101
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Lai L, Wang L, Chen H, Zhang J, Yan Q, Ou M, Lin H, Hou X, Chen S, Dai Y, Sui W. T cell repertoire following kidney transplantation revealed by high-throughput sequencing. Transpl Immunol 2016; 39:34-45. [PMID: 27561238 DOI: 10.1016/j.trim.2016.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 08/19/2016] [Accepted: 08/20/2016] [Indexed: 10/25/2022]
Abstract
Delayed T cell recovery and restricted T cell receptor (TCR) diversity after kidney transplantation are associated with increased risks of infection and malignancy. Technical challenges limit the faithful measurement of TCR diversity after kidney transplantation. In this study, we used a combination of multiplex-PCR, Illumina sequencing and IMGT/HighV-QUEST to directly assess millions of TCRs per individual before and at two time points after kidney transplantation (1days and 7days after transplantation) in a cohort of 10 patients compared to a normal control (NC) group (n=10). We identified the most commonly observed CDR3 length, VD indel length, and DJ indel length in transplantation group and normal group. In addition, we found that the TCR repertoire diversity of transplantation groups was relatively lower compared to NC group. T cell depletion in Post-1 group can be observed, which resulted in the altered distribution characteristics of clonotype abundance. A modest proportion of high abundance clones were shared among the pre-1 group, post-1 group and post-7 group, and it did not exist in the NC group, which exhibited a signature of antigen selection. Moreover, our results also demonstrated that various TRBV expression increased and some public sequences at different time points after kidney transplantation, which may provide biomarkers to monitor the immune status of transplant patients.
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Affiliation(s)
- Liusheng Lai
- Department of Nephrology, The Affiliated Guilin Hospital of Southern Medical University, Guilin, Guangxi 541002, PR China
| | - Lei Wang
- Department of Nephrology, The Affiliated Guilin Hospital of Southern Medical University, Guilin, Guangxi 541002, PR China
| | - Huaizhou Chen
- Department of Nephrology, Guilin 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, PR China
| | - Jiaxing Zhang
- Department of Nephrology, The Affiliated Guilin Hospital of Southern Medical University, Guilin, Guangxi 541002, PR China
| | - Qiang Yan
- Department of Nephrology, The Affiliated Guilin Hospital of Southern Medical University, Guilin, Guangxi 541002, PR China
| | - Minglin Ou
- Department of Nephrology, Guilin 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, PR China
| | - Hua Lin
- Department of Nephrology, Guilin 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, PR China
| | - Xianliang Hou
- Department of Nephrology, Guilin 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, PR China
| | - Sisi Chen
- Beijing Genomics Institute, Shenzhen 518083, PR China
| | - Yong Dai
- Department of Nephrology, Guilin 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, PR China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, PR China
| | - Weiguo Sui
- Department of Nephrology, The Affiliated Guilin Hospital of Southern Medical University, Guilin, Guangxi 541002, PR China; Department of Nephrology, Guilin 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, PR China.
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102
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Chen Y, Xu Y, Zhao M, Liu Y, Gong M, Xie C, Wu H, Wang Z. High-throughput T cell receptor sequencing reveals distinct repertoires between tumor and adjacent non-tumor tissues in HBV-associated HCC. Oncoimmunology 2016; 5:e1219010. [PMID: 27853640 DOI: 10.1080/2162402x.2016.1219010] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/16/2016] [Accepted: 07/26/2016] [Indexed: 12/17/2022] Open
Abstract
T lymphocytes, which recognize antigen peptides through specific T cell receptors (TCRs), play an important role in the human adaptive immune response. TCR diversity is closely associated with host immune response and cancer prognosis. Although tumor-infiltrating T lymphocytes have implications for tumor prognosis, few studies have performed a detailed characterization of TCR diversity in both tumor and non-tumor tissues in hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC). Here, we performed high-throughput sequencing of the TCRβ chain complementarity determining region 3 (CDR3) of liver-infiltrating T cells from 48 HBV-associated HCC patients. A significantly higher average number of CDR3 aa clonotypes (2259 vs. 1324, p < 0.001), and significantly higher TCR diversity (Gini coefficient, p < 0.001; Simpson index, p < 0.01; Shannon entropy, p < 0.001) were observed in tumor tissues compared with adjacent non-tumor tissues. The ratio of highly expanded clones (HECs) was significantly higher in non-tumor tissues than in tumor tissues when the HEC threshold was defined as 2% or greater (p < 0.05). Our analysis of the median Morisita-Horn index indicated weak TCR repertoire similarity between tumor and matched non-tumor tissues. The median number of shared clones in tumor tissue and matched non-tumor tissue from each patient was 360.5, representing 5.1-15.8% (10.6 ± 0.4%) of all clones in each patient. We observed extensive heterogeneity of T lymphocytes in tumors and higher HEC ratios in adjacent non-tumor tissues of HCC patients. The differential T cell repertoires in tumor and non-tumor tissues suggest a distinct T cell immune microenvironment in patients with HBV-associated HCC.
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Affiliation(s)
- Yunqing Chen
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Ying Xu
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Miaoxian Zhao
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Yu Liu
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Mingxing Gong
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Cantao Xie
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Hongkai Wu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University , Guangzhou, China
| | - Zhanhui Wang
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
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103
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Mehta RS, Rezvani K. Immune reconstitution post allogeneic transplant and the impact of immune recovery on the risk of infection. Virulence 2016; 7:901-916. [PMID: 27385018 DOI: 10.1080/21505594.2016.1208866] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Infection is the leading cause of non-relapse mortality after allogeneic haematopoietic cell transplantation (HCT). This occurs as a result of dysfunction to the host immune system from the preparative regimen used prior to HCT, combined with a delay in reconstitution of the donor-derived immune system after HCT. In this article, we elaborate on the process of immune reconstitution post-HCT that begins with the innate system and is followed by recovery of adaptive immunity. Simultaneously, we describe how the tempo of immune reconstitution influences the risk of various infections. We explain some of the key differences in immune reconstitution and the consequent risk of infections in recipients of peripheral blood stem cell, bone marrow or umbilical cord blood grafts. Other factors that impact on immune recovery are also highlighted. Finally, we allude to various strategies that are being tested to enhance immune reconstitution post-HCT.
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Affiliation(s)
- Rohtesh S Mehta
- a Division of Hematology, Oncology and Transplantation, University of Minnesota , Minneapolis , MN , USA
| | - Katayoun Rezvani
- b Department of Stem Cell Transplantation and Cellular Therapy , MD Anderson Cancer Center , Houston , TX , USA
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104
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Landscape of tumor-infiltrating T cell repertoire of human cancers. Nat Genet 2016; 48:725-32. [PMID: 27240091 PMCID: PMC5298896 DOI: 10.1038/ng.3581] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/04/2016] [Indexed: 02/05/2023]
Abstract
We developed a computational method to infer the complementarity determining region 3 (CDR3) sequences of tumor infiltrating T-cells in 9,142 RNA-seq samples across 29 cancer types. We identified over 600 thousand CDR3 sequences, including 15% with full-length. CDR3 sequence length distribution and amino acid conservation, as well as variable gene usage of infiltrating T-cells in many tumors, except brain and kidney cancers, resembled those in the peripheral blood of healthy donors. We observed a strong association between T-cell diversity and tumor mutation load, and predicted SPAG5 and TSSK6 as putative immunogenic cancer/testis antigens in multiple cancers. Finally, we identified 3 potential immunogenic somatic mutations based on their co-occurrence with CDR3 sequences. One of them, PRAMEF4 F300V, was predicted to bind strongly to both MHC-I and MHC-II, with matched HLA types in its carriers. Our analyses have the potential to simultaneously identify immunogenic neoantigens and the tumor-reactive T-cell clonotypes.
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105
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Kanakry CG, Coffey DG, Towlerton AMH, Vulic A, Storer BE, Chou J, Yeung CCS, Gocke CD, Robins HS, O'Donnell PV, Luznik L, Warren EH. Origin and evolution of the T cell repertoire after posttransplantation cyclophosphamide. JCI Insight 2016; 1. [PMID: 27213183 DOI: 10.1172/jci.insight.86252] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Posttransplantation cyclophosphamide (PTCy) effectively prevents graft-versus-host disease (GVHD), but its immunologic impact is poorly understood. We assessed lymphocyte reconstitution via flow cytometry (n = 74) and antigen receptor sequencing (n = 35) in recipients of myeloablative, HLA-matched allogeneic BM transplantation using PTCy. Recovering T cells were primarily phenotypically effector memory with lower T cell receptor β (TRB) repertoire diversity than input donor repertoires. Recovering B cells were predominantly naive with immunoglobulin heavy chain locus (IGH) repertoire diversity similar to donors. Numerical T cell reconstitution and TRB diversity were strongly associated with recipient cytomegalovirus seropositivity. Global similarity between input donor and recipient posttransplant repertoires was uniformly low at 1-2 months after transplant but increased over the balance of the first posttransplant year. Blood TRB repertoires at ≥3 months after transplant were often dominated by clones present in the donor blood/marrow memory CD8+ compartment. Limited overlap was observed between the TRB repertoires of T cells infiltrating the skin or gastrointestinal tract versus the blood. Although public TRB sequences associated with herpesvirus- or alloantigen-specific CD8+ T cells were detected in some patients, posttransplant TRB and IGH repertoires were unique to each individual. These data define the immune dynamics occurring after PTCy and establish a benchmark against which immune recovery after other transplantation approaches can be compared.
