CD8+ tissue-resident immunity to primary and heterotypic Influenza A controlled by commensal microbiota

Project Summary/Abstract Neonates have the highest infection-related mortality of any age group with viral pneumonia causing the majority of these estimated 1 million deaths per year. A majority of neonates in the neonatal intensive care unit (NICU) receive empiric antibiotic therapy. This antibiotic exposure dysregulates the development of immunity, including influenza-specific CD8+ T cells, although exactly how early-life antibiotic exposure affects the formation and function of tissue-resident CD8+ T cells is unclear. With their canonical role as adaptive responders to viral infection, CD8+ T cells are key effector immune cells in both immediate and long-term host defense against serious viral pneumonia. It is essential to better define how exactly early-life antibiotic exposure disrupts tissue-resident CD8+ T cell formation and function in order to lessen the substantial pneumonia-related mortality in neonates. Preliminary flow cytometry data in this proposal shows that early-life antibiotic exposure reduces the formation of influenza-specific CD8+ T cells, which leads to higher viral burden and morbidity. Preliminary single cell RNA (scRNA-) and single cell Assay for Transposase-accessible Chromatin sequencing (scATACseq) data shows a similar reduction in lung CD8+ T cells that is controlled by specific alterations in gene regulatory networks. This data drives the overall hypothesis of this proposal that early-life antibiotic exposure leads to a decrease in the formation and functions of tissue-resident CD8+ T cells following both primary and heterotypic Influenza A infection. This proposal will test this hypothesis by determining the effect of early-life antibiotic exposure on the formation and function of CD8+ T cells in the lungs following challenge with Influenza A (Aim 1) and determining regulatory mechanisms governing how this early-life antibiotic exposure affects the functions of CD8+ T cells (Aim 2). Collectively, this work will provide novel, mechanistic insights into how early-life antibiotic exposure is affecting the functions of influenza-specific tissue-resident CD8+ T cells. These Aims expect to show an antibiotic-mediated reduction in CD8+ T cell cytotoxicity, cytokine production, and proliferation, as well as changes in specific gene regulatory networks underlying the functional dysregulation. The candidate driving this proposal is currently an MD/PhD student at Cincinnati Children’s Hospital in the laboratory of Dr. Hitesh Deshmukh, who will use this proposal to set a foundation for an independent career as a physician-scientist. The candidate will use this proposal to support his future in the clinic as a pediatric intensivist, where findings from this proposal will uncover new strategies leading to better outcomes for the most vulnerable neonates.