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Oon ML, Lim JQ, Lee B, Leong SM, Soon GST, Wong ZW, Lim EH, Li Z, Yeoh AEJ, Chen S, Ban KHK, Chung TH, Tan SY, Chuang SS, Kato S, Nakamura S, Takahashi E, Ho YH, Khoury JD, Au-Yeung RKH, Cheng CL, Lim ST, Chng WJ, Tripodo C, Rotzschke O, Ong CK, Ng SB. T-Cell Lymphoma Clonality by Copy Number Variation Analysis of T-Cell Receptor Genes. Cancers (Basel) 2021; 13:cancers13020340. [PMID: 33477749 PMCID: PMC7832336 DOI: 10.3390/cancers13020340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 01/11/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary T-cells defend the human body from pathogenic invasion via specific recognition by T-cell receptors (TCRs). The TCR genes undergo recombination (rearrangement) in a myriad of possible ways to generate different TCRs that can recognize a wide diversity of foreign antigens. However, in patients with T-cell lymphoma (TCL), a particular T-cell becomes malignant and proliferates, resulting in a population of genetically identical cells with same TCR rearrangement pattern. To help diagnose patients with TCL, a polymerase chain reaction (PCR)-based assay is currently used to determine if neoplastic cells in patient samples are of T-cell origin and bear identical (monoclonal) TCR rearrangement pattern. Herein, we report the application of a novel segmentation and copy number computation algorithm to accurately identify different TCR rearrangement patterns using data from the whole genome sequencing of patient materials. Our approach may improve the diagnostic accuracy of TCLs and can be similarly applied to the diagnosis of B-cell lymphomas. Abstract T-cell lymphomas arise from a single neoplastic clone and exhibit identical patterns of deletions in T-cell receptor (TCR) genes. Whole genome sequencing (WGS) data represent a treasure trove of information for the development of novel clinical applications. However, the use of WGS to identify clonal T-cell proliferations has not been systematically studied. In this study, based on WGS data, we identified monoclonal rearrangements (MRs) of T-cell receptors (TCR) genes using a novel segmentation algorithm and copy number computation. We evaluated the feasibility of this technique as a marker of T-cell clonality using T-cell lymphomas (TCL, n = 44) and extranodal NK/T-cell lymphomas (ENKTLs, n = 20), and identified 98% of TCLs with one or more TCR gene MRs, against 91% detected using PCR. TCR MRs were absent in all ENKTLs and NK cell lines. Sensitivity-wise, this platform is sufficiently competent, with MRs detected in the majority of samples with tumor content under 25% and it can also distinguish monoallelic from biallelic MRs. Understanding the copy number landscape of TCR using WGS data may engender new diagnostic applications in hematolymphoid pathology, which can be readily adapted to the analysis of B-cell receptor loci for B-cell clonality determination.
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Affiliation(s)
- Ming Liang Oon
- Department of Pathology, National University Hospital, National University Health System, Singapore 119074, Singapore; (M.L.O.); (G.S.-T.S.); (Z.W.W.); (S.-Y.T.)
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore;
- Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Bernett Lee
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Singapore 138632, Singapore; (B.L.); (O.R.)
| | - Sai Mun Leong
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore;
| | - Gwyneth Shook-Ting Soon
- Department of Pathology, National University Hospital, National University Health System, Singapore 119074, Singapore; (M.L.O.); (G.S.-T.S.); (Z.W.W.); (S.-Y.T.)
| | - Zi Wei Wong
- Department of Pathology, National University Hospital, National University Health System, Singapore 119074, Singapore; (M.L.O.); (G.S.-T.S.); (Z.W.W.); (S.-Y.T.)
| | - Evelyn Huizi Lim
- Viva-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; (E.H.L.); (Z.L.); (A.E.J.Y.)
| | - Zhenhua Li
- Viva-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; (E.H.L.); (Z.L.); (A.E.J.Y.)
| | - Allen Eng Juh Yeoh
- Viva-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; (E.H.L.); (Z.L.); (A.E.J.Y.)
