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Vujović M, Marcatili P, Chain B, Kaplinsky J, Andresen TL. Signatures of T cell immunity revealed using sequence similarity with TCRDivER algorithm. Commun Biol 2023; 6:357. [PMID: 37002292 PMCID: PMC10066310 DOI: 10.1038/s42003-023-04702-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Changes in the T cell receptor (TCR) repertoires have become important markers for monitoring disease or therapy progression. With the rise of immunotherapy usage in cancer, infectious and autoimmune disease, accurate assessment and comparison of the "state" of the TCR repertoire has become paramount. One important driver of change within the repertoire is T cell proliferation following immunisation. A way of monitoring this is by investigating large clones of individual T cells believed to bind epitopes connected to the disease. However, as a single target can be bound by many different TCRs, monitoring individual clones cannot fully account for T cell cross-reactivity. Moreover, T cells responding to the same target often exhibit higher sequence similarity, which highlights the importance of accounting for TCR similarity within the repertoire. This complexity of binding relationships between a TCR and its target convolutes comparison of immune responses between individuals or comparisons of TCR repertoires at different timepoints. Here we propose TCRDivER algorithm (T cell Receptor Diversity Estimates for Repertoires), a global method of T cell repertoire comparison using diversity profiles sensitive to both clone size and sequence similarity. This approach allowed for distinction between spleen TCR repertoires of immunised and non-immunised mice, showing the need for including both facets of repertoire changes simultaneously. The analysis revealed biologically interpretable relationships between sequence similarity and clonality. These aid in understanding differences and separation of repertoires stemming from different biological context. With the rise of availability of sequencing data we expect our tool to find broad usage in clinical and research applications.
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Affiliation(s)
- Milena Vujović
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Paolo Marcatili
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Benny Chain
- UCL Division of Infection and Immunity, University College London, London, UK.
| | - Joseph Kaplinsky
- Ludwig Institute for Cancer Research Ltd, University of Oxford, Nuffield Department of Medicine, Oxford, UK.
| | - Thomas Lars Andresen
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.
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2
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Sharma H, Moroni L. Recent Advancements in Regenerative Approaches for Thymus Rejuvenation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100543. [PMID: 34306981 PMCID: PMC8292900 DOI: 10.1002/advs.202100543] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/04/2021] [Indexed: 05/29/2023]
Abstract
The thymus plays a key role in adaptive immunity by generating a diverse population of T cells that defend the body against pathogens. Various factors from disease and toxic insults contribute to the degeneration of the thymus resulting in a fewer output of T cells. Consequently, the body is prone to a wide host of diseases and infections. In this review, first, the relevance of the thymus is discussed, followed by thymic embryological organogenesis and anatomy as well as the development and functionality of T cells. Attempts to regenerate the thymus include in vitro methods, such as forming thymic organoids aided by biofabrication techniques that are transplantable. Ex vivo methods that have shown promise in enhancing thymic regeneration are also discussed. Current regenerative technologies have not yet matched the complexity and functionality of the thymus. Therefore, emerging techniques that have shown promise and the challenges that lie ahead are explored.
