (ART). Using a combination of ImmunoPET imaging, single-genome analysis of plasma SHIV RNA and cell-associated SHIV DNA, the researchers demonstrated that the gastrointestinal tract is a major site of viral RNA persistence that is capable of early SHIV.C.CH505 expansion following ATI, but virus reactivation in other tissues likely contributes to rebound viremia as ATI progresses.


 AAV Capsid Variants with Brain-wide Transgene Expression and Decreased Liver Targeting After Intravenous Delivery in Mouse and Marmoset

Goertsen, David et al., Nature Neuroscience. 09 December 2021. 25(1):106-115.

Genetic intervention is increasingly being explored as a therapeutic option for debilitating disorders of the central nervous system (CNS). This project focused on organ-specific targeting of adeno-associated virus (AAV) capsids after intravenous delivery. These results constitute an important step forward toward achieving the goal of engineered AAV vectors that can be used to broadly deliver gene therapies to the CNS in humans. Supported by ORIP U24 OD026638 and awarded to Dr. Guoping Feng at Massachusetts Institute of Technology, Cambridge, MA, USA.


 The Pigtail Macaque (Macaca nemestrina) Model of COVID-19 Reproduces Diverse Clinical Outcomes and Reveals New and Complex Signatures of Disease

Melton, Alexandra et al., PLoS Pathogens. 20 December 2021;17(12):e1010162.

Animal models that recapitulate human COVID-19 disease are critical for understanding SARS-CoV-2 viral and immune dynamics, mechanisms of disease, and testing of vaccines and therapeutics. A group of male pigtail macaques (PTM) were euthanized either 6- or 21-days after SARS-CoV-2 viral challenge and demonstrated mild-to-moderate COVID-19 disease. Pulmonary infiltrates were dominated by T cells, virus-targeting T cells were predominantly CD4+, increases in circulating inflammatory and coagulation markers, pulmonary pathologic lesions, and the development of neutralizing antibodies were observed. Collectively, the data suggests PTMs are a valuable model to study COVID-19 pathogenesis and may be useful for testing vaccines and therapeutics. Supported by ORIP (P51OD011104) and NIAID.


 Cannabinoid Control of Gingival Immune Activation in Chronically SIV-Infected Rhesus Macaques Involves Modulation of the Indoleamine-2,3-Dioxygenase-1 Pathway and Salivary Microbiome

McDew-White, Marina et al., EBioMedicine. 23 December 2021;75:103769; online ahead of print.

HIV-associated periodontal disease (PD) affects people living with HIV (PLWH) on combination anti-retroviral therapy (cART). Researchers used a systems biology approach to investigate the molecular, metabolome, and microbiome changes underlying PD and its modulation by phytocannabinoids (Δ9-THC) in rhesus macaques. Δ9-THC reduced IDO1 protein expression. The findings suggest that phytocannabinoids may help reduce gingival/systemic inflammation, salivary dysbiosis, and potentially metabolic disease in PLWH on cART.


 HDAC Inhibitor Titration of Transcription and Axolotl Tail Regeneration

Voss, S. Randal, et al., Frontiers in Cell and Development Biology. 31 December 2021; 31,9:76377. PMC8759488

New patterns of gene expression are enacted and regulated during tissue regeneration. Romidepsin, an FDA-approved HDAC inhibitor, potently blocks axolotl embryo tail regeneration by altering initial transcriptional responses to injury. Regeneration inhibitory concentrations of romidepsin increased and decreased the expression of key genes. Single-nuclei RNA-Seq at 6 HPA illustrated that key genes were altered by romidepsin in the same direction across multiple cell types. These results implicate HDAC activity as a transcriptional mechanism that operates across cell types to regulate the alternative expression of genes that associate with regenerative success versus failure outcomes.




 Fluorescence-based Sorting of Caenorhabditis Elegans via Acoustofluidics

Zhang, Jinxin et al. Lab on a Chip. 19 May 2020(10):1729-1739. PMC7239761.

