51
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Wang X, Zhang B, Yang Y, Zhu J, Cheng S, Mao Y, Feng L, Xiao T. Characterization of Distinct T Cell Receptor Repertoires in Tumor and Distant Non-tumor Tissues from Lung Cancer Patients. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:287-296. [PMID: 31479759 PMCID: PMC6818398 DOI: 10.1016/j.gpb.2018.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/12/2018] [Accepted: 10/23/2018] [Indexed: 01/10/2023]
Abstract
T cells and T cell receptors (TCRs) play pivotal roles in adaptive immune responses against tumors. The development of next-generation sequencing technologies has enabled the analysis of the TCRβ repertoire usage. Given the scarce investigations on the TCR repertoire in lung cancer tissues, in this study, we analyzed TCRβ repertoires in lung cancer tissues and the matched distant non-tumor lung tissues (normal lung tissues) from 15 lung cancer patients. Based on our results, the general distribution of T cell clones was similar between cancer tissues and normal lung tissues; however, the proportion of highly expanded clones was significantly higher in normal lung tissues than in cancer tissues (0.021% ± 0.002% vs. 0.016% ± 0.001%, P = 0.0054, Wilcoxon signed rank test). In addition, a significantly higher TCR diversity was observed in cancer tissues than in normal lung tissues (431.37 ± 305.96 vs. 166.20 ± 101.58, P = 0.0075, Mann-Whitney U test). Moreover, younger patients had a significantly higher TCR diversity than older patients (640.7 ± 295.3 vs. 291.8 ± 233.6, P = 0.036, Mann-Whitney U test), and the higher TCR diversity in tumors was significantly associated with worse cancer outcomes. Thus, we provided a comprehensive comparison of the TCR repertoires between cancer tissues and matched normal lung tissues and demonstrated the presence of distinct T cell immune microenvironments in lung cancer patients.
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Affiliation(s)
- Xiang Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Botao Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yikun Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jiawei Zhu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shujun Cheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yousheng Mao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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52
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Zhuang Y, Zhang C, Wu Q, Zhang J, Ye Z, Qian Q. Application of immune repertoire sequencing in cancer immunotherapy. Int Immunopharmacol 2019; 74:105688. [PMID: 31276974 DOI: 10.1016/j.intimp.2019.105688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 05/05/2019] [Accepted: 06/05/2019] [Indexed: 12/21/2022]
Abstract
With the prominent breakthrough in the field of tumor immunology, diverse cancer immunotherapies have attracted great attention in the last decade. The immune checkpoint inhibitors, adoptive cell therapies, and therapeutic cancer vaccines have already achieved impressive clinical success. However, the fact that only a small subset of patients with specific tumor types can benefit from these treatments limits the application of cancer immunotherapy. To seek out the molecular mechanisms behind this challenge and to select cancer precision medicine for different individuals, researchers apply the immune repertoire sequencing (IRS) to evaluate genetic responses of each patient to current immunotherapies. This review summarizes the technical advances and recent applications of IRS in cancer immunotherapy, indicates the limitations of this technique, and predicts future perspectives both in basic studies and clinical trials.
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Affiliation(s)
- Yuan Zhuang
- Shanghai Baize Medical Laboratory, Shanghai, China
| | - Changzheng Zhang
- Shanghai Baize Medical Laboratory, Shanghai, China; Shanghai Engineering Research Center for Cell Therapy, Shanghai, China
| | - Qiong Wu
- Shanghai Baize Medical Laboratory, Shanghai, China
| | - Jing Zhang
- Shanghai Baize Medical Laboratory, Shanghai, China
| | - Zhenlong Ye
- Shanghai Baize Medical Laboratory, Shanghai, China; Shanghai Cell Therapy Research Institute, Shanghai, China; Shanghai Engineering Research Center for Cell Therapy, Shanghai, China.
| | - Qijun Qian
- Shanghai Baize Medical Laboratory, Shanghai, China; Shanghai Cell Therapy Research Institute, Shanghai, China; Shanghai Engineering Research Center for Cell Therapy, Shanghai, China.
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53
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Chapuis AG, Egan DN, Bar M, Schmitt TM, McAfee MS, Paulson KG, Voillet V, Gottardo R, Ragnarsson GB, Bleakley M, Yeung CC, Muhlhauser P, Nguyen HN, Kropp LA, Castelli L, Wagener F, Hunter D, Lindberg M, Cohen K, Seese A, McElrath MJ, Duerkopp N, Gooley TA, Greenberg PD. T cell receptor gene therapy targeting WT1 prevents acute myeloid leukemia relapse post-transplant. Nat Med 2019; 25:1064-1072. [PMID: 31235963 DOI: 10.1038/s41591-019-0472-9] [Citation(s) in RCA: 220] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/23/2019] [Accepted: 04/26/2019] [Indexed: 01/12/2023]
Abstract
Relapse after allogeneic hematopoietic cell transplantation (HCT) is the leading cause of death in patients with acute myeloid leukemia (AML) entering HCT with poor-risk features1-3. When HCT does produce prolonged relapse-free survival, it commonly reflects graft-versus-leukemia effects mediated by donor T cells reactive with antigens on leukemic cells4. As graft T cells have not been selected for leukemia specificity and frequently recognize proteins expressed by many normal host tissues, graft-versus-leukemia effects are often accompanied by morbidity and mortality from graft-versus-host disease5. Thus, AML relapse risk might be more effectively reduced with T cells expressing receptors (TCRs) that target selected AML antigens6. We therefore isolated a high-affinity Wilms' Tumor Antigen 1-specific TCR (TCRC4) from HLA-A2+ normal donor repertoires, inserted TCRC4 into Epstein-Bar virus-specific donor CD8+ T cells (TTCR-C4) to minimize graft-versus-host disease risk and enhance transferred T cell survival7,8, and infused these cells prophylactically post-HCT into 12 patients ( NCT01640301 ). Relapse-free survival was 100% at a median of 44 months following infusion, while a concurrent comparative group of 88 patients with similar risk AML had 54% relapse-free survival (P = 0.002). TTCR-C4 maintained TCRC4 expression, persisted long-term and were polyfunctional. This strategy appears promising for preventing AML recurrence in individuals at increased risk of post-HCT relapse.
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Affiliation(s)
- Aude G Chapuis
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington School of Medicine, Seattle, WA, USA
| | - Daniel N Egan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington School of Medicine, Seattle, WA, USA
| | - Merav Bar
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington School of Medicine, Seattle, WA, USA
| | - Thomas M Schmitt
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Megan S McAfee
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kelly G Paulson
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington School of Medicine, Seattle, WA, USA
| | - Valentin Voillet
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gunnar B Ragnarsson
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Landspítali Háskólasjúkrahús, Reykjavík, Iceland
| | - Marie Bleakley
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington School of Medicine, Seattle, WA, USA
| | - Cecilia C Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington School of Medicine, Seattle, WA, USA
| | | | - Hieu N Nguyen
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Alpine Biotech, Seattle, WA, USA
| | - Lara A Kropp
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Therapeutic Products Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Luca Castelli
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Therapeutic Products Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Felecia Wagener
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel Hunter
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marcus Lindberg
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Kristen Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Aaron Seese
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - M Juliana McElrath
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington School of Medicine, Seattle, WA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Natalie Duerkopp
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ted A Gooley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Philip D Greenberg
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,University of Washington School of Medicine, Seattle, WA, USA. .,Departments of Immunology and Medicine, University of Washington, Seattle, WA, USA.
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54
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Zhang JL, Zhong XS, Yang SB, Kang X, Li Y, Chen JX, Li WB. Features and therapeutic potential of T-cell receptors in high-grade glioma. Chin Med J (Engl) 2019; 132:1435-1440. [PMID: 31205101 PMCID: PMC6629323 DOI: 10.1097/cm9.0000000000000282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Previous studies have shown that endogenous T cells play an important role in the prolonged survival time of high-grade glioma (HGG) patients. Our objectives were to investigate the features of T-cell receptor (TCR) repertoires in HGG patients and to elucidate any potential therapeutic value. METHODS During November 2011 and December 2018, tumor tissues and blood samples of 35 patients with HGG who underwent surgery at Beijing Tiantan Hospital or Beijing Shijitan Hospital were selected after surgery. After isolating DNA from samples, multiple rounds of PCR were performed to establish a DNA immune repertoire (IR). Then, the sequences and frequencies of the complementarity-determining 3 (CDR3) region in TCR beta chain (TRB) were identified by high-throughput sequencing and IR analysis. A survival follow-up was conducted monthly thereafter until December 2018. Finally, the t test and Mann-Whitney test were used to compare statistical differences between two sets of data. RESULTS The Shannon diversity index (SHDI) of TRB sequences of HGG patients was significantly lower than that of healthy individuals (7.34 vs. 8.45, P = 0.001). The SHDI of TRB sequences of glioblastoma (GBM) patients with more than 16 months survival time was much higher than that of GBM patients with shorter survival times in both tumor tissues (3.48 ± 0.31 vs. 6.21 ± 0.33, t = -5.49, P = 0.002) and blood cells (6.02 ± 0.66 vs. 7.44 ± 0.32, t = -2.20, P = 0.036). In addition, patients achieved a distinctly higher proportion compared to that of healthy individuals in the proportion of TRBV9 and TRBV5 functional regions (9.83% vs. 6.83%, P = 0.001). Surgical tissue from patients who survived more than 16 months yielded a much higher proportion of TRBV4 and TRBV9 regions (7.14% vs. 3.28%, t = 3.18, P = 0.019). In surgical tissues from two GBM patients who survived for longer than 46 months, we found a potentially therapeutic TCR sequence. CONCLUSIONS HGG patients have less species diversity of TCR repertoires compared with that of healthy individuals. TRBV9 regions in TCRs may be protective factors for long-term survival of GBM patients.