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Affiliation(s)
- Christopher G Kanakry
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David G Coffey
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Andrea M H Towlerton
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA
| | - Ante Vulic
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Barry E Storer
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA
| | - Jeffrey Chou
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Cecilia C S Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Christopher D Gocke
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Harlan S Robins
- Public Health Sciences Division, FHCRC, Seattle, Washington, USA
| | - Paul V O'Donnell
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Leo Luznik
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Edus H Warren
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
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106
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Lin C. Analysis of TCR repertoires for tracking and evaluating distinct T cell subsets. Stem Cell Investig 2016; 3:12. [PMID: 27358903 DOI: 10.21037/sci.2016.04.01] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/08/2016] [Indexed: 02/04/2023]
Affiliation(s)
- Chen Lin
- Department of Microbiology and Immunology, Medical College, Jinan University, Guangzhou 510632, China
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107
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Lucchini G, Perales MA, Veys P. Immune reconstitution after cord blood transplantation: peculiarities, clinical implications and management strategies. Cytotherapy 2016; 17:711-722. [PMID: 25946726 DOI: 10.1016/j.jcyt.2015.03.614] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/12/2015] [Indexed: 12/26/2022]
Abstract
Umbilical cord blood (UCB) is now widely used as an alternative hematopoietic stem cell source for patients lacking closely matched related or unrelated adult donors. UCB transplantation has traditionally been associated with delayed engraftment, poor immune reconstitution and consequent increased risk of infection. More recent clinical studies, however, suggest that conditioning regimens and in particular the omission of in vivo T-cell depletion may play a crucial role in post-transplant T-cell expansion, facilitating a uniquely rapid immune recovery after UCB transplantation. The peculiar characteristics of UCB cells, the importance of thymic function and the role of conditioning regimens and graft-versus-host disease influencing immune reconstitution are described. The last part of the review reports available data on UCB, as well as third-party peripheral blood derived anti-viral cell therapy, which provides a novel approach to rescue UCB recipients with viral complications in the post-transplant period.
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Affiliation(s)
- Giovanna Lucchini
- Bone Marrow Transplantation Department, Great Ormond Street Hospital, London, United Kingdom.
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, and Weill Cornell Medical College, New York, USA
| | - Paul Veys
- Bone Marrow Transplantation Department, Great Ormond Street Hospital, London, United Kingdom
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108
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Link CS, Eugster A, Heidenreich F, Rücker-Braun E, Schmiedgen M, Oelschlägel U, Kühn D, Dietz S, Fuchs Y, Dahl A, Domingues AMJ, Klesse C, Schmitz M, Ehninger G, Bornhäuser M, Schetelig J, Bonifacio E. Abundant cytomegalovirus (CMV) reactive clonotypes in the CD8(+) T cell receptor alpha repertoire following allogeneic transplantation. Clin Exp Immunol 2016; 184:389-402. [PMID: 26800118 DOI: 10.1111/cei.12770] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Indexed: 12/15/2022] Open
Abstract
Allogeneic stem cell transplantation is potentially curative, but associated with post-transplantation complications, including cytomegalovirus (CMV) infections. An effective immune response requires T cells recognizing CMV epitopes via their T cell receptors (TCRs). Little is known about the TCR repertoire, in particular the TCR-α repertoire and its clinical relevance in patients following stem cell transplantation. Using next-generation sequencing we examined the TCR-α repertoire of CD8(+) T cells and CMV-specific CD8(+) T cells in four patients. Additionally, we performed single-cell TCR-αβ sequencing of CMV-specific CD8(+) T cells. The TCR-α composition of human leucocyte antigen (HLA)-A*0201 CMVpp65- and CMVIE -specific T cells was oligoclonal and defined by few dominant clonotypes. Frequencies of single clonotypes reached up to 11% of all CD8(+) T cells and half of the total CD8(+) T cell repertoire was dominated by few CMV-reactive clonotypes. Some TCR-α clonotypes were shared between patients. Gene expression of the circulating CMV-specific CD8(+) T cells was consistent with chronically activated effector memory T cells. The CD8(+) T cell response to CMV reactivation resulted in an expansion of a few TCR-α clonotypes to dominate the CD8(+) repertoires. These results warrant further larger studies to define the ability of oligoclonally expanded T cell clones to achieve an effective anti-viral T cell response in this setting.
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Affiliation(s)
- C S Link
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus.,DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - A Eugster
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - F Heidenreich
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus
| | - E Rücker-Braun
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus
| | - M Schmiedgen
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus
| | - U Oelschlägel
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus
| | - D Kühn
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - S Dietz
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Y Fuchs
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - A Dahl
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany.,BIOTEChnology Center, TU Dresden, Dresden, Germany
| | - A M J Domingues
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - C Klesse
- DKMS Clinical Trials Unit, Dresden, Germany
| | - M Schmitz
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany.,Institut Für Immunologie, Medizinische Fakultät, TU Dresden, Dresden, Germany
| | - G Ehninger
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus.,DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - M Bornhäuser
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus.,DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - J Schetelig
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus.,DKMS Clinical Trials Unit, Dresden, Germany
| | - E Bonifacio
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
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109
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Control of T cell antigen reactivity via programmed TCR downregulation. Nat Immunol 2016; 17:379-86. [PMID: 26901151 PMCID: PMC4803589 DOI: 10.1038/ni.3386] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/22/2015] [Indexed: 12/17/2022]
Abstract
The T cell receptor (TCR) is unique in that its affinity for ligand is unknown prior to encounter and can vary by orders of magnitude. How the immune system regulates individual T cells that display highly different reactivity to antigen remains unclear. Here we identified that activated CD4+ T cells, at the peak of clonal expansion, persistently downregulate TCR expression in proportion to the strength of initial antigen recognition. This programmed response increases the threshold for cytokine production and recall proliferation in a clone-specific manner, ultimately excluding clones with the highest antigen reactivities. Thus, programmed TCR downregulation represents a negative feedback mechanism to constrain T cell effector function with a suitable time delay, thereby allowing pathogen control while avoiding excess inflammatory damage.
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110
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Alachkar H, Nakamura Y. Deep-sequencing of the T-cell receptor repertoire in patients with haplo-cord and matched-donor transplants. CHIMERISM 2016; 6:47-9. [PMID: 26745665 DOI: 10.1080/19381956.2015.1128624] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Haplo-cord transplant has emerged as a feasible and reliable approach for haematopoietic stem cell transplant in patients who are unable to find matched-donor. This approach provides fast myeloid recovery, low incidence of graft vs host disease (GVHD) and favorable graft versus leukemia (GVL) effects. T cell recovery plays an important role in preventing infectious complications; it also mediates the GVHD and the GVL effects. Here, we utilized a novel RNA-based sequencing approach to quantitatively characterize the T cell receptor (TCRs) repertoire in patients underwent haplo-cord transplant in comparison with those underwent matched-donor transplant. Our study shows that higher percentage of cord cells early post transplant were associated with significantly higher TCR diversity. TCR diversity was significantly lower in patients with GVHD and in relapsed patients. A larger cohort study is needed to validate these data and to provide useful information on the specific TCR clones correlated with clinical outcome.
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Affiliation(s)
- Houda Alachkar
- a School of Pharmacy, University of Southern California , Los Angeles , CA , USA
| | - Yusuke Nakamura
- b Section of Hematology/Oncology, Department of Medicine, The University of Chicago , Chicago , IL , USA
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111
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Abdul Razzaq B, Scalora A, Koparde VN, Meier J, Mahmood M, Salman S, Jameson-Lee M, Serrano MG, Sheth N, Voelkner M, Kobulnicky DJ, Roberts CH, Ferreira-Gonzalez A, Manjili MH, Buck GA, Neale MC, Toor AA. Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides Demonstrates Different Alloreactivity Potential in HLA-Matched and -Mismatched Donor-Recipient Pairs. Biol Blood Marrow Transplant 2015; 22:850-61. [PMID: 26688192 DOI: 10.1016/j.bbmt.2015.11.1103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/29/2015] [Indexed: 12/11/2022]
Abstract
Immune reconstitution kinetics and subsequent clinical outcomes in HLA-matched recipients of allogeneic stem cell transplantation (SCT) are variable and difficult to predict. Considering SCT as a dynamical system may allow sequence differences across the exomes of the transplant donors and recipients to be used to simulate an alloreactive T cell response, which may allow better clinical outcome prediction. To accomplish this, whole exome sequencing was performed on 34 HLA-matched SCT donor-recipient pairs (DRPs) and the nucleotide sequence differences translated to peptides. The binding affinity of the peptides to the relevant HLA in each DRP was determined. The resulting array of peptide-HLA binding affinity values in each patient was considered as an operator modifying a hypothetical T cell repertoire vector, in which each T cell clone proliferates in accordance with the logistic equation of growth. Using an iterating system of matrices, each simulated T cell clone's growth was calculated with the steady-state population being proportional to the magnitude of the binding affinity of the driving HLA-peptide complex. Incorporating competition between T cell clones responding to different HLA-peptide complexes reproduces a number of features of clinically observed T cell clonal repertoire in the simulated repertoire, including sigmoidal growth kinetics of individual T cell clones and overall repertoire, Power Law clonal frequency distribution, increase in repertoire complexity over time with increasing clonal diversity, and alteration of clonal dominance when a different antigen array is encountered, such as in SCT. The simulated, alloreactive T cell repertoire was markedly different in HLA-matched DRPs. The patterns were differentiated by rate of growth and steady-state magnitude of the simulated T cell repertoire and demonstrate a possible correlation with survival. In conclusion, exome wide sequence differences in DRPs may allow simulation of donor alloreactive T cell response to recipient antigens and may provide a quantitative basis for refining donor selection and titration of immunosuppression after SCT.
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Affiliation(s)
- Badar Abdul Razzaq
- Virginia Commonwealth University School of Engineering, Virginia Commonwealth University, Richmond, VA 23298
| | - Allison Scalora
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298
| | - Vishal N Koparde
- Center for Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298
| | - Jeremy Meier
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298
| | - Musa Mahmood
- Virginia Commonwealth University School of Engineering, Virginia Commonwealth University, Richmond, VA 23298
| | - Salman Salman
- Virginia Commonwealth University School of Engineering, Virginia Commonwealth University, Richmond, VA 23298
| | - Max Jameson-Lee
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298
| | - Myrna G Serrano
- Center for Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298
| | - Nihar Sheth
- Center for Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298
| | - Mark Voelkner
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298
| | - David J Kobulnicky
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298
| | - Catherine H Roberts
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298
| | | | - Masoud H Manjili
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298
| | - Gregory A Buck
- Center for Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298
| | - Michael C Neale
- Department of Psychiatry and Statistical Genomics, Virginia Commonwealth University, Richmond, VA 23298
| | - Amir A Toor
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298.
