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@ARTICLE{Volkmar:286105,
      author       = {M. Volkmar and E. Fakhr and S. Zens$^*$ and A. Bury and R.
                      Offringa$^*$ and J. Gordon and E. Huduti and T. Wölfel$^*$
                      and C. Wölfel$^*$},
      title        = {{I}dentification of {TRDV}-{TRAJ} {V} domains in human and
                      mouse {T}-cell receptor repertoires.},
      journal      = {Frontiers in immunology},
      volume       = {14},
      issn         = {1664-3224},
      address      = {Lausanne},
      publisher    = {Frontiers Media},
      reportid     = {DKFZ-2023-02681},
      pages        = {1286688},
      year         = {2023},
      note         = {HI-TRON},
      abstract     = {Here, we describe the identification of two T-cell
                      receptors (TRs) containing TRDV genes in their TRA chains,
                      the first one in human and the second one in mouse. First,
                      using 5'RACE on a mixed lymphocyte-tumor cell culture
                      (MLTC), we identified TRDV1 5'-untranslated region (UTR) and
                      complete coding sequence rearranged productively to TRAJ24.
                      Single-cell TR RNA sequencing (RNA-seq) of the MLTC,
                      conducted to identify additional clonotypes, revealed that
                      the analysis software detected the hybrid TRDV-TRAJ TRA
                      (TRA) chain but excluded it from the final results. In a
                      separate project, we performed TR sequencing of
                      tumor-infiltrating lymphocytes (TILs) in a murine tumor
                      model. Here, the predominant clonotype contained a TRA chain
                      with a TRDV2-2-TRAJ49 rearrangement. Again, the hybrid TRA
                      chain was not reported in the final results. Transfection of
                      both TR cDNAs resulted in cell surface localization of TR
                      together with CD3, suggesting a productive protein in both
                      cases. Tumor recognition of the Homo sapiens (Homsap)
                      TRDV1-containing TR could be demonstrated by IFN Gamma ELISA
                      ELISpot kit, whereas the Mus musculus (Musmus) TR did not
                      recognize a tumor-derived cell line. To determine whether
                      the TRDV-containing TRA chains we detected were rare events
                      or whether TRDV genes are commonly incorporated into TRA
                      chains, we queried the NCBI Sequence Read Archive for TR
                      single-cell RNA-seq data and analyzed 21 human and 23 murine
                      datasets. We found that especially Homsap TRDV1, Musmus
                      TRDV1, and to some extent Musmus TRDV2-2 are more commonly
                      incorporated into TRA chains than several TRAV genes, making
                      those TRDV genes a relevant contribution to TRA diversity.
                      TRDV-containing TRA chains are currently excluded from the
                      final results of V-(D)-J dataset analyses with the
                      CellRanger software. We provide a work-around to avoid
                      exclusion of those hybrid TRA chains from the final analysis
                      results.},
      keywords     = {T cell receptor (TR) (Other) / TCR (Other) / TRDV-TRAJ
                      (Other) / TRDV1 (Other) / V-(D)-J rearrangement (Other) /
                      hybrid V-domain (Other)},
      cin          = {D200 / FM01},
      ddc          = {610},
      cid          = {I:(DE-He78)D200-20160331 / I:(DE-He78)FM01-20160331},
      pnm          = {314 - Immunologie und Krebs (POF4-314)},
      pid          = {G:(DE-HGF)POF4-314},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:38077312},
      pmc          = {pmc:PMC10702483},
      doi          = {10.3389/fimmu.2023.1286688},
      url          = {https://inrepo02.dkfz.de/record/286105},
}