%0 Journal Article
%A Volkmar, Michael
%A Fakhr, Elham
%A Zens, Stefan
%A Bury, Alice
%A Offringa, Rienk
%A Gordon, Jessica
%A Huduti, Enes
%A Wölfel, Thomas
%A Wölfel, Catherine
%T Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires.
%J Frontiers in immunology
%V 14
%@ 1664-3224
%C Lausanne
%I Frontiers Media
%M DKFZ-2023-02681
%P 1286688
%D 2023
%Z HI-TRON
%X 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.
%K T cell receptor (TR) (Other)
%K TCR (Other)
%K TRDV-TRAJ (Other)
%K TRDV1 (Other)
%K V-(D)-J rearrangement (Other)
%K hybrid V-domain (Other)
%F PUB:(DE-HGF)16
%9 Journal Article
%$ pmid:38077312
%2 pmc:PMC10702483
%R 10.3389/fimmu.2023.1286688
%U https://inrepo02.dkfz.de/record/286105