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112
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Shah GL, Shune L, Purtill D, Devlin S, Lauer E, Lubin M, Bhatt V, McElrath C, Kernan NA, Scaradavou A, Giralt S, Perales MA, Ponce DM, Young JW, Shah M, Papanicolaou G, Barker JN. Robust Vaccine Responses in Adult and Pediatric Cord Blood Transplantation Recipients Treated for Hematologic Malignancies. Biol Blood Marrow Transplant 2015; 21:2160-2166. [PMID: 26271191 PMCID: PMC4672874 DOI: 10.1016/j.bbmt.2015.08.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/05/2015] [Indexed: 01/04/2023]
Abstract
Because cord blood (CB) lacks memory T and B cells and recent decreases in herd immunity to vaccine-preventable diseases in many developed countries have been documented, vaccine responses in CB transplantation (CBT) survivors are of great interest. We analyzed vaccine responses in double-unit CBT recipients transplanted for hematologic malignancies. In 103 vaccine-eligible patients, graft-versus-host disease (GVHD) most commonly precluded vaccination. Sixty-five patients (63%; engrafting units median HLA-allele match 5/8; range, 2 to 7/8) received protein conjugated vaccines, and 63 patients (median age, 34 years; range, .9 to 64) were evaluated for responses. Median vaccination time was 17 months (range, 7 to 45) post-CBT. GVHD (n = 42) and prior rituximab (n = 13) delayed vaccination. Responses to Prevnar 7 and/or 13 vaccines (serotypes 14, 19F, 23F) were seen in children and adults (60% versus 49%, P = .555). Responses to tetanus, diphtheria, pertussis, Haemophilus influenzae, and polio were observed in children (86% to 100%) and adults (53% to 89%) even if patients had prior GVHD or rituximab. CD4(+)CD45RA(+) and CD19(+) cell recovery significantly influenced tetanus and polio responses. In a smaller cohort responses were seen to measles (65%), mumps (50%), and rubella (100%) vaccines. No vaccine side effects were identified, and all vaccinated patients survived (median follow-up, 57 months). Although GVHD and rituximab can delay vaccination, CBT recipients (including adults and those with prior GVHD) have similar vaccine response rates to adult donor allograft recipients supporting vaccination in CBT recipients.
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Affiliation(s)
- Gunjan L Shah
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leyla Shune
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Duncan Purtill
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sean Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Lauer
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marissa Lubin
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Valkal Bhatt
- Department of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Courtney McElrath
- Department of Nursing, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy A Kernan
- Bone Marrow Transplantation Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andromachi Scaradavou
- Bone Marrow Transplantation Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sergio Giralt
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Miguel A Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Doris M Ponce
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - James W Young
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Monica Shah
- Department of Medicine, Weill Cornell Medical College, New York, New York; Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Genovefa Papanicolaou
- Department of Medicine, Weill Cornell Medical College, New York, New York; Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Juliet N Barker
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York.
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113
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Klarenbeek PL, Doorenspleet ME, Esveldt REE, van Schaik BDC, Lardy N, van Kampen AHC, Tak PP, Plenge RM, Baas F, de Bakker PIW, de Vries N. Somatic Variation of T-Cell Receptor Genes Strongly Associate with HLA Class Restriction. PLoS One 2015; 10:e0140815. [PMID: 26517366 PMCID: PMC4627806 DOI: 10.1371/journal.pone.0140815] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/29/2015] [Indexed: 01/18/2023] Open
Abstract
Every person carries a vast repertoire of CD4+ T-helper cells and CD8+ cytotoxic T cells for a healthy immune system. Somatic VDJ recombination at genomic loci that encode the T-cell receptor (TCR) is a key step during T-cell development, but how a single T cell commits to become either CD4+ or CD8+ is poorly understood. To evaluate the influence of TCR sequence variation on CD4+/CD8+ lineage commitment, we sequenced rearranged TCRs for both α and β chains in naïve T cells isolated from healthy donors and investigated gene segment usage and recombination patterns in CD4+ and CD8+ T-cell subsets. Our data demonstrate that most V and J gene segments are strongly biased in the naïve CD4+ and CD8+ subsets with some segments increasing the odds of being CD4+ (or CD8+) up to five-fold. These V and J gene associations are highly reproducible across individuals and independent of classical HLA genotype, explaining ~11% of the observed variance in the CD4+ vs. CD8+ propensity. In addition, we identified a strong independent association of the electrostatic charge of the complementarity determining region 3 (CDR3) in both α and β chains, where a positively charged CDR3 is associated with CD4+ lineage and a negatively charged CDR3 with CD8+ lineage. Our findings suggest that somatic variation in different parts of the TCR influences T-cell lineage commitment in a predominantly additive fashion. This notion can help delineate how certain structural features of the TCR-peptide-HLA complex influence thymic selection.
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Affiliation(s)
- Paul L. Klarenbeek
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Clinical Immunology and Rheumatology, Laboratory for Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Laboratory for Genome Analysis, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Marieke E. Doorenspleet
- Department of Clinical Immunology and Rheumatology, Laboratory for Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Laboratory for Genome Analysis, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Rebecca E. E. Esveldt
- Department of Clinical Immunology and Rheumatology, Laboratory for Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Barbera D. C. van Schaik
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam, Amsterdam, The Netherlands
| | - Neubury Lardy
- Department of Immunogenetics, Sanquin Diagnostic Services, Amsterdam, The Netherlands
| | - Antoine H. C. van Kampen
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul P. Tak
- Department of Clinical Immunology and Rheumatology, Laboratory for Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Robert M. Plenge
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Frank Baas
- Laboratory for Genome Analysis, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul I. W. de Bakker
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Epidemiology, University Medical Center, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center, Utrecht, The Netherlands
- * E-mail:
| | - Niek de Vries
- Department of Clinical Immunology and Rheumatology, Laboratory for Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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114
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Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing. PLoS One 2015; 10:e0141561. [PMID: 26509579 PMCID: PMC4624875 DOI: 10.1371/journal.pone.0141561] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/10/2015] [Indexed: 01/05/2023] Open
Abstract
Monitoring antigen-specific T cells is critical for the study of immune responses and development of biomarkers and immunotherapeutics. We developed a novel multiplex assay that combines conventional immune monitoring techniques and immune receptor repertoire sequencing to enable identification of T cells specific to large numbers of antigens simultaneously. We multiplexed 30 different antigens and identified 427 antigen-specific clonotypes from 5 individuals with frequencies as low as 1 per million T cells. The clonotypes identified were validated several ways including repeatability, concordance with published clonotypes, and high correlation with ELISPOT. Applying this technology we have shown that the vast majority of shared antigen-specific clonotypes identified in different individuals display the same specificity. We also showed that shared antigen-specific clonotypes are simpler sequences and are present at higher frequencies compared to non-shared clonotypes specific to the same antigen. In conclusion this technology enables sensitive and quantitative monitoring of T cells specific for hundreds or thousands of antigens simultaneously allowing the study of T cell responses with an unprecedented resolution and scale.
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115
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Choudhury NJ, Kiyotani K, Yap KL, Campanile A, Antic T, Yew PY, Steinberg G, Park JH, Nakamura Y, O'Donnell PH. Low T-cell Receptor Diversity, High Somatic Mutation Burden, and High Neoantigen Load as Predictors of Clinical Outcome in Muscle-invasive Bladder Cancer. Eur Urol Focus 2015; 2:445-452. [PMID: 28723478 DOI: 10.1016/j.euf.2015.09.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/19/2015] [Indexed: 12/22/2022]
Abstract
BACKGROUND The success of cancer immunotherapies has highlighted the potent ability of local adaptive immune responses to eradicate cancer cells by targeting neoantigens generated by somatic alterations. However, how these factors interact to drive the natural history of muscle-invasive bladder cancer (MIBC) is not well understood. OBJECTIVE To investigate the role of immune regulation in MIBC disease progression, we performed massively parallel T-cell receptor (TCR) sequencing of tumor-infiltrating T cells (TILs), in silico neoantigen prediction from exome sequences, and expression analysis of immune-related genes. DESIGN, SETTING, AND PARTICIPANTS We analyzed 38 MIBC tissues from patients who underwent definitive surgery with a minimum clinical follow-up of 2 yr. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Recurrence-free survival (RFS) was determined. TCR diversity was quantified using Simpson's diversity index. The main analyses involved the Mann-Whitney U test, Kaplan-Meier survival analysis, and Cox proportional hazards models. RESULTS AND LIMITATIONS Low TCRβ chain diversity, correlating with oligoclonal TIL expansion, was significantly correlated with longer RFS, even after adjustment for pathologic tumor stage, node status, and receipt of adjuvant chemotherapy (hazard ratio 2.67, 95% confidence interval 1.08-6.60; p=0.03). Patients with both a high number of neoantigens and low TCRβ diversity had longer RFS compared to those with fewer neoantigens and high TCR diversity (median RFS 275 vs 30 wk; p=0.03). Higher expression of immune cytolytic genes was associated with nonrecurrence among patients with low TCR diversity or fewer neoantigens. Limitations include the sample size and the inability to distinguish CD8+ and CD4+ T cells using TCR sequencing. CONCLUSIONS These findings are the first to show that detailed tumor immune-genome analysis at definitive surgery can identify molecular patterns of antitumor immune response contributing to better clinical outcomes in MIBC. PATIENT SUMMARY We discovered that clonal expansion of certain T cells in tumor tissue, possibly targeting cancer-specific antigens, contributes to prevention of bladder cancer recurrence.
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116
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Li Y, Xu L. Evaluation of TCR repertoire diversity in patients after hematopoietic stem cell transplantation. Stem Cell Investig 2015; 2:17. [PMID: 27358885 DOI: 10.3978/j.issn.2306-9759.2015.09.01] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/19/2015] [Indexed: 12/16/2022]
Abstract
T-cell receptor (TCR) repertoire analyses have been widely used to identify T cell populations of interest in cancer and autoimmunity and for characterizing immune repertoire reconstitution after hematopoietic stem cell transplantation (HSCT). Several decades of development and progress have led to the use of techniques for evaluating TCR repertoires in a more comprehensive, unbiased and fast manner, and the mechanisms of T cell immune reconstitution after HSCT and the new approaches used for recovering T cell repertoire diversity post HSCT have been more exhaustively documented to some degree. To better understand and characterize this progress, here we review recent studies on TCR repertoire diversity recovery in patients with leukemia and autoimmune disease who have received HSCT, impact factors and improvements in approaches for TCR repertoire recovery after HSCT.
