Distinct contributions of CCR4 versus CCR7 to thymocyte localization and central tolerance

PROJECT ABSTRACTSome COVID-19 patients fare well, experiencing asymptomatic or mild disease, while up to 20% of patients havesevere symptoms that can be fatal. Recent studies reveal elevated inflammatory cytokines and a reducednumber of T cells in patients with severe disease, indicating that variation in immune responses may underliedifferences in disease outcomes. However, features of protective versus pathologic immune responses to SARS-CoV-2 are not well understood. Furthermore, children tend to experience milder symptoms, while elderlyindividuals are more susceptible to severe disease, but it is not known if this is a function of age-associateddifferences in immune responses. In Aim 1, we propose to carry out paired single-cell transcriptomics,proteomics, and TCR repertoire sequencing of longitudinal blood samples from COVID-19 patients of differentages and disease severities in order to comprehensively profile the trajectory of immune responses to SARS-CoV-2 and identify candidate immune signatures that correlate with disease severity and age. Candidatesignatures will be tested and refined in a larger patient cohort. Current vaccine efforts are focused on elicitingneutralizing antibodies against SARS-CoV-2. CD4+ T-cell responses are required to activate B cells to produceneutralizing antibodies and to support differentiation of CD8+ T cells, which can promote viral clearance andmaintain immunologic memory. However, viral epitopes that activate protective T-cell responses remainunknown. In Aim 2, we will activate T cells from the longitudinal patient samples used for single-cell profiling inAim 1 with "megapools" of overlapping peptides, spanning individual SARS-CoV-2 antigens. Activated T cellswill be subjected to single-cell multi-omics analysis, allowing us to identify TCR sequences of clones that respondto each viral protein. Retrospective analysis of datasets from Aim 1 will enable us to follow the natural progressionof these individual clones to evaluate frequencies and differentiation over the course of disease. Using thesedata, we will determine which viral antigens activate specific T-cell clones during effector and memory phasesthat correlate with favorable outcomes at each age, informing vaccine design. The increased incidence inautoimmune syndromes, such as the Kawasaki-like disease reported in pediatric patients, suggests that SARS-CoV-2 may induce autoimmunity; conversely, patients with autoimmune syndromes may be more susceptible tosevere disease due to immune dysregulation. In Aim 3, we will explore both possibilities. Specifically, we willretrospectively determine if autoimmunity predisposes patients to severe disease and if autoimmune patientshave more inflammatory T cell responses to SARS-CoV-2 antigens. We will also evaluate whether autoantigenswith high sequence similarity to SARS-CoV-2 peptides activate a higher frequency of T cells in COVID-19patients versus uninfected controls, and we will determine if COVID-19 patients develop autoantibodies. Thesestudies will identify specific immune correlates of disease severity at each age to stratify patients into risk groups,inform vaccine design, and test links between autoimmunity and COVID-19 for informed clinical care.