- VIVA—University Children’s Cancer Centre, Khoo Teck Puat–National University Children’s Medical Institute, National University Hospital, National University Health System, Singapore 119074, Singapore
| | - Shangying Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore; (S.C.); (K.H.K.B.)
| | - Kenneth Hon Kim Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore; (S.C.); (K.H.K.B.)
| | - Tae-Hoon Chung
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (T.-H.C.); (W.-J.C.)
| | - Soo-Yong Tan
- Department of Pathology, National University Hospital, National University Health System, Singapore 119074, Singapore; (M.L.O.); (G.S.-T.S.); (Z.W.W.); (S.-Y.T.)
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore;
| | - Shih-Sung Chuang
- Department of Pathology, Chi-Mei Medical Center, Tainan 71004, Taiwan;
| | - Seiichi Kato
- Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya 466-8560, Japan; (S.K.); (S.N.)
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya 464-0021, Japan
| | - Shigeo Nakamura
- Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya 466-8560, Japan; (S.K.); (S.N.)
| | - Emiko Takahashi
- Department of Pathology, Aichi Medical University Hospital, Nagakute 480-1195, Japan;
| | - Yong-Howe Ho
- Department of Pathology, Tan Tock Seng Hospital, Singapore 308433, Singapore;
| | - Joseph D. Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Rex K. H. Au-Yeung
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China;
| | - Chee-Leong Cheng
- Department of Pathology, Singapore General Hospital, Singapore 169608, Singapore;
| | - Soon-Thye Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore;
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (T.-H.C.); (W.-J.C.)
- Department of Hematology-Oncology, National University Cancer Institute Singapore, National University Hospital, National University Health System, Singapore 119074, Singapore
| | - Claudio Tripodo
- Tumor Immunology Unit, University of Palermo School of Medicine, 90134 Palermo, Italy;
| | - Olaf Rotzschke
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Singapore 138632, Singapore; (B.L.); (O.R.)
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore;
- Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
- Genome Institute of Singapore, A*STAR (Agency for Science, Technology and Research), Singapore 138632, Singapore
- Correspondence: (C.K.O.); (S.-B.N.); Tel.: +65-6436-8269 (C.K.O.); +65-6772-4709 (S-B.N.)
| | - Siok-Bian Ng
- Department of Pathology, National University Hospital, National University Health System, Singapore 119074, Singapore; (M.L.O.); (G.S.-T.S.); (Z.W.W.); (S.-Y.T.)
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore;
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (T.-H.C.); (W.-J.C.)
- Correspondence: (C.K.O.); (S.-B.N.); Tel.: +65-6436-8269 (C.K.O.); +65-6772-4709 (S-B.N.)
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Abstract
T lymphocytes belong to 2 distinct sublineages that express either αβ or γδ T-cell receptor (TCR) complex. Although malignancy is a great instigator of lineage infidelity, as exemplified by aberrant expression of numerous lineage markers in lymphoma cells, malignant T cells rarely coexpress αβ and γδ TCR complexes. Similarly, only rare cases of CD4/CD8 double-positive primary cutaneous T-cell lymphoma have been reported. In this report, we describe a remarkable case of primary cutaneous T-cell lymphoma coexpressing αβ and γδ TCR complexes, strong diffuse CD8, and a very restricted coexpression of CD4 and CD8. A 66-year-old man was referred to our center for treatment of a persistent eczematoid eruption of 6 years of duration. An initial biopsy demonstrated not only marked spongiosis, but also an epidermotropic population of CD4 small mature T cells with partial expression of CD8. The process remained indolent for another year, followed by an abrupt progression with development of plaques and tumors. Repeat biopsies of these lesions demonstrated a superimposed population of large anaplastic T cells extensively involving the dermis and epidermis. The large cells showed a strong uniform expression of CD3, CD8, CD45RA, CD5, granzyme, TIA1, perforin, TCR-β, and TCR-γ and a weaker but unambiguous expression of CD4, CD25, CD2, and CD56. TCR gene rearrangement studies showed clonal rearrangements for TCR-β and TCR-γ with identical peaks to those seen in the biopsy from a year earlier. The patient developed lymphadenopathy, with a biopsy showing nodal involvement by a morphologically and phenotypically identical neoplastic T-cell population. The disease showed partial response to systemic chemotherapy with development of new plaques, but these new lesions have regressed with radiation therapy.
