Repertoire-based mapping and time-tracking of T helper cell subsets in scRNA-Seq

Area of Science:

• Immunology
• Genomics
• Computational Biology

Background:

• CD4+ T helper (Th) cell subsets are crucial for adaptive immunity.
• Single-cell RNA sequencing (scRNA-Seq) reveals Th cell diversity, but mapping to traditional subsets is challenging.
• Distinguishing between Th17 and Th22 subsets, and understanding cytotoxic CD4+ T cell origins, remain areas of ambiguity.

Purpose of the Study:

• To develop and validate a method (TCR-Track) for precisely mapping phenotypically sorted Th subsets onto scRNA-Seq profiles.
• To resolve ambiguities in Th subset identification and explore clonal relationships within CD4+ T cells.
• To investigate the role of Th cells in SARS-CoV-2 infection.

Main Methods:

• Development of TCR-Track, a method utilizing immune repertoire data to map Th subsets to scRNA-Seq data.
• Comparison of TCR-Track mapping accuracy against CITE-Seq.
• Analysis of repertoire overlap at the scRNA-Seq level.
• Integration of scRNA-Seq, TCR-Track, and CITE-Seq data from 122 donors.

Main Results:

• TCR-Track accurately maps Th1, Th1-17, Th17, Th22, Th2a, Th2, T follicular helper (Tfh), and regulatory T-cell (Treg) subsets.
• Mapping reveals clonal independence among Th1, Th2, Th2a, Th17, Th22, and Treg subsets, but suggests cytotoxic CD4+ T cells arise from Th1 clones.
• Distinguishes bona fide Th17 cells from a mixed population previously classified as Th17, and identifies CCR10+ Th cells with a Th22 cluster.
• Severe SARS-CoV-2 infection is associated with systemic type 1 interferon activation in naive Th cells, with effector IFN-induced Th cells correlating with moderate disease.

Conclusions:

• TCR-Track provides a robust method for defining Th subsets within scRNA-Seq data, highlighting intrinsic program stability of circulating Th clones.
• The study clarifies the distinct identities of Th17 and Th22 subsets, with implications for vaccine and T-cell therapy development.
• Provides a comprehensive Th scRNA-Seq reference map for future immunological and clinical research.