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Bo H, Jiang H, Xiong J, Zhang W, Shi Y, Pan C, Wang H. T cell receptor repertoire deciphers anti-tuberculosis immunity. Int Immunopharmacol 2024; 138:112252. [PMID: 38976948 DOI: 10.1016/j.intimp.2024.112252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 07/10/2024]
Abstract
T cell induced cellular immunity is considered to be extremely important for the control of tuberculosis (TB). T cell receptor (TCR), the key component responsible for the specificity and clustering of T cells, holds the potential to advance our understanding of T cell immunity against TB infection. This review systematically expounded the study progressions made in the field of TB-relevant TCRs based on single cell sequencing together with GLIPH2 technology and initiated a comparison of the T cell distribution between peripheral blood and infected organs. We divided clonal expanded T cell clones into recirculation subsets and local subsets to summarize their distinctions in clonal abundance, TCR sequences and antigenic specificity. Notably, local expansion appears to drive the primary variances in T cell subsets between these two contexts, indicating the necessity for further exploration into the functions and specificity of local subsets.
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Affiliation(s)
- Haohui Bo
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Haiqin Jiang
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China.
| | - Jingshu Xiong
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Wenyue Zhang
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Ying Shi
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Chun Pan
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Hongsheng Wang
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China; Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
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2
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Shao MM, Yi FS, Huang ZY, Peng P, Wu FY, Shi HZ, Zhai K. T Cell Receptor Repertoire Analysis Reveals Signatures of T Cell Responses to Human Mycobacterium tuberculosis. Front Microbiol 2022; 13:829694. [PMID: 35197957 PMCID: PMC8859175 DOI: 10.3389/fmicb.2022.829694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/03/2022] [Indexed: 11/17/2022] Open
Abstract
Characterization of T cell receptor (TCR) repertoires is essential for understanding the mechanisms of Mycobacterium tuberculosis (Mtb) infection involving T cell adaptive immunity. The characteristics of TCR sequences and distinctive signatures of T cell subsets in tuberculous patients are still unclear. By combining single-cell TCR sequencing (sc-TCR seq) with single-cell RNA sequencing (sc-RNA seq) and flow cytometry to characterize T cells in tuberculous pleural effusions (TPEs), we identified 41,718 CD3+ T cells in TPEs and paired blood samples, including 30,515 CD4+ T cells and 11,203 CD8+ T cells. Compared with controls, no differences in length and profile of length distribution were observed in complementarity determining region 3 (CDR3) in both CD4+ and CD8+ T cells in TPE. Altered hydrophobicity was demonstrated in CDR3 in CD8+ T cells and a significant imbalance in the TCR usage pattern of T cells with preferential expression of TRBV4-1 in TPE. A significant increase in clonality was observed in TCR repertoires in CD4+ T cells, but not in CD8+ T cells, