High-throughput and high-dimensional single-cell analysis of antigen-specific CD4⁺ T cells in COVID-19 and influenza

This study aims to elucidate the tissue-specific dynamics of antigen-specific CD4+ T cells in response to SARS-CoV-2 and influenza. We have developed TetTCRII-SeqHD, a novel high-throughput, high-dimensional single-cell analysis platform that utilizes barcoded tetramers for antigen-specific TCR sequencing. It enables simultaneous profiling of CD4+ T cells' antigen specificities, TCR sequences, gene and surface-protein expression in human tissues. Using this technology, we have profiled >50,000 SARS-CoV-2-specific CD4+ T cells from lung, lung-associated lymph node, spleen, and blood.

Our results show distinct TCR repertoires and responses of CD4+ T cells in COVID-19 and influenza. Tissue-isolated CD4+ T cells display overlapping core signatures, yet distinct tissue cues influence their phenotype, pointing to site-specific functions. In COVID-19, unique transcriptional profiles of CD4+ T cells is characterized by a pronounced cytotoxic signature and a reduction in Treg, in contrast to flu-specific cells. We also observed that tissue context influences the Treg TCR repertoire, with clonal diversity tending to be more restricted in lung tissues compared to the spleen.

This study provides a comprehensive understanding of CD4+ T cell heterogeneity and function in tissues during viral infections. The novel TetTCRII-SeqHD platform presents an advancement in analyzing tissue-localized immune responses, offering potential implications for future immune research and vaccine strategies.