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Affiliation(s)
- Himal Sharma
- MERLN Institute for Technology‐Inspired Regenerative MedicineDepartment of Complex Tissue RegenerationMaastricht UniversityMaastricht6229 ERNetherlands
| | - Lorenzo Moroni
- MERLN Institute for Technology‐Inspired Regenerative MedicineDepartment of Complex Tissue RegenerationMaastricht UniversityMaastricht6229 ERNetherlands
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3
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Ho CC, Tung JK, Zehnder JL, Zhang BM. Validation of a Next-Generation Sequencing-Based T-Cell Receptor Gamma Gene Rearrangement Diagnostic Assay: Transitioning from Capillary Electrophoresis to Next-Generation Sequencing. J Mol Diagn 2021; 23:805-815. [PMID: 33892183 DOI: 10.1016/j.jmoldx.2021.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 03/15/2021] [Accepted: 03/25/2021] [Indexed: 01/23/2023] Open
Abstract
Assessment of T-cell receptor γ gene (TRG) rearrangements is an importants consideration in the diagnostic workup of lymphoproliferative diseases. Although fragment analysis by PCR and capillary electrophoresis (CE) is the current standard of such assessment in clinical molecular diagnostic laboratories, it does not provide sequence information and is only semi-quantitative. Next-generation sequencing (NGS)-based assays are an attractive alternative to the conventional fragment size-based methods, given that they generate results with specific clonotype sequence information and allow for more accurate quantitation. The present study evaluated various test parameters and performance characteristics of a commercially available NGS-based TRG gene-rearrangement assay by testing 101 clinical samples previously characterized by fragment analysis. The NGS TRG assay showed an overall accuracy of 83% and an analytical specificity of 100%. The concordance rates were 88% to 95% in the Vγ1-8, Vγ10, and Vγ11 gene families, but lower in the Vγ9 gene family. This difference was mostly attributed to the incomplete polyclonal symmetry resulting from the two-tube CE assay versus the one-tube design of the NGS assay. The NGS assay also demonstrated strengths in distinguishing clonotypes of the same fragment size. This clinical validation demonstrated robust performance of the NGS-based TRG assay and identified potential pitfalls associated with CE assay design that are important for understanding the observed discrepancies with the CE-based assay.
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Affiliation(s)
- Chandler C Ho
- Molecular Pathology Laboratory, Stanford Health Care, Stanford, California
| | - Jack K Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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4
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Li G, Li J, Zhang H, Zhang Y, Liu D, Hao Y, Han J, Du J, Zhu L, Zeng Y, Li B, Li R, Song C, Zhang F, Chen C, Zhao H, Zeng H. Partial recovery of disturbed V-J pairing profiles of T-cell receptor in people living with HIV receiving long-term antiretroviral therapy. SCIENCE CHINA-LIFE SCIENCES 2020; 64:152-161. [PMID: 32567004 PMCID: PMC7306449 DOI: 10.1007/s11427-020-1718-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/16/2020] [Indexed: 02/07/2023]
Abstract
Chronic human immunodeficiency virus (HIV) infection not only causes a gradual loss of CD4+ T cells but also leads to a disturbance of the T cell receptor (TCR) repertoire. In people living with HIV (PLWH), monitoring TCR repertoire is challenged by the inconsistency of complementarity determining region 3 (CDR3) and limited cell numbers in clinical samples. Thus, a quantitative method is necessary for monitoring the TCR repertoire in PLWH. We characterized the TCR V-J pairing profile of naïve and memory CD4+ T cells in healthy donors, HIV-infected antiretroviral therapy (ART)-naïve patients and long-term (over 5 years) ART-experienced patients by performing TCR sequencing. We developed a V-J index with 18 parameters which were subdivided into five categories (expression coverage, cumulative percentage of the top tenth percentile, diversity, intra-individual similarity and inter-individual similarity). In ART-naïve patients, 14 of the 18 parameters were significantly altered. Long-term ART recovered ten parameters. The four unrecovered parameters were related to inter-individual similarity. Therefore, these findings indicate that long-term ART could only partially recover TCR V-J pairs and introduce newly impacted V-J pairs. Moreover, these results provide new insights into the V-J pairing of the TCR and into the disturbance of TCR repertoire in HIV infection.
