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Kumari S, Zemek RM, Palendira U, Ebert LM. Celebrating 100 years of Immunology & Cell Biology - a special focus on the field of tumor immunology in Australia. Immunol Cell Biol 2023; 101:783-788. [PMID: 37694341 DOI: 10.1111/imcb.12690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
In this Commentary article, as part of the 100-year celebrations of the journal, we reflect on the contribution of articles published in ICB in the field of tumor immunology. A highlight is a series of interviews conducted with three Australian-based ICB authors who have contributed key papers over the years: Rajiv Khanna, Delia Nelson and Ian Frazer.
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Affiliation(s)
- Snehlata Kumari
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
- Translational Research Institute, Brisbane, QLD, Australia
| | - Rachael M Zemek
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Umaimainthan Palendira
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Lisa M Ebert
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Cancer Clinical Trials Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
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Smith C, Corvino D, Beagley L, Rehan S, Neller MA, Crooks P, Matthews KK, Solomon M, Le Texier L, Campbell S, Francis RS, Chambers D, Khanna R. T cell repertoire remodeling following post-transplant T cell therapy coincides with clinical response. J Clin Invest 2020; 129:5020-5032. [PMID: 31415240 DOI: 10.1172/jci128323] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/08/2019] [Indexed: 01/31/2023] Open
Abstract
BACKGROUNDImpaired T cell immunity in transplant recipients is associated with infection-related morbidity and mortality. We recently reported the successful use of adoptive T cell therapy (ACT) against drug-resistant/recurrent cytomegalovirus in solid-organ transplant recipients.METHODSIn the present study, we used high-throughput T cell receptor Vβ sequencing and T cell functional profiling to delineate the impact of ACT on T cell repertoire remodeling in the context of pretherapy immunity and ACT products.RESULTSThese analyses indicated that a clinical response was coincident with significant changes in the T cell receptor Vβ landscape after therapy. This restructuring was associated with the emergence of effector memory T cells in responding patients, while nonresponders displayed dramatic pretherapy T cell expansions with minimal change following ACT. Furthermore, immune reconstitution included both adoptively transferred clonotypes and endogenous clonotypes not detected in the ACT products.CONCLUSIONThese observations demonstrate that immune control following ACT requires significant repertoire remodeling, which may be impaired in nonresponders because of the preexisting immune environment. Immunological interventions that can modulate this environment may improve clinical outcomes.TRIAL REGISTRATIONAustralian New Zealand Clinical Trial Registry, ACTRN12613000981729.FUNDINGThis study was supported by funding from the National Health and Medical Research Council, Australia (APP1132519 and APP1062074).
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Affiliation(s)
- Corey Smith
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Dillon Corvino
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Leone Beagley
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sweera Rehan
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Michelle A Neller
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Pauline Crooks
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Katherine K Matthews
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Matthew Solomon
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Laetitia Le Texier
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Scott Campbell
- Department of Nephrology, Princess Alexandra Hospital, Brisbane, Queensland, Australia.,School of Clinical Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Ross S Francis
- Department of Nephrology, Princess Alexandra Hospital, Brisbane, Queensland, Australia.,School of Clinical Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Daniel Chambers
- School of Clinical Medicine, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - Rajiv Khanna
- QIMR Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,School of Clinical Medicine, The University of Queensland, Brisbane, Queensland, Australia
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Stervbo U, Nienen M, Weist BJD, Kuchenbecker L, Hecht J, Wehler P, Westhoff TH, Reinke P, Babel N. BKV Clearance Time Correlates With Exhaustion State and T-Cell Receptor Repertoire Shape of BKV-Specific T-Cells in Renal Transplant Patients. Front Immunol 2019; 10:767. [PMID: 31024575 PMCID: PMC6468491 DOI: 10.3389/fimmu.2019.00767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 03/22/2019] [Indexed: 01/08/2023] Open
