SARS-CoV-2-reactive tissue-resident memory T cells in healthy and cancer subjects

PROJECT Summary: This multi-PI proposal titled "SARS-CoV-2-reactivesubjects" is written in response to 'RFA-CA-20-039' -tissue-resident memory T cells in healthy and cancerResearch projects in SARS-CoV-2 Serological Sciences.Recent studies have shown that antibody responses to SARS-CoV-2 infection decline rapidly over time, implyinga lack of durable protective humoral (B cell) immunity. Whether this is also true for cellular immunity (e.g., Tcells) is poorly understood. It is well established that CD8+ TRM cells are the first line of defense in viral infectionsat mucosal/barrier sites. They are also known to protect hosts against homologous or heterologous re-infections.Our group was the first to show that TRM cells are pivotal players in driving effective anti-tumor immune responsesin lung cancer, and that TRM cells are the primary cellular targets of anti-PD1 therapies. These key findings werepossible because of the ongoing collaboration between Dr. Vijayanand, Dr. Ay, and Dr. Ottensmeier (Multi-PI).This team brings together experience in T cell immunology, single-cell genomics, bioinformatics, and cancerimmunology. Our Multi-PI team has recently performed the first and largest single-cell RNA-seq and TCR-seqanalysis of SARS-CoV-2-reactive CD8+ and CD4+ T cells (~300,000 single-cells) from COVID-19 patients. Here,to understand TRM responses to SARS-CoV-2, we will capitalize on a cohort of cancer (n=100) and non-cancer(n=100) patients, who will provide excess airway (nasal, oropharynx, larynx), lung and tumor tissue specimensobtained during routine surgery. In AIM 1, we will define the properties of SARS-CoV-2 reactive TRM cells fromcancer and non-cancer patients with or without previous SARS-CoV-2 infection. We will perform combinedsingle-cell RNA-seq and TCR-seq analysis of CD8+ TRM cells in the airways (nasal, oropharynx), lung, and tumortissue. In parallel, by stimulating PBMCs with SARS-CoV-2 peptide pool, we will determine the transcriptomicand TCR sequence of SARS-CoV-2 reactive T cells. We will utilize this TCR sequence information to define thenumbers and properties of SARS-CoV-2 reactive-TRM cells in mucosal and tumor tissues. Recent studies in non-exposed individuals (pre-COVID-19 pandemic) indicate pre-existing, circulating CD8+ T cells, with humancoronavirus cross-reactivity. Here, we will measure the quantity and quality of pre-existing SARS-CoV-2 cross-reactive TRM responses in subjects without clinical or serological evidence of previous SARS-CoV-2 infection. InAIM 2, we will assess the impact of SARS-CoV-2 infection on anti-tumor and other anti-viral TRM responses. Wewill stimulate matched PBMCs (as above) with peptide pools targeting (i) common respiratory RNA viruses(influenza (FLU), RSV), (ii) persistent DNA viruses (CMV, EBV), and (iii) a tumor-driving virus (HPV) to definethe TCR sequence of the respective virus-specific and tumor(HPV)-specific CD8+ T cells; we will utilize the TCRinformation to determine frequency and properties of other virus/tumor-reactive TRM cells in mucosal and tumor-tissue cells.