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MESH Headings
- Adult
- Anti-Retroviral Agents/therapeutic use
- CD4 Lymphocyte Count
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
- Female
- HIV Infections/drug therapy
- HIV Infections/genetics
- HIV Infections/immunology
- Humans
- Immunoglobulin Joining Region/genetics
- Immunoglobulin Joining Region/immunology
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/immunology
- Immunologic Memory/immunology
- Male
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Time Factors
- Young Adult
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Affiliation(s)
- Guoli Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Jiarui Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Henghui Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Yu Zhang
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Di Liu
- Computational Virology Group, Center for Bacteria and Virus Resources and Application, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yu Hao
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Junyan Han
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Juan Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Liuluan Zhu
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Yongqin Zeng
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Bei Li
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Rui Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Chuan Song
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Fujie Zhang
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Chen Chen
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China.
| | - Hongxin Zhao
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
| | - Hui Zeng
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China.
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5
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Faghih Z, Deihimi S, Talei A, Ghaderi A, Erfani N. Analysis of T cell receptor repertoire based on Vβ chain in patients with breast cancer. Cancer Biomark 2018; 22:733-745. [DOI: 10.3233/cbm-181295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zahra Faghih
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Safoora Deihimi
- Perelman School of Medicine, University of Pennsylvania, Abramson Cancer Center, Philadelphia, PA, USA
| | - Abdolrasoul Talei
- Breast Disease Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Ghaderi
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasrollah Erfani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Zewde M, Kiyotani K, Park JH, Fang H, Yap KL, Yew PY, Alachkar H, Kato T, Mai TH, Ikeda Y, Matsuda T, Liu X, Ren L, Deng B, Harada M, Nakamura Y. The era of immunogenomics/immunopharmacogenomics. J Hum Genet 2018; 63:865-875. [PMID: 29785006 DOI: 10.1038/s10038-018-0468-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 11/09/2022]
Abstract
Although germline alterations and somatic mutations in disease cells have been extensively analyzed, molecular changes in immune cells associated with disease conditions have not been characterized in depth. It is clear that our immune system has a critical role in various biological and pathological conditions, such as infectious diseases, autoimmune diseases, drug-induced skin and liver toxicity, food allergy, and rejection of transplanted organs. The recent development of cancer immunotherapies, particularly drugs modulating the immune checkpoint molecules, has clearly demonstrated the importance of host immune cells in cancer treatments. However, the molecular mechanisms by which these new therapies kill tumor cells are still not fully understood. In this regard, we have begun to explore the role of newly developed tools such as next-generation sequencing in the genetic characterization of both cancer cells and host immune cells, a field that is called immunogenomics/ immunopharmacogenomics. This new field has enormous potential to help us better understand changes in our immune system during the course of various disease conditions. Here we report the potential of deep sequencing of T-cell and B-cell receptors in capturing the molecular contribution of the immune system, which we believe plays critical roles in the pathogenesis of various human diseases.
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Affiliation(s)
- Makda Zewde
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Kazuma Kiyotani
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.,Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Jae-Hyun Park
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Hua Fang
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Kai Lee Yap
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Poh Yin Yew
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Houda Alachkar
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Taigo Kato
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Tu H Mai
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Yuji Ikeda
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Tatsuo Matsuda
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiao Liu
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Lili Ren
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Boya Deng
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Makiko Harada
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Yusuke Nakamura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
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7
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Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq. Genome Med 2016; 8:80. [PMID: 27460926 PMCID: PMC4962388 DOI: 10.1186/s13073-016-0335-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 07/11/2016] [Indexed: 11/24/2022] Open
Abstract
Accurate characterization of the repertoire of the T-cell receptor (TCR) alpha and beta chains is critical to understanding adaptive immunity. Such characterization has many applications across such fields as vaccine development and response, clone-tracking in cancer, and immunotherapy. Here we present a new methodology called single-cell TCRseq (scTCRseq) for the identification and assembly of full-length rearranged V(D)J T-cell receptor sequences from paired-end single-cell RNA sequencing reads. The method allows accurate identification of the V(D)J rearrangements for each individual T-cell and has the novel ability to recover paired alpha and beta segments. Source code is available at https://github.com/ElementoLab/scTCRseq.