Abstract
Reactivation of the BK polyomavirus is known to lead to severe complications in kidney transplant patients. The current treatment strategy relies on decreasing the immunosuppression to allow the immune system to clear the virus. Recently, we demonstrated a clear association between the resolution of BKV reactivation and reconstitution of BKV-specific CD4+ T-cells. However, which factors determine the duration of viral infection clearance remains so far unclear. Here we apply a combination of in-depth multi-parametric flow cytometry and NGS-based CDR3 beta chain receptor repertoire analysis of BKV-specific T-cells to a cohort of 7 kidney transplant patients during the clinical course of BKV reactivation. This way we followed TCR repertoires at single clone levels and functional activity of BKV-specific T-cells during the resolution of BKV infection. The duration of BKV clearance did not depend on the number of peripheral blood BKV-specific T-cells nor on a few immunodominant BKV-specific T-cell clones. Rather, the T-cell receptor repertoire diversity and exhaustion status of BKV-specific T-cells affected the duration of viral clearance: high clonotype diversity and lack of PD1 and TIM3 exhaustion markers on BKV-specific T-cells was associated with short clearance time. Our data thus demonstrate how the diversity and the exhaustion state of the T-cells can determine the clinical course of BKV infection.
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Affiliation(s)
- Ulrik Stervbo
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mikalai Nienen
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Institute for Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Labor Berlin-Charité Vivantes GmbH, Berlin, Germany
| | - Benjamin J D Weist
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Leon Kuchenbecker
- Applied Bioinformatics, Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, Germany
| | - Jochen Hecht
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Patrizia Wehler
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Timm H Westhoff
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Petra Reinke
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Center for Advanced Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nina Babel
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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5
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Cárdenas D, Vélez G, Orfao A, Herrera MV, Solano J, Olaya M, Uribe AM, Saavedra C, Duarte M, Rodríguez M, López M, Fiorentino S, Quijano S. Epstein-Barr virus-specific CD8(+) T lymphocytes from diffuse large B cell lymphoma patients are functionally impaired. Clin Exp Immunol 2015; 182:173-83. [PMID: 26174440 PMCID: PMC4608507 DOI: 10.1111/cei.12682] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2015] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) is a persistent virus with oncogenic capacity that has been implicated in the development of aggressive B cell lymphomas, primarily in immunosuppressed individuals, although it can be present in immunocompetent individuals. Changes in the function and clonal diversity of T lymphocytes might be implied by viral persistence and lymphoma development. The aim of the present study was to evaluate the frequency, phenotype, function and clonotypical distribution of EBV-specific T cells after peripheral blood stimulation with a virus lysate in newly diagnosed patients with diffuse large B cell lymphoma (DLBCL) aged more than 50 years without prior histories of clinical immunosuppression compared with healthy controls. Our results showed impaired EBV-specific immune responses among DLBCL patients that were associated primarily with decreased numbers of central and effector memory CD8(+) T lymphocytes. In contrast to healthy controls, only a minority of the patients showed CD4(+)/tumour necrosis factor (TNF)-α(+) T cells expressing T cell receptor (TCR)-Vβ17 and CD8(+)/TNF-α(+) T cells with TCR-Vβ5·2, Vβ9 and Vβ18 in response to EBV. Notably, the production of TNF-α was undetectable among TCR-Vβ5·3(+), Vβ11(+), Vβ12(+), Vβ16(+) and Vβ23(+) CD8(+) T cells. In addition, we observed decreased numbers of CD4(+)/TNF-α(+) and CD8(+)/TNF-α(+), CD8(+)/interleukin (IL)-2(+) and CD8(+)/TNF-α(+)/IL-2(+) T lymphocytes in the absence of T cells capable of producing TNF-α, IL-2 and IFN-γ after EBV stimulation simultaneously. Moreover, DLBCL patients displayed higher IL-10 levels both under baseline conditions and after EBV stimulation. These findings were also observed in patients with positive EBV viral loads. Prospective studies including a large number of patients are needed to confirm these findings.
