PROJECT SUMMARY/ABSTRACT The overarching goal of the proposed study is to better understand COVID-19 vaccine immunogenicity in immunocompromised individuals, particularly patients with connective tissue diseases (CTDs) and other musculoskeletal disorders. A paucity of data exists regarding vaccine safety, immunogenicity, efficacy, durability and especially mechanisms of vaccine responses in AID patients, leading to an unmet need to elucidate these critical mechanisms. We performed a “systems vaccinology” study of the BNT162b2 (Pfizer-BioNTech) mRNA vaccine in 18 patients with systemic lupus erythematosus (SLE), using multiple methods including single cell profiling technologies. We showed vaccination was generally safe but led to minor disease flares in a subset of patients. Vaccine efficacy, based on anti-spike IgG responses and pseudovirus neutralization assays for multiple SARS-CoV-2 variants of concern (VoC), were highly variable and not fully explained by immunosuppressive medications. Vaccine nonresponders (NR) had severely blunted induction of IFN-γ, CXCL9, CXCL10, and CXCL11 proteins following vaccine boost. SLE patients had universally lower frequency of CD8+ and CD4+ spike-specific T cells throughout the vaccination series. This R01 application proposes 3 aims. Aim 1 will enroll an expanded SLE longitudinal COVID-19 vaccine cohort and a new SSc vaccine cohort. We will continue to follow the SLE inception cohort to determine how their immune responses evolve with future COVID vaccines. In parallel, we will enroll two new cohorts, one in SLE and the second in SSc, a disease which shares several features including AAb, anti-cytokine AAbs (ACA), and lung and skin pathology. We will test the hypothesis that immune mechanisms of vaccine responses will be shared between diseases, but that differences in autoreactive B and T cell receptors, antibody repertoires, and innate immunity will be discovered. We will compare CTDs with each other and with healthy people, across vaccine platforms (e.g., mRNA vaccines, protein vaccines, and DNA vaccines) currently in development for COVID-19 prevention. Aim 2 will characterize adaptive immune responses. We will characterize antibodies, T cells, and B cells. Antibodies will be measured using custom, bead-based arrays for measurement of AAbs and ACA to ensure vaccines do not enhance secretion of existing or new AAb after vaccination; and anti-viral IgG responses, including in vitro and pseudoviral functional blocking assays against emerging VoC over time. B cell studies will include B cell receptor (BCR) repertoires and transcription modules, and creation and analysis of recombinant monoclonal Ab (rMAb); T cell studies will include phenotyping of virus-specific T cells using MHC Class I and II spheromers. T cell populations known to be associated with AID, will be studied. Aim 3 will characterize COVID-19 vaccine responses in the innate immune compartment. The role of innate immune cells will be explored us...