The authors present an integrated acoustofluidic chip capable of identifying worms of interest based on expression of a fluorescent protein in a continuous flow and then separate them in a high-throughput manner. Utilizing planar fiber optics, their acoustofluidic device requires no temporary immobilization of worms for interrogation/detection, thereby improving the throughput. The device can sort worms of different developmental stages (L3 and L4 stage worms) at high throughput and accuracy. In their acoustofluidic chip, the time to complete the detection and sorting of one worm is only 50 ms, which outperforms nearly all existing microfluidics-based worm sorting devices. Supported by ORIP (R43 OD024963), NIEHS, NIDDK.


 3-D Printed Customizable Vitrification Devices for Preservation of Genetic Resources of Aquatic Species

Tiersch, Connor J., et al. Aquac Eng. 2020 Aug; 90:102097 (PMC7434064)

Sperm vitrification as an alternative approach to conventional cryopreservation allows quick and low-cost sample preservation and is suitable for small-bodied aquatic species with miniscule testis, fieldwork at remote locations, and small-scale freezing for research purposes. Tiersch et al. report the developing of operational prototypes of 3-dimensional (3-D) printed vitrification devices. This study demonstrated the feasibility of developing standardized low-cost devices fabricated by 3-D printing with functions including vitrification, volume control, labeling, protection, and storage. These prototypes can be further developed to assist development of germplasm repositories to protect the genetic resources of aquatic species by breeders, hatcheries, aquariums, and researchers. Supported by ORIP (R24 OD010441).


 Epidemiological and Molecular Characterization of a Novel Adenovirus of Squirrel Monkeys after Fatal Infection during Immunosuppression

Rogers, Donna L. et al. Microb Genom. 2020 Sep; 6(9):mgen000395 (PMC7643968)

Adenoviruses frequently cause upper respiratory tract infections often causing disseminated disease in immunosuppressed patients. A novel adenovirus was identified, squirrel monkey adenovirus 1 (SqMAdV-1), as the cause of a fatal infection in an immunocompromised squirrel monkey (Saimiri boliviensis). A nucleotide polymorphism at the stop codon of the DNA polymerase gene results in a 126 amino acid extension at the carboxy terminus. A single adenovirus variant, SqMAdV-3, has similarity to tufted capuchin (Sapajus apella) adenoviruses. The largest group of adenovirus variants detected, SqMAdV-2.0-2.16, has high similarity (93-99 %) to the TMAdV, suggesting that squirrel monkeys may be the natural host of the TMAdV. Supported by ORIP (P40 OD010938, R24 OD018553), NIAID.


 Induction and Characterization of Pancreatic Cancer in a Transgenic Pig Model

Boas, F. Edward et al., PLoS One. 2020 Sep 21;15(9):e0239391

Preclinical testing of new therapies for pancreatic cancer has been challenging due to lack of a suitable large animal model. Pigs, however, have similar physiology and immune response to humans. Boas et al report the development of a porcine model of pancreatic cancer. H&E and immunohistochemical stains revealed undifferentiated carcinomas, like those of human pancreatobiliary systems. In several pigs, angiographies revealed that the artery supplying the pancreatic tumor could be catheterized using a 2.4 F microcatheter. In summary, pancreatic cancer can be induced in a transgenic pig, and intra-arterial procedures using catheters designed for human interventions were feasible in this model. Supported by ORIP (U42 OD011140), NCI.


 Intra-Strain Genetic Variation of Platyfish (Xiphophorus maculatus) Strains Determines Tumorigenic Trajectory

Lu, Yuan et al., Frontiers in Genetics 2020 Oct 6;11:562594

Xiphophorus interspecies hybrids represent a valuable model system to study heritable tumorigenesis. Although the ancestors of the two X. maculatus parental lines, Jp163 A and Jp163 B, were siblings produced by the same mother, backcross interspecies hybrid progeny between X. hellerii and X. maculatus Jp163 A develop spontaneous melanoma initiating at the dorsal fin due to a regulator encoded by the X. maculatus genome; the backcross hybrid progeny with X. hellerii or X. couchianus and Jp163 B exhibit melanoma on their flanks. Comparative genomic analyses revealed genetic differences are associated with pathways highlighting fundamental cellular functions. Disruption of these baselines may give rise to spontaneous or inducible tumorigenesis. Supported by ORIP (R24 OD-011120), NCI, NIGMS.


