PT Journal AU Lukyanov, DK Kriukova, VV Ladell, K Shagina, IA Staroverov, DB Minasian, BE Fedosova, AS Shelyakin, P Suchalko, ON Komkov, AY Blagodatskikh, KA Miners, KL Britanova, OV Franke, A Price, DA Chudakov, DM TI Repertoire-based mapping and time-tracking of T helper cell subsets in scRNA-Seq SO Frontiers in immunology JI Front. Immunol. PY 2025 BP 1536302 VL 16 PU Frontiers Media SA DI 10.3389/fimmu.2025.1536302 WP https://macau.uni-kiel.de/receive/macau_mods_00005883 LA en DE T-Lymphocyte Subsets; T-Lymphocytes, Helper-Inducer; Humans; Sequence Analysis, RNA; Single-Cell Analysis; RNA-Seq; Single-Cell Gene Expression Analysis; T cell memory; helper T cell subsets; Th17; Th22; Scrna-seq; Immune Repertoires; Sctcr-seq; Cytotoxic Cd4+ T Cells SN 1664-3224 AB This approach accurately positions the Th1, Th1-17, Th17, Th22, Th2a, Th2, T follicular helper (Tfh), and regulatory T-cell (Treg) subsets, outperforming mapping based on CITE-Seq. Remarkably, the mapping is tightly focused on specific scRNA-Seq clusters, despite 4-year interval between subset sorting and the effector CD4+ scRNA-Seq experiment. These findings highlight the intrinsic program stability of Th clones circulating in peripheral blood. Repertoire overlap analysis at the scRNA-Seq level confirms that the circulating Th1, Th2, Th2a, Th17, Th22, and Treg subsets are clonally independent. However, a significant clonal overlap between the Th1 and cytotoxic CD4+ T-cell clusters suggests that cytotoxic CD4+ T cells differentiate from Th1 clones. In addition, this study resolves a longstanding ambiguity: we demonstrate that, while CCR10+ Th cells align with a specific Th22 scRNA-Seq cluster, CCR10-CCR6+CXCR3-CCR4+ cells, typically classified as Th17, represent a mixture of bona fide Th17 cells and clonally unrelated CCR10low Th22 cells. The clear distinction between the Th17 and Th22 subsets should influence the development of vaccine- and T-cell-based therapies. Furthermore, we show that severe acute SARS-CoV-2 infection induces systemic type 1 interferon (IFN) activation of naive Th cells. An increased proportion of effector IFN-induced Th cells is associated with a moderate course of the disease but remains low in critical COVID-19 cases. Using integrated scRNA-Seq, TCR-Track, and CITE-Seq data from 122 donors, we provide a comprehensive Th scRNA-Seq reference that should facilitate further investigation of Th subsets in fundamental and clinical studies. PI Lausanne ER