{
  "abstract": "Mucosal-associated invariant T (MAIT) cells and invariant natural killer T (iNKT) cells are conventionally identified using invariant or semi-invariant TCRα chains, antigen-loaded tetramers, or transcriptomic phenotypes. These requirements limit their detection in public and clinical immune-repertoire datasets that contain only TCRβ sequences. Here we present UcTCRp, a TCRβ-only framework for detecting and profiling relative MAIT- and iNKT-associated signals in bulk immune repertoires. We first identified model-informative TCRβ features, including biased V-gene usage and reproducible CDR3β amino acid composition, in collected human and mouse MAIT and iNKT TCRβ sequences. UcTCRp subsequently integrates these features using species-specific transformer-based representation pretrained separately on large human and mouse TCRβ repertoires, followed by independent supervised modeling with curated MAIT, iNKT, and conventional T cell references for each species. The resulting species-specific models generalized robustly across independent human and mouse cohorts. In paired scRNA-seq/scTCR-seq datasets, UcTCRp recovered transcriptome-defined MAIT and iNKT cells and identified additional MAIT-like candidates supported by receptor evidence but missed by expression-only annotation. Bulk calibration against paired single-cell references and synthetic spike-in experiments established operating characteristics for repertoire-level abundance estimation. These results establish unpaired TCRβ repertoires as an actionable substrate for detecting relative unconventional T cell-associated immune signals, enabling archived repertoire resources to be repurposed for systems-level studies of tissue immunity, disease, and therapeutic response.",
  "abstract_shown": true,
  "affiliations": [
    "Academy of Medical Engineering and Translational Medicine, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China.",
    "State Key Laboratory of Advanced Medical Materials and Devices, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China.",
    "Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China.",
    "Beijing Institute of Basic Medical Sciences, No. 27, Taiping Road, Haidian District, Beijing 100850, China.",
    "Beijing Institute of Radiation Medicine, No. 27, Taiping Road, Haidian District, Beijing 100850, China.",
    "Institute of Health Service and Transfusion Medicine, No. 27, Taiping Road, Haidian District, Beijing 100850, China."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 12,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Linlin Chen"
    },
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Yueyi Li"
    },
    {
      "affs": [
        0
      ],
      "name": "Shiwen Shan"
    },
    {
      "affs": [
        0
      ],
      "name": "Kaixuan Wang"
    },
    {
      "affs": [
        3
      ],
      "name": "Chao Feng"
    },
    {
      "affs": [
        0
      ],
      "name": "Yunsheng Dou"
    },
    {
      "affs": [
        0
      ],
      "name": "Qihang Xu"
    },
    {
      "affs": [
        0
      ],
      "name": "Linru Cai"
    },
    {
      "affs": [
        0
      ],
      "name": "Hao Wang"
    },
    {
      "affs": [
        4
      ],
      "name": "Haiyang Wang"
    },
    {
      "affs": [
        0,
        5
      ],
      "name": "Xiaochen Bo"
    },
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Jian Zhang",
      "orcid": "0000-0002-4966-2086"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/209pxx32sj03h.bib",
  "cited_by": 0,
  "doi": "10.1093/bib/bbag553",
  "fulltext_url": "https://europepmc.org/articles/PMC13677069",
  "id": "209pxx32sj03h",
  "issns": [
    "1467-5463",
    "1477-4054"
  ],
  "landing_url": "https://europepmc.org/article/MED/42893562",
  "language": "eng",
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2403|T-cell and B-cell Immunology"
    ]
  ],
  "openalex": "W7222874053",
  "pdf_url": "https://europepmc.org/articles/PMC13677069?pdf=render",
  "pmcid": "PMC13677069",
  "pmid": "42893562",
  "published": "2026-09-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/209pxx32sj03h.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:18Z",
      "native_id": "MED:42893562",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42893562"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:2403|T-cell and B-cell Immunology",
      "subfield": "immunology"
    }
  ],
  "title": "UcTCRp: a TCRβ-based framework for identifying and profiling MAIT- and iNKT-associated repertoire signals.",
  "title_text": "UcTCRp: a TCRβ-based framework for identifying and profiling MAIT- and iNKT-associated repertoire signals.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:18Z",
  "url": "https://research.draconitic.com/paper/209pxx32sj03h",
  "venue": "Briefings in bioinformatics",
  "versions": []
}