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Affiliation(s)
- Yangqiu Li
- 1 Institute of Hematology, Medical College, 2 Department of Hematology, First Affiliated Hospital, 3 Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou 510632, China
| | - Ling Xu
- 1 Institute of Hematology, Medical College, 2 Department of Hematology, First Affiliated Hospital, 3 Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou 510632, China
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117
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Bai X, Zhang Q, Wu S, Zhang X, Wang M, He F, Wei T, Yang J, Lou Y, Cai Z, Liang T. Characteristics of Tumor Infiltrating Lymphocyte and Circulating Lymphocyte Repertoires in Pancreatic Cancer by the Sequencing of T Cell Receptors. Sci Rep 2015; 5:13664. [PMID: 26329277 PMCID: PMC4556988 DOI: 10.1038/srep13664] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/03/2015] [Indexed: 01/20/2023] Open
Abstract
Pancreatic cancer has a poor prognosis and few effective treatments. The failure of treatment is partially due to the high heterogeneity of cancer cells within the tumor. T cells target and kill cancer cells by the specific recognition of cancer-associated antigens. In this study, T cells from primary tumor and blood of sixteen patients with pancreatic cancer were characterized by deep sequencing. T cells from blood of another eight healthy volunteers were also studied as controls. By analyzing the complementary determining region 3 (CDR3) gene sequence, we found no significant differences in the T cell receptor (TCR) repertoires between patients and healthy controls. Types and length of CDR3 were similar among groups. However, two clusters of patients were identified according to the degree of CDR3 overlap within tumor sample group. In addition, clonotypes with low frequencies were found in significantly higher numbers in primary pancreatic tumors compared to blood samples from patients and healthy controls. This study is the first to characterize the TCR repertoires of pancreatic cancers in both primary tumors and matched blood samples. The results imply that specific types of pancreatic cancer share potentially important immunological characteristics.
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Affiliation(s)
- Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Song Wu
- National-regional Key Technology Engineering Laboratory for Clinical Application of Cancer Genomics, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Xiaoyu Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mingbang Wang
- Shenzhen Following Precision Medical Research Institute
| | - Fusheng He
- Shenzhen Following Precision Medical Research Institute
| | - Tao Wei
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaqi Yang
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Lou
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhiming Cai
- National-regional Key Technology Engineering Laboratory for Clinical Application of Cancer Genomics, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang University; Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
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118
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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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119
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Reconstitution of T Cell Immunity after Umbilical Cord Blood Transplantation. Biol Blood Marrow Transplant 2015; 21:1151-2. [DOI: 10.1016/j.bbmt.2015.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 04/30/2015] [Indexed: 12/29/2022]
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120
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Postow MA, Manuel M, Wong P, Yuan J, Dong Z, Liu C, Perez S, Tanneau I, Noel M, Courtier A, Pasqual N, Wolchok JD. Peripheral T cell receptor diversity is associated with clinical outcomes following ipilimumab treatment in metastatic melanoma. J Immunother Cancer 2015; 3:23. [PMID: 26085931 PMCID: PMC4469400 DOI: 10.1186/s40425-015-0070-4] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/08/2015] [Indexed: 11/14/2022] Open
Abstract
Background Ipilimumab improves overall survival in a subset of patients with metastatic melanoma. Peripheral blood T cell receptor (TCR) repertoire diversity has been associated with favorable outcomes in patients with cancer, but its relevance as a biomarker for ipilimumab outcomes remains unknown. Findings In this pilot study, we analyzed the pre-treatment peripheral blood TCR repertoire in 12 patients with metastatic melanoma who received ipilimumab at 3 mg/kg (clinical benefit, n = 4; no clinical benefit, n = 8). TCR diversity was evaluated using a polymerase chain reaction assay which measures TCR combinatorial diversity between V and J genes from genomic DNA. TCR repertoire diversity was studied through richness (observed V-J rearrangements) and evenness (similarity between the frequencies of specific V-J rearrangements). The Wilcoxon rank sum test was used to compare patients with clinical benefit and those without. Association with benefit in a dichotomized analysis was assessed through a Fisher’s exact test. Overall survival was studied through log-rank analysis. There was a significant difference in richness (p = 0.033) and evenness (p = 0.028) between patients with and without clinical benefit. Dichotomized analysis showed that none of the patients with low richness (n = 0/5, p = 0.081) nor low evenness (n = 0/7, p = 0.01) achieved clinical benefit. There were no significant differences in overall survival. Conclusions In this small group of patients, baseline TCR diversity in the peripheral blood was associated with clinical outcomes. Further investigation is ongoing in larger cohorts of patients to explore these preliminary findings and determine whether TCR diversity can be used as a predictive biomarker in cancer immunotherapy. Electronic supplementary material The online version of this article (doi:10.1186/s40425-015-0070-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael A Postow
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA ; Weill Cornell Medical College, 525 E 68th Street, New York, 10065 USA ; Assistant Attending Physician, Melanoma and Immunotherapeutics Oncology Service, Memorial Sloan Kettering Cancer Center, 1300 East 66th Street, New York, NY 10065 USA
| | | | - Phillip Wong
- Immune Monitoring Core Facility, Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York City, NY 10065 USA
| | - Jianda Yuan
- Immune Monitoring Core Facility, Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York City, NY 10065 USA
| | - Zhiwan Dong
- Immune Monitoring Core Facility, Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York City, NY 10065 USA
| | - Cailian Liu
- Immune Monitoring Core Facility, Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York City, NY 10065 USA
| | | | | | | | | | | | - Jedd D Wolchok
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA ; Weill Cornell Medical College, 525 E 68th Street, New York, 10065 USA
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121
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Yew PY, Alachkar H, Yamaguchi R, Kiyotani K, Fang H, Yap KL, Liu HT, Wickrema A, Artz A, van Besien K, Imoto S, Miyano S, Bishop MR, Stock W, Nakamura Y. Quantitative characterization of T-cell repertoire in allogeneic hematopoietic stem cell transplant recipients. Bone Marrow Transplant 2015; 50:1227-34. [PMID: 26052909 PMCID: PMC4559843 DOI: 10.1038/bmt.2015.133] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 04/26/2015] [Accepted: 04/28/2015] [Indexed: 12/25/2022]
Abstract
Allogeneic hematopoietic stem cell transplantation (HSCT) is one of curative treatment options for patients with hematologic malignancies. Although GVHD mediated by the donor's T lymphocytes remains the most challenging toxicity of allo-HSCT, graft-versus-leukemia (GVL) effect targeting leukemic cells, has an important role in affecting the overall outcome of patients with AML. Here we comprehensively characterized the TCR repertoire in patients who underwent matched donor or haplo-cord HSCT using next-generation sequencing approach. Our study defines the functional kinetics of each TCRA and TCRB clone, and changes in T-cell diversity (with identification of CDR3 sequences) and the extent of clonal expansion of certain T-cells. Using this approach, our study demonstrates that higher percentage of cord-blood cells at 30 days after transplant was correlated with higher diversity of TCR repertoire, implicating the role of cord-chimerism in enhancing immune recovery. Importantly, we found that GVHD and relapse, exclusive of each other, were correlated with lower TCR repertoire diversity and expansion of certain T-cell clones. Our results highlight novel insights into the balance between GVHD and GVL effect, suggesting that higher diversity early after transplant possibly implies lower risks of both GVHD and relapse following the HSCT transplantation.
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Affiliation(s)
- P Y Yew
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - H Alachkar
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - R Yamaguchi
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - K Kiyotani
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - H Fang
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - K L Yap
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - H T Liu
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - A Wickrema
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - A Artz
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - K van Besien
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - S Imoto
- Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - S Miyano
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - M R Bishop
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - W Stock
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Y Nakamura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA.,Department of Surgery, The University of Chicago, Chicago, IL, USA
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122
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Integration of humoral and cellular HLA-specific immune responses in cord blood allograft rejection. Bone Marrow Transplant 2015; 50:1187-94. [PMID: 26030050 DOI: 10.1038/bmt.2015.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 04/03/2015] [Accepted: 04/08/2015] [Indexed: 11/08/2022]
Abstract
In allo-stem cell transplantation (SCT), it is unclear whether donor-specific anti-HLA Abs (DSAs) can actually mediate graft rejection or if they are simply surrogate markers for the cellular immunity that causes graft rejection. Here, we first analyzed a case of cord blood allograft rejection in which DSA and cytotoxic T lymphocyte (CTL) specific for donor HLA-B*54:01 were detected at the time of graft rejection. Both the DSA and CTL inhibited colony formation by unrelated bone marrow mononuclear cells sharing HLA-B*54:01, suggesting that the humoral and cellular immune responses were involved in the graft rejection. Interestingly, the DSA and CTL were also detected in cryopreserved pre-transplant patient blood, raising a hypothesis that the presence of anti-HLA Abs could be an indicator for corresponding HLA-specific T cells. We then evaluated the existence of HLA-specific CD8(+) T cells in other patient blood specimens having anti-HLA class I Abs. Interferon-γ enzyme-linked immunospot assays clearly confirmed the existence of corresponding HLA-specific T-cell precursors in three of seven patients with anti-HLA Abs. In conclusion, our data demonstrate that integrated humoral and cellular immunity recognizing the same alloantigen of the donor can mediate graft rejection in DSA-positive patients undergoing HLA-mismatched allo-SCT. Further studies generalizing our observation are warranted.
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123
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Comprehensive analysis of the T-cell receptor beta chain gene in rhesus monkey by high throughput sequencing. Sci Rep 2015; 5:10092. [PMID: 25961410 PMCID: PMC4426732 DOI: 10.1038/srep10092] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/30/2015] [Indexed: 01/24/2023] Open
Abstract
Profiling immune repertoires by high throughput sequencing enhances our understanding of immune system complexity and immune-related diseases in humans. Previously, cloning and Sanger sequencing identified limited numbers of T cell receptor (TCR) nucleotide sequences in rhesus monkeys, thus their full immune repertoire is unknown. We applied multiplex PCR and Illumina high throughput sequencing to study the TCRβ of rhesus monkeys. We identified 1.26 million TCRβ sequences corresponding to 643,570 unique TCRβ sequences and 270,557 unique complementarity-determining region 3 (CDR3) gene sequences. Precise measurements of CDR3 length distribution, CDR3 amino acid distribution, length distribution of N nucleotide of junctional region, and TCRV and TCRJ gene usage preferences were performed. A comprehensive profile of rhesus monkey immune repertoire might aid human infectious disease studies using rhesus monkeys.