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8
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Flinn AM, Gennery AR. Extracoporeal photopheresis treatment of acute graft-versus-host disease following allogeneic haematopoietic stem cell transplantation. F1000Res 2016; 5. [PMID: 27408705 PMCID: PMC4926758 DOI: 10.12688/f1000research.8118.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/22/2016] [Indexed: 01/03/2023] Open
Abstract
Acute graft-versus-host disease (aGvHD) continues to be a major obstacle to allogeneic haematopoietic stem cell transplantation. Thymic damage secondary to aGvHD along with corticosteroids and other non-selective T lymphocyte-suppressive agents used in the treatment of aGvHD concurrently impair thymopoiesis and negatively impact on immunoreconstitution of the adaptive immune compartment and ultimately adversely affect clinical outcome. Extracorporeal photopheresis (ECP) is an alternative therapeutic strategy that appears to act in an immunomodulatory fashion, potentially involving regulatory T lymphocytes and dendritic cells. By promoting immune tolerance and simultaneously avoiding systemic immunosuppression, ECP could reduce aGvHD and enable a reduction in other immunosuppression, allowing thymic recovery, restoration of normal T lymphopoiesis, and complete immunoreconstitution with improved clinical outcome. Although the safety and efficacy of ECP has been demonstrated, further randomised controlled studies are needed as well as elucidation of the underlying mechanisms responsible and the effect of ECP on thymic recovery.
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Affiliation(s)
- Aisling M Flinn
- Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew R Gennery
- Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK; Paediatric Haematopoietic Stem Cell Unit, Great North Children's Hospital, Newcastle upon Tyne, UK
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9
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Characterization of T-cell Receptor Repertoire in Inflamed Tissues of Patients with Crohn's Disease Through Deep Sequencing. Inflamm Bowel Dis 2016; 22:1275-85. [PMID: 27135481 DOI: 10.1097/mib.0000000000000752] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Intestinal tissues of patients with Crohn's disease (CD) contain expanded populations of T cells which are believed to mediate inflammation. We performed a detailed characterization of these T-cell repertoires. METHODS We obtained biopsies from the neoterminal ileum of 12 patients undergoing evaluation for postoperative recurrent CD and 4 individuals with normal terminal ileum and no history of inflammatory bowel disease (controls). Samples of diseased terminal ileum were obtained from 5 patients undergoing surgery for stricturing or penetrating CD. Total RNA was extracted from tissues and peripheral blood mononuclear cells, and cDNAs were generated. We used next-generation sequencing to characterize T-cell receptor (TCR)-α and TCR-β cDNAs in ileal mucosal tissue and matched peripheral blood mononuclear cells of 17 patients with CD to identify oligoclonal expansions of T-cell populations associated with CD. RESULTS TCR diversity in mucosal tissue was significantly lower than that of matched peripheral blood mononuclear cells, indicating expansion of certain T-cell populations in inflamed intestinal tissue. A single TCR-β clonotype, CASSWTNGEQYF (TRBV10-1-TRBJ2-7), was enriched at a frequency of 7.0% to 28.9% in the neoterminal ileum of 4 of 12 patients with recurrent CD. The abundance of this clonotype significantly correlated with the severity of disease recurrence, based on Rutgeerts score (P = 0.015). CONCLUSIONS Specific populations of T cells are expanded in the inflamed intestinal mucosa of patients with CD; their abundance correlates with severity of disease recurrence. Studies of these T cells could provide information about mechanisms of CD pathogenesis. Deep TCR sequencing is a powerful tool that rapidly provides in-depth, real-time assessment of the T-cell repertoire.
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10
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Ritter J, Seitz V, Balzer H, Gary R, Lenze D, Moi S, Pasemann S, Seegebarth A, Wurdack M, Hennig S, Gerbitz A, Hummel M. Donor CD4 T Cell Diversity Determines Virus Reactivation in Patients After HLA-Matched Allogeneic Stem Cell Transplantation. Am J Transplant 2015; 15:2170-9. [PMID: 25873100 PMCID: PMC4654256 DOI: 10.1111/ajt.13241] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/18/2014] [Accepted: 01/17/2015] [Indexed: 01/25/2023]
Abstract
Delayed reconstitution of the T cell compartment in recipients of allogeneic stem cell grafts is associated with an increase of reactivation of latent viruses. Thereby, the transplanted T cell repertoire appears to be one of the factors that affect T cell reconstitution. Therefore, we studied the T cell receptor beta (TCRβ) gene rearrangements of flow cytometry-sorted CD4(+) and CD8(+) T cells from the peripheral blood of 23 allogeneic donors before G-CSF administration and on the day of apheresis. For this purpose, TCRβ rearrangements were amplified by multiplex PCR followed by high-throughput amplicon sequencing. Overall, CD4(+) T cells displayed a significantly higher TCRβ diversity compared to CD8(+) T cells irrespective of G-CSF administration. In line, no significant impact of G-CSF treatment on the TCR Vβ repertoire usage was found. However, correlation of the donor T cell repertoire with clinical outcomes of the recipient revealed that a higher CD4(+) TCRβ diversity after G-CSF treatment is associated with lower reactivation of cytomegalovirus and Epstein-Barr virus. By contrast, no protecting correlation was observed for CD8(+) T cells. In essence, our deep TCRβ analysis identifies the importance of the CD4(+) T cell compartment for the control of latent viruses after allogeneic stem cell transplantation.
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Affiliation(s)
- J Ritter
- Institute of Pathology, Charité - University Medicine Berlin, Campus Benjamin FranklinBerlin, Germany
| | - V Seitz
- Institute of Pathology, Charité - University Medicine Berlin, Campus Benjamin FranklinBerlin, Germany,HS Diagnomics GmbHBerlin, Germany
| | - H Balzer
- Department of Internal Medicine 5 - Hematology/Oncology, University of ErlangenErlangen, Germany
| | - R Gary
- Department of Internal Medicine 5 - Hematology/Oncology, University of ErlangenErlangen, Germany
| | - D Lenze
- Institute of Pathology, Charité - University Medicine Berlin, Campus Benjamin FranklinBerlin, Germany
| | - S Moi
- Department of Internal Medicine 5 - Hematology/Oncology, University of ErlangenErlangen, Germany
| | - S Pasemann
- Department of Internal Medicine 5 - Hematology/Oncology, University of ErlangenErlangen, Germany
| | - A Seegebarth
- Institute of Pathology, Charité - University Medicine Berlin, Campus Benjamin FranklinBerlin, Germany
| | - M Wurdack
- Department of Internal Medicine 5 - Hematology/Oncology, University of ErlangenErlangen, Germany
| | - S Hennig
- HS Diagnomics GmbHBerlin, Germany
| | - A Gerbitz
- Department of Internal Medicine 5 - Hematology/Oncology, University of ErlangenErlangen, Germany
| | - M Hummel
- Institute of Pathology, Charité - University Medicine Berlin, Campus Benjamin FranklinBerlin, Germany,*Corresponding author: Michael Hummel,
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11
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Yang J, Lu H, Guo R, Yan D, Ye P, Jin L, Chen C, Cao H, Diao H, Li L. Molecular profile of the T cell receptor beta variable in peripheral blood lymphocytes from chronic asymptomatic HBV carriers. Pathog Dis 2014; 73:1-9. [PMID: 25722488 DOI: 10.1093/femspd/ftu018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Jiezuan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Haifeng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Renyong Guo
- Department of Laboratory Medicine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Dong Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Ping Ye
