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T cell receptor sequencing of HNSCC patient and healthy donor peripheral blood

ABSTRACT: This dataset comprises TCR-seq data from peripheral blood CD4+ and CD8+ T cells of head and neck squamous cell carcinoma (HNSCC) patients and healthy donors. Viable peripheral blood mononuclear cells (PBMCs) were sorted into CD45+CD3+CD4+ (CD4+ T cells) and CD45+CD3+CD8+ (CD8+ T cells) subsets, and RNA was isolated using the Qiagen AllPrep DNA/RNA Micro kit. TCR libraries were prepared with the SMART-Seq Human TCR-seq with UMIs kit (Takara Bio) and sequenced on an Illumina NovaSeq X Plus platform. This dataset includes samples from 27 tumor patients and five healthy donors (HDs). The study aims to investigate the phenotype, function, and spatial localization of T cells in HNSCC patients. This peripheral blood dataset focuses on characterizing circulating immune determinants of anti-HNSCC immunity and linking circulating T cell clones to those identified in patient-matched tumor scRNA-seq data.

ORGANISM(S): Homo sapiens

PROVIDER: GSE285951 | GEO | 2025/08/06

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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T cell receptor sequencing of HNSCC patient and healthy donor peripheral blood

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