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Abstract
Primary cutaneous γδ T-cell lymphomas (PCGD-TCLs) are considered a subgroup of aggressive cytotoxic T-cell lymphomas (CTCLs). We have taken advantage of a new, commercially available antibody that recognizes the T-cell receptor-γ (TCR-γ) subunit of the TCR in paraffin-embedded tissue. We have analyzed a series of 146 primary cutaneous T-cell lymphomas received for consultation or a second opinion in the CNIO Pathology Department. Cases were classified according to the World Health Organization 2008 classification as mycosis fungoides (MF; n=96), PCGD-TCLs (n=5), pagetoid reticulosis (n=6), CD30(+) primary cutaneous anaplastic large cell lymphomas (n=5), primary cutaneous CD8 aggressive epidermotropic CTCLs (n=3), primary cutaneous CTCL, not otherwise specified (n=4), and extranodal nasal-type NK/T-cell lymphomas primarily affecting the skin or subcutaneous tissue (n=11). Sixteen cases of the newly named lymphomatoid papulosis type D (LyP-D; n=16) were also included. In those cases positive for TCR-γ, a further panel of 13 antibodies was used for analysis, including TIA-1, granzyme B, and perforin. Clinical and follow-up data were recorded in all cases. Twelve cases (8.2%) were positive for TCR-γ, including 5 PCGD-TCLs, 2 MFs, and 5 LyP-Ds. All 5 PCGD-TCL patients and 1 MF patient died of the disease, whereas the other MF patient and all those with LyP-D were alive. All cases expressed cytotoxic markers, were frequently CD3(+)/CD8(+), and tended to lose CD5 and CD7 expressions. Eight of 12 and 5 of 11 cases were CD30(+) and CD56(+), respectively. Interestingly, 5/12 TCR-γ-positive cases also expressed TCR-BF1. All cases analyzed were negative for Epstein-Barr virus-encoded RNA. In conclusion, TCR-γ expression seems to be rare and is confined to cytotoxic primary cutaneous TCLs. Nevertheless, its expression is not exclusive to PCGD-TCLs, as TCR-γ protein can be found in other CTCLs. Moreover, its expression does not seem to be associated with bad prognosis by itself, as it can be found in cases with good and bad outcomes.
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Lee YN, Alt FW, Reyes J, Gleason M, Zarrin AA, Jung D. Differential utilization of T cell receptor TCR alpha/TCR delta locus variable region gene segments is mediated by accessibility. Proc Natl Acad Sci U S A 2009; 106:17487-92. [PMID: 19805067 PMCID: PMC2765100 DOI: 10.1073/pnas.0909723106] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Indexed: 01/15/2023] Open
Abstract
T cell receptor (TCR) variable region exons are assembled from germline V, (D), and J gene segments, each of which is flanked by recombination signal (RS) sequences that are composed of a conserved heptamer, a spacer of 12 or 23 bp, and a characteristic nonamer. V(D)J recombination only occurs between V, D, and J segments flanked by RS sequences that contain, respectively, 12(12-RS)- and 23(23-RS)-bp spacers (12/23 rule). Additional mechanisms can restrict joining of 12/23 RS matched segments beyond the 12/23 rule (B12/23). The TCRdelta locus is contained within the TCRalpha locus; TCRalpha variable region exons are encoded by TRAV and TRAJ segments and those of TCRdelta by TRDV, TRDD, and TRDJ segments. On the basis of the 12/23 rule, both TRAV and TRDV gene segments are compatible to rearrange with TRDD gene segments; however, TRAV-to-TRDD joins are not observed in vivo. Absence of TRAV-to-TRDD rearrangement might be explained either by B12/23 restriction or by differential accessibility of the TRDV versus TRAV gene segments for rearrangement to TRDD. We used in vitro substrate analysis to reveal that both TRAV and TRDV 23-RSs mediate rearrangements to the 5'TRDD1 12-RS, demonstrating that B12/23 restriction does not explain these rearrangement biases. However, targeted replacement of TRDD1 and its 12-RSs with TRAJ38 and its 12-RS showed that TRDV gene segments rearrange with the ectopic TRAJ38, whereas TRAV segments do not. Our results demonstrate that sorting of TRAV and TRDV gene segments is determined by differential locus accessibility during T cell development.