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Affiliation(s)
- Jie-Lin Zhang
- General Department of Neuro-oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Xiao-Song Zhong
- The Clinical Center of Gene and Cell Engineering, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Shou-Bo Yang
- General Department of Neuro-oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Xun Kang
- General Department of Neuro-oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Yan Li
- Department of Glioma, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Jian-Xin Chen
- Department of Glioma, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Wen-Bin Li
- General Department of Neuro-oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
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55
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George AP, Kuzel TM, Zhang Y, Zhang B. The Discovery of Biomarkers in Cancer Immunotherapy. Comput Struct Biotechnol J 2019; 17:484-497. [PMID: 31011407 PMCID: PMC6465579 DOI: 10.1016/j.csbj.2019.03.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
- Anil P George
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Illinois College of Medicine, United States of America
| | - Timothy M Kuzel
- Department of Medicine, Division of Hematology/Oncology/Cell Therapy, Rush University Medical Center, United States of America
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Bin Zhang
- Department of Medicine, Division of Hematology/Oncology, Northwestern University Feinberg School of Medicine, United States of America
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56
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Lee M, Park C, Woo J, Kim J, Kho I, Nam DH, Park WY, Kim YS, Kong DS, Lee HW, Kim TJ. Preferential Infiltration of Unique Vγ9Jγ2-Vδ2 T Cells Into Glioblastoma Multiforme. Front Immunol 2019; 10:555. [PMID: 30967876 PMCID: PMC6440384 DOI: 10.3389/fimmu.2019.00555] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 03/01/2019] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma multiforme (GBM) is clinically highly aggressive as a result of evolutionary dynamics induced by cross-talk between cancer cells and a heterogeneous group of immune cells in tumor microenvironment. The brain harbors limited numbers of immune cells with few lymphocytes and macrophages; thus, innate-like lymphocytes, such as γδ T cells, have important roles in antitumor immunity. Here, we characterized GBM-infiltrating γδ T cells, which may have roles in regulating the GBM tumor microenvironment and cancer cell gene expression. V(D)J repertoires of tumor-infiltrating and blood-circulating γδ T cells from four patients were analyzed by next-generation sequencing-based T-cell receptor (TCR) sequencing in addition to mutation and immune profiles in four GBM cases. In all tumor tissues, abundant innate and effector/memory lymphocytes were detected, accompanied by large numbers of tumor-associated macrophages and closely located tumor-infiltrating γδ T cells, which appear to have anti-tumor activity. The immune-related gene expression analysis using the TCGA database showed that the signature gene expression extent of γδ T cells were more associated with those of cytotoxic T and Th1 cells and M1 macrophages than those of Th2 cells and M2 macrophages. Although the most abundant γδ T cells were Vγ9Vδ2 T cells in both tumor tissues and blood, the repertoire of intratumoral Vγ9Vδ2 T cells was distinct from that of peripheral blood Vγ9Vδ2 T cells and was dominated by Vγ9Jγ2 sequences, not by canonical Vγ9JγP sequences that are mostly commonly found in blood γδ T cells. Collectively, unique GBM-specific TCR clonotypes were identified by comparing TCR repertoires of peripheral blood and intra-tumoral γδ T cells. These findings will be helpful for the elucidation of tumor-specific antigens and development of anticancer immunotherapies using tumor-infiltrating γδ T cells.
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Affiliation(s)
- Mijeong Lee
- Department of Health Science and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul, South Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, South Korea
| | - Chanho Park
- Division of Immunobiology, Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Jeongmin Woo
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Jinho Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Inseong Kho
- Division of Immunobiology, Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Do-Hyun Nam
- Department of Health Science and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul, South Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, South Korea.,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Woong-Yang Park
- Department of Health Science and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul, South Korea.,Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Yeon-Soo Kim
- Department of New Drug Discovery and Development, Chungnam National University, Daejeon, South Korea
| | - Doo-Sik Kong
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, South Korea.,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hye Won Lee
- Department of Health Science and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul, South Korea.,Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea.,Single Cell Network Research Center, Sungkyunkwan University, Seoul, South Korea
| | - Tae Jin Kim
- Department of Health Science and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul, South Korea.,Division of Immunobiology, Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
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57
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Dupic T, Marcou Q, Walczak AM, Mora T. Genesis of the αβ T-cell receptor. PLoS Comput Biol 2019; 15:e1006874. [PMID: 30830899 PMCID: PMC6417744 DOI: 10.1371/journal.pcbi.1006874] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 03/14/2019] [Accepted: 02/17/2019] [Indexed: 11/18/2022] Open
Abstract
The T-cell (TCR) repertoire relies on the diversity of receptors composed of two chains, called α and β, to recognize pathogens. Using results of high throughput sequencing and computational chain-pairing experiments of human TCR repertoires, we quantitively characterize the αβ generation process. We estimate the probabilities of a rescue recombination of the β chain on the second chromosome upon failure or success on the first chromosome. Unlike β chains, α chains recombine simultaneously on both chromosomes, resulting in correlated statistics of the two genes which we predict using a mechanistic model. We find that ∼35% of cells express both α chains. Altogether, our statistical analysis gives a complete quantitative mechanistic picture that results in the observed correlations in the generative process. We learn that the probability to generate any TCRαβ is lower than 10(-12) and estimate the generation diversity and sharing properties of the αβ TCR repertoire.
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MESH Headings
- Chromosomes, Human
- Humans
- Probability
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombination, Genetic
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Affiliation(s)
- Thomas Dupic
- Laboratoire de physique théorique et hautes énergies, CNRS and Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
| | - Quentin Marcou
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
- * E-mail: (AMW); (TM)
| | - Thierry Mora
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
- * E-mail: (AMW); (TM)
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58
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Luo S, Yu JA, Li H, Song YS. Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans. Life Sci Alliance 2019; 2:2/2/e201800221. [PMID: 30808649 PMCID: PMC6391684 DOI: 10.26508/lsa.201800221] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 12/31/2022] Open
Abstract
This article presents a comprehensive study of the IGHV and TRBV gene families in a globally diverse sample of humans and shows that the two gene families exhibit starkly different patterns of variation. The immunoglobulin heavy variable (IGHV) and T cell beta variable (TRBV) loci are among the most complex and variable regions in the human genome. Generated through a process of gene duplication/deletion and diversification, these loci can vary extensively between individuals in copy number and contain genes that are highly similar, making their analysis technically challenging. Here, we present a comprehensive study of the functional gene segments in the IGHV and TRBV loci, quantifying their copy number and single-nucleotide variation in a globally diverse sample of 109 (IGHV) and 286 (TRBV) humans from over a 100 populations. We find that the IGHV and TRBV gene families exhibit starkly different patterns of variation. In addition to providing insight into the different evolutionary paths of the IGHV and TRBV loci, our results are also important to the adaptive immune repertoire sequencing community, where the lack of frequencies of common alleles and copy number variants is hampering existing analytical pipelines.
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Affiliation(s)
- Shishi Luo
- Computer Science Division, University of California, Berkeley, Berkeley, CA, USA.,Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Jane A Yu
- Computer Science Division, University of California, Berkeley, Berkeley, CA, USA
| | - Heng Li
- Department of Biostatistics, Harvard Medical School, Boston, MA, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, Berkeley, CA, USA .,Department of Statistics, University of California, Berkeley, Berkeley, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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59
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Comprehensive Analysis of TCR-β Repertoire in Patients with Neurological Immune-mediated Disorders. Sci Rep 2019; 9:344. [PMID: 30674904 PMCID: PMC6344574 DOI: 10.1038/s41598-018-36274-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/30/2018] [Indexed: 12/02/2022] Open
Abstract
In this study we characterized the TCR repertoire profiles in patients with chronic progressive inflammatory neurological disorders including HAM/TSP, associated with human T-cell lymphotropic virus type I (HTLV-I) infection, and multiple sclerosis (MS), an inflammatory, demyelinating disease of the CNS of unknown etiology. We hypothesized that a T-cell receptor (TCR) clonal repertoire ‘signature’ could distinguish HAM/TSP patients from healthy controls, as well as from patients with a more heterogeneous CNS-reactive inflammatory disease such as MS. In this study, we applied an unbiased molecular technique – unique molecular identifier (UMI) library-based strategy to investigate with high accuracy the TCR clonal repertoire by high throughput sequencing (HTS) technology. cDNA-TCR β-chain libraries were sequenced from 2 million peripheral mononuclear cells (PBMCs) in 14 HAM/TSP patients, 34 MS patients and 20 healthy controls (HC). While HAM/TSP patients showed a higher clonal T-cell expansion compared to MS and HC, increase of the TCR clonal expansion was inversely correlated with the diversity of TCR repertoire in all subjects. In addition, longitudinal analysis of TCR repertoires from HAM/TSP patients demonstrated a correlation of the TCR clonal expansion with HTLV-I proviral load. Surprisingly, MS patients showed a higher diversity of TCR repertoires than other groups. Despite higher TCR clonal expansions in HAM/TSP patients, no disease-specific TCRs were shared among patients. Only non-shared or “private” TCR repertoires was observed. While no clones that shared the same CDR3 amino acid sequences were seen in either HC or MS patients, there was a cluster of related CDR3 amino acid sequences observed for 18 out of 34 MS patients when evaluated by phylogenetic tree analysis. This suggests that a TCR-repertoire signature may be identified in a subset of patients with MS.
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60
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Uddin I, Joshi K, Oakes T, Heather JM, Swanton C, Chain B. An Economical, Quantitative, and Robust Protocol for High-Throughput T Cell Receptor Sequencing from Tumor or Blood. Methods Mol Biol 2019; 1884:15-42. [PMID: 30465193 DOI: 10.1007/978-1-4939-8885-3_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The T cell receptor repertoire provides a window to the cellular adaptive immune response within a tumor, and has the potential to identify specific and personalized biomarkers for tracking host responses during cancer therapy, including immunotherapy. We describe a protocol for amplifying, sequencing, and analyzing T cell receptors which is economical, robust, sensitive, and versatile. The key experimental step is the ligation of a single-stranded oligonucleotide to the 3' end of the T cell receptor cDNA, which allows easy amplification of all possible rearrangements using only a single set of primers per locus, while simultaneously introducing a unique molecular identifier to label each starting cDNA molecule. After sequencing, this molecular identifier can be used to correct both sequence errors and the effects of differential PCR amplification efficiency, thus producing a more accurate measure of the true T cell receptor frequency within the sample. This method has been applied to the analysis of unfractionated human tumor lysates, subpopulations of tumor-infiltrating lymphocytes, and peripheral blood samples from patients with a variety of solid tumors.
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MESH Headings
- Antineoplastic Agents, Immunological/therapeutic use
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/immunology
- Biomarkers, Tumor/metabolism
- High-Throughput Nucleotide Sequencing/economics
- High-Throughput Nucleotide Sequencing/instrumentation
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Neoplasms/blood
- Neoplasms/drug therapy
- Neoplasms/immunology
- Neoplasms/pathology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Treatment Outcome
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Affiliation(s)
- Imran Uddin
- Division of Infection and Immunity, UCL, London, UK
| | - Kroopa Joshi
- Cancer Immunology Unit, UCL Cancer Institute, UCL, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, UCL, London, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, UCL, London, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK
| | - Benny Chain
- Division of Infection and Immunity, UCL, London, UK.
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61
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de Jong A, Jabbari A, Dai Z, Xing L, Lee D, Li MM, Duvic M, Hordinsky M, Norris DA, Price V, Mackay-Wiggan J, Clynes R, Christiano AM. High-throughput T cell receptor sequencing identifies clonally expanded CD8+ T cell populations in alopecia areata. JCI Insight 2018; 3:121949. [PMID: 30282836 DOI: 10.1172/jci.insight.121949] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/29/2018] [Indexed: 01/04/2023] Open
Abstract
Alopecia areata (AA) is an autoimmune disease in which cytotoxic T cells specifically target growing hair follicles. We used high-throughput TCR sequencing in the C3H/HeJ mouse model of AA and in human AA patients to gain insight into pathogenic T cell populations and their dynamics, which revealed clonal CD8+ T cell expansions in lesional skin. In the C3H/HeJ model, we observed interindividual sharing of TCRβ chain protein sequences, which strongly supports a model of antigenic drive in AA. The overlap between the lesional TCR repertoire and a population of CD8+NKG2D+ T cells in skin-draining lymph nodes identified this subset as pathogenic effectors. In AA patients, treatment with the oral JAK inhibitor tofacitinib resulted in a decrease in clonally expanded CD8+ T cells in the scalp but also revealed that many expanded lesional T cell clones do not completely disappear from either skin or blood during treatment with tofacitinib, which may explain in part the relapse of disease after stopping treatment.