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124
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van der Geest KSM, Abdulahad WH, Horst G, Lorencetti PG, Bijzet J, Arends S, van der Heiden M, Buisman AM, Kroesen BJ, Brouwer E, Boots AMH. Quantifying Distribution of Flow Cytometric TCR-Vβ Usage with Economic Statistics. PLoS One 2015; 10:e0125373. [PMID: 25923356 PMCID: PMC4414620 DOI: 10.1371/journal.pone.0125373] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/23/2015] [Indexed: 11/19/2022] Open
Abstract
Measuring changes of the T cell receptor (TCR) repertoire is important to many fields of medicine. Flow cytometry is a popular technique to study the TCR repertoire, as it quickly provides insight into the TCR-Vβ usage among well-defined populations of T cells. However, the interpretation of the flow cytometric data remains difficult, and subtle TCR repertoire changes may go undetected. Here, we introduce a novel means for analyzing the flow cytometric data on TCR-Vβ usage. By applying economic statistics, we calculated the Gini-TCR skewing index from the flow cytometric TCR-Vβ analysis. The Gini-TCR skewing index, which is a direct measure of TCR-Vβ distribution among T cells, allowed us to track subtle changes of the TCR repertoire among distinct populations of T cells. Application of the Gini-TCR skewing index to the flow cytometric TCR-Vβ analysis will greatly help to gain better understanding of the TCR repertoire in health and disease.
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Affiliation(s)
- Kornelis S. M. van der Geest
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- * E-mail:
| | - Wayel H. Abdulahad
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerda Horst
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pedro G. Lorencetti
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Johan Bijzet
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Suzanne Arends
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marieke van der Heiden
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Center for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Anne-Marie Buisman
- Center for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Bart-Jan Kroesen
- Department Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Elisabeth Brouwer
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Annemieke M. H. Boots
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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125
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CMV reactivation drives posttransplant T-cell reconstitution and results in defects in the underlying TCRβ repertoire. Blood 2015; 125:3835-50. [PMID: 25852054 DOI: 10.1182/blood-2015-03-631853] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/26/2015] [Indexed: 12/21/2022] Open
Abstract
Although cytomegalovirus (CMV) reactivation has long been implicated in posttransplant immune dysfunction, the molecular mechanisms that drive this phenomenon remain undetermined. To address this, we combined multiparameter flow cytometric analysis and T-cell subpopulation sorting with high-throughput sequencing of the T-cell repertoire, to produce a thorough evaluation of the impact of CMV reactivation on T-cell reconstitution after unrelated-donor hematopoietic stem cell transplant. We observed that CMV reactivation drove a >50-fold specific expansion of Granzyme B(high)/CD28(low)/CD57(high)/CD8(+) effector memory T cells (Tem) and resulted in a linked contraction of all naive T cells, including CD31(+)/CD4(+) putative thymic emigrants. T-cell receptor β (TCRβ) deep sequencing revealed a striking contraction of CD8(+) Tem diversity due to CMV-specific clonal expansions in reactivating patients. In addition to querying the topography of the expanding CMV-specific T-cell clones, deep sequencing allowed us, for the first time, to exhaustively evaluate the underlying TCR repertoire. Our results reveal new evidence for significant defects in the underlying CD8 Tem TCR repertoire in patients who reactivate CMV, providing the first molecular evidence that, in addition to driving expansion of virus-specific cells, CMV reactivation has a detrimental impact on the integrity and heterogeneity of the rest of the T-cell repertoire. This trial was registered at www.clinicaltrials.gov as #NCT01012492.
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126
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Hobbs GS, Perales MA. Effects of T-Cell Depletion on Allogeneic Hematopoietic Stem Cell Transplantation Outcomes in AML Patients. J Clin Med 2015; 4:488-503. [PMID: 26239251 PMCID: PMC4470141 DOI: 10.3390/jcm4030488] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 01/19/2015] [Accepted: 01/19/2015] [Indexed: 01/25/2023] Open
Abstract
Graft versus host disease (GVHD) remains one of the leading causes of morbidity and mortality associated with conventional allogeneic hematopoietic stem cell transplantation (HCT). The use of T-cell depletion significantly reduces this complication. Recent prospective and retrospective data suggest that, in patients with AML in first complete remission, CD34+ selected grafts afford overall and relapse-free survival comparable to those observed in recipients of conventional grafts, while significantly decreasing GVHD. In addition, CD34+ selected grafts allow older patients, and those with medical comorbidities or with only HLA-mismatched donors to successfully undergo transplantation. Prospective data are needed to further define which groups of patients with AML are most likely to benefit from CD34+ selected grafts. Here we review the history of T-cell depletion in AML, and techniques used. We then summarize the contemporary literature using CD34+ selection in recipients of matched or partially mismatched donors (7/8 or 8/8 HLA-matched), and provide a summary of the risks and benefits of using T-cell depletion.
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Affiliation(s)
- Gabriela Soriano Hobbs
- Adult Leukemia Service, Massachusetts General Hospital, Boston, MA 02114, USA.
- Harvard Medical School, Boston, MA 02115, USA.
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
- Weill Cornell Medical College, New York, NY 10065, USA.
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127
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Hunsucker SA, McGary CS, Vincent BG, Enyenihi AA, Waugh JP, McKinnon KP, Bixby LM, Ropp PA, Coghill JM, Wood WA, Gabriel DA, Sarantopoulos S, Shea TC, Serody JS, Alatrash G, Rodriguez-Cruz T, Lizée G, Buntzman AS, Frelinger JA, Glish GL, Armistead PM. Peptide/MHC tetramer-based sorting of CD8⁺ T cells to a leukemia antigen yields clonotypes drawn nonspecifically from an underlying restricted repertoire. Cancer Immunol Res 2015; 3:228-35. [PMID: 25576336 PMCID: PMC4351150 DOI: 10.1158/2326-6066.cir-14-0001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Testing of T cell-based cancer therapeutics often involves measuring cancer antigen-specific T-cell populations with the assumption that they arise from in vivo clonal expansion. This analysis, using peptide/MHC tetramers, is often ambiguous. From a leukemia cell line, we identified a CDK4-derived peptide epitope, UNC-CDK4-1 (ALTPVVVTL), that bound HLA-A*02:01 with high affinity and could induce CD8⁺ T-cell responses in vitro. We identified UNC-CDK4-1/HLA-A*02:01 tetramer⁺ populations in 3 of 6 patients with acute myeloid leukemia who had undergone allogeneic stem cell transplantation. Using tetramer-based, single-cell sorting and T-cell receptor β (TCRβ) sequencing, we identified recurrent UNC-CDK4-1 tetramer-associated TCRβ clonotypes in a patient with a UNC-CDK4-1 tetramer⁺ population, suggesting in vivo T-cell expansion to UNC-CDK4-1. In parallel, we measured the patient's TCRβ repertoire and found it to be highly restricted/oligoclonal. The UNC-CDK4-1 tetramer-associated TCRβ clonotypes represented >17% of the entire TCRβ repertoire-far in excess of the UNC-CDK4-1 tetramer⁺ frequency-indicating that the recurrent TCRβ clonotypes identified from UNC-CDK-4-1 tetramer⁺ cells were likely a consequence of the extremely constrained T-cell repertoire in the patient and not in vivo UNC-CDK4-1-driven clonal T-cell expansion. Mapping recurrent TCRβ clonotype sequences onto TCRβ repertoires can help confirm or refute antigen-specific T-cell expansion in vivo.
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Affiliation(s)
| | - Colleen S McGary
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | | | - Atim A Enyenihi
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Jennifer P Waugh
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Karen P McKinnon
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | - Lisa M Bixby
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | - Patricia A Ropp
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | - James M Coghill
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - William A Wood
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Don A Gabriel
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Stefanie Sarantopoulos
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Thomas C Shea
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Gheath Alatrash
- Section of Transplantation Immunology, Department of Stem Cell Transplant and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tania Rodriguez-Cruz
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory Lizée
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Adam S Buntzman
- Department of Immunobiology, University of Arizona, Tucson, Arizona
| | | | - Gary L Glish
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Paul M Armistead
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Medicine, University of North Carolina, Chapel Hill, North Carolina.
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128
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Eugster A, Lindner A, Catani M, Heninger AK, Dahl A, Klemroth S, Kühn D, Dietz S, Bickle M, Ziegler AG, Bonifacio E. High diversity in the TCR repertoire of GAD65 autoantigen-specific human CD4+ T cells. THE JOURNAL OF IMMUNOLOGY 2015; 194:2531-8. [PMID: 25681349 DOI: 10.4049/jimmunol.1403031] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Autoreactive CD4(+) T cells are an essential feature of type 1 diabetes mellitus. We applied single-cell TCR α- and β-chain sequencing to peripheral blood GAD65-specific CD4(+) T cells, and TCR α-chain next-generation sequencing to bulk memory CD4(+) T cells to provide insight into TCR diversity in autoimmune diabetes mellitus. TCRs obtained for 1650 GAD65-specific CD4(+) T cells isolated from GAD65 proliferation assays and/or GAD65 557I tetramer staining in 6 patients and 10 islet autoantibody-positive children showed large diversity with 1003 different TCRs identified. TRAV and TRBV gene usage was broad, and the TRBV5.1 gene was most prominent within the GAD65 557I tetramer(+) cells. Limited overlap (<5%) was observed between TCRs of GAD65-proliferating and GAD65 557I tetramer(+) CD4(+) T cells. Few TCRs were repeatedly found in GAD65-specific cells at different time points from individual patients, and none was seen in more than one subject. However, single chains were often shared between patients and used in combination with different second chains. Next-generation sequencing revealed a wide frequency range (<0.00001-1.62%) of TCR α-chains corresponding to GAD65-specific T cells. The findings support minor selection of genes and TCRs for GAD65-specific T cells, but fail to provide strong support for TCR-targeted therapies.
