TY  - JOUR
AU  - Volkmar, Michael
AU  - Fakhr, Elham
AU  - Zens, Stefan
AU  - Bury, Alice
AU  - Offringa, Rienk
AU  - Gordon, Jessica
AU  - Huduti, Enes
AU  - Wölfel, Thomas
AU  - Wölfel, Catherine
TI  - Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires.
JO  - Frontiers in immunology
VL  - 14
SN  - 1664-3224
CY  - Lausanne
PB  - Frontiers Media
M1  - DKFZ-2023-02681
SP  - 1286688
PY  - 2023
N1  - HI-TRON
AB  - 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.
KW  - T cell receptor (TR) (Other)
KW  - TCR (Other)
KW  - TRDV-TRAJ (Other)
KW  - TRDV1 (Other)
KW  - V-(D)-J rearrangement (Other)
KW  - hybrid V-domain (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:38077312
C2  - pmc:PMC10702483
DO  - DOI:10.3389/fimmu.2023.1286688
UR  - https://inrepo02.dkfz.de/record/286105
ER  -