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Affiliation(s)
- Yu Nee Lee
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
| | - Frederick W. Alt
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
| | - Julia Reyes
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
| | - Megan Gleason
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
| | - Ali A. Zarrin
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
| | - David Jung
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
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Huang CY, Sleckman BP. Developmental stage-specific regulation of TCR-alpha-chain gene assembly by intrinsic features of the TEA promoter. THE JOURNAL OF IMMUNOLOGY 2007; 179:449-54. [PMID: 17579065 DOI: 10.4049/jimmunol.179.1.449] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The TCR delta- and alpha-chain genes lie in a single complex locus, the TCRalpha/delta locus. TCRdelta-chain genes are assembled in CD4(-)CD8(-) (double negative (DN)) thymocytes and TCRalpha-chain genes are assembled in CD4(+)CD8(+) (double positive) thymocytes due, in part, to the developmental stage-specific activities of the TCRdelta and TCRalpha enhancers (Edelta and Ealpha), respectively. Edelta functions with TCRdelta promoters to mediate TCRdelta-chain gene assembly in DN thymocytes. However, Edelta is unable to function with TCRalpha promoters such as the TEA promoter to drive TCRalpha-chain gene assembly in these cells. This is important, because the premature assembly of TCRalpha-chain genes in DN thymocytes would disrupt alphabeta and gammadelta T cell development. The basis for TEA inactivity in DN thymocytes is unclear, because Edelta can activate the Vdelta5 gene segment promoter that lies only 4 kb upstream of TEA promoter. In this study, we use gene targeting to construct a modified TCRalpha/delta locus (TCRalpha/delta(5DeltaT)) in which the TEA promoter lies in the same location as the Vdelta5 gene segment on the wild-type TCRalpha/delta allele. Remarkably, the TEA promoter on this allele exhibits normal developmental stage-specific regulation, being active in double positive thymocytes but not in DN thymocytes as is the case with the Vdelta5 promoter. Thus, the inactivity of the TEA promoter in DN thymocytes is due primarily to intrinsic developmental stage-specific features of the promoter itself and not to its location relative to other cis-acting elements in the locus, such as Edelta.
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MESH Headings
- Animals
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Enhancer Elements, Genetic/immunology
- Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor
- Gene Rearrangement, delta-Chain T-Cell Antigen Receptor
- Gene Targeting
- Genes, T-Cell Receptor alpha/immunology
- Genes, T-Cell Receptor delta
- Genetic Markers/immunology
- Immunoglobulin Joining Region/genetics
- Immunoglobulin Joining Region/metabolism
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/metabolism
- Mice
- Mice, Knockout
- Promoter Regions, Genetic/immunology
- Protein Processing, Post-Translational/genetics
- Protein Processing, Post-Translational/immunology
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/deficiency
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/biosynthesis
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- T-Lymphocyte Subsets/cytology
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- Transcription, Genetic/immunology
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Affiliation(s)
- Ching-Yu Huang
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
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