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Developmental features and unique characteristics of peptide-specific PLZF+ innate-like T cells

ABSTRACT: Innate-like T cells are considered a family of T lymphocytes capable of mounting quick responses, yet restricted to conserved antigens of non-peptide nature. Here, we performed single-cell transcriptomic analyses of peptide-specific PLZF+ innate-like T (PILT) cells and compared them to other members of the innate-like T cell family. Our data revealed that PILT cells share similar transcriptional profiles and overlapping developmental trajectories with invariant Natural Killer T (iNKT) cells as well as mucosal-associated invariant T (MAIT) cells. Yet, in contrast to iNKT and MAIT cells, PILT cells displayed a polyclonal T cell receptor (TCR) repertoire closely resembling the one of conventional CD8 T cells, inferring MHC I restriction and a broader range of antigen specificity. We further show that artificial thymic organoid cultures (ATOC) support selection and development of PILT cells in vitro exhibiting similar transcriptional profiles to their counterparts maturing in the thymus. Lastly, using an “on-time” T-cell receptor retrogenic ATOC system, we demonstrate that PILT1 derived TCR clonotypes favour acquisition of PILT1 innate-like phenotype during T cell development in vitro suggesting an instructive role of TCR specificity in PILT cell lineage commitment and functional differentiation.

ORGANISM(S): Mus musculus

PROVIDER: GSE279513 | GEO | 2025/05/14

REPOSITORIES: GEO

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Project description:A recently identified unconventional T cell population known as mucosal-associated invariant T (MAIT) cells are characterized by the expression of semi-invariant T cell receptor (TCR) with a canonical TRAV1-2/TRAJ33 (Vα7.2/Jα33). These evolutionary conserved, innate-like T cells recognize vitamin B metabolites, derived from some bacteria and fungi. Due to their presence not only in the T cell repertoire of mucosal surfaces but also in peripheral blood and liver, and their significant involvement in a wide range of diseases, in-depth characterization of human MAIT cells is a timely requirement. Studies that examined the transcriptome, immunoproteome, and whole-cell proteome characterized the role of cytotoxic molecules and cytokines in effector functions of MAIT cells and their relationship with some other immune cell subsets. As MAIT cells are classified under the CD3+ T cell compartment and the majority express surface receptor CD8, identifying their proteomic relationship with CD3+ and CD8+ T cells is pivotal. Thus, a high-resolution dataset was generated using the cell populations sorted from peripheral blood mononuclear cells of three healthy volunteers to describe the whole cell proteomes of MAIT, CD3+, and CD8+ T cells. Trypsin-digested peptide samples obtained from the methanol co-precipitation method were analyzed using an Orbitrap FusionTM TribridTM mass spectrometer (Thermo Fisher Scientific, USA) inline coupled to nanoACQUITY ultra-performance liquid chromatography system (Waters, USA) to acquire data-dependent shotgun proteomic data (DDA-MS) for label-free quantification. Analysis of raw DDA-MS data using MaxQuant software and maxLFQ identified and quantified 4,442 protein groups at a 1% false discovery rate. Further analysis identified 3,680 proteins which were detected with a single UniProt accession and a minimum of 2 unique or razor peptides. Thus this proteomic dataset can be used as a reference proteome for future studies on human MAIT cells.

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Developmental features and unique characteristics of peptide-specific PLZF+ innate-like T cells

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