000K utf8 1100 $c2025 1500 eng 2050 urn:nbn:de:gbv:8:3-2025-00352-7 2051 10.3389/fimmu.2025.1536302 3000 Lukyanov, Daniil K 3010 Blagodatskikh, Konstantin A 3010 Britanova, Olga V 3010 Chudakov, Dmitry M 3010 Fedosova, Anna S 3010 Franke, Andre 3010 Komkov, Alexander Y 3010 Kriukova, Valeriia V 3010 Ladell, Kristin 3010 Minasian, Bella E 3010 Miners, Kelly L 3010 Price, David A 3010 Shagina, Irina A 3010 Shelyakin, Pavel 3010 Staroverov, Dmitry B 3010 Suchalko, Oleg N 4000 Repertoire-based mapping and time-tracking of T helper cell subsets in scRNA-Seq$hFrontiers Media SA [Lukyanov, Daniil K] 4030 $nFrontiers Media SA 4209 This approach accurately positions the Th1, Th1-17, Th17, Th22, Th2a, Th2, T follicular helper (Tfh), and regulatory T-cell (Treg) subsets, outperforming mapping based on CITE-Seq. Remarkably, the mapping is tightly focused on specific scRNA-Seq clusters, despite 4-year interval between subset sorting and the effector CD4+ scRNA-Seq experiment. These findings highlight the intrinsic program stability of Th clones circulating in peripheral blood. Repertoire overlap analysis at the scRNA-Seq level confirms that the circulating Th1, Th2, Th2a, Th17, Th22, and Treg subsets are clonally independent. However, a significant clonal overlap between the Th1 and cytotoxic CD4+ T-cell clusters suggests that cytotoxic CD4+ T cells differentiate from Th1 clones. In addition, this study resolves a longstanding ambiguity: we demonstrate that, while CCR10+ Th cells align with a specific Th22 scRNA-Seq cluster, CCR10-CCR6+CXCR3-CCR4+ cells, typically classified as Th17, represent a mixture of bona fide Th17 cells and clonally unrelated CCR10low Th22 cells. The clear distinction between the Th17 and Th22 subsets should influence the development of vaccine- and T-cell-based therapies. Furthermore, we show that severe acute SARS-CoV-2 infection induces systemic type 1 interferon (IFN) activation of naive Th cells. An increased proportion of effector IFN-induced Th cells is associated with a moderate course of the disease but remains low in critical COVID-19 cases. Using integrated scRNA-Seq, TCR-Track, and CITE-Seq data from 122 donors, we provide a comprehensive Th scRNA-Seq reference that should facilitate further investigation of Th subsets in fundamental and clinical studies. 4950 https://doi.org/10.3389/fimmu.2025.1536302$xR$3Volltext$534 4950 https://nbn-resolving.org/urn:nbn:de:gbv:8:3-2025-00352-7$xR$3Volltext$534 4961 https://macau.uni-kiel.de/receive/macau_mods_00005883 5051 610 5550 Cytotoxic Cd4+ T Cells 5550 helper T cell subsets 5550 Humans 5550 Immune Repertoires 5550 RNA-Seq 5550 Scrna-seq 5550 Sctcr-seq 5550 Sequence Analysis, RNA 5550 Single-Cell Analysis 5550 Single-Cell Gene Expression Analysis 5550 T cell memory 5550 Th17 5550 Th22 5550 T-Lymphocytes, Helper-Inducer 5550 T-Lymphocyte Subsets