 Antiretroviral Therapy Does Not Reduce Tuberculosis Reactivation in a Tuberculosis-HIV Coinfection Model

Ganatra, Shashank R. et al., Journal of Clinical Investigation. 2020 October;130(10):5171-5179

Despite treatment of HIV with antiretroviral therapy (ART), the risk of tuberculosis (TB) reactivation is higher in HIV-infected than HIV-uninfected persons. Researchers used Mycobacterium tuberculosis/SIV-coinfected rhesus macaques to model the impact of ART on TB reactivation due to HIV-induced immunosuppression. ART significantly reduced viral loads and increased CD4+ T-cell counts in blood, spleen, and bronchoalveolar lavage samples, but it did not reduce the risk of SIV-induced TB reactivation during the early phase of treatment. This study offers a translational model for the investigation of TB/SIV coinfection and the evaluation of treatment regimens to prevent TB reactivation in HIV-infected individuals. Supported by ORIP (P51OD011133, P51OD011132) and NIAID.


 Fructose Stimulated De Novo Lipogenesis Is Promoted by Inflammation

Jelena et al., Nat Metab. 2020 Oct; 2(10):1034-1045

Non-alcoholic fatty liver disease (NAFD) affects 30% of adult Americans. While NAFD starts as simple steatosis with little liver damage, its severe manifestation as non-alcoholic steatohepatitis (NASH) is a leading cause of liver failure, cirrhosis, and cancer. Fructose consumption is proposed to increase the risk of hepatosteatosis and NASH. Excessive intake of fructose causes barrier deterioration and low-grade endotoxemia. Using a mouse model, the study examined the mechanism of how fructose triggers these alterations and their roles in hepatosteatosis and NASH pathogenesis. The results demonstrated that microbiota-derived Toll-like receptor (TLR) agonists promote hepatosteatosis without affecting fructose-1-phosphate (F1P) and cytosolic acetyl-CoA. Activation of mucosal-regenerative gp130 signaling, administration of the YAP-induced matricellular protein CCN1 or expression of the antimicrobial peptide Reg3b (beta) counteract fructose-induced barrier deterioration, which depends on endoplasmic-reticulum stress and subsequent endotoxemia. Endotoxin engages TLR4 to trigger TNF production by liver macrophages, thereby inducing lipogenic enzymes that convert F1P and acetyl-CoA to fatty acid in both mouse and human hepatocytes. The finding may be of relevance to several common liver diseases and metabolic disorders. Supported by ORIP (S10OD020025), NCI, NIEHS, NIDDK, NIAID, and NIAAA.


 Estrogen Acts Through Estrogen Receptor 2b to Regulate Hepatobiliary Fate During Vertebrate Development

Chaturantabut, Saireudee et al. Hepatology. 2020 Nov;72(5):1786-1799

During liver development, bipotent progenitor cells differentiate into hepatocytes and biliary epithelial cells to ensure a functional liver. The developmental cues controlling the differentiation of committed progenitors into these cell types are not completely understood. These authors report an essential role for estrogenic regulation in vertebrate liver development to affect hepatobiliary fate decisions. The studies identify17β-estradiol (E2), nuclear estrogen receptor 2b (esr2b), and downstream bone morphogenetic protein (BMP) activity as important regulators of hepatobiliary fate decisions during vertebrate liver development. These results have significant implications for liver development in infants exposed to abnormal estrogen levels or estrogenic compounds during pregnancy. Supported by ORIP (R24 OD017870), NIDDK.