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Affiliation(s)
| | | | | | - Luzhou Xing
- Department of Pathology, Columbia University, New York, New York, USA
| | | | | | - Madeleine Duvic
- Department of Dermatology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Maria Hordinsky
- Department of Dermatology, University of Minnesota, Minneapolis, Minnesota, USA
| | - David A Norris
- Department of Dermatology, University of Colorado, Denver, Colorado, USA
| | - Vera Price
- Department of Dermatology, UCSF, San Francisco, California, USA
| | | | | | - Angela M Christiano
- Department of Dermatology and.,Department of Genetics and Development, Columbia University, New York, New York, USA
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62
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DeWolf S, Grinshpun B, Savage T, Lau SP, Obradovic A, Shonts B, Yang S, Morris H, Zuber J, Winchester R, Sykes M, Shen Y. Quantifying size and diversity of the human T cell alloresponse. JCI Insight 2018; 3:121256. [PMID: 30089728 PMCID: PMC6129121 DOI: 10.1172/jci.insight.121256] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/28/2018] [Indexed: 01/19/2023] Open
Abstract
Alloreactive T lymphocytes are the primary mediators of immune responses in transplantation, both in the graft-versus-host and host-versus-graft directions. While essentially all clones comprising the human T cell repertoire have been selected on self-peptide presented by self-human leukocyte antigens (self-HLAs), much remains to be understood about the nature of clones capable of responding to allo-HLA molecules. Quantitative tools to study these cells are critical to understand fundamental features of this important response; however, the large size and diversity of the alloreactive T cell repertoire in humans presents a great technical challenge. We have developed a high-throughput T cell receptor (TCR) sequencing approach to characterize the human alloresponse. We present a statistical method to model T cell clonal frequency distribution and quantify repertoire diversity. Using these approaches, we measured the diversity and frequency of distinct alloreactive CD4+ and CD8+ T cell populations in HLA-mismatched responder-stimulator pairs. Our findings indicate that the alloimmune repertoire is highly specific for a given pair of individuals, that most alloreactive clones circulate at low frequencies, and that a high proportion of TCRs is likely able to recognize alloantigens.
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Affiliation(s)
- Susan DeWolf
- Center for Translational Immunology, Department of Medicine
| | | | - Thomas Savage
- Center for Translational Immunology, Department of Medicine
| | - Sai Ping Lau
- Center for Translational Immunology, Department of Medicine
| | | | | | - Suxiao Yang
- Center for Translational Immunology, Department of Medicine
| | - Heather Morris
- Center for Translational Immunology, Department of Medicine
| | - Julien Zuber
- Center for Translational Immunology, Department of Medicine
| | | | - Megan Sykes
- Center for Translational Immunology, Department of Medicine
| | - Yufeng Shen
- Department of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, New York, USA
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63
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Heather JM, Ismail M, Oakes T, Chain B. High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform 2018; 19:554-565. [PMID: 28077404 PMCID: PMC6054146 DOI: 10.1093/bib/bbw138] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information. The latest generation of bioinformatics tools allows millions of DNA sequences to be accurately and rapidly assigned to their respective variable V and J gene segments, and to reconstruct an almost error-free representation of the non-templated additions and deletions that occur. High-level processing can measure the diversity of the repertoire in different samples, quantify V and J usage and identify private and public T-cell receptors. Finally, we discuss the major challenge of linking T-cell receptor sequence to function, and specifically to antigen recognition. Sophisticated machine learning algorithms are being developed that can combine the paradoxical degeneracy and cross-reactivity of individual T-cell receptors with the specificity of the overall T-cell immune response. Computational analysis will provide the key to unlock the potential of the T-cell receptor repertoire to give insight into the fundamental biology of the adaptive immune system and to provide powerful biomarkers of disease.
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Affiliation(s)
| | | | | | - Benny Chain
- Division of Infection and Immunity, University College of London, Bloomsbury, UK
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64
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Jiang Q, Zhao T, Zheng W, Zhou J, Wang H, Dong H, Chen Y, Tang X, Liu C, Ye L, Mao Q, Wang C, Han J, Shang X, Wu Y. Patient-shared TCRβ-CDR3 clonotypes correlate with favorable prognosis in chronic hepatitis B. Eur J Immunol 2018; 48:1539-1549. [PMID: 29856484 DOI: 10.1002/eji.201747327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 03/22/2018] [Accepted: 05/24/2018] [Indexed: 01/12/2023]
Abstract
The presence of shared T-cell clonotypes was found in several different diseases, but its relationship with the progression of disease remains unclear. By sequencing the complementary determining region 3 of T-cell receptor (TCR) β chains from the purified antigen-experienced CD8+ T cells, we characterized the T-cell repertoire in a prospective cohort study among 75 patients with chronic hepatitis B in China, as well as a healthy control and a validation cohort. We found that most T-cell clones from patients harbored the "patient-specific" TCR sequences. However, "patient-shared" TCR clonotypes were also widely found, which correlated with the favorable turnover of disease. Interestingly, the frequency of the "patient-shared" clonotypes can serve as a biomarker for favorable prognosis. Based on the clonotypes in those patients with favorable outcomes, we created a database including several clusters of protective anti-HBV CD8+ T-cell clonotypes that might be a reasonable target for therapeutic vaccine development or adoptive cell transfer therapy. These findings were validated in an additional independent cohort of patients. These results suggest that the "patient-shared" TCR clonotypes may serve as a valuable prognostic tool in the treatment of chronic hepatitis B and possibly other chronic viral diseases.
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Affiliation(s)
- Qiong Jiang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Tingting Zhao
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Wenhong Zheng
- Department of Health, Third Military Medical University, Chongqing, P. R. China
| | - Jijun Zhou
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Haoliang Wang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Hui Dong
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Yongwen Chen
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Xiaoqin Tang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Cong Liu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Lilin Ye
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Qing Mao
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Chunlin Wang
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Jian Han
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Xiaoyun Shang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
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65
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Abstract
Probabilistic modeling is fundamental to the statistical analysis of complex data. In addition to forming a coherent description of the data-generating process, probabilistic models enable parameter inference about given datasets. This procedure is well developed in the Bayesian perspective, in which one infers probability distributions describing to what extent various possible parameters agree with the data. In this paper, we motivate and review probabilistic modeling for adaptive immune receptor repertoire data then describe progress and prospects for future work, from germline haplotyping to adaptive immune system deployment across tissues. The relevant quantities in immune sequence analysis include not only continuous parameters such as gene use frequency but also discrete objects such as B-cell clusters and lineages. Throughout this review, we unravel the many opportunities for probabilistic modeling in adaptive immune receptor analysis, including settings for which the Bayesian approach holds substantial promise (especially if one is optimistic about new computational methods). From our perspective, the greatest prospects for progress in probabilistic modeling for repertoires concern ancestral sequence estimation for B-cell receptor lineages, including uncertainty from germline genotype, rearrangement, and lineage development.
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Affiliation(s)
- Branden Olson
- Computational Biology Program Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail stop: M1-B514 Seattle, WA 98109-1024 phone: +1 206 667 7318
| | - Frederick A. Matsen
- Computational Biology Program Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail stop: M1-B514 Seattle, WA 98109-1024 phone: +1 206 667 7318
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66
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Sun G, Qiu L, Cheng Z, Pan W, Qiu J, Zou C, Xie N, Liu S, Zhu P, Zeng J, Dai Y. Association of the characteristics of B- and T-cell repertoires with papillary thyroid carcinoma. Oncol Lett 2018; 16:1584-1592. [PMID: 30008841 PMCID: PMC6036450 DOI: 10.3892/ol.2018.8800] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 11/16/2017] [Indexed: 11/16/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Complementarity-determining region 3 (CDR3) of B-cell receptors (BCRs) and T-cell receptors are the major site of antigen recognition, which determines a unique clone type, and are considered to be the representative of the disease. In the present study, high-throughput sequencing was used to analyze the association of characteristics of the BCR immunoglobulin heavy chain (IGH) and the T-cell receptor β chain (TRB) CDR3 genes in PTC and corresponding pericarcinous tissues from patients. A difference of CDR3 length distributions of total IGH CDR3 sequences between the two groups was revealed. IGHV3-11/IGHJ6, TRBV2/TRBJ1-2 and TRBV2/TRBJ1-1 may be biomarkers for the development of PTC. Furthermore, it was revealed that the extent of the common clonotype expressions at the amino acid level was slightly higher compared with the nucleotide level. The Shannon entropy demonstrated a diversity reduction in PTC compared with the pericarcinous group, and the highly expended clone (HEC) expression of PTC was higher compared with that of the corresponding pericarcinous group. Additionally, the highest clone frequency percentage of IGH and TRB was at 0.1–1.0% degree of expansion, as HEC expression was higher in PTC compared with the matched group. There was no shared clone of HECs in the two groups either at the amino acid level or at the nucleotide expression level. The differential expression of CDR3 sequences of PTC have been identified in the present study. Further research is required for assessing the immune repertoire size, diversity, cloning tracking and finding public clones of T-cell and B-cell populations in the development of PTC.
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Affiliation(s)
- Guoping Sun
- Core Laboratory, Pingshan New District People's Hospital, Shenzhen, Guangdong 518118, P.R. China
| | - Lumei Qiu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Zhiqiang Cheng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Weibing Pan
- Core Laboratory, Pingshan New District People's Hospital, Shenzhen, Guangdong 518118, P.R. China
| | - Jingjun Qiu
- Core Laboratory, Pingshan New District People's Hospital, Shenzhen, Guangdong 518118, P.R. China
| | - Chang Zou
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Ni Xie
- Core Laboratory, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518035, P.R. China
| | - Song Liu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Peng Zhu
- Core Laboratory, Pingshan New District People's Hospital, Shenzhen, Guangdong 518118, P.R. China
| | - Jun Zeng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
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67
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Lindner M, Klotz L, Wiendl H. Mechanisms underlying lesion development and lesion distribution in CNS autoimmunity. J Neurochem 2018; 146:122-132. [PMID: 29574788 DOI: 10.1111/jnc.14339] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 12/30/2022]
Abstract
It is widely accepted that development of autoimmunity in the central nervous system (CNS) is triggered by autoreactive T cells, that are activated in the periphery and gain the capacity to migrate through endothelial cells at the blood-brain barrier (BBB) into the CNS. Upon local reactivation, an inflammatory cascade is initiated, that subsequently leads to a recruitment of additional immune cells ultimately causing demyelination and axonal damage. Even though the interaction of immune cells with the BBB has been in the focus of research for many years, the exact mechanisms of how immune cells enter and exit the CNS remains poorly understood. In this line, the factors deciding immune cell entry routes, lesion formation, cellular composition as well as distribution within the CNS have also not been elucidated. The following factors have been proposed to represent key determinants for lesion evaluation and distribution: (i) presence and density of (auto) antigens in the CNS, (ii) local immune milieu at sites of lesion development and resolution, (iii) trafficking routes and specific trafficking requirements, especially at the BBB and (iv) characteristics and phenotypes of CNS infiltrating cells and cell subsets (e.g. features of T helper subtypes or CD8 cells). The heterogeneity of lesion development within inflammatory demyelinating diseases remains poorly understood until today, but here especially orphan inflammatory CNS disorders such as neuromyelitis optica spectrum disorder (NMOSD), Rasmussen encephalitis or SUSAC syndrome might give important insights in critical determinants of lesion topography. Finally, investigating the interaction of T cells with the BBB using in vitro approaches or tracking of T cells in vivo in animals or even human patients, as well as the discovery of lymphatic vasculature in the CNS are teaching us new aspects during the development of CNS autoimmunity. In this review, we discuss recent findings which help to unravel mechanisms underlying lesion topography and might lead to new diagnostic or therapeutic approaches in neuroinflammatory disorders including multiple sclerosis (MS).