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Affiliation(s)
- Anne Eugster
- German Research Foundation Center for Regenerative Therapies Dresden, Dresden University of Technology, 01307 Dresden, Germany;
| | - Annett Lindner
- German Research Foundation Center for Regenerative Therapies Dresden, Dresden University of Technology, 01307 Dresden, Germany
| | - Mara Catani
- German Research Foundation Center for Regenerative Therapies Dresden, Dresden University of Technology, 01307 Dresden, Germany
| | - Anne-Kristin Heninger
- German Research Foundation Center for Regenerative Therapies Dresden, Dresden University of Technology, 01307 Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing Group, Collaborative Research Center 655/BIOTEC, Biotechnology Center, Dresden University of Technology, 01307 Dresden, Germany
| | - Sylvia Klemroth
- Deep Sequencing Group, Collaborative Research Center 655/BIOTEC, Biotechnology Center, Dresden University of Technology, 01307 Dresden, Germany
| | - Denise Kühn
- German Research Foundation Center for Regenerative Therapies Dresden, Dresden University of Technology, 01307 Dresden, Germany
| | - Sevina Dietz
- German Research Foundation Center for Regenerative Therapies Dresden, Dresden University of Technology, 01307 Dresden, Germany
| | - Marc Bickle
- Technology Development Studio, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anette-Gabrielle Ziegler
- Institute of Diabetes Mellitus Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Forschergruppe Diabetes Mellitus, Klinikum Rechts der Isar, Technische Universität München, 81664 Munich, Germany
| | - Ezio Bonifacio
- German Research Foundation Center for Regenerative Therapies Dresden, Dresden University of Technology, 01307 Dresden, Germany; Paul Langerhans Institute Dresden, German Center for Diabetes Mellitus Research, Dresden University of Technology, 01307 Dresden, Germany; and Institute for Diabetes Mellitus and Obesity, Helmholtz Zentrum München, 85764 Neuherberg, Germany Germany
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129
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Zhang Q, Jia Q, Deng T, Song B, Li L. Heterogeneous expansion of CD4+ tumor-infiltrating T-lymphocytes in clear cell renal cell carcinomas. Biochem Biophys Res Commun 2015; 458:70-6. [PMID: 25637538 DOI: 10.1016/j.bbrc.2015.01.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 01/16/2015] [Indexed: 11/18/2022]
Abstract
Aberrant expression of tumor-associated antigens (TAAs) mediates the effective mounting of adaptive immunity in human solid tumors. The foundations of this tumor-host interaction strongly depend on specific recognition via TAA-cognate-receptors in T-cell repertoires. Previous studies focused on the phenotypic and functional properties of CD4+/CD8+ tumor-infiltrating T-lymphocytes (TILs), but the detailed composition of T-cell repertoires of these fundamental subsets remains largely unknown. This study recruited 10 clear cell renal cell carcinoma (ccRCC) patients and obtained samples from various tissues, including tumors, adjacent healthy renal tissue and peripheral blood. We utilized deep sequencing of T-cell receptor beta chains (TCRB), which serve as a unique identifier for each T clonotype, to characterize the CD4+/CD8+ TIL repertoire in ccRCC patients, assess the diversity and clonality of infiltrated T-cells in distinct tissues from patients and depict the clonal expansion events that occur in anti-tumor immune responses. We found that the CD4+ TIL repertoire exhibited signatures of heterogeneous T-cell expansion, which were characterized by divergent TRBV/J usage and an enrichment of expanded dominant clones. Taken together, our findings provide additional evidence of CD4+ T-cell-mediated anti-tumor immunity. The identification of the underlying molecular mechanisms of this process may provide novel avenues for targeted immunotherapeutic interventions.
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MESH Headings
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/pathology
- CD4-Positive T-Lymphocytes/physiology
- CD8-Positive T-Lymphocytes/pathology
- Carcinoma, Renal Cell/immunology
- Carcinoma, Renal Cell/pathology
- Humans
- Kidney Neoplasms/immunology
- Kidney Neoplasms/pathology
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/pathology
- Lymphocytes, Tumor-Infiltrating/physiology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Tumor Microenvironment/genetics
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Affiliation(s)
- Qian Zhang
- Department of Urology, XinQiao Hospital, Third Military Medical University, Chongqing, China; Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Qingzhu Jia
- Biomedical Analysis Center, Third Military Medical University, Chongqing, China
| | - Tianxing Deng
- Department of Urology, XinQiao Hospital, Third Military Medical University, Chongqing, China
| | - Bo Song
- Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing, China.
| | - Longkun Li
- Department of Urology, XinQiao Hospital, Third Military Medical University, Chongqing, China.
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130
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131
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Fang H, Yamaguchi R, Liu X, Daigo Y, Yew PY, Tanikawa C, Matsuda K, Imoto S, Miyano S, Nakamura Y. Quantitative T cell repertoire analysis by deep cDNA sequencing of T cell receptor α and β chains using next-generation sequencing (NGS). Oncoimmunology 2015; 3:e968467. [PMID: 25964866 DOI: 10.4161/21624011.2014.968467] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/19/2014] [Indexed: 11/19/2022] Open
Abstract
Immune responses play a critical role in various disease conditions including cancer and autoimmune diseases. However, to date, there has not been a rapid, sensitive, comprehensive, and quantitative analysis method to examine T-cell or B-cell immune responses. Here, we report a new approach to characterize T cell receptor (TCR) repertoire by sequencing millions of cDNA of TCR α and β chains in combination with a newly-developed algorithm. Using samples from lung cancer patients treated with cancer peptide vaccines as a model, we demonstrate that detailed information of the V-(D)-J combination along with complementary determining region 3 (CDR3) sequences can be determined. We identified extensive abnormal splicing of TCR transcripts in lung cancer samples, indicating the dysfunctional splicing machinery in T lymphocytes by prior chemotherapy. In addition, we found three potentially novel TCR exons that have not been described previously in the reference genome. This newly developed TCR NGS platform can be applied to better understand immune responses in many disease areas including immune disorders, allergies, and organ transplantations.
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Key Words
- APC, antigen presenting cell
- CDCA1, cell division cycle-associated protein 1
- CDR3, complementary determining region 3
- CTL, cytotoxic T lymphocytes
- CTLA-4, cytotoxic T-lymphocyte antigen-4
- ELISPOT, enzyme-linked immunospot
- FDA, Food and Drug Administration
- IFA, incomplete Freund's adjuvant
- IFNγ, γ-interferon
- IRB, institutional review board
- KIF20A, kinesin family member 20A
- LY6K, lymphocyte antigen 6 complex locus K
- MHC, major histocompatibility complex
- NGS, Next Generation Sequencing
- NSCLC, non-small cell lung cancer
- ORF, Open reading frames
- OS, overall survival
- PBL, peripheral blood lymphocyte
- PGM, Personal Genome Machine
- RACE, rapid amplification of cDNA end
- T cell repertoire
- TCR, T cell receptor
- cancer peptide vaccines
- complementary determining region 3
- immune responses
- next-generation sequencing
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Affiliation(s)
- Hua Fang
- Committee on Clinical Pharmacology and Pharmacogenomics; The University of Chicago ; Chicago, IL USA ; Section of Hematology/Oncology; Department of Medicine; The University of Chicago ; Chicago, IL USA
| | - Rui Yamaguchi
- Human Genome Center; Institute of Medical Science; The University of Tokyo ; Tokyo, Japan
| | - Xiao Liu
- Section of Hematology/Oncology; Department of Medicine; The University of Chicago ; Chicago, IL USA
| | - Yataro Daigo
- Department of Medical Oncology; Shiga University of Medical Science Hospital ; Shiga, Japan
| | - Poh Yin Yew
- Section of Hematology/Oncology; Department of Medicine; The University of Chicago ; Chicago, IL USA
| | - Chizu Tanikawa
- Human Genome Center; Institute of Medical Science; The University of Tokyo ; Tokyo, Japan
| | - Koichi Matsuda
- Human Genome Center; Institute of Medical Science; The University of Tokyo ; Tokyo, Japan
| | - Seiya Imoto
- Human Genome Center; Institute of Medical Science; The University of Tokyo ; Tokyo, Japan
| | - Satoru Miyano
- Human Genome Center; Institute of Medical Science; The University of Tokyo ; Tokyo, Japan
| | - Yusuke Nakamura
- Committee on Clinical Pharmacology and Pharmacogenomics; The University of Chicago ; Chicago, IL USA ; Section of Hematology/Oncology; Department of Medicine; The University of Chicago ; Chicago, IL USA ; Department of Surgery; The University of Chicago ; Chicago, IL USA ; Center for Personalized Therapeutics; The University of Chicago ; Chicago, IL, USA
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132
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van den Brink MRM, Velardi E, Perales MA. Immune reconstitution following stem cell transplantation. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2015; 2015:215-219. [PMID: 26637724 DOI: 10.1182/asheducation-2015.1.215] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Marcel R M van den Brink
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY; Weill Cornell Medical College, New York, NY; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY; and
| | - Enrico Velardi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY; and Division of Pharmacology, Department of Medicine, University of Perugia, Perugia, Italy
| | - Miguel-Angel Perales
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY; Weill Cornell Medical College, New York, NY
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133
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Calis JJA, Rosenberg BR. Characterizing immune repertoires by high throughput sequencing: strategies and applications. Trends Immunol 2014; 35:581-590. [PMID: 25306219 PMCID: PMC4390416 DOI: 10.1016/j.it.2014.09.004] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/05/2014] [Accepted: 09/09/2014] [Indexed: 01/09/2023]
Abstract
As the key cellular effectors of adaptive immunity, T and B lymphocytes utilize specialized receptors to recognize, respond to, and neutralize a diverse array of extrinsic threats. These receptors (immunoglobulins in B lymphocytes, T cell receptors in T lymphocytes) are incredibly variable, the products of specialized genetic diversification mechanisms that generate complex lymphocyte repertoires with extensive collections of antigen specificities. Recent advances in high throughput sequencing (HTS) technologies have transformed our ability to examine antigen receptor repertoires at single nucleotide, and more recently, single cell, resolution. Here we review current approaches to examining antigen receptor repertoires by HTS, and discuss inherent biological and technical challenges. We further describe emerging applications of this powerful methodology for exploring the adaptive immune system.