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Linfeng Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Chunlei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Hongcui Cao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Hongyan Diao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
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Britanova OV, Putintseva EV, Shugay M, Merzlyak EM, Turchaninova MA, Staroverov DB, Bolotin DA, Lukyanov S, Bogdanova EA, Mamedov IZ, Lebedev YB, Chudakov DM. Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling. THE JOURNAL OF IMMUNOLOGY 2014; 192:2689-98. [PMID: 24510963 DOI: 10.4049/jimmunol.1302064] [Citation(s) in RCA: 303] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The decrease of TCR diversity with aging has never been studied by direct methods. In this study, we combined high-throughput Illumina sequencing with unique cDNA molecular identifier technology to achieve deep and precisely normalized profiling of TCR β repertoires in 39 healthy donors aged 6-90 y. We demonstrate that TCR β diversity per 10(6) T cells decreases roughly linearly with age, with significant reduction already apparent by age 40. The percentage of naive T cells showed a strong correlation with measured TCR diversity and decreased linearly up to age 70. Remarkably, the oldest group (average age 82 y) was characterized by a higher percentage of naive CD4(+) T cells, lower abundance of expanded clones, and increased TCR diversity compared with the previous age group (average age 62 y), suggesting the influence of age selection and association of these three related parameters with longevity. Interestingly, cross-analysis of individual TCR β repertoires revealed a set >10,000 of the most representative public TCR β clonotypes, whose abundance among the top 100,000 clones correlated with TCR diversity and decreased with aging.
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Affiliation(s)
- Olga V Britanova
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia
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Tzifi F, Kanariou M, Tzanoudaki M, Mihas C, Paschali E, Chrousos G, Kanaka-Gantenbein C. Flow cytometric analysis of the CD4+ TCR Vβ repertoire in the peripheral blood of children with type 1 diabetes mellitus, systemic lupus erythematosus and age-matched healthy controls. BMC Immunol 2013; 14:33. [PMID: 23915345 PMCID: PMC3750582 DOI: 10.1186/1471-2172-14-33] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 07/31/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Data regarding the quantitative expression of TCR Vβ subpopulations in children with autoimmune diseases provided interesting and sometimes conflicting results. The aim of the present study was to assess by comparative flow cytometric analysis the peripheral blood CD4+ TCR Vβ repertoire of children with an organ-specific autoimmune disorder, such as type 1 diabetes mellitus (T1DM), in comparison to children with a systemic autoimmune disease, such as Systemic Lupus Erythematosus (SLE) in comparison to healthy age-matched controls of the same ethnic origin. The CD4+ TCR Vβ repertoire was analysed by flow cytometry in three groups of participants: a) fifteen newly diagnosed children with T1DM (mean age: 9.2 ± 4.78 years old), b) nine newly diagnosed children with SLE, positive for ANA and anti-dsDNA, prior to treatment (mean age: 12.8 ±1.76 years old) and c) 31 healthy age-matched controls (mean age: 6.58 ± 3.65 years old), all of Hellenic origin. RESULTS CD4 + TCR Vβ abnormalities (± 3SD of controls) were observed mainly in SLE patients. Statistical analysis revealed that the CD4 + Vβ4 chain was significantly increased in patients with T1DM (p < 0.001), whereas CD4 + Vβ16 one was significantly increased in SLE patients (p < 0.001) compared to controls. CONCLUSIONS CD4 + Vβ4 and CD4 + Vβ16 chains could be possibly involved in the cascade of events precipitating the pathogenesis of T1DM and SLE in children, respectively.