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MESH Headings
- Aged
- Aged, 80 and over
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/virology
- Epstein-Barr Virus Infections/blood
- Epstein-Barr Virus Infections/immunology
- Epstein-Barr Virus Infections/virology
- Female
- Flow Cytometry
- Herpesvirus 4, Human/immunology
- Herpesvirus 4, Human/physiology
- Host-Pathogen Interactions/immunology
- Humans
- Interferon-gamma/immunology
- Interferon-gamma/metabolism
- Interleukin-10/immunology
- Interleukin-10/metabolism
- Interleukin-2/immunology
- Interleukin-2/metabolism
- Lymphocyte Count
- Lymphoma, Large B-Cell, Diffuse/blood
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/virology
- Male
- Middle Aged
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Tumor Necrosis Factor-alpha/immunology
- Tumor Necrosis Factor-alpha/metabolism
- Viral Load/immunology
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Affiliation(s)
- D Cárdenas
- Grupo De Inmunobiología Y Biología Celular Departamento De Microbiología Facultad De Ciencias Pontificia Universidad JaverianaBogotá, Colombia
| | - G Vélez
- Grupo De Inmunobiología Y Biología Celular Departamento De Microbiología Facultad De Ciencias Pontificia Universidad JaverianaBogotá, Colombia
| | - A Orfao
- Servicio General De Citometría Y Departamento De Medicina, Centro De Investigación Del Cáncer (Instituto De Biología Molecular Y Celular Del Cáncer and IBSAL; CSIC-USAL), Universidad De SalamancaSalamanca, España
| | - M V Herrera
- Servicio De Hematología Hospital Universitario San Ignacio-Centro De Oncología Javeriano
| | - J Solano
- Servicio De Hematología Hospital Universitario San Ignacio-Centro De Oncología Javeriano
| | - M Olaya
- Departamento de Patología, Pontificia Universidad Javeriana, Hospital Universitario San Ignacio
| | - A M Uribe
- Departamento de Patología, Pontificia Universidad Javeriana, Hospital Universitario San Ignacio
| | - C Saavedra
- Grupo De Patología Fundación Santa Fe De Bogotá
| | - M Duarte
- Servicio De Hematología Fundación Santa Fe De BogotáBogotá, Colombia
| | - M Rodríguez
- Servicio De Hematología Fundación Santa Fe De BogotáBogotá, Colombia
| | - M López
- Fundación Cardiovascular De ColombiaFloridablanca, Colombia
| | - S Fiorentino
- Grupo De Inmunobiología Y Biología Celular Departamento De Microbiología Facultad De Ciencias Pontificia Universidad JaverianaBogotá, Colombia
| | - S Quijano
- Grupo De Inmunobiología Y Biología Celular Departamento De Microbiología Facultad De Ciencias Pontificia Universidad JaverianaBogotá, Colombia
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Plaisted WC, Weinger JG, Walsh CM, Lane TE. T cell mediated suppression of neurotropic coronavirus replication in neural precursor cells. Virology 2013; 449:235-43. [PMID: 24418558 PMCID: PMC3894587 DOI: 10.1016/j.virol.2013.11.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 09/17/2013] [Accepted: 11/14/2013] [Indexed: 02/02/2023]
Abstract
Neural precursor cells (NPCs) are the subject of intense investigation for their potential to treat neurodegenerative disorders, yet the consequences of neuroinvasive virus infection of NPCs remain unclear. This study demonstrates that NPCs support replication following infection by the neurotropic JHM strain of mouse hepatitis virus (JHMV). JHMV infection leads to increased cell death and dampens IFN-γ-induced MHC class II expression. Importantly, cytokines secreted by CD4+ T cells inhibit JHMV replication in NPCs, and CD8+ T cells specifically target viral peptide-pulsed NPCs for lysis. Furthermore, treatment with IFN-γ inhibits JHMV replication in a dose-dependent manner. Together, these findings suggest that T cells play a critical role in controlling replication of a neurotropic virus in NPCs, a finding which has important implications when considering immune modulation for NPC-based therapies for treatment of human neurologic diseases. Murine neural precursor cells are infected by JHMV in a CEACAM1a-dependent manner. Peptide-pulsed NPCs are targeted for lysis by virus-specific CD8+ T cells. JHMV replication in NPCs is suppressed by CD4+ T cells through IFN-γ secretion. IFN-γ dampens CEACAM1a expression and JHMV protein production in NPCs.
