Defining antiviral T cell responses restricted to the non-classical MHC class Ib molecule, Qa-1

PROJECT SUMMARY The basis of cellular immunity is the recognition by T cells of foreign peptides in association with major histocompatibility complex (MHC) proteins on the cell surface. CD8 T cells, the subset most associated with cytolysis, are conventionally believed to recognize peptides bound to the classical, hyper-polymorphic MHC class Ia molecules (HLA-A, B, and C in humans); however, a handful of studies have suggested that CD8 T cells can also recognize pathogen-derived peptides in the context of MHC-E (Qa-1 in mice, HLA-E in humans), a nearly invariant non-classical MHC-Ib molecule typically associated with the regulation of natural killer cell function. In limited cases, MHC-E-restricted CD8 T cells have been shown to exert potent antiviral effects, but extremely little is known about how common these responses are in viral infections, what kinds of effector functions they generally exhibit, how they are regulated, and what antigen presentation pathways drive them. This proposal will shed light on this enigmatic aspect of cellular immunity, taking advantage of a recently identified Qa-1-restricted CD8 T cell epitope from influenza A virus called M-SL9. This epitope drives a CD8 T cell response that is co- dominant with conventional MHC-Ia-restricted epitopes and in preliminary studies appears to protect mice from weight loss and clinical severity during flu infection. Aim 1 of this research plan will detail the cellular pathways by which this model Qa-1-restricted epitope is processed, transported, and presented in flu-infected cells. These studies will be facilitated by an M-SL9-specific CD8 T cell hybridoma line that acts as a highly sensitive reporter of M-SL9/Qa-1 presentation. Aim 2 will test the hypothesis that Qa-1-restricted CD8 T cells occur commonly in viral infections and that they protect the host from severe disease, similarly to MHC-Ia-restricted CD8 T cells. An immunopeptidomics approach will be used to discover Qa-1 epitopes in the context of influenza A virus and mouse hepatitis virus 1, a beta-coronavirus in the same family as SARS-CoV-2. An mRNA-based vaccination strategy will be used to raise CD8 T cells against identified Qa-1 epitopes in mice, followed by a challenge with the corresponding virus and monitoring of disease severity. These results will illuminate a promising but poorly understood aspect of the cellular immune response, with potential benefits for the design of new vaccines or immune therapies against infectious diseases and cancer. This proposal will promote the applicant’s career goals of initiating an independent research career with a rapid pace of productivity, laying a foundation of valuable data that will enable several viable follow-up studies, and ultimately gaining better understanding the importance of unconventional forms of antigen presentation in human health. This study will also take place in a broader context that prioritizes the applicant’s career development by emphasizing feedback from senior scientists, mentoring trainees, and engaging with current literature and innovative research on and off campus.