Selected Grantee Publications
Multiplexed Drug-Based Selection and Counterselection Genetic Manipulations in Drosophila
Matinyan et al., Cell Reports. 2021.
https://www.cell.com/cell-reports/pdf/S2211-1247(21)01147-5.pdf
Many highly efficient methods exist which enable transgenic flies to contribute to diagnostics and therapeutics for human diseases. In this study, researchers describe a drug-based genetic platform with four selection and two counterselection markers, increasing transgenic efficiency by more than 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 Drosophila melanogaster but many other model organisms for biomedical research. Supported by ORIP (P40OD018537, P40OD010949, R21OD022981), NCI, NHGRI, NIGMS, and NIMH.
IL-21 Enhances Influenza Vaccine Responses in Aged Macaques with Suppressed SIV Infection
Kvistad et al., JCI Insight. 2021.
https://doi.org/10.1172/jci.insight.150888
Aging with HIV is associated with low-grade systemic inflammation, immune senescence, and impaired antibody (Ab) responses to such vaccines 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.
Circulating Integrin α4β7+ CD4 T Cells Are Enriched for Proliferative Transcriptional Programs in HIV Infection
Lakshmanappa et al., Federation of European Biochemical Societies Letters. 2021.
https://doi.org/10.1002/1873-3468.14163
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.
PD-1 Blockade and Vaccination Provide Therapeutic Benefit Against SIV by Inducing Broad and Functional CD8+ T Cells in Lymphoid Tissue
Rahman et al., Science Immunology. 2021.
https://doi.org/10.1126/sciimmunol.abh3034
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) and NIAID.
MIC-Drop: A Platform for Large-scale In Vivo CRISPR Screens
Parvez et al., Science. 2021.
https://pubmed.ncbi.nlm.nih.gov/34413171/
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 (R24OD017870), NIGMS, and NHLBI.
The Bowfin Genome Illuminates the Developmental Evolution of Ray-Finned Fishes
Thompson et al., Nature Genetics. 2021.
https://www.nature.com/articles/s41588-021-00914-y
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 (R01OD011116).
Neuropeptide S Receptor 1 is a Nonhormonal Treatment Target in Endometriosis
Tapmeier et al., Science Translational Medicine. 2021.
https://pubmed.ncbi.nlm.nih.gov/34433639
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 for 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, P51OD011106).
Blocking α4β7 Integrin Delays Viral Rebound in SHIVSF162P3-Infected Macaques Treated with Anti-HIV Broadly Neutralizing Antibodies
Frank et al., Science Translational Medicine. 2021.
https://doi.org/10.1126/scitranslmed.abf7201
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 6 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.
A Noncoding RNA Modulator Potentiates Phenylalanine Metabolism in Mice
Li et al., Science. 2021.
https://pubmed.ncbi.nlm.nih.gov/34353949/
The role of long noncoding RNAs (lncRNAs) in phenylketonuria (PKU), 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) and others.
TGF-β1 Signaling Is Essential for Tissue Regeneration in the Xenopus Tadpole Tail
Nakamura et al., Biochemical and Biophysical Research Communications. 2021.
https://www.sciencedirect.com/science/article/pii/S0006291X21008731
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 (P40OD010997, R24OD030008).