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Affiliation(s)
| | - Brad R Rosenberg
- The Rockefeller University, New York, NY, USA; John C. Whitehead Presidential Fellows Program, The Rockefeller University, New York, NY, USA.
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134
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Luo W, He WT, Wen Q, Chen S, Wu J, Chen XP, Ma L. Changes of TCR repertoire diversity in colorectal cancer after Erbitux (cetuximab) in combination with chemotherapy. Am J Cancer Res 2014; 4:924-933. [PMID: 25520880 PMCID: PMC4266724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 09/23/2014] [Indexed: 06/04/2023] Open
Abstract
We have previous found a positive correlation between post-therapy TCR repertoire normalization and remission of colorectal cancer (CRC) patients following fluorouracil, leucovorin, and irinotecan (FOLFIRI) plus bevacizumab or Rh-endostatin therapy. To further define the TCR repertoire diversity changes following treatment in CRC patients, and confirm its potential prognostic value, the present study extended the sample size of follow-up and used an alternative therapy regime to investigate changes of TCR repertoires following Erbitux plus FOLFIRI therapy. Inclusion and exclusion criteria have been established to screen out 26 patients to receive Erbitux plus FOLFIRI therapy. Efficacy and toxicity assessment have been made for them after 3 months' treatment as well as the TCR repertoire diversity has been determined. A CDR3 complex scoring system was used to quantify the diversity of TCR repertoire. The results showing that the diversity of CD4(+) T cells in PR group was significantly higher than that of SD and PD groups, and the difference was enlargement after treatment. The diversity of CD8(+) T cells in PR group has no difference before and after treatment, but significant decrease in SD and PD group after treatment. In conclusion, analysis the diversity of T cell repertoire has an important prognosis value for CRC patients.
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Affiliation(s)
- Wei Luo
- Institute of Molecular Immunology, School of Biotechnology, Southern Medical UniversityGuangzhou 510515, China
| | - Wen-Ting He
- Institute of Molecular Immunology, School of Biotechnology, Southern Medical UniversityGuangzhou 510515, China
| | - Qian Wen
- Institute of Molecular Immunology, School of Biotechnology, Southern Medical UniversityGuangzhou 510515, China
| | - Shu Chen
- Cancer Research Institute, Foshan First People’s HospitalFoshan, Guangdong 528000, China
| | - Jing Wu
- Cancer Research Institute, Foshan First People’s HospitalFoshan, Guangdong 528000, China
| | - Xiang-Ping Chen
- Cancer Research Institute, Foshan First People’s HospitalFoshan, Guangdong 528000, China
| | - Li Ma
- Institute of Molecular Immunology, School of Biotechnology, Southern Medical UniversityGuangzhou 510515, China
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135
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Feliu J, Clay J, Raj K, Barber L, Devlia V, Shaw B, Pagliuca A, Mufti G. Transplant-acquired food allergy (TAFA) following cord blood stem cell transplantation in two adult patients with haematological malignancies. Br J Haematol 2014; 167:426-8. [PMID: 24962133 DOI: 10.1111/bjh.12992] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jesus Feliu
- Haematology Department, King's College Hospital, London, UK; Department of Haematological Medicine, King's College London, Rayne Institute, London, UK.
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136
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Dahi PB, Perales MA, Devlin SM, Olson A, Lubin M, Gonzales AM, Scaradavou A, Kernan NA, O'Reilly RJ, Giralt S, Jakubowski A, Koehne G, Papadopoulos EB, Ponce DM, Sauter C, Papanicolaou G, Barker JN. Incidence, nature and mortality of cytomegalovirus infection after double-unit cord blood transplant. Leuk Lymphoma 2014; 56:1799-805. [PMID: 25224458 DOI: 10.3109/10428194.2014.963079] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cord blood transplant (CBT) extends allograft access but is associated with a significant risk for cytomegalovirus (CMV) infection. We analyzed CMV infection in 157 CBT recipients transplanted for hematological malignancies. As compared with antigenemia testing, routine polymerase chain reaction (PCR) monitoring was associated with increased and earlier CMV infection detection (1-year incidence if seropositive 67% [median onset 41 days] vs. 100% at an earlier 33-day median [p < 0.001]) and decreased gastrointestinal disease. One-year CMV-related transplant-related mortality was 11% in CMV+ patients with 7/9 deaths associated with initial infection. Disease-free survival was lower in seropositive compared with seronegative patients (1-year: 55% vs. 73%, p = 0.02). However, in multivariate analysis adjusting for age, treatment failure risk in CMV+ patients was not significant (hazard ratio 1.52, p = 0.11). CMV infection is a major challenge in seropositive CBT recipients. While PCR surveillance permits early detection of viremia, new prophylaxis and therapeutic strategies are needed.
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Affiliation(s)
- Parastoo B Dahi
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center , New York, NY , USA
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137
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The role of the thymus in T-cell immune reconstitution after umbilical cord blood transplantation. Blood 2014; 124:3201-11. [PMID: 25287708 DOI: 10.1182/blood-2014-07-589176] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Umbilical cord blood (UCB) is an alternative source of hematopoietic stem cells for patients without HLA-matched adult donors. UCB contains a low number of nucleated cells and mostly naive T cells, resulting in prolonged time to engraftment and lack of transferred T-cell memory. Although the first phase of T-cell reconstitution after UCB transplantation (UCBT) depends on peripheral expansion of transferred T cells, permanent T-cell reconstitution is mediated via a central mechanism, which depends on de novo production of naive T lymphocytes by the recipient's thymus from donor-derived lymphoid-myeloid progenitors (LMPs). Thymopoiesis can be assessed by quantification of recent thymic emigrants, T-cell receptor excision circle levels, and T-cell receptor repertoire diversity. These assays are valuable tools for monitoring posttransplantation thymic recovery, but more importantly they have shown the significant prognostic value of thymic reconstitution for clinical outcomes after UCBT, including opportunistic infections, disease relapse, and overall survival. Strategies to improve thymic entry and differentiation of LMPs and to accelerate recovery of the thymic stromal microenvironment may improve thymic lymphopoiesis. Here, we discuss the mechanisms and clinical implications of thymic recovery and new approaches to improve reconstitution of the T-cell repertoire after UCBT.
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138
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Assessing T cell clonal size distribution: a non-parametric approach. PLoS One 2014; 9:e108658. [PMID: 25275470 PMCID: PMC4183510 DOI: 10.1371/journal.pone.0108658] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 08/25/2014] [Indexed: 11/24/2022] Open
Abstract
Clonal structure of the human peripheral T-cell repertoire is shaped by a number of homeostatic mechanisms, including antigen presentation, cytokine and cell regulation. Its accurate tuning leads to a remarkable ability to combat pathogens in all their variety, while systemic failures may lead to severe consequences like autoimmune diseases. Here we develop and make use of a non-parametric statistical approach to assess T cell clonal size distributions from recent next generation sequencing data. For 41 healthy individuals and a patient with ankylosing spondylitis, who undergone treatment, we invariably find power law scaling over several decades and for the first time calculate quantitatively meaningful values of decay exponent. It has proved to be much the same among healthy donors, significantly different for an autoimmune patient before the therapy, and converging towards a typical value afterwards. We discuss implications of the findings for theoretical understanding and mathematical modeling of adaptive immunity.
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139
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Linnemann C, Mezzadra R, Schumacher TNM. TCR repertoires of intratumoral T-cell subsets. Immunol Rev 2014; 257:72-82. [PMID: 24329790 DOI: 10.1111/imr.12140] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The infiltration of human tumors by T cells is a common phenomenon, and over the past decades, it has become increasingly clear that the nature of such intratumoral T-cell populations can predict disease course. Furthermore, intratumoral T cells have been utilized therapeutically in clinical studies of adoptive T-cell therapy. In this review, we describe how novel methods that are either based on T-cell receptor (TCR) sequencing or on cancer exome analysis allow the analysis of the tumor reactivity and antigen-specificity of the intratumoral TCR repertoire with unprecedented detail. Furthermore, we discuss studies that have started to utilize these techniques to probe the link between cancer exomes and the intratumoral TCR pool. Based on the observation that both the cancer epitope repertoire and intratumoral TCR repertoire appear highly individual, we outline strategies, such as 'autologous TCR gene therapy', that exploit the tumor-resident TCR repertoire for the development of personalized immunotherapy.
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Affiliation(s)
- Carsten Linnemann
- Division of Immunology, The Netherlands Cancer Institute (NKI-AVL), Amsterdam, the Netherlands
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140
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Image-guided intrathymic injection of multipotent stem cells supports lifelong T-cell immunity and facilitates targeted immunotherapy. Blood 2014; 123:2797-805. [PMID: 24652996 DOI: 10.1182/blood-2013-10-535401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
T-cell deficiency related to disease, medical treatment, or aging represents a major clinical challenge and is associated with significant morbidity and mortality in cancer and bone marrow transplantation recipients. This study describes several innovative and clinically relevant strategies to manipulate thymic function based on an interventional radiology technique for intrathymic injection of cells or drugs. We show that intrathymic injection of multipotent hematopoietic stem/progenitor cells into irradiated syngeneic or allogeneic young or aged recipients resulted in efficient and long-lasting generation of functional donor T cells. Persistence of intrathymic donor cells was associated with intrathymic presence of cells resembling long-term hematopoietic stem cells, suggesting a self-renewal capacity of the intrathymically injected cells. Furthermore, our approach enabled the induction of long-term antigen-specific T-cell-mediated antitumor immunity following intrathymic injection of progenitor cells harboring a transgenic T-cell receptor gene. The intrathymic injection of interleukin-7 prior to irradiation conferred radioprotection. In addition, thymopoiesis of aged mice improved with a single intrathymic administration of low-dose keratinocyte growth factor, an effect that was sustained even in the setting of radiation-induced injury. Taken together, we established a preclinical framework for the development of novel clinical protocols to establish lifelong antigen-specific T-cell immunity.