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Blanchfield JL, Shorter SK, Evavold BD. Monitoring the Dynamics of T Cell Clonal Diversity Using Recombinant Peptide:MHC Technology. Front Immunol 2013; 4:170. [PMID: 23840195 PMCID: PMC3699728 DOI: 10.3389/fimmu.2013.00170] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/14/2013] [Indexed: 12/31/2022] Open
Abstract
The capacity to probe antigen specific T cells within the polyclonal repertoire has been revolutionized by the advent of recombinant peptide:MHC (pMHC) technology. Monomers and multimers of pMHC molecules can enrich for and identify antigen specific T cells to elucidate the contributions of T cell frequency, localization, and T cell receptor (TCR) affinity during immune responses. Two-dimensional (2D) measurements of TCR–pMHC interactions are at the forefront of this field because the biological topography is replicated such that TCR and pMHC are membrane anchored on opposing cells, allowing for biologically pertinent measures of TCR antigen specificity and diversity. 2D measurements of TCR-pMHC kinetics have also demonstrated increased fidelity compared to three-dimensional surface plasmon resonance data and are capable of detecting T cell affinities that are below the detection level of most pMHC multimers. Importantly, 2D techniques provide a platform to evaluate T cell affinity and antigen specificity against multiple protein epitopes within the polyclonal repertoire directly ex vivo from sites of ongoing immune responses. This review will discuss how antigen specific pMHC molecules, with a focus on 2D technologies, can be used as effective tools to evaluate the range of TCR affinities that comprise an immune response and more importantly how the breadth of affinities determine functional outcome against a given exposure to antigen.
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Affiliation(s)
- J Lori Blanchfield
- Department of Microbiology and Immunology, Emory University, Atlanta, GA , USA
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van Heijst JWJ, Ceberio I, Lipuma LB, Samilo DW, Wasilewski GD, Gonzales AMR, Nieves JL, van den Brink MRM, Perales MA, Pamer EG. Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation. Nat Med 2013; 19:372-7. [PMID: 23435170 PMCID: PMC3594333 DOI: 10.1038/nm.3100] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 07/16/2012] [Indexed: 12/19/2022]
Abstract
Delayed T-cell recovery and restricted T-cell receptor (TCR) diversity after allogeneic hematopoietic stem cell transplantation (allo-HSCT) are associated with increased risks of infection and cancer relapse. Technical challenges have limited faithful measurement of TCR diversity following allo-HSCT. Here we combined 5′-RACE PCR with deep sequencing, to quantify TCR diversity in 28 allo-HSCT recipients using a single oligonucleotide pair. Analysis of duplicate blood samples confirmed that the frequency of individual TCRs was accurately determined. After 6 months, cord blood graft recipients approximated the TCR diversity of healthy individuals, whereas recipients of T-cell-depleted peripheral blood stem cell grafts had a 28-fold and 14-fold lower CD4+ and CD8+ T-cell diversity, respectively. After 12 months, these deficiencies had improved for the CD4+, but not the CD8+ T-cell compartment. Overall, this method provides unprecedented views of T-cell repertoire recovery after allo-HSCT and may identify patients at high risk of infection or relapse.
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Affiliation(s)
- Jeroen W J van Heijst
- Immunology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.
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Rempala GA, Seweryn M. Methods for diversity and overlap analysis in T-cell receptor populations. J Math Biol 2012; 67:1339-68. [PMID: 23007599 DOI: 10.1007/s00285-012-0589-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 08/29/2012] [Indexed: 12/13/2022]
Abstract
The paper presents some novel approaches to the empirical analysis of diversity and similarity (overlap) in biological or ecological systems. The analysis is motivated by the molecular studies of highly diverse mammalian T-cell receptor (TCR) populations, and is related to the classical statistical problem of analyzing two-way contingency tables with missing cells and low cell counts. The new measures of diversity and overlap are proposed, based on the information-theoretic as well as geometric considerations, with the capacity to naturally up-weight or down-weight the rare and abundant population species. The consistent estimates are derived by applying the Good-Turing sample-coverage correction. In particular, novel consistent estimates of the Shannon entropy function and the Morisita-Horn index are provided. Data from TCR populations in mice are used to illustrate the empirical performance of the proposed methods vis a vis the existing alternatives.
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Affiliation(s)
- Grzegorz A Rempala
- Department of Biostatistics and Cancer Research Center, Georgia Health Sciences University, Augusta, GA, 30912, USA,
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