1
|
Volkmar M, Fakhr E, Zens S, Bury A, Offringa R, Gordon J, Huduti E, Wölfel T, Wölfel C. Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires. Front Immunol 2023; 14:1286688. [PMID: 38077312 PMCID: PMC10702483 DOI: 10.3389/fimmu.2023.1286688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
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.
Collapse
Affiliation(s)
- Michael Volkmar
- TCR Discovery Platform, Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, Germany
| | - Elham Fakhr
- TCR Discovery Platform, Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, Germany
| | - Stefan Zens
- Department D200, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alice Bury
- Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, Germany
| | - Rienk Offringa
- Department D200, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica Gordon
- BioNtech, Deptartment Immunotherapies & Preclinical Research, Cellular Biomarker and Immunology Research Team, Mainz, Germany
| | - Enes Huduti
- Helmholtz Institute for Translational Oncology (HI-TRON) Mainz, Mainz, Germany
| | - Thomas Wölfel
- Internal 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, Germany
| | - Catherine Wölfel
- Internal 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, Germany
| |
Collapse
|
2
|
Sun QX, Huang XN, Pan Y, Yao CL. Promoter analysis of TLR5M and TLR5S revealed NF-κB might be a conserved cis-element in TLR5S promoter of large yellow croaker. Comp Biochem Physiol B Biochem Mol Biol 2021; 257:110675. [PMID: 34637922 DOI: 10.1016/j.cbpb.2021.110675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/12/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022]
Abstract
Toll like receptor 5 (TLR5) plays a crucial role in the innate immune response by recognizing bacterial flagellin proteins. In the present study, the genomic and 5'-flanking sequences of LcTLR5M (membrane) and LcTLR5S (soluble) were cloned from the large yellow croaker, Larimichthys crocea. Then, their promoter activities were determined in human embryonic kidney (HEK293T) cells. LcTLR5M contained 4 exons and 3 introns, and LcTLR5S contained 2 exons and 1 intron. Bioinformatic prediction of transcription factor binding sites (TFBSs) indicated that the promoter structures were different between LcTLR5M and LcTLR5S. A dual luciferase assay showed that the deletion mutant -471 to +189 of LcTLR5M promoter possessed the greatest activity with 36 times activity of the control (P < 0.05). For LcTLR5S, two deletion mutants, -1687 to +106 and - 720 to +106, showed high promoter activity. Furthermore, site-directed mutation demonstrated that a -392 to -391 AT/GG substitution in Oct-1 binding site, and a -104 to -103 GG/TT and a -98 to -97 CC/AA substitution in the NF-κB binding site of TLR5S caused a significant decline of luciferase activity (P < 0.05). Moreover, the co-transfection of an NF-κB/p65 over-expression plasmid with wild type TLR5S (-720 to +106) resulted in an extremely significant increase of promoter activity by more than 9 times compared with the NF-kB mutant (P < 0.01). Our findings suggest that the genomic organization and promoter structure may differ between LcTLR5M and LcTLR5S. Oct1 and NF-κB binding sites might be cis-regulatory elements in the LcTLR5S promoter. NF-κB/p65 plays an important role in LcTLR5S promoter activation through binding with the NF-κB binding site.
Collapse
Affiliation(s)
- Qing-Xue Sun
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Xue-Na Huang
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Ying Pan
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian 352103, China
| | - Cui-Luan Yao
- Fisheries College, Jimei University, Xiamen 361021, China.
| |
Collapse
|
3
|
Antonacci R, Massari S, Linguiti G, Caputi Jambrenghi A, Giannico F, Lefranc MP, Ciccarese S. Evolution of the T-Cell Receptor (TR) Loci in the Adaptive Immune Response: The Tale of the TRG Locus in Mammals. Genes (Basel) 2020; 11:E624. [PMID: 32517024 PMCID: PMC7349638 DOI: 10.3390/genes11060624] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022] Open
Abstract
T lymphocytes are the principal actors of vertebrates' cell-mediated immunity. Like B cells, they can recognize an unlimited number of foreign molecules through their antigen-specific heterodimer receptors (TRs), which consist of αβ or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, β, γ, and δ chains. For each chain, multi-gene families are arranged in a TR locus, and their expression is guaranteed by the somatic recombination process. A great plasticity of the gene organization within the TR loci exists among species. Marked structural differences affect the TR γ (TRG) locus. The recent sequencing of multiple whole genome provides an opportunity to examine the TR gene repertoire in a systematic and consistent fashion. In this review, we report the most recent findings on the genomic organization of TRG loci in mammalian species in order to show differences and similarities. The comparison revealed remarkable diversification of both the genomic organization and gene repertoire across species, but also unexpected evolutionary conservation, which highlights the important role of the T cells in the immune response.
