Selected Grantee Publications
Efficient Ex Vivo Expansion of Conserved Element Vaccine-Specific CD8+ T Cells from SHIV-Infected, ART-Suppressed Nonhuman Primates
Dross et al., Frontiers in Immunology. 2023.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10189133/
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.
Therapeutic Blocking of VEGF Binding to Neuropilin-2 Diminishes PD-L1 Expression to Activate Antitumor Immunity in Prostate Cancer
Wang et al., Science Translational Medicine. 2023.
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.
Cell-Type Memory in a Single-Cell Eukaryote Requires the Continuous Presence of a Specific Transcription Regulator
Lee et al., PNAS. 2023.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10214202/
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.
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.
https://pubmed.ncbi.nlm.nih.gov/37243143/
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 (K01OD026529), NIAID, and NCI.
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 et al., Journal of Virology. 2023.
https://journals.asm.org/doi/10.1128/jvi.01864-22
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.
An E1–E2 Fusion Protein Primes Antiviral Immune Signaling in Bacteria
Ledvina et al., Nature. 2023.
https://www.nature.com/articles/s41586-022-05647-4
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.
High-Resolution Genomes of Multiple Xiphophorus Species Provide New Insights into Microevolution, Hybrid Incompatibility, and Epistasis
Lu et al., Genome Research. 2023.
https://pubmed.ncbi.nlm.nih.gov/37147111/
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.
Resolution of Structural Variation in Diverse Mouse Genomes Reveals Chromatin Remodeling due to Transposable Elements
Ferraj et al., Cell Genomics. 2023.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10203049/
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.
Topologically Associating Domain Boundaries Are Required for Normal Genome Function
Rajderkar et al., Communications Biology. 2023.
https://www.nature.com/articles/s42003-023-04819-w
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.
Identification of a Heterogeneous and Dynamic Ciliome during Embryonic Development and Cell Differentiation
Elliott et al., Development. 2023.
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.