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Affiliation(s)
- Warren C Plaisted
- Department of Molecular Biology & Biochemistry, University of California, Irvine 92697-3900, USA; Sue and Bill Gross Stem Cell Center, University of California, Irvine 92697-3900, USA
| | - Jason G Weinger
- Department of Molecular Biology & Biochemistry, University of California, Irvine 92697-3900, USA; Sue and Bill Gross Stem Cell Center, University of California, Irvine 92697-3900, USA
| | - Craig M Walsh
- Department of Molecular Biology & Biochemistry, University of California, Irvine 92697-3900, USA; Sue and Bill Gross Stem Cell Center, University of California, Irvine 92697-3900, USA; Multiple Sclerosis Research Center, University of California, Irvine 92697-3900, USA; Institute for Immunology, University of California, Irvine 92697-3900, USA
| | - Thomas E Lane
- Department of Molecular Biology & Biochemistry, University of California, Irvine 92697-3900, USA; Sue and Bill Gross Stem Cell Center, University of California, Irvine 92697-3900, USA; Multiple Sclerosis Research Center, University of California, Irvine 92697-3900, USA; Institute for Immunology, University of California, Irvine 92697-3900, USA.
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7
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Knowlton ER, Lepone LM, Li J, Rappocciolo G, Jenkins FJ, Rinaldo CR. Professional antigen presenting cells in human herpesvirus 8 infection. Front Immunol 2013; 3:427. [PMID: 23346088 PMCID: PMC3549500 DOI: 10.3389/fimmu.2012.00427] [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: 08/27/2012] [Accepted: 12/24/2012] [Indexed: 12/18/2022] Open
Abstract
Professional antigen presenting cells (APC), i.e., dendritic cells (DC), monocytes/macrophages, and B lymphocytes, are critically important in the recognition of an invading pathogen and presentation of antigens to the T cell-mediated arm of immunity. Human herpesvirus 8 (HHV-8) is one of the few human viruses that primarily targets these APC for infection, altering their cytokine profiles, manipulating their surface expression of MHC molecules, and altering their ability to activate HHV-8-specific T cells. This could be why T cell responses to HHV-8 antigens are not very robust. Of these APC, only B cells support complete, lytic HHV-8 infection. However, both complete and abortive virus replication cycles in APC could directly affect viral pathogenesis and progression to Kaposi's sarcoma (KS) and HHV-8-associated B cell cancers. In this review, we discuss the effects of HHV-8 infection on professional APC and their relationship to the development of KS and B cell lymphomas.
