Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires
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...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-11-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1286688/full |
| _version_ | 1797492713618145280 |
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| author | Michael Volkmar Elham Fakhr Stefan Zens Alice Bury Rienk Offringa Jessica Gordon Enes Huduti Thomas Wölfel Catherine Wölfel |
| author_facet | Michael Volkmar Elham Fakhr Stefan Zens Alice Bury Rienk Offringa Jessica Gordon Enes Huduti Thomas Wölfel Catherine Wölfel |
| author_sort | Michael Volkmar |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T01:07:38Z |
| format | Article |
| id | doaj.art-a94935e9201446238650f1a5f250b8d8 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-03-10T01:07:38Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Immunology |
| spelling | doaj.art-a94935e9201446238650f1a5f250b8d82023-11-23T14:24:23ZengFrontiers Media S.A.Frontiers in Immunology1664-32242023-11-011410.3389/fimmu.2023.12866881286688Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoiresMichael Volkmar0Elham Fakhr1Stefan Zens2Alice Bury3Rienk Offringa4Jessica Gordon5Enes Huduti6Thomas Wölfel7Catherine Wölfel8TCR Discovery Platform, Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, GermanyTCR Discovery Platform, Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, GermanyDepartment D200, German Cancer Research Center (DKFZ), Heidelberg, GermanyHelmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, GermanyDepartment D200, German Cancer Research Center (DKFZ), Heidelberg, GermanyBioNtech, Deptartment Immunotherapies & Preclinical Research, Cellular Biomarker and Immunology Research Team, Mainz, GermanyHelmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, GermanyInternal Medicine III, University Cancer Center (UCT), Research Center for Immunotherapy (FZI), University Medical Center (UMC) of the Johannes Gutenberg University Mainz and German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Mainz, GermanyInternal Medicine III, University Cancer Center (UCT), Research Center for Immunotherapy (FZI), University Medical Center (UMC) of the Johannes Gutenberg University Mainz and German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Mainz, GermanyHere, 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.https://www.frontiersin.org/articles/10.3389/fimmu.2023.1286688/fullT cell receptor (TR)TCRTRDV-TRAJhybrid V-domainV-(D)-J rearrangementTRDV1 |
| spellingShingle | Michael Volkmar Elham Fakhr Stefan Zens Alice Bury Rienk Offringa Jessica Gordon Enes Huduti Thomas Wölfel Catherine Wölfel Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires Frontiers in Immunology T cell receptor (TR) TCR TRDV-TRAJ hybrid V-domain V-(D)-J rearrangement TRDV1 |
| title | Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires |
| title_full | Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires |
| title_fullStr | Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires |
| title_full_unstemmed | Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires |
| title_short | Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires |
| title_sort | identification of trdv traj v domains in human and mouse t cell receptor repertoires |
| topic | T cell receptor (TR) TCR TRDV-TRAJ hybrid V-domain V-(D)-J rearrangement TRDV1 |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1286688/full |
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