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Affiliation(s)
- Maren Lindner
- Department of Neurology, University Hospital Münster, Münster, DE, Germany
| | - Luisa Klotz
- Department of Neurology, University Hospital Münster, Münster, DE, Germany
| | - Heinz Wiendl
- Department of Neurology, University Hospital Münster, Münster, DE, Germany.,Sydney Medical School, University of Sydney, Sydney, AU, Australia
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68
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Zhang C, Björkman A, Cai K, Liu G, Wang C, Li Y, Xia H, Sun L, Kristiansen K, Wang J, Han J, Hammarström L, Pan-Hammarström Q. Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire. Front Immunol 2018; 9:908. [PMID: 29755475 PMCID: PMC5934425 DOI: 10.3389/fimmu.2018.00908] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/11/2018] [Indexed: 12/18/2022] Open
Abstract
The dietary pattern can influence the immune system directly, but may also modulate it indirectly by regulating the gut microbiota. Here, we investigated the effect of a 3-months lacto-ovo-vegetarian diet on the diversity of gut microbiota and the immune system in healthy omnivorous volunteers, using high-throughput sequencing technologies. The short-term vegetarian diet did not have any major effect on the diversity of the immune system and the overall composition of the metagenome. The prevalence of bacterial genera/species with known beneficial effects on the intestine, including butyrate-producers and probiotic species and the balance of autoimmune-related variable genes/families were, however, altered in the short-term vegetarians. A number of bacterial species that are associated with the expression level of IgA, a key immunoglobulin class that protects the gastrointestinal mucosal system, were also identified. Furthermore, a lower diversity of T-cell repertoire and expression level of IgE, as well as a reduced abundance of inflammation-related genes in the gut microbiota were potentially associated with a control group with long-term vegetarians. Thus, the composition and duration of the diet may have an impact on the balance of pro-/anti-inflammatory factors in the gut microbiota and immune system.
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Affiliation(s)
| | - Andrea Björkman
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Chunlin Wang
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Yin Li
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,iCarbonX, Shenzhen, China
| | - Jian Han
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
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69
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Liu X, Wu J. History, applications, and challenges of immune repertoire research. Cell Biol Toxicol 2018; 34:441-457. [PMID: 29484527 DOI: 10.1007/s10565-018-9426-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 02/14/2018] [Indexed: 12/19/2022]
Abstract
The diversity of T and B cells in terms of their receptor sequences is huge in the vertebrate's immune system and provides broad protection against the vast diversity of pathogens. Immune repertoire is defined as the sum of T cell receptors and B cell receptors (also named immunoglobulin) that makes the organism's adaptive immune system. Before the emergence of high-throughput sequencing, the studies on immune repertoire were limited by the underdeveloped methodologies, since it was impossible to capture the whole picture by the low-throughput tools. The massive paralleled sequencing technology suits perfectly the researches on immune repertoire. In this article, we review the history of immune repertoire studies, in terms of technologies and research applications. Particularly, we discuss several aspects of challenges in this field and highlight the efforts to develop potential solutions, in the era of high-throughput sequencing of the immune repertoire.
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Affiliation(s)
- Xiao Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
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70
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Lang Kuhs KA, Lin SW, Hua X, Schiffman M, Burk RD, Rodriguez AC, Herrero R, Abnet CC, Freedman ND, Pinto LA, Hamm D, Robins H, Hildesheim A, Shi J, Safaeian M. T cell receptor repertoire among women who cleared and failed to clear cervical human papillomavirus infection: An exploratory proof-of-principle study. PLoS One 2018; 13:e0178167. [PMID: 29385144 PMCID: PMC5791954 DOI: 10.1371/journal.pone.0178167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 05/08/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND It is unknown why a minority of women fail to clear human papillomavirus (HPV) and develop precancer/cancer. Differences in T-cell receptor (TCR) repertoires may identify HPV16-infected women at highest-risk for progression to cancer. We conducted a proof-of-principle study nested within the Guanacaste HPV Natural History Study to evaluate the utility of next-generation sequencing for interrogating the TCR repertoires among women who cleared and failed to clear cervical HPV16. METHODS TCR repertoires of women with HPV16-related intraepithelial neoplasia grade 3 or higher (CIN3+; n = 25) were compared to women who cleared an incident HPV16 infection without developing precancer/cancer (n = 25). TCR diversity (richness and evenness) and relative abundance (RA) of gene segment (V [n = 51], D [n = 2], J [n = 13]) usage was evaluated; receiver operating curve analysis assessed the ability to differentiate case-control status. RESULTS TCR repertoire richness was associated with CIN3+ status (P = 0.001). Relative abundance (RA) of V-gene segments was enriched for associations between cases and controls. A single V-gene (TRBV6-7) was significantly associated with CIN3+ status (RA = 0.11%, 0.16%, among cases and controls, respectively, Bonferroni P = 0.0008). The estimated area under the curve using richness and V-gene segment RA was 0.83 (95% confidence interval: 0.73-0.90). CONCLUSIONS Substantial differences in TCR repertoire among women with CIN3+ compared to women who cleared infection were observed. IMPACT This is the first study to use next-generation sequencing to investigate TCR repertoire in the context of HPV infection. These findings suggest that women with HPV16-associated cervical lesions have significantly different TCR repertoires from disease-free women who cleared HPV16 infection.
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Affiliation(s)
- Krystle A. Lang Kuhs
- National Cancer Institute, NIH, Bethesda, Maryland, United States of America
- Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Shih-Wen Lin
- National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Xing Hua
- National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Mark Schiffman
- National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Robert D. Burk
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | | | - Rolando Herrero
- Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
- Prevention and Implementation Group, International Agency for Research on Cancer, Lyon, France
| | - Christian C. Abnet
- National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Neal D. Freedman
- National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Ligia A. Pinto
- HPV Immunology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - David Hamm
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Harlan Robins
- Adaptive Biotechnologies, Seattle, Washington, United States of America
- Fred Hutchinson Cancer Research Cancer, Seattle, Washington, United States of America
| | - Allan Hildesheim
- National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Jianxin Shi
- National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Mahboobeh Safaeian
- National Cancer Institute, NIH, Bethesda, Maryland, United States of America
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71
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Nie J, Zhang Y, Li X, Chen M, Liu C, Han W. DNA demethylating agent decitabine broadens the peripheral T cell receptor repertoire. Oncotarget 2018; 7:37882-37892. [PMID: 27191266 PMCID: PMC5122357 DOI: 10.18632/oncotarget.9352] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 04/28/2016] [Indexed: 01/08/2023] Open
Abstract
Purpose Decitabine, a promising epi-immunotherapeutic agent has shown clinical responses in solid tumor patients, while the anti-tumor mechanisms were unclear. We aimed to investigate the immunomodulatory effect of decitabine in peripheral T cells. Experimental design We applied next-generation sequencing to investigate the complementarity-determining region 3 (CDR3) of the TCRβ gene, the diversity of which acts as the prerequisite for the host immune system to recognize the universal foreign antigens. We collected the peripheral blood mononuclear cells (PBMCs) from 4 patients, at baseline and after 2 cycles of low-dose decitabine therapy. Results An increase of the unique productive sequences of the CDR3 of TCRβ was observed in all of the 4 patients after decitabine treatment, which was characterized by a lower abundance of expanded clones and increased TCR diversity compared with before decitabine treatment. Further analysis showed a tendency for CD4 T cells with an increased CD4/CD8 ratio in response to decitabine therapy. In addition, the genome-wide expression alterations confirmed the effects of decitabine on immune reconstitution, and the increase of TCR excision circles (TRECs) was validated. Conclusions The low-dose DNMT inhibitor decitabine broadens the peripheral T cell repertoire, providing a novel role for the epigenetic modifying agent in anti-tumor immune enhancement.
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Affiliation(s)
- Jing Nie
- Department of Immunology, Institute of Basic Medical Science, PLA General Hospital, Beijing, 100853, China
| | - Yan Zhang
- Department of Biological Therapy, PLA General Hospital, Beijing, 100853, China
| | - Xiang Li
- Department of Immunology, Institute of Basic Medical Science, PLA General Hospital, Beijing, 100853, China
| | - Meixia Chen
- Department of Biological Therapy, PLA General Hospital, Beijing, 100853, China
| | - Chuanjie Liu
- Department of Immunology, Institute of Basic Medical Science, PLA General Hospital, Beijing, 100853, China
| | - Weidong Han
- Department of Immunology, Institute of Basic Medical Science, PLA General Hospital, Beijing, 100853, China.,Department of Biological Therapy, PLA General Hospital, Beijing, 100853, China
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72
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Kovaltsuk A, Krawczyk K, Galson JD, Kelly DF, Deane CM, Trück J. How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data. Front Immunol 2017; 8:1753. [PMID: 29276518 PMCID: PMC5727015 DOI: 10.3389/fimmu.2017.01753] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/27/2017] [Indexed: 12/24/2022] Open
Abstract
Next-generation sequencing of immunoglobulin gene repertoires (Ig-seq) allows the investigation of large-scale antibody dynamics at a sequence level. However, structural information, a crucial descriptor of antibody binding capability, is not collected in Ig-seq protocols. Developing systematic relationships between the antibody sequence information gathered from Ig-seq and low-throughput techniques such as X-ray crystallography could radically improve our understanding of antibodies. The mapping of Ig-seq datasets to known antibody structures can indicate structurally, and perhaps functionally, uncharted areas. Furthermore, contrasting naïve and antigenically challenged datasets using structural antibody descriptors should provide insights into antibody maturation. As the number of antibody structures steadily increases and more and more Ig-seq datasets become available, the opportunities that arise from combining the two types of information increase as well. Here, we review how these data types enrich one another and show potential for advancing our knowledge of the immune system and improving antibody engineering.
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Affiliation(s)
| | - Konrad Krawczyk
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Jacob D Galson
- Division of Immunology and the Children's Research Center, University Children's Hospital, University of Zürich, Zürich, Switzerland
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Johannes Trück
- Division of Immunology and the Children's Research Center, University Children's Hospital, University of Zürich, Zürich, Switzerland
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73
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Brunner PM, Emerson RO, Tipton C, Garcet S, Khattri S, Coats I, Krueger JG, Guttman-Yassky E. Nonlesional atopic dermatitis skin shares similar T-cell clones with lesional tissues. Allergy 2017; 72:2017-2025. [PMID: 28599078 DOI: 10.1111/all.13223] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND Atopic dermatitis (AD) is characterized by robust immune activation. Various T-cell subsets, including Th2/Th22 cells, are increased in lesional and nonlesional skin. However, there is conflicting literature on the diversity of the T-cell receptor (TCR) repertoire in lesional AD, and its relation to nonlesional skin remains unclear. METHODS We performed high-throughput deep sequencing of the β-TCR repertoire in 29 lesional and 19 nonlesional AD biopsies, compared to six healthy control and six cutaneous T-cell lymphoma (CTCL) samples from previously published cohorts. RESULTS While greater T-cell infiltrates were observed in lesional vs nonlesional AD, TCR repertoire diversity was similar in lesional and nonlesional tissues, and absolute numbers of unique T-cell clones correlated with respective T-cell counts. Most (87%) top expanded lesional T-cell clones were shared with nonlesional tissues, and they were largely maintained after 16 weeks of successful treatment with topical triamcinolone. Nevertheless, both lesional and nonlesional AD showed a highly polyclonal TCR pattern, without evidence of oligoclonal expansion, or a preferred usage of certain V-β genes in AD skin. Size of the overall T-cell infiltrate, but not the level of clonality, correlated with mRNA levels of key inflammatory mediators (e.g., IL-13, CCL17, IL23p19, CXCL10). CONCLUSION While AD harbors a highly polyclonal T-cell receptor repertoire, and despite the lack of information on TCR antigen specificity, the sharing of top abundant clones between lesional and nonlesional skin, and their persistence after months of therapy, points to the continuous presence of potentially pathogenic skin resident memory T cells well beyond clinically inflamed lesions.