 Lipocalin-2 Is an Anorexigenic Signal in Primates

Petropoulou, Peristera-Ioanna et al., eLife. 2020 Nov; 9:e58949.

The hormone Lipocalin-2 (LCN2) suppresses food intake in mice. Researchers demonstrated that LCN2 increases after a meal and reduces hunger in people with normal weight or overweight, but not in obese individuals. The researchers also showed that LCN2 crosses the blood-brain barrier and binds to the hypothalamus in vervet monkeys. LCN2 was found to bind to the hypothalamus in human, baboon, and rhesus macaque brain sections. When injected into vervets, LCN2 suppressed food intake and lowered body weight without toxic effects in short-term experiments. These findings lay the groundwork to investigate whether LCN2 might be a useful treatment for obesity. Supported by ORIP (P40OD010965), NCATS, NIDDK, NIA, NHLBI, and National Institute of Food and Agriculture.


 A Frog with Three Sex Chromosomes that Co-Mingle Together in Nature: Xenopus tropicalis Has a Degenerate W and a Y that Evolved from a Z Chromosome

Furman, Benjamin L. S., et al. PLoS Genet. 2020 Nov 9; 16(11):e1009121 (PMC7652241)

Genetic systems governing sexual differentiation vary among species. Furman et al. investigated a frog with three sex chromosomes, the Western clawed frog, Xenopus tropicalis. They demonstrate that natural populations from the western and eastern edges of Ghana have a young Y chromosome, and that a male-determining factor on this Y chromosome is in a similar genomic location as a previously known female-determining factor on the W chromosome. Their findings are consistent with theoretical expectations associated with recombination suppression on sex chromosomes and demonstrate that several characteristics of old and established sex chromosomes can arise well before they become cytogenetically distinguished. Supported by ORIP (P40 OD010997), NICHD.


 Infant Isoflurane Exposure Affects Social Behaviours, but Does Not Impair Specific Cognitive Domains in Juvenile Non-human Primates

Neudecker, Viola et al., British Journal of Anaesthesia. 14 November 2020

Researchers investigated the impact of extended (5 hours) isoflurane anesthetic exposure (1-3 exposures) of rhesus macaque (RM) infants of both sexes on cognitive testing and behavioral assessments. Cognitive function did not differ among groups; however, compared to controls, RMs exposed three times during infancy exhibited less close social behavior. One isoflurane exposure resulted in increased anxiety-related behaviors and more inhibition towards novel objects. These findings are consistent with behavioral alterations observed in social settings of human clinical studies. Supported by ORIP (P51OD011092).


 Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4+ T Cells in COVID-19

Meckiff, Cell. 2020 Nov 25;183(5):1340-1353.e16.

It is not clear why COVID-19 is deadly in some people and mild in others. To understand the underlying mechanism, investigators studied the contribution of CD4+ T cells in immune responses to SARS-CoV-2 infection. They analyzed single-cell transcriptomic data of >100,000 viral antigen-reactive CD4+ T cells from 40 COVID-19 patients. In hospitalized patients compared to non-hospitalized patients, they found increased proportions of cytotoxic follicular helper cells (TFH) and cytotoxic T helper (TH) cells responding to SARS-CoV-2 and reduced proportion of SARS-CoV-2-reactive regulatory T cells (TREG). Importantly, in hospitalized COVID-19 patients, a strong cytotoxic TFH response was observed early in the illness, which correlated negatively with antibody levels to SARS-CoV-2 spike protein. Polyfunctional TH1 and TH17 cell subsets were underrepresented in the repertoire of SARS-CoV-2-reactive CD4+ T cells compared to influenza-reactive CD4+ T cells. Together, these analyses provided insights into the gene expression patterns of SARS-CoV-2-reactive CD4+ T cells in distinct disease severities. Supported by ORIP (S10RR027366 and S10OD025052), NIAID, NHLBI, NIGMS and other sources.