Collapse
Affiliation(s)
- Rachele Antonacci
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, 73100 Lecce, Italy;
| | - Giovanna Linguiti
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
| | - Anna Caputi Jambrenghi
- Department of Agricultural and Environmental Science, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.C.J.); (F.G.)
| | - Francesco Giannico
- Department of Agricultural and Environmental Science, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.C.J.); (F.G.)
| | - Marie-Paule Lefranc
- IMGT, the International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR9002 CNRS, Université de Montpellier, CEDEX 5, 34396 Montpellier, France;
| | - Salvatrice Ciccarese
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
| |
Collapse
|
4
|
Ofir R, Novick I, Krup M, Cleveland JL, Ihle JN, Weinstein Y. Structural and functional analysis of the promoter of the murine V gamma 1.1 T cell receptor gene. Eur J Immunol 1995; 25:3070-8. [PMID: 7489745 DOI: 10.1002/eji.1830251113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The expression of the germ-line gene V gamma 1.1-C gamma 4 of the T cell receptor (TcR) gamma chain depends on interleukin (IL)-3 induction in hematopoietic cells, while in T cells, the rearranged gene is expressed constitutively. To understand the mechanism that controls TcR gamma gene expression, we cloned and characterized the structure and function of the V gamma 1.1-C gamma 4 TcR promoter. IL-3-dependent cell lines and T cell lines utilized the same transcriptional start sites. In chloramphenicol acetyltransferase (CAT) assays, the minimal 70-bp promoter confers strong transcriptional activity which is 50-60% of the Moloney long terminal repeat promoter activity. The 500-bp promoter region linked to the CAT gene exhibits IL-3 dependency similar to the endogenous TcR gamma gene. The immediate 3' and 5' flanking sequences inhibit the promoter activity two- to fourfold. The promoter lacks an obvious TATA box or CAAT box sequences, but contains a GC box in the untranslated region 3' to the promoter. The GC box is the core sequence of the element which binds Sp1-like proteins. Cloning of this Sp1 binding element in front of the thymidine kinase (TK) promoter and mutations generated in this site demonstrate its function as a silencer. Ultraviolet cross-linking analysis with the Sp1 binding site from the TcR gamma promoter revealed binding of a 90-100-kDa protein in a T cell line (EL-4) and 40-50 and 90-100-kDa proteins in FDC-P1 cells. The possible function of the Sp1-like protein in silencing the minimal promoter activity is discussed.
Collapse
Affiliation(s)
- R Ofir
- Department of Microbiology and Immunology, Ben Gurion University of the Negev, Beer Sheva, Israel
| | | | | | | | | | | |
Collapse
|
5
|
Hettmann T, Cohen A. Identification of a T cell-specific transcriptional enhancer 3' of the human T cell receptor gamma locus. Mol Immunol 1994; 31:315-22. [PMID: 8139585 DOI: 10.1016/0161-5890(94)90129-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Positive and negative transcriptional regulatory mechanisms are thought to play a major role in the expression of T cell antigen receptor (TCR) genes. Since the alpha beta and gamma delta T cell receptor heterodimers are expressed in a mutually exclusive fashion and since TCR genes are sequentially activated during T cell ontogeny, transcriptional activation and repression must at least in part determine T lineage-specific and developmental-specific expression of these genes. We have identified a transcriptional enhancer located 6.5 kb downstream from the human T cell receptor gamma (TRG) locus. The nucleotide sequence of the enhancer core element shows strong sequence homology to the recently identified murine C gamma 1 enhancer. The enhancer demonstrates T cell-specific activity, but not gamma delta sublineage-specificity in combination with either a heterologous or gene-specific promoter. Thus, additional regulatory elements may be required to repress the expression of rearranged TRG genes in non-gamma delta T cells.