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Affiliation(s)
- P. M. Brunner
- The Laboratory for Investigative Dermatology; The Rockefeller University; New York NY USA
| | - R. O. Emerson
- Adaptive Biotechnologies Corporation; Seattle WA USA
| | - C. Tipton
- Adaptive Biotechnologies Corporation; Seattle WA USA
| | - S. Garcet
- The Laboratory for Investigative Dermatology; The Rockefeller University; New York NY USA
| | - S. Khattri
- Department of Dermatology and the Laboratory for Inflammatory Skin Diseases; Icahn School of Medicine at Mount Sinai; New York NY USA
| | - I. Coats
- The Laboratory for Investigative Dermatology; The Rockefeller University; New York NY USA
| | - J. G. Krueger
- The Laboratory for Investigative Dermatology; The Rockefeller University; New York NY USA
| | - E. Guttman-Yassky
- The Laboratory for Investigative Dermatology; The Rockefeller University; New York NY USA
- Department of Dermatology and the Laboratory for Inflammatory Skin Diseases; Icahn School of Medicine at Mount Sinai; New York NY USA
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74
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Affiliation(s)
- Siranush Sarkizova
- Siranush Sarkizova is at the Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; the Broad Institute of MIT and Harvard, Cambridge, Massachusetts; and the Department of Biomedical Informatics, Harvard Medical School, Boston
| | - Nir Hacohen
- Nir Hacohen is at the Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA, and at the Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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75
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Liu S, Pan W, Cheng Z, Sun G, Zhu P, Chan F, Hu Y, Zhang X, Dai Y. Characterization of the T-cell receptor repertoire by deep T cell receptor sequencing in tissues from patients with prostate cancer. Oncol Lett 2017; 15:1744-1752. [PMID: 29399194 PMCID: PMC5774533 DOI: 10.3892/ol.2017.7479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 11/21/2017] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PC) is the most prevalent urological cancer in men. T cells serve a central role in the cancer's immunological microenvironment. In the present study, we applied multiplex PCR and Illumina next-generation sequencing to study the clonal diversity of the T-cell receptor (TCR) repertoire in cancer tissues and paracancer tissues from patients with PC. It was found that the TCR repertoire in the PC samples had a notably more skewed clonotype composition, with a greater number of highly expanded clones (HECs) compared with the prostate paracancer samples. The amino acid sequences ATSRVAGETQY (1.008 vs. 0.002%), ATSRTGRWETQY (3.985 vs. 0.007%), ATSDSSDYEQY (12.464 vs. 0.027%), ATSDFRGQPQETQY (2.205 vs. 0.06%), ASSQQDEAF (1.109 vs. 0.002%) and ARPTRTEETQY (1.263 vs. 0.002%) were found to vary markedly between cancer and paracancer tissues, respectively. In conclusion, the present study identified PC-specific HECs, which are critical to improving understanding of the TCR repertoire in PC. This may accelerate the screening process for potential new autoantigens and provide information for generating more effective T cell-targeted diagnostic and therapeutic strategies.
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Affiliation(s)
- Song Liu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China
| | - Weibing Pan
- Urology Division of Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, P.R. China
| | - Zhiqiang Cheng
- Department of Pathology, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China
| | - Guoping Sun
- Central Lab of Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, P.R. China
| | - Peng Zhu
- Central Lab of Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, P.R. China
| | - Franky Chan
- Cancer Biology and Experimental Therapeutics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Yunlong Hu
- Cancer Research Center, Shenzhen University School of Medicine, Shenzhen, Guangdong 518000, P.R. China
| | - Xinzhou Zhang
- Department of Nephrology, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China
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76
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Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol 2017; 8:1418. [PMID: 29163494 PMCID: PMC5671925 DOI: 10.3389/fimmu.2017.01418] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/12/2017] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1–3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail. It holds significant promise for diagnostic and therapy-guiding applications. New technology often spreads rapidly, sometimes more rapidly than the understanding of how to make the products of that technology reliable, reproducible, or usable by others. As complex technologies have developed, scientific communities have come together to adopt common standards, protocols, and policies for generating and sharing data sets, such as the MIAME protocols developed for microarray experiments. The Adaptive Immune Receptor Repertoire (AIRR) Community formed in 2015 to address similar issues for HTS data of immune repertoires. The purpose of this perspective is to provide an overview of the AIRR Community’s founding principles and present the progress that the AIRR Community has made in developing standards of practice and data sharing protocols. Finally, and most important, we invite all interested parties to join this effort to facilitate sharing and use of these powerful data sets (join@airr-community.org).
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Florian Rubelt
- Department of Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Christian E Busse
- Division of B Cell Immunology, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Jason A Vander Heiden
- Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
| | - Scott Christley
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | | | - Adrian Thorogood
- entre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Frederick A Matsen Iv
- Public Health Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yariv Wine
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Uri Laserson
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David Klatzmann
- Immunology-Immunopathology-Immunotherapy (i3 & i2B), Sorbonne Université, Paris, France
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Marie-Paule Lefranc
- IMGT, LIGM, Institut de Génétique Humaine IGH, CNRS, University of Montpellier, Montpellier, France
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Tania Bubela
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Steven H Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jamie K Scott
- Faculty of Health Sciences, Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,Department of Mathematics and Statistics, Boston University, Boston, MA, United States
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77
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Oakes T, Heather JM, Best K, Byng-Maddick R, Husovsky C, Ismail M, Joshi K, Maxwell G, Noursadeghi M, Riddell N, Ruehl T, Turner CT, Uddin I, Chain B. Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile. Front Immunol 2017; 8:1267. [PMID: 29075258 PMCID: PMC5643411 DOI: 10.3389/fimmu.2017.01267] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/22/2017] [Indexed: 11/13/2022] Open
Abstract
The T cell receptor (TCR) repertoire can provide a personalized biomarker for infectious and non-infectious diseases. We describe a protocol for amplifying, sequencing, and analyzing TCRs which is robust, sensitive, and versatile. The key experimental step is ligation of a single-stranded oligonucleotide to the 3' end of the TCR cDNA. This allows amplification of all possible rearrangements using a single set of primers per locus. It also introduces a unique molecular identifier to label each starting cDNA molecule. This molecular identifier is used to correct for sequence errors and for effects of differential PCR amplification efficiency, thus producing more accurate measures of the true TCR frequency within the sample. This integrated experimental and computational pipeline is applied to the analysis of human memory and naive subpopulations, and results in consistent measures of diversity and inequality. After error correction, the distribution of TCR sequence abundance in all subpopulations followed a power law over a wide range of values. The power law exponent differed between naïve and memory populations, but was consistent between individuals. The integrated experimental and analysis pipeline we describe is appropriate to studies of T cell responses in a broad range of physiological and pathological contexts.
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Affiliation(s)
- Theres Oakes
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - James M. Heather
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Katharine Best
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Rachel Byng-Maddick
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Connor Husovsky
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Kroopa Joshi
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Gavin Maxwell
- Unilever Safety and Environmental Assurance Centre, Unilever, Sharnbrook, United Kingdom
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Natalie Riddell
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Tabea Ruehl
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Carolin T. Turner
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
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78
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Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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79
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Hess GT, Tycko J, Yao D, Bassik MC. Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes. Mol Cell 2017; 68:26-43. [PMID: 28985508 PMCID: PMC5997582 DOI: 10.1016/j.molcel.2017.09.029] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 12/26/2022]
Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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Affiliation(s)
- Gaelen T Hess
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Josh Tycko
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - David Yao
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA.
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80
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Wendel BS, He C, Qu M, Wu D, Hernandez SM, Ma KY, Liu EW, Xiao J, Crompton PD, Pierce SK, Ren P, Chen K, Jiang N. Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children. Nat Commun 2017; 8:531. [PMID: 28912592 PMCID: PMC5599618 DOI: 10.1038/s41467-017-00645-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/15/2017] [Indexed: 12/03/2022] Open
Abstract
Accurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important for understanding repertoire responses to infection and vaccination. We develop molecular identifier clustering-based immune repertoire sequencing (MIDCIRS) and use it to study age-related antibody repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12-47 months old) with 4-8 ml of blood. Here, we show this accurate and high-coverage repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody repertoire diversification in infants and toddlers.Somatic hypermutation of antibodies can occur in infants but are difficult to track. Here the authors present a new method called MIDCIRS for deep quantitative repertoire sequencing with few cells, and show infants as young as 3 months can expand antibody lineage complexity in response to malaria infection.
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Affiliation(s)
- Ben S Wendel
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Chenfeng He
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Mingjuan Qu
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- School of Life Sciences, Ludong University, Yantai, Shandong, 264025, China
| | - Di Wu
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Stefany M Hernandez
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ke-Yue Ma
- Institute for Cellular and Molecular Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Eugene W Liu
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Atlanta, 30329, GA, USA
| | - Jun Xiao
- ImmuDX, LLC, Austin, TX, 78750, USA
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Susan K Pierce
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Pengyu Ren
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Keke Chen
- Department of Computer Science and Engineering, Wright State University, Dayton, OH, 45435, USA
| | - Ning Jiang
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
- Institute for Cellular and Molecular Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, 78712, USA.
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81
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Wendel BS, He C, Crompton PD, Pierce SK, Jiang N. A Streamlined Approach to Antibody Novel Germline Allele Prediction and Validation. Front Immunol 2017; 8:1072. [PMID: 28928742 PMCID: PMC5591497 DOI: 10.3389/fimmu.2017.01072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022] Open
Abstract
Advancements in high-throughput sequencing and molecular identifier-based error correction have opened the door to antibody repertoire sequencing with single mutation precision, increasing both the breadth and depth of immune response characterization. However, improvements in sequencing technology cannot resolve one key aspect of antibody repertoire sequencing accuracy: the possibility of undocumented novel germline alleles. Somatic hypermutation (SHM) calling requires a reference germline sequence, and the antibody variable region gene alleles collected by the IMGT database, although large in number, are not comprehensive. Mismatches, resulted from single nucleotide polymorphisms or other genetic variation, between the true germline sequence and the closest IMGT allele can inflate SHM counts, leading to inaccurate antibody repertoire analysis. Here, we developed a streamlined approach to novel allele prediction and validation using bulk PBMC antibody repertoire sequencing data and targeted genomic DNA amplification and sequencing using PBMCs from only 4 ml of blood to quickly and effectively improve the fidelity of antibody repertoire analysis. This approach establishes a framework for comprehensively annotating novel alleles using a small amount of blood sample, which is extremely useful in studying young children’s immune systems.
