Research towards a cure for human immunodeficiency virus (HIV) and mitigation of the impact of HIV/ tuberculosis co-infections are NIH priorities. Both research areas rely on studies of macaque monkeys experimentally infected with simian immunodeficiency virus (SIV). Interventions to elicit effective CD8+ T cell responses to SIV and Mycobacterium tuberculosis (MTb) in macaques are under active develop- ment. These studies are limited by the dearth of SIV- and MTb-specific CD8+ T cell responses restricted by common macaque major histocompatibility complex (MHC) class I alleles. We began addressing this problem in the previous grant period and identified dozens of novel CD8+ T cell responses in SIV and MTb, as well as in Zika virus, ebolavirus, and influenza. We also realized that conventional T cell epitope discovery and characterization is unwieldy, slow, and cumbersome. Consequently, we demonstrated that MHC class I binding to millions of peptides can be measured si- multaneously, providing a transformative and extremely rapid way to define CD8+ T cell epitopes. The purpose of this competitive revision is to use this new technology to define CD8+ T cell epitopes in SIV and MTb restricted by 16 common macaque MHC class I alleles. Specifically, we will:
Aim 1 : Identify SIV and MTb CD8+ T cell responses restricted by 16 common macaque MHC class I molecules. We will assess peptide binding of each 8-, 9-, 10, and 11-mer peptide in the pro- teomes of every SIV and SHIV genome currently in Genbank and the MTb Erdman strain using an ul- tradense peptide array. MHC:peptide tetramers will be produced for responses that are experimentally validated.
Aim 2 : Define peptide binding motifs for the 16 common MHC class I molecules by determining the impact of every amino acid substitution at each residue in CD8+ T cell epitopes on peptide binding. The peptide binding motifs can be used to improve algorithms for in silico prediction of MHC:peptide binding. Research resources from this study will be made available to the research community through real-time sharing of peptide array data, deposition of experimentally validated CD8+ T cell epitopes in the Immune Epitope Database, and distribution of MHC:peptide tetramers through the NIH Tetramer Core Facility. Furthermore, the definition of CD8+ T cell epitopes using ultradense peptide arrays is generalizable and could revolutionize the identification of pathogen-specific epitopes in all species, including humans.

Public Health Relevance

We recently showed that millions of peptides can be assayed for binding major histocompatibility com- plex (MHC) class I molecules simultaneously. In this grant, we will use this technology to identify CD8+ T cell epitopes in simian immunodeficiency virus and Mycobacterium tuberculosis (MTb) that are re- stricted by common macaque MHC class I alleles with unprecedented throughput. These responses, as well as MHC:peptide tetramers that can specifically stain subpopulations of CD8+ T cells responding to these epitopes, are a vital research-resource for investigators studying HIV cures and HIV/MTb co-infec- tions -- high priority research areas in the trans-NIH plan for HIV-related research.

National Institute of Health (NIH)
Office of The Director, National Institutes of Health (OD)
Resource-Related Research Projects (R24)
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Special Emphasis Panel (ZRG1)
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Zou, Sige
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University of Wisconsin Madison
Schools of Medicine
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Aliota, Matthew T; Dudley, Dawn M; Newman, Christina M et al. (2018) Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics. PLoS Pathog 14:e1006964
Wu, Helen L; Wiseman, Roger W; Hughes, Colette M et al. (2018) The Role of MHC-E in T Cell Immunity Is Conserved among Humans, Rhesus Macaques, and Cynomolgus Macaques. J Immunol 200:49-60
Ellis, Amy; Balgeman, Alexis; Rodgers, Mark et al. (2017) Characterization of T Cells Specific for CFP-10 and ESAT-6 in Mycobacterium tuberculosis-Infected Mauritian Cynomolgus Macaques. Infect Immun 85:
Bailey, Adam L; Buechler, Connor R; Matson, Daniel R et al. (2017) Pegivirus avoids immune recognition but does not attenuate acute-phase disease in a macaque model of HIV infection. PLoS Pathog 13:e1006692
Ericsen, Adam J; Lauck, Michael; Mohns, Mariel S et al. (2016) Microbial Translocation and Inflammation Occur in Hyperacute Immunodeficiency Virus Infection and Compromise Host Control of Virus Replication. PLoS Pathog 12:e1006048
Ayala, Victor I; Trivett, Matthew T; Coren, Lori V et al. (2016) A novel SIV gag-specific CD4(+)T-cell clone suppresses SIVmac239 replication in CD4(+)T cells revealing the interplay between antiviral effector cells and their infected targets. Virology 493:100-12
Gellerup, Dane D; Balgeman, Alexis J; Nelson, Chase W et al. (2016) Conditional Immune Escape during Chronic Simian Immunodeficiency Virus Infection. J Virol 90:545-52
Dudley, Dawn M; Aliota, Matthew T; Mohr, Emma L et al. (2016) A rhesus macaque model of Asian-lineage Zika virus infection. Nat Commun 7:12204
Mohns, Mariel S; Greene, Justin M; Cain, Brian T et al. (2015) Expansion of Simian Immunodeficiency Virus (SIV)-Specific CD8 T Cell Lines from SIV-Naive Mauritian Cynomolgus Macaques for Adoptive Transfer. J Virol 89:9748-57