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Affiliation(s)
- Emilee R Knowlton
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh Pittsburgh, PA, USA
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8
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Egli A, Humar A, Kumar D. State-of-the-Art Monitoring of Cytomegalovirus-Specific Cell-Mediated Immunity After Organ Transplant: A Primer for the Clinician. Clin Infect Dis 2012; 55:1678-89. [DOI: 10.1093/cid/cis818] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Galleu A, Fozza C, Simula MP, Contini S, Virdis P, Corda G, Pardini S, Cottoni F, Pruneddu S, Angeloni A, Ceccarelli S, Longinotti M. CD4+ and CD8+ T-cell skewness in classic Kaposi sarcoma. Neoplasia 2012; 14:487-94. [PMID: 22787430 PMCID: PMC3394191 DOI: 10.1596/neo.11646] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Revised: 04/23/2012] [Accepted: 04/24/2012] [Indexed: 11/17/2022]
Abstract
It is widely accepted that a deranged immune system plays a key role in the onset and evolution of classic Kaposi sarcoma (CKS). Nevertheless, the usage of the T-cell receptor (TCR) β-variable (BV) chain repertoire expressed by peripheral blood lymphocytes in patients with CKS is still unknown. With the aim of providing some further insights into the complex role of the immune system in CKS pathogenesis, we performed an extensive analysis of the TCR BV repertoire in both CD4(+) and CD8(+) T cells in 30 human herpesvirus 8-positive Sardinian patients with CKS and an equal number of age-matched healthy controls. We used a panel of monoclonal antibodies covering approximately 70% of human BV subfamilies and third complementarity determining region (CDR3) spectratyping. Patients with CKS showed an increased frequency of BV expansions in both CD4(+) and CD8(+) lymphocytes, with no prevalent clones. On spectratyping analysis, most of the 720 BV CDR3 profiles obtained from both CD4(+) and CD8(+) T cells in patients with CKS were skewed. In particular, the surprising increase of BV skewing observed in CD4(+) lymphocytes mimics the pattern of progressive TCR BV narrowing described in responses to persistent viral antigen stimulations. Our findings support the hypothesis that CKS evolution is associated with inadequate activation rather than impairment of the immune system.
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Affiliation(s)
- Antonio Galleu
- Haematology Section, Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
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Memon SA, Sportès C, Flomerfelt FA, Gress RE, Hakim FT. Quantitative analysis of T cell receptor diversity in clinical samples of human peripheral blood. J Immunol Methods 2012; 375:84-92. [PMID: 21986106 PMCID: PMC3253939 DOI: 10.1016/j.jim.2011.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 09/21/2011] [Accepted: 09/23/2011] [Indexed: 12/19/2022]
Abstract
The analysis of T cell receptor diversity provides a clinically relevant and sensitive marker of repertoire loss, gain, or skewing. Spectratyping is a broadly utilized technique to measure global TCR diversity by the analysis of the lengths of CDR3 fragments in each Vβ family. However the common use of large numbers of T cells to obtain a global view of TCR Vβ CDR3 diversity has restricted spectratyping analyses when limited T-cell numbers are available in clinical setting, such as following transplant regimens. We here demonstrate that one hundred thousand T cells are sufficient to obtain a robust, highly reproducible measure of the global TCR Vβ repertoire diversity among twenty Vβ families in human peripheral blood. We also show that use of lower cell number results not in a dwindling of observed diversity but rather in non-reproducible patterns in replicate spectratypes. Finally, we report here a simple to use but sensitive method to quantify repertoire divergence in patient samples by comparison to a standard repertoire profile we generated from fifteen normal donors. We provide examples using this method to statistically evaluate the changes in the global TCR Vβ repertoire diversity that may take place during T subset immune reconstitution after hematopoietic stem cell transplantation or after immune modulating therapies.
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MESH Headings
- CD8-Positive T-Lymphocytes/chemistry
- CD8-Positive T-Lymphocytes/immunology
- Clinical Laboratory Techniques/methods
- Hematopoietic Stem Cell Transplantation/methods
- Humans
- Leukocytes, Mononuclear/chemistry
- Leukocytes, Mononuclear/immunology
- Monitoring, Immunologic/methods
- Receptors, Antigen, T-Cell/blood
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Reproducibility of Results
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Affiliation(s)
- Sarfraz A Memon
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1203, United States.