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Affiliation(s)
- Ben S Wendel
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Chenfeng He
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Susan K Pierce
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Ning Jiang
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States.,College of Natural Sciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
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82
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Fu L, Li X, Zhang W, Wang C, Wu J, Yang H, Wang J, Liu X. A comprehensive profiling of T- and B-lymphocyte receptor repertoires from a Chinese-origin rhesus macaque by high-throughput sequencing. PLoS One 2017; 12:e0182733. [PMID: 28813462 PMCID: PMC5559085 DOI: 10.1371/journal.pone.0182733] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 07/24/2017] [Indexed: 12/28/2022] Open
Abstract
Due to the close genetic background, high similarity of physiology, and susceptibility to infectious and metabolic diseases with humans, rhesus macaques have been widely used as an important animal model in biomedical research, especially in the study of vaccine development and human immune-related diseases. In recent years, high-throughput sequencing based immune repertoire sequencing (IR-SEQ) has become a powerful tool to study the dynamic adaptive immune responses. Several previous studies had analyzed the responses of B cells to HIV-1 trimer vaccine or T cell repertoire of rhesus macaques using this technique, however, there are little studies that had performed a comprehensive analysis of immune repertoire of rhesus macaques, including T and B lymphocytes. Here, we did a comprehensive analysis of the T and B cells receptor repertoires of a Chinese rhesus macaque based on the 5’—RACE and IR-SEQ. The detailed analysis includes the distribution of CDR3 length, the composition of amino acids and nucleotides of CDR3, V, J and V-J combination usage, the insertion and deletion length distribution and somatic hypermutation rates of the framework region 3 (FR3). In addition, we found that several positions of FR3 region have high mutation frequencies, which may indicate the existence of new genes/alleles that have not been discovered and/or collected into IMGT reference database. We believe that a comprehensive profiling of immune repertoire of rhesus macaque will facilitate the human immune-related diseases studies.
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Affiliation(s)
- Longfei Fu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Xinyang Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Changxi Wang
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Jinghua Wu
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, BGI-Shenzhen, Shenzhen, China
- * E-mail:
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83
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Zhao Y, Forst CV, Sayegh CE, Wang IM, Yang X, Zhang B. Molecular and genetic inflammation networks in major human diseases. MOLECULAR BIOSYSTEMS 2017; 12:2318-41. [PMID: 27303926 DOI: 10.1039/c6mb00240d] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It has been well-recognized that inflammation alongside tissue repair and damage maintaining tissue homeostasis determines the initiation and progression of complex diseases. Albeit with the accomplishment of having captured the most critical inflammation-involved molecules, genetic susceptibilities, epigenetic factors, and environmental factors, our schemata on the role of inflammation in complex diseases remain largely patchy, in part due to the success of reductionism in terms of research methodology per se. Omics data alongside the advances in data integration technologies have enabled reconstruction of molecular and genetic inflammation networks which shed light on the underlying pathophysiology of complex diseases or clinical conditions. Given the proven beneficial role of anti-inflammation in coronary heart disease as well as other complex diseases and immunotherapy as a revolutionary transition in oncology, it becomes timely to review our current understanding of the molecular and genetic inflammation networks underlying major human diseases. In this review, we first briefly discuss the complexity of infectious diseases and then highlight recently uncovered molecular and genetic inflammation networks in other major human diseases including obesity, type II diabetes, coronary heart disease, late onset Alzheimer's disease, Parkinson's disease, and sporadic cancer. The commonality and specificity of these molecular networks are addressed in the context of genetics based on genome-wide association study (GWAS). The double-sword role of inflammation, such as how the aberrant type 1 and/or type 2 immunity leads to chronic and severe clinical conditions, remains open in terms of the inflammasome and the core inflammatome network features. Increasingly available large Omics and clinical data in tandem with systems biology approaches have offered an exciting yet challenging opportunity toward reconstruction of more comprehensive and dynamic molecular and genetic inflammation networks, which hold great promise in transiting network snapshots to video-style multi-scale interplays of disease mechanisms, in turn leading to effective clinical intervention.
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Affiliation(s)
- Yongzhong Zhao
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Camil E Sayegh
- Vertex Pharmaceuticals (Canada) Incorporated, 275 Armand-Frappier, Laval, Quebec H7V 4A7, Canada
| | - I-Ming Wang
- Informatics and Analysis, Merck Research Laboratories, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90025, USA.
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
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84
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Díez P, Ibarrola N, Dégano RM, Lécrevisse Q, Rodriguez-Caballero A, Criado I, Nieto WG, Góngora R, González M, Almeida J, Orfao A, Fuentes M. A systematic approach for peptide characterization of B-cell receptor in chronic lymphocytic leukemia cells. Oncotarget 2017; 8:42836-42846. [PMID: 28467808 PMCID: PMC5522109 DOI: 10.18632/oncotarget.17076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/22/2017] [Indexed: 01/09/2023] Open
Abstract
A wide variety of immunoglobulins (Ig) is produced by the immune system thanks to different mechanisms (V(D)J recombination, somatic hypermutation, and antigen selection). The profiling of Ig sequences (at both DNA and peptide levels) are of great relevance to developing targeted vaccines or treatments for specific diseases or infections. Thus, genomics and proteomics techniques (such as Next-Generation Sequencing (NGS) and mass spectrometry (MS)) have notably increased the knowledge in Ig sequencing and serum Ig peptide profiling in a high-throughput manner. However, the peptide characterization of membrane-bound Ig (e.g., B-cell receptors, BCR) is still a challenge mainly due to the poor recovery of mentioned Ig.Herein, we have evaluated three different sample processing methods for peptide sequencing of BCR belonging to chronic lymphocytic leukemia (CLL) B cells identifying up to 426 different peptide sequences (MS/MS data are available via ProteomeXchange with identifier PXD004466). Moreover, as a consequence of the results here obtained, recommended guidelines have been described for BCR-sequencing of B-CLL samples by MS approaches.For this purpose, an in-house algorithm has been designed and developed to compare the MS/MS results with those obtained by molecular biology in order to integrate both proteomics and genomics results and establish the steps to follow when sequencing membrane-bound Ig by MS/MS.
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MESH Headings
- Aged
- Aged, 80 and over
- Amino Acid Sequence
- Female
- Genomics/methods
- High-Throughput Nucleotide Sequencing
- Humans
- Immunoglobulin Heavy Chains/chemistry
- Immunoglobulin Heavy Chains/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Male
- Middle Aged
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Proteomics/methods
- Receptors, Antigen, B-Cell/chemistry
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Tandem Mass Spectrometry
- Workflow
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Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Nieves Ibarrola
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Rosa M. Dégano
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Quentin Lécrevisse
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Arancha Rodriguez-Caballero
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Ignacio Criado
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Wendy G. Nieto
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Marcos González
- Hematology Service, Institute of Biomedical Research of Salamanca, University Hospital of Salamanca, Cancer Research and Institute of Molecular Biology and Cellular Oncology, 37007 Salamanca, Spain
| | - Julia Almeida
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
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85
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Liu XS, Mardis ER. Applications of Immunogenomics to Cancer. Cell 2017; 168:600-612. [PMID: 28187283 DOI: 10.1016/j.cell.2017.01.014] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 01/05/2023]
Abstract
Cancer immunogenomics originally was framed by research supporting the hypothesis that cancer mutations generated novel peptides seen as "non-self" by the immune system. The search for these "neoantigens" has been facilitated by the combination of new sequencing technologies, specialized computational analyses, and HLA binding predictions that evaluate somatic alterations in a cancer genome and interpret their ability to produce an immune-stimulatory peptide. The resulting information can characterize a tumor's neoantigen load, its cadre of infiltrating immune cell types, the T or B cell receptor repertoire, and direct the design of a personalized therapeutic.
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Affiliation(s)
- X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, 450 Brookline Ave, Boston MA 02215, USA.
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, and The Ohio State University College of Medicine, 575 Children's Crossroad, Columbus OH 43205, USA.
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86
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Multidisciplinary study of the secondary immune response in grandparents re-exposed to chickenpox. Sci Rep 2017; 7:1077. [PMID: 28439065 PMCID: PMC5430877 DOI: 10.1038/s41598-017-01024-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/23/2017] [Indexed: 11/25/2022] Open
Abstract
Re-exposure to chickenpox may boost varicella-zoster virus (VZV) immunity in the elderly. This secondary immune response is hypothesized to confer protection against herpes zoster. We longitudinally sampled 36 adults over the course of one year after re-exposure to chickenpox. The resulting 183 samples and those of 14 controls were assessed for VZV-specific T-cell immunity and antibody titres. The percentages of VZV-specific CD4+ IL-2-producing T-cells were increased in re-exposed grandparents compared to control participants up to 9 months after re-exposure. Using a longitudinal mixture modelling approach, we found that 25% and 17% of re-exposed grandparents showed a boosting of VZV-specific CD4+ IL-2-producing T-cells and VZV-specific antibodies, respectively. The antibody boosting occurred exclusively in cytomegalovirus (CMV) IgG-positive participants. CMV IgG-positive participants also had higher VZV IE62-specific CD4+ IFN-γ-producing T-cell percentages and VZV-specific antibody titres. The protective effect of re-exposure to chickenpox is likely limited, as boosting only occurred in 17–25% of the VZV re-exposed grandparents and for less than one year.
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87
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Roles of tumor heterogeneity in the development of drug resistance: A call for precision therapy. Semin Cancer Biol 2017; 42:13-19. [DOI: 10.1016/j.semcancer.2016.11.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/08/2016] [Indexed: 12/13/2022]
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88
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Callan CG, Mora T, Walczak AM. Repertoire sequencing and the statistical ensemble approach to adaptive immunity. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2016.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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89
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Chen H, Zou M, Teng D, Zhang J, He W. Characterization of the diversity of T cell receptor γδ complementary determinant region 3 in human peripheral blood by Immune Repertoire Sequencing. J Immunol Methods 2017; 443:9-17. [PMID: 28159550 DOI: 10.1016/j.jim.2017.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/12/2016] [Accepted: 01/26/2017] [Indexed: 01/05/2023]
Abstract
γδ T cells function as sentinels in early host response to infections and malignancies. Although γδ T cells are regarded as innate immune cells and recognize antigens in a non-MHC restricted manner, they possess a huge diversity of complementary determinant region 3 (CDR3) of T cell receptor (TCR) generated by the rearrangement of germ-line gene V- (D) -J-C fragments. However, the detailed characteristics of the TCRγδ CDR3 repertoire remain unclear. A comprehensive analysis would answer fundamental questions about the diversity of the TCRγδ CDR3 repertoire and elucidate the mechanism underlying γδ T cell recognition of pathogens and tumor antigens. In this study, we used Immune Repertoire Sequencing (IR-SEQ) to analyze the diversity of TCRγδ CDR3 repertoires from 30 healthy donors. The results show that IR-SEQ had sufficient repeatability to analyze the TCRγδ CDR3 repertoire. The diversity of TCRγδ CDR3 repertoire is quite dispersed and individually different. The TCR δ chain (TRD) repertoire displayed more diversity and less sharing among individuals compared with TCR γ chain (TRG). To our knowledge, this is the first study to use IR-SEQ to characterize the repertoire of TCRγδ CDR3 in human peripheral blood γδ T cells by using IR-SEQ. Our findings provide a basic understanding of the diversity of TCRγδ repertoire in the physiological condition, which provides a clue to the underlying mechanism of γδ T cell recognition of pathogens and tumor antigens.