 Biological Activities of a New Crotamine-like Peptide from Crotalus Oreganus Helleri on C2C12 and CHO Cell Lines, and Ultrastructural Changes on Motor Endplate and Striated Muscle

Salazar et al. Toxicon. 2020 December;188:95-107 (PMC7720416)

Crotamine and crotamine-like peptides are non-enzymatic polypeptides found in high concentration in the Crotalus genus venom. Helleramine was isolated and purified from the venom of the rattlesnake, Crotalus oreganus helleri. Purified helleramine increased intracellular Ca2+ in Chinese Hamster Ovary (CHO) cell line, inhibited cell viability of C2C12 (immortalized skeletal myoblast) and promoted early apoptosis and cell death. Skeletal muscle harvested from mice 24 h after helleramine injection showed contracted myofibrils and profound vacuolization, with loss of plasmatic and basal membrane integrity. The effects of helleramine provide evidence of myotoxic activities of crotamine-like peptides and their possible role in crotalid envenoming. Supported by ORIP (P40 OD010960) and other sources.


 The Immune Landscape in Tuberculosis Reveals Populations Linked to Disease and Latency

Esaulova et al., Cell Host Microbe. 2020 Dec 16;S1931-3128(20)30635-1

Mycobacterium tuberculosis infection of adult rhesus macaques (RMs), predominantly males (81%), recapitulates both latent (LTBI) and active pulmonary TB (PTB) observed in humans. The immune characterization in lungs of RMs with PTB exhibited an influx of plasmacytoid dendritic cells, an interferon-responsive macrophage population, and activated T cell responses. In contrast, a CD27+ natural killer (NK) cell subset accumulated in the lungs of RMs with LTBI. This NK cell population was also detected in the circulation of humans with LTBI. This characterization of lung immune cells enhances our understanding of TB immunopathogenesis and provides potential targets for therapies and vaccines for TB control. Supported by ORIP (P51OD011104 and P51OD011133), NHLBI and NIAID.


 Sequence Diversity Analyses of an Improved Rhesus Macaque Genome Enhance its Biomedical Utility

Warren et al., Science. 18 December 2020: Vol. 370, Issue 6523, eabc6617

Investigators sequenced and assembled an Indian-origin female rhesus macaque (RM) genome using a multiplatform genomics approach that included long-read sequencing, extensive manual curation, and experimental validation to generate a new comprehensive annotated reference genome. As a result, 99.7% of the gaps in the earlier draft genome are now closed, and more than 99% of the genes are represented. Whole-genome sequencing of 853 RMs of both sexes identified 85.7 million single-nucleotide variants and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay. The improved assembly of segmental duplications, new lineage-specific genes and expanded gene families provide a framework for developing noninvasive NHP models of human disease as well as studies of genetic variation and phenotypic consequences. Supported by ORIP (P51OD011106, P51OD011107, P51OD011132, P51OD011104, U42OD024282, U42OD010568, R24OD011173, R24OD021324, and R24OD010962), NHGRI, NIMH, NHLBI, and NIGMS.


 Responses to Acute Infection with SARS-CoV-2 in the Lungs of Rhesus Macaques, Baboons and Marmosets

Singh, Dhiraj K. et al., Nature Microbiology, 18 December 2020

Investigators compared acute SARS-CoV-2 infection in young and old rhesus macaques and baboons. Macaques had clinical signs of viral infection, mild to moderate pneumonitis and extra-pulmonary pathologies; both age groups recovered within two weeks. Baboons had prolonged viral RNA shedding and more lung inflammation compared with macaques; inflammation in bronchoalveolar lavage was increased in old versus young baboons. Macaques developed T-cell memory responses and bystander cytokine production. Old macaques had lower titers of SARS-CoV-2-specific IgG antibody levels compared with young macaques. The results indicate macaques and baboons experience acute respiratory distress that recapitulates the progression of COVID-19 in humans. Supported by ORIP (P51OD111033 and U42OD010442) and NIAID.