High-throughput Biomolecular Technologies and Computational Analysis for Antigen-specific CD8 T cells

Abstract

Cytotoxic CD8 T cell responses represent a major element of the adaptive immune response. Elucidating the relationships between the antigen specificity, TCR clonotype, and T cell functionality, however, has remained an unsolved problem. Here, we present an integrated experimental-computational framework designed for the high-throughput capturing and analysis of antigen-specific CD8 T cells. First, we introduce Antigen-TCR Pairing and Multiomic Analysis of T-cells (APMAT) to profile SARS-CoV-2 specific T cells from a large cohort of COVID-19 participants. We systematically demonstrate how distinct physicochemical features of the antigen-TCR pairs strongly associate with both T cell phenotype and persistence. Next, we present a high- throughput cancer-specific TCR discovery strategy against neoantigens using artificial antigen-presenting cells based on single-chain-trimer (SCT) peptide - major histocompatibility complex (pMHC), identifying potential TCR targets for adoptive cell therapy. Additionally, we introduce peptide-loaded cleavable-SCT (pCSCT), a highly stable, versatile, and easy-to-use reagent for efficient capturing of antigen-specific CD8 T cells. We then demonstrate the high-throughput application of pCSCT to profile antigen-specific T cells in Human papillomavirus-16 (HPV16)- positive individuals. In summary, we have leveraged high-throughput peptide-MHC technologies, single-cell multi-omics analysis, and TCR engineering to better understand the CD8 T cell response. Our findings offer valuable insights into adaptive immunity across infectious disease, vaccination, and cancer immunotherapy.