Collapse
Affiliation(s)
- T Hettmann
- Division of Immunology and Cancer Research, Hospital for Sick Children, Toronto, Ontario, Canada
| | | |
Collapse
|
6
|
Hettmann T, Doherty PJ, Cohen A. The human T cell receptor gamma genes are transcribed from TATA-less promoters containing a conserved heptamer sequence. Mol Immunol 1992; 29:1073-80. [PMID: 1386651 DOI: 10.1016/0161-5890(92)90039-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have used the anchored polymerase chain reaction (A-PCR) to clone and compare the 5' upstream regions of the human T cell receptor gamma (TRG) genes. Whereas little homology was found among subgroups I, II, III and IV, sequence alignment of TRG subgroup I members revealed a high degree of homology in the 5' sequences. A conserved heptamer sequence (CTGCAGG), which was found upstream from the translation initiation site of all TRG genes in our analysis. Determination of the transcription initiation site located the conserved heptamer 65 base pairs upstream from the cap sites of V5. No TATA box or other cis-acting promoter sequences could be identified in any of the human TRG upstream sequences.
Collapse
Affiliation(s)
- T Hettmann
- Department of Immunology and Cancer Research, Hospital For Sick Children, Toronto, Ontario, Canada
| | | | | |
Collapse
|
7
|
Yoshikawa K, Seto M, Ueda R, Obata Y, Notake K, Yokochi T, Takahashi T. Molecular cloning of the gene coding for the human T cell differentiation antigen CD7. Immunogenetics 1991; 33:352-60. [PMID: 1711009 DOI: 10.1007/bf00216694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The CD7 molecule is a differentiation antigen found on the surface of T lymphocytes and also on a very minor fraction of acute nonlymphocytic leukemia (ANLL). To study the genomic structure of the CD7 gene, two clones (SY4 and SY22) were isolated by screening a genomic library with a CD7 cDNA probe. Restriction mapping of these two phage clones showed that both overlapped each other, covering a total length of 23 kilobases (kb). Transfection of mouse L cells demonstrated that SY22 contains the gene expressing the CD7 antigen reactive with monoclonal CD7 antibody (Tp40), while SY4 does not. Subcloning of a 10.5 kb fragment from a 14.4 kb insert of SY22 contained the structural gene for the CD7 antigen. Detailed restriction mapping and partial sequence analysis revealed the CD7 gene to consist of four exons. By RNase protection assay, multiple initiation sites -122 base pairs (bp) to -38 bp from ATG translation initiation site were demonstrated. The promoter region had high G + C content and contained two SP1 binding sites (CCGCCC) and an AP2 binding site (CCCCAGGC), but lacked CAAT and TATA motifs.
Collapse
Affiliation(s)
- K Yoshikawa
- Department of Microbiology, Aichi Medical University, Japan
| | | | | | | | | | | | | |
Collapse
|
8
|
Lefranc MP, Rabbitts TH. Genetic organization of the human T cell receptor gamma locus. Curr Top Microbiol Immunol 1991; 173:3-9. [PMID: 1655357 DOI: 10.1007/978-3-642-76492-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- M P Lefranc
- Laboratoire d'Immunogénétique Moléculaire, URA CNRS 1191, Université Montpellier II, France
| | | |
Collapse
|
9
|
Lefranc MP, Rabbitts TH. Genetic organization of the human T-cell receptor gamma and delta loci. RESEARCH IN IMMUNOLOGY 1990; 141:565-77. [PMID: 1965674 DOI: 10.1016/0923-2494(90)90058-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- M P Lefranc
- Laboratoire d'Immunogénétique Moléculaire, URA CNRS 1191, Université Montpellier II, France
| | | |
Collapse
|
10
|
Affiliation(s)
- M P Lefranc
- Laboratoire d'Immunogénétique moléculaire, URA CNRS 1191, Université Montpellier II, France
| | | |
Collapse
|