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Affiliation(s)
- Hui Chen
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China
| | - Mingjin Zou
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan 250012, China
| | - Da Teng
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China
| | - Jianmin Zhang
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China.
| | - Wei He
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China.
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90
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Lee DW, Khavrutskii IV, Wallqvist A, Bavari S, Cooper CL, Chaudhury S. BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires. Front Immunol 2017; 7:681. [PMID: 28144239 PMCID: PMC5239784 DOI: 10.3389/fimmu.2016.00681] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/21/2016] [Indexed: 11/13/2022] Open
Abstract
The somatic diversity of antigen-recognizing B-cell receptors (BCRs) arises from Variable (V), Diversity (D), and Joining (J) (VDJ) recombination and somatic hypermutation (SHM) during B-cell development and affinity maturation. The VDJ junction of the BCR heavy chain forms the highly variable complementarity determining region 3 (CDR3), which plays a critical role in antigen specificity and binding affinity. Tracking the selection and mutation of the CDR3 can be useful in characterizing humoral responses to infection and vaccination. Although tens to hundreds of thousands of unique BCR genes within an expressed B-cell repertoire can now be resolved with high-throughput sequencing, tracking SHMs is still challenging because existing annotation methods are often limited by poor annotation coverage, inconsistent SHM identification across the VDJ junction, or lack of B-cell lineage data. Here, we present B-cell repertoire inductive lineage and immunosequence annotator (BRILIA), an algorithm that leverages repertoire-wide sequencing data to globally improve the VDJ annotation coverage, lineage tree assembly, and SHM identification. On benchmark tests against simulated human and mouse BCR repertoires, BRILIA correctly annotated germline and clonally expanded sequences with 94 and 70% accuracy, respectively, and it has a 90% SHM-positive prediction rate in the CDR3 of heavily mutated sequences; these are substantial improvements over existing methods. We used BRILIA to process BCR sequences obtained from splenic germinal center B cells extracted from C57BL/6 mice. BRILIA returned robust B-cell lineage trees and yielded SHM patterns that are consistent across the VDJ junction and agree with known biological mechanisms of SHM. By contrast, existing BCR annotation tools, which do not account for repertoire-wide clonal relationships, systematically underestimated both the size of clonally related B-cell clusters and yielded inconsistent SHM frequencies. We demonstrate BRILIA’s utility in B-cell repertoire studies related to VDJ gene usage, mechanisms for adenosine mutations, and SHM hot spot motifs. Furthermore, we show that the complete gene usage annotation and SHM identification across the entire CDR3 are essential for studying the B-cell affinity maturation process through immunosequencing methods.
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Affiliation(s)
- Donald W Lee
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Ilja V Khavrutskii
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Anders Wallqvist
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Sina Bavari
- Molecular and Translational Sciences, U.S. Army Medical Research Institute of Infectious Diseases , Frederick, MD , USA
| | - Christopher L Cooper
- Molecular and Translational Sciences, U.S. Army Medical Research Institute of Infectious Diseases , Frederick, MD , USA
| | - Sidhartha Chaudhury
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
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91
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T cell receptor repertoire usage in cancer as a surrogate marker for immune responses. Semin Immunopathol 2017; 39:255-268. [PMID: 28074285 DOI: 10.1007/s00281-016-0614-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/15/2016] [Indexed: 12/21/2022]
Abstract
Characterizing the interaction of cancer cells with the host adaptive immune system is critical for understanding tumor immunology and the modus operandi of immunotherapeutic interventions to treat cancer. As the key cellular effectors of adaptive immunity, T cells are endowed with specialized receptors (the T cell receptor; TCR), to recognize and to eliminate cancer cells. The diversity of the TCR repertoire results from specialized genetic diversification mechanisms that generate an incredible variability allowing recognizing extensive collections of antigens. Based on the attainment and function of the TCR, the TCR repertoire is a mirror of the human immune response, and the dynamic changes of its usage can be assumed as a promising biomarker to monitor immunomodulatory therapies. Recent advances in multiplexed PCR amplification and massive parallel sequencing technologies have facilitated the characterization of TCR repertoires at high resolution even when only biomaterial of limited quantity and quality, such as formalin-fixed paraffin-embedded (FFPE) archived tissues, is available. Here, we review the concept framework and current experimental approaches to characterize the TCR repertoire usage in cancer including inherent technical and biological challenges.
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92
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Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol 2017. [PMID: 29163494 DOI: 10.3389/fimmu.2017.01418/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1-3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail. It holds significant promise for diagnostic and therapy-guiding applications. New technology often spreads rapidly, sometimes more rapidly than the understanding of how to make the products of that technology reliable, reproducible, or usable by others. As complex technologies have developed, scientific communities have come together to adopt common standards, protocols, and policies for generating and sharing data sets, such as the MIAME protocols developed for microarray experiments. The Adaptive Immune Receptor Repertoire (AIRR) Community formed in 2015 to address similar issues for HTS data of immune repertoires. The purpose of this perspective is to provide an overview of the AIRR Community's founding principles and present the progress that the AIRR Community has made in developing standards of practice and data sharing protocols. Finally, and most important, we invite all interested parties to join this effort to facilitate sharing and use of these powerful data sets (join@airr-community.org).
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Florian Rubelt
- Department of Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Christian E Busse
- Division of B Cell Immunology, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Jason A Vander Heiden
- Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
| | - Scott Christley
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | | | - Adrian Thorogood
- entre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Frederick A Matsen Iv
- Public Health Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yariv Wine
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Uri Laserson
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David Klatzmann
- Immunology-Immunopathology-Immunotherapy (i3 & i2B), Sorbonne Université, Paris, France
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Marie-Paule Lefranc
- IMGT, LIGM, Institut de Génétique Humaine IGH, CNRS, University of Montpellier, Montpellier, France
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Tania Bubela
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Steven H Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jamie K Scott
- Faculty of Health Sciences, Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States
- Department of Mathematics and Statistics, Boston University, Boston, MA, United States
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93
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T Cell Repertoire Diversity Is Decreased in Type 1 Diabetes Patients. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:338-348. [PMID: 28024918 PMCID: PMC5200939 DOI: 10.1016/j.gpb.2016.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 10/13/2016] [Accepted: 10/25/2016] [Indexed: 02/01/2023]
Abstract
Type 1 diabetes mellitus (T1D) is an immune-mediated disease. The autoreactive T cells in T1D patients attack and destroy their own pancreatic cells. In order to systematically investigate the potential autoreactive T cell receptors (TCRs), we used a high-throughput immune repertoire sequencing technique to profile the spectrum of TCRs in individual T1D patients and controls. We sequenced the T cell repertoire of nine T1D patients, four type 2 diabetes (T2D) patients, and six nondiabetic controls. The diversity of the T cell repertoire in T1D patients was significantly decreased in comparison with T2D patients (P=7.0E-08 for CD4+ T cells, P=1.4E-04 for CD8+ T cells) and nondiabetic controls (P=2.7E-09 for CD4+ T cells, P=7.6E-06 for CD8+ T cells). Moreover, T1D patients had significantly more highly-expanded T cell clones than T2D patients (P=5.2E-06 for CD4+ T cells, P=1.9E-07 for CD8+ T cells) and nondiabetic controls (P=1.7E-07 for CD4+ T cells, P=3.3E-03 for CD8+ T cells). Furthermore, we identified a group of highly-expanded T cell receptor clones that are shared by more than two T1D patients. Although further validation in larger cohorts is needed, our data suggest that T cell receptor diversity measurements may become a valuable tool in investigating diabetes, such as using the diversity as an index to distinguish different types of diabetes.
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94
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Thome JJC, Grinshpun B, Kumar BV, Kubota M, Ohmura Y, Lerner H, Sempowski GD, Shen Y, Farber DL. Longterm maintenance of human naive T cells through in situ homeostasis in lymphoid tissue sites. Sci Immunol 2016; 1. [PMID: 28361127 DOI: 10.1126/sciimmunol.aah6506] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Naïve T cells develop in the thymus and coordinate immune responses to new antigens; however, mechanisms for their long-term persistence over the human lifespan remain undefined. Here, we investigated human naïve T cell development and maintenance in primary and secondary lymphoid tissues obtained from individual organ donors aged 3 months-73 years. In the thymus, the frequency of double-positive thymocytes declined sharply in donors over age 40 coincident with reduced recent thymic emigrants (RTE) in lymphoid tissues, while naïve T cells were functionally maintained predominantly in lymph nodes (LN). Analysis of TCR clonal distribution by CDR3 sequencing of naïve CD4+ and CD8+ T cells in spleen and LNs reveal site-specific clonal expansions of naïve T cells from individuals >40 years of age with minimal clonal overlap between lymphoid tissues. We also identified biased naïve T cell clonal distribution within specific lymph nodes based on VJ usage. Together these results suggest prolonged maintenance of naïve T cells through in situ homeostasis and retention in lymphoid tissue.
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Affiliation(s)
- Joseph J C Thome
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Boris Grinshpun
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Brahma V Kumar
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Masa Kubota
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Yoshiaki Ohmura
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | | | | | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
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Sweis RF, Galsky MD. Emerging role of immunotherapy in urothelial carcinoma-Immunobiology/biomarkers. Urol Oncol 2016; 34:556-565. [PMID: 27836246 PMCID: PMC5709811 DOI: 10.1016/j.urolonc.2016.10.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 09/21/2016] [Accepted: 10/05/2016] [Indexed: 12/13/2022]
Abstract
Urothelial bladder cancer is one of the first cancers recognized to be immunogenic since 40 years ago when the use of bacillus Calmette-Guerin was shown to prevent recurrence. Since that time, our knowledge of immune biology of cancer has expanded tremendously, and patients with bladder cancer finally have new active immunotherapeutic drugs on the horizon. Anti-programmed cell death-1 (PD-1)/programmed cell death ligand-1 (PD-L1) therapy has shown impressively durable responses in urothelial bladder cancer (UBC), but the reported response rates warrant improvement. To outline potential strategies to overcome tumor immune resistance, herein, we summarize current models of tumor immunology with a specific focus on bladder cancer. Recognition of tumor-specific antigens through cross-presentation, T-cell priming and activation, and trafficking of immune cells to the tumor microenvironment are some of the critical steps we now understand to be necessary for an effective antitumor immune response. Many of the involved steps are important targets for therapeutic interventions. As new immunotherapies are developed, predictive biomarkers would also be important to select patients most likely to respond and to better understand tumor biology. Several potential biomarkers are reviewed including PD-L1 expression, identification of T-cell-inflamed/non-T-cell-inflamed tumors based on immune gene expression, intrinsic molecular subtyping based on luminal/basal or the cancer genome atlas (TCGA) groups, T-cell receptor sequencing, and somatic mutational density. Even within the past few years, our current knowledge of immune biology has exploded, and we are highly optimistic about the future of UBC therapy that will be available to patients.