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141
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Niklas N, Pröll J, Weinberger J, Zopf A, Wiesinger K, Krismer K, Bettelheim P, Gabriel C. Qualifying high-throughput immune repertoire sequencing. Cell Immunol 2014; 288:31-8. [PMID: 24607567 DOI: 10.1016/j.cellimm.2014.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 11/06/2013] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
Abstract
Diversity of B and T cell receptors, achieved by gene recombination and somatic hypermutation, allows the immune system for recognition and targeted reaction against various threats. Next-generation sequencing for assessment of a cell's gene composition and variation makes deep analysis of one individual's immune spectrum feasible. An easy to apply but detailed analysis and visualization strategy is necessary to process all sequences generated. We performed sequencing utilizing the 454 system for CLL and control samples, utilized the IMGT database and applied the presented analysis tools. With the applied protocol, malignant clones are found and characterized, mutational status compared to germline identity is elaborated in detail showing that the CLL mutation status is not as monoclonal as generally thought. On the other hand, this strategy is not solely applicable to the 454 sequencing system but can easily be transferred to any other next-generation sequencing platform.
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Affiliation(s)
- Norbert Niklas
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Johannes Pröll
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Johannes Weinberger
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Agnes Zopf
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Karin Wiesinger
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Konstantin Krismer
- University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria.
| | - Peter Bettelheim
- Division of Hematology/Oncology, Elisabethinen Hospital Linz, Fadingerstraße 1, 4020 Linz, Austria.
| | - Christian Gabriel
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
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142
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Muraro PA, Robins H, Malhotra S, Howell M, Phippard D, Desmarais C, de Paula Alves Sousa A, Griffith LM, Lim N, Nash RA, Turka LA. T cell repertoire following autologous stem cell transplantation for multiple sclerosis. J Clin Invest 2014; 124:1168-72. [PMID: 24531550 DOI: 10.1172/jci71691] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 12/13/2013] [Indexed: 12/21/2022] Open
Abstract
Autologous hematopoietic stem cell transplantation (HSCT) is commonly employed for hematologic and non-hematologic malignancies. In clinical trials, HSCT has been evaluated for severe autoimmunity as a method to "reset" the immune system and produce a new, non-autoimmune repertoire. While the feasibility of eliminating the vast majority of mature T cells is well established, accurate and quantitative determination of the relationship of regenerated T cells to the baseline repertoire has been difficult to assess. Here, in a phase II study of HSCT for poor-prognosis multiple sclerosis, we used high-throughput deep TCRβ chain sequencing to assess millions of individual TCRs per patient sample. We found that HSCT has distinctive effects on CD4+ and CD8+ T cell repertoires. In CD4+ T cells, dominant TCR clones present before treatment were undetectable following reconstitution, and patients largely developed a new repertoire. In contrast, dominant CD8+ clones were not effectively removed, and the reconstituted CD8+ T cell repertoire was created by clonal expansion of cells present before treatment. Importantly, patients who failed to respond to treatment had less diversity in their T cell repertoire early during the reconstitution process. These results demonstrate that TCR characterization during immunomodulatory treatment is both feasible and informative, and may enable monitoring of pathogenic or protective T cell clones following HSCT and cellular therapies.
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143
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Weng WK, Armstrong R, Arai S, Desmarais C, Hoppe R, Kim YH. Minimal Residual Disease Monitoring with High-Throughput Sequencing of T Cell Receptors in Cutaneous T Cell Lymphoma. Sci Transl Med 2013; 5:214ra171. [DOI: 10.1126/scitranslmed.3007420] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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144
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Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, Mora T, Thomas-Vaslin V, Walczak AM, Boudinot P. The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis. Front Immunol 2013; 4:413. [PMID: 24348479 PMCID: PMC3841818 DOI: 10.3389/fimmu.2013.00413] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/12/2013] [Indexed: 01/09/2023] Open
Abstract
T and B cell repertoires are collections of lymphocytes, each characterized by its antigen-specific receptor. We review here classical technologies and analysis strategies developed to assess immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe recent advances in the field. First, we describe the broad range of available methodological tools developed in the past decades, each of which answering different questions and showing complementarity for progressive identification of the level of repertoire alterations: global overview of the diversity by flow cytometry, IG repertoire descriptions at the protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies, and related molecular quantification or dynamics of T/B cell differentiation. Additionally, we introduce the recent technological advances in molecular biology tools allowing deeper analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence analysis, V allele identification with a quantitative dimension, therefore requiring high-throughput analysis tools development. In this line, we discuss the recent efforts made for nomenclature standardization and ontology development. We then present the variety of available statistical analysis and modeling approaches developed with regards to the various levels of diversity analysis, and reveal the increasing sophistication of those modeling approaches. To conclude, we provide some examples of recent mathematical modeling strategies and perspectives that illustrate the active rise of a "next-generation" of repertoire analysis.
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Affiliation(s)
- Adrien Six
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Maria Encarnita Mariotti-Ferrandiz
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Wahiba Chaara
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Susana Magadan
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
| | - Hang-Phuong Pham
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Institut de Génétique Humaine, UPR CNRS 1142, Université Montpellier 2 , Montpellier , France
| | - Thierry Mora
- Laboratoire de Physique Statistique, UMR8550, CNRS and Ecole Normale Supérieure , Paris , France
| | - Véronique Thomas-Vaslin
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, UMR8549, CNRS and Ecole Normale Supérieure , Paris , France
| | - Pierre Boudinot
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
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145
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Making the genomic leap in HCT: application of second-generation sequencing to clinical advances in hematopoietic cell transplantation. Eur J Hum Genet 2013; 22:715-23. [PMID: 24253860 DOI: 10.1038/ejhg.2013.247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 09/20/2013] [Accepted: 09/27/2013] [Indexed: 12/30/2022] Open
Abstract
Recent developments in second-generation sequencing (SGS) technologies provide an avenue for achieving rapid and accurate high-throughput analysis of human and microbial genomic diversity. SGS technologies have the potential to transform existing medical management of complex and life-threatening medical conditions by enabling clinicians to develop disease-targeted clinical care plans for each patient. In this review, we outline how innovative SGS-based approaches can improve the care of recipients of allogeneic hematopoietic cell transplantation (HCT), a life-saving procedure that carries a 1-year mortality risk of over 30%. We specifically evaluate foreseeable applications of SGS-based technology in facilitating rapid, phase-sensitive human leukocyte antigen (HLA) typing, assessment of non-HLA genomic compatibility, identifying patients at high risk for adverse drug reactions, and post-HCT monitoring for engraftment, minimal residual disease and infection. We conclude that innovative SGS approaches have the capacity to revolutionize the HCT recipient risk assessment process, support non-invasive clinical monitoring and improve patient outcomes, thereby setting the stage for a new era of genomically informed patient-centered medicine.
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146
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Woodsworth DJ, Castellarin M, Holt RA. Sequence analysis of T-cell repertoires in health and disease. Genome Med 2013; 5:98. [PMID: 24172704 PMCID: PMC3979016 DOI: 10.1186/gm502] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
T-cell antigen receptor (TCR) variability enables the cellular immune system to discriminate between self and non-self. High-throughput TCR sequencing (TCR-seq) involves the use of next generation sequencing platforms to generate large numbers of short DNA sequences covering key regions of the TCR coding sequence, which enables quantification of T-cell diversity at unprecedented resolution. TCR-seq studies have provided new insights into the healthy human T-cell repertoire, such as revised estimates of repertoire size and the understanding that TCR specificities are shared among individuals more frequently than previously anticipated. In the context of disease, TCR-seq has been instrumental in characterizing the recovery of the immune repertoire after hematopoietic stem cell transplantation, and the method has been used to develop biomarkers and diagnostics for various infectious and neoplastic diseases. However, T-cell repertoire sequencing is still in its infancy. It is expected that maturation of the field will involve the introduction of improved, standardized tools for data handling, deposition and statistical analysis, as well as the emergence of new and equivalently large-scale technologies for T-cell functional analysis and antigen discovery. In this review, we introduce this nascent field and TCR-seq methodology, we discuss recent insights into healthy and diseased TCR repertoires, and we examine the applications and challenges for TCR-seq in the clinic.
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Affiliation(s)
- Daniel J Woodsworth
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
- Genome Sciences & Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Mauro Castellarin
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Robert A Holt
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
- Genome Sciences & Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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147
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Robins H. Immunosequencing: applications of immune repertoire deep sequencing. Curr Opin Immunol 2013; 25:646-52. [DOI: 10.1016/j.coi.2013.09.017] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 10/01/2013] [Accepted: 09/30/2013] [Indexed: 01/25/2023]
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148
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Tyler EM, Koehne G. The emergence of WT1-specific T-cell responses following allogeneic T cell-depleted hematopoietic stem cell transplantation and low-dose donor lymphocyte infusions is associated with a graft-vs.- myeloma effect. Oncoimmunology 2013; 2:e24963. [PMID: 24073375 PMCID: PMC3782135 DOI: 10.4161/onci.24963] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 05/08/2013] [Indexed: 11/19/2022] Open
Abstract
The development of T-cell responses specific for myeloma-associated antigens correlates with improved clinical outcomes in multiple myeloma patients undergoing allogeneic T cell-depleted hematopoietic stem cell transplantation and donor lymphocyte infusions. Thus, immunotherapeutic strategies that further increase the frequency of Wilms tumor 1 (WT1)-specific T cells may provide clinical benefits to multiple myeloma patients.
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Affiliation(s)
- Eleanor M Tyler
- Immunology and Microbial Pathogenesis Program; Weill Cornell Graduate School of Medical Sciences; New York, NY USA ; Sloan-Kettering Institute; New York, NY USA
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149
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Abstract
Application of high-throughput DNA sequencing to the analysis of B- and T-lymphocyte antigen receptors has great potential for improving the monitoring of lymphoid malignancies, assessing immune reconstitution after hematopoietic cell transplantation, and characterizing the composition of lymphocyte repertoires. Current technology can define the number and frequency of immunoglobulin heavy, T-cell receptor (TCR)α, TCRβ, or TCRγ chains expressed in a population of lymphocytes; techniques for determining the number of antigen receptor heterodimers, such as TCRαβ pairs, expressed in the population are under development.
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