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Smith C, Miles JJ, Khanna R. Advances in direct T-cell alloreactivity: function, avidity, biophysics and structure. Am J Transplant 2012; 12:15-26. [PMID: 22152064 DOI: 10.1111/j.1600-6143.2011.03863.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Although T-cell-based adaptive immunity plays a crucial role in protection against infectious pathogens and uncontrolled outgrowth of malignant cells, a large portion of these T cells are also capable of responding to allogeneic HLA molecules, violating the paradigm of self-major histocompatibility complex (MHC) restriction. Recent studies have provided insights into the mechanisms by which these T cells recognize allogeneic targets. The role of antiviral T cells in direct alloreactivity through peptide-dependent molecular mimicry and alternate peptide-MHC docking modes has emerged as major models for the human alloresponse. Here, we review in depth recent advances in this field and discuss how molecular interactions between T cells and HLA molecules drive the activation of these effector cells and its potential implications for alloreactivity in human transplantation.
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Affiliation(s)
- C Smith
- Australian Centre for Vaccine Development, Tumour Immunology Laboratory, Queensland Institute of Medical Research, Herston, Brisbane, Australia
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12
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Carbone J, del Pozo N, Gallego A, Sarmiento E. Immunological risk factors for infection after immunosuppressive and biologic therapies. Expert Rev Anti Infect Ther 2011; 9:405-13. [PMID: 21504398 DOI: 10.1586/eri.10.178] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Immunosuppressive and biologic therapies are costly and can involve a considerable risk of infection. Noninvasive diagnostic tools for early prediction of infection before and after administration of these therapies are of major interest. Serial longitudinal immune monitoring would provide data on immunocompetence and complement clinical follow-up protocols. Biomarkers of immune response may be useful to identify patients at risk of developing infection and who could be candidates for immunosuppressant dose reduction. This article focuses on the potential use of biomarkers of immune response to predict development of infection after immunosuppressive and biologic therapies in selected settings of autoimmune disease (rituximab for treatment of rheumatoid arthritis) and solid organ transplantation.
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Affiliation(s)
- Javier Carbone
- Transplant Immunology Group, Clinical Immunology Department, University Hospital Gregorio Marañon, Doctor Esquerdo 46, 28007 Madrid, Spain.
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Nguyen P, Ma J, Pei D, Obert C, Cheng C, Geiger TL. Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics 2011; 12:106. [PMID: 21310087 PMCID: PMC3045962 DOI: 10.1186/1471-2164-12-106] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 02/11/2011] [Indexed: 12/22/2022] Open
Abstract
Background Recent advances in massively parallel sequencing have increased the depth at which T cell receptor (TCR) repertoires can be probed by >3log10, allowing for saturation sequencing of immune repertoires. The resolution of this sequencing is dependent on its accuracy, and direct assessments of the errors formed during high throughput repertoire analyses are limited. Results We analyzed 3 monoclonal TCR from TCR transgenic, Rag-/- mice using Illumina® sequencing. A total of 27 sequencing reactions were performed for each TCR using a trifurcating design in which samples were divided into 3 at significant processing junctures. More than 20 million complementarity determining region (CDR) 3 sequences were analyzed. Filtering for lower quality sequences diminished but did not eliminate sequence errors, which occurred within 1-6% of sequences. Erroneous sequences were pre-dominantly of correct length and contained single nucleotide substitutions. Rates of specific substitutions varied dramatically in a position-dependent manner. Four substitutions, all purine-pyrimidine transversions, predominated. Solid phase amplification and sequencing rather than liquid sample amplification and preparation appeared to be the primary sources of error. Analysis of polyclonal repertoires demonstrated the impact of error accumulation on data parameters. Conclusions Caution is needed in interpreting repertoire data due to potential contamination with mis-sequence reads. However, a high association of errors with phred score, high relatedness of erroneous sequences with the parental sequence, dominance of specific nt substitutions, and skewed ratio of forward to reverse reads among erroneous sequences indicate approaches to filter erroneous sequences from repertoire data sets.
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Affiliation(s)
- Phuong Nguyen
- Department of Pathology, St, Jude Children's Research Hospital, 262 Danny Thomas Pl., Memphis, TN 38105, USA
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