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MESH Headings
- Adjuvants, Immunologic/therapeutic use
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal, Humanized
- Antigen-Presenting Cells/immunology
- Antigens, Neoplasm/immunology
- Antineoplastic Agents, Immunological/adverse effects
- Antineoplastic Agents, Immunological/therapeutic use
- B7-H1 Antigen/antagonists & inhibitors
- B7-H1 Antigen/immunology
- Carcinoma, Transitional Cell/chemistry
- Carcinoma, Transitional Cell/drug therapy
- Carcinoma, Transitional Cell/immunology
- Carcinoma, Transitional Cell/therapy
- Clinical Trials as Topic
- Costimulatory and Inhibitory T-Cell Receptors/immunology
- Humans
- Immunotherapy
- Lymphocyte Activation
- Lymphocytes, Tumor-Infiltrating/immunology
- Molecular Targeted Therapy
- Mutation
- Neoplasm Proteins/antagonists & inhibitors
- Neoplasm Proteins/immunology
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Programmed Cell Death 1 Receptor/immunology
- Receptors, Antigen, T-Cell/immunology
- T-Lymphocytes, Cytotoxic/immunology
- Therapies, Investigational
- Tumor Escape/immunology
- Tumor Microenvironment/immunology
- Urinary Bladder Neoplasms/chemistry
- Urinary Bladder Neoplasms/drug therapy
- Urinary Bladder Neoplasms/immunology
- Urinary Bladder Neoplasms/therapy
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Affiliation(s)
- Randy F Sweis
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL
| | - Matthew D Galsky
- Division of Hematology & Medical Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY.
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96
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Salson M, Giraud M, Caillault A, Grardel N, Duployez N, Ferret Y, Duez M, Herbert R, Rocher T, Sebda S, Quief S, Villenet C, Figeac M, Preudhomme C. High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones. Leuk Res 2016; 53:1-7. [PMID: 27930944 DOI: 10.1016/j.leukres.2016.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/28/2016] [Accepted: 11/11/2016] [Indexed: 01/22/2023]
Abstract
Minimal residual disease (MRD) is known to be an independent prognostic factor in patients with acute lymphoblastic leukemia (ALL). High-throughput sequencing (HTS) is currently used in routine practice for the diagnosis and follow-up of patients with hematological neoplasms. In this retrospective study, we examined the role of immunoglobulin/T-cell receptor-based MRD in patients with ALL by HTS analysis of immunoglobulin H and/or T-cell receptor gamma chain loci in bone marrow samples from 11 patients with ALL, at diagnosis and during follow-up. We assessed the clinical feasibility of using combined HTS and bioinformatics analysis with interactive visualization using Vidjil software. We discuss the advantages and drawbacks of HTS for monitoring MRD. HTS gives a more complete insight of the leukemic population than conventional real-time quantitative PCR (qPCR), and allows identification of new emerging clones at each time point of the monitoring. Thus, HTS monitoring of Ig/TR based MRD is expected to improve the management of patients with ALL.
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Affiliation(s)
- Mikaël Salson
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.
| | - Mathieu Giraud
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.
| | - Aurélie Caillault
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France.
| | - Nathalie Grardel
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France.
| | - Nicolas Duployez
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France
| | - Yann Ferret
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France
| | - Marc Duez
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Ryan Herbert
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France
| | - Tatiana Rocher
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France
| | - Shéhérazade Sebda
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France
| | - Sabine Quief
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France
| | - Céline Villenet
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France
| | - Martin Figeac
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France; Univ. Lille, CHU Lille, Cellule bioinformatique, plateau commun de séquençage, F-59000 Lille, France
| | - Claude Preudhomme
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France.
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97
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Autoimmune susceptibility imposed by public TCRβ chains. Sci Rep 2016; 6:37543. [PMID: 27869234 PMCID: PMC5116635 DOI: 10.1038/srep37543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/01/2016] [Indexed: 11/21/2022] Open
Abstract
Although the TCR repertoire is highly diverse, a small fraction of TCR chains, referred to as public, preferentially form and are shared by most individuals. Prior studies indicated that public TCRβ may be preferentially deployed in autoimmunity. We hypothesized that if these TCRβ modulate the likelihood of a TCRαβ heterodimer productively engaging autoantigen, because they are widely present in the population and often high frequency within individual repertoires, they could also broadly influence repertoire responsiveness to specific autoantigens. We assess this here using a series of public and private TCRβ derived from autoimmune encephalomyelitis-associated TCR. Transgenic expression of public, but not private, disease-associated TCRβ paired with endogenously rearranged TCRα endowed unprimed T cells with autoantigen reactivity. Further, two of six public, but none of five private TCRβ provoked spontaneous early-onset autoimmunity in mice. Our findings indicate that single TCRβ are sufficient to confer on TCRαβ chains reactivity toward disease-associated autoantigens in the context of diverse TCRα. They further suggest that public TCR can skew autoimmune susceptibility, and that subsets of public TCR sequences may serve as disease- specific biomarkers or therapeutic targets.
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98
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Brodin J, Zanini F, Thebo L, Lanz C, Bratt G, Neher RA, Albert J. Establishment and stability of the latent HIV-1 DNA reservoir. eLife 2016; 5. [PMID: 27855060 PMCID: PMC5201419 DOI: 10.7554/elife.18889] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/01/2016] [Indexed: 12/11/2022] Open
Abstract
HIV-1 infection cannot be cured because the virus persists as integrated proviral DNA in long-lived cells despite years of suppressive antiretroviral therapy (ART). In a previous paper (Zanini et al, 2015) we documented HIV-1 evolution in 10 untreated patients. Here we characterize establishment, turnover, and evolution of viral DNA reservoirs in the same patients after 3–18 years of suppressive ART. A median of 14% (range 0–42%) of the DNA sequences were defective due to G-to-A hypermutation. Remaining DNA sequences showed no evidence of evolution over years of suppressive ART. Most sequences from the DNA reservoirs were very similar to viruses actively replicating in plasma (RNA sequences) shortly before start of ART. The results do not support persistent HIV-1 replication as a mechanism to maintain the HIV-1 reservoir during suppressive therapy. Rather, the data indicate that DNA variants are turning over as long as patients are untreated and that suppressive ART halts this turnover. DOI:http://dx.doi.org/10.7554/eLife.18889.001
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Affiliation(s)
- Johanna Brodin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Fabio Zanini
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Lina Thebo
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Christa Lanz
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Göran Bratt
- Department of Clinical Science and Education, Stockholm South General Hospital, Stockholm, Sweden.,Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
| | - Richard A Neher
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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99
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Masucci GV, Cesano A, Hawtin R, Janetzki S, Zhang J, Kirsch I, Dobbin KK, Alvarez J, Robbins PB, Selvan SR, Streicher HZ, Butterfield LH, Thurin M. Validation of biomarkers to predict response to immunotherapy in cancer: Volume I - pre-analytical and analytical validation. J Immunother Cancer 2016; 4:76. [PMID: 27895917 PMCID: PMC5109744 DOI: 10.1186/s40425-016-0178-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022] Open
Abstract
Immunotherapies have emerged as one of the most promising approaches to treat patients with cancer. Recently, there have been many clinical successes using checkpoint receptor blockade, including T cell inhibitory receptors such as cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death-1 (PD-1). Despite demonstrated successes in a variety of malignancies, responses only typically occur in a minority of patients in any given histology. Additionally, treatment is associated with inflammatory toxicity and high cost. Therefore, determining which patients would derive clinical benefit from immunotherapy is a compelling clinical question. Although numerous candidate biomarkers have been described, there are currently three FDA-approved assays based on PD-1 ligand expression (PD-L1) that have been clinically validated to identify patients who are more likely to benefit from a single-agent anti-PD-1/PD-L1 therapy. Because of the complexity of the immune response and tumor biology, it is unlikely that a single biomarker will be sufficient to predict clinical outcomes in response to immune-targeted therapy. Rather, the integration of multiple tumor and immune response parameters, such as protein expression, genomics, and transcriptomics, may be necessary for accurate prediction of clinical benefit. Before a candidate biomarker and/or new technology can be used in a clinical setting, several steps are necessary to demonstrate its clinical validity. Although regulatory guidelines provide general roadmaps for the validation process, their applicability to biomarkers in the cancer immunotherapy field is somewhat limited. Thus, Working Group 1 (WG1) of the Society for Immunotherapy of Cancer (SITC) Immune Biomarkers Task Force convened to address this need. In this two volume series, we discuss pre-analytical and analytical (Volume I) as well as clinical and regulatory (Volume II) aspects of the validation process as applied to predictive biomarkers for cancer immunotherapy. To illustrate the requirements for validation, we discuss examples of biomarker assays that have shown preliminary evidence of an association with clinical benefit from immunotherapeutic interventions. The scope includes only those assays and technologies that have established a certain level of validation for clinical use (fit-for-purpose). Recommendations to meet challenges and strategies to guide the choice of analytical and clinical validation design for specific assays are also provided.
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Affiliation(s)
- Giuseppe V Masucci
- Department of Oncology-Pathology, Karolinska Institutet, 171 76 Stockholm, Sweden
| | | | - Rachael Hawtin
- Nodality, Inc, 170 Harbor Way, South San Francisco, 94080 CA USA
| | - Sylvia Janetzki
- ZellNet Consulting, Inc, 555 North Avenue, Fort Lee, 07024 NJ USA
| | - Jenny Zhang
- Covaris Inc, 14 Gill St, Woburn, MA 01801 USA
| | - Ilan Kirsch
- Adaptive Biotechnologies, Inc, 1551 Eastlake Ave. E, Seattle, WA 98102 USA
| | - Kevin K Dobbin
- Department of Epidemiology and Biostatistics, College of Public Health, The University of Georgia, 101 Buck Road, Athens, 30602 GA USA
| | - John Alvarez
- Janssen Research & Development, LLC, Spring House, PA 19477 USA
| | | | - Senthamil R Selvan
- Omni Array Biotechnology, 15601 Crabbs Branch Way, Rockville, 20855 MD USA
| | - Howard Z Streicher
- National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, 20892 MD USA
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Magdalena Thurin
- National Cancer Institute, Cancer Diagnosis Program, DCTD, National Institutes of Health, 9609 Medical Center Drive, Bethesda, 20892 MD USA ; Adaptive Biotechnologies, Inc, 1551 Eastlake Ave. E, Seattle, WA 98102 USA
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100
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Hughes CE, Benson RA, Bedaj M, Maffia P. Antigen-Presenting Cells and Antigen Presentation in Tertiary Lymphoid Organs. Front Immunol 2016; 7:481. [PMID: 27872626 PMCID: PMC5097899 DOI: 10.3389/fimmu.2016.00481] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 10/20/2016] [Indexed: 12/18/2022] Open
Abstract
Tertiary lymphoid organs (TLOs) form in territorialized niches of peripheral tissues characterized by the presence of antigens; however, little is known about mechanism(s) of antigen handling by ectopic lymphoid structures. In this mini review, we will discuss the role of antigen-presenting cells and mechanisms of antigen presentation in TLOs, summarizing what is currently known about this facet of the formation and function of these tissues as well as identifying questions yet to be addressed.
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Affiliation(s)
- Catherine E Hughes
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow , Glasgow , UK
| | - Robert A Benson
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow , Glasgow , UK
| | - Marija Bedaj
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK; Rheumatology Research Group, Centre for Translational Inflammation Research, School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Pasquale Maffia
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK; BHF Centre of Excellence in Vascular Science and Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK; Department of Pharmacy, University of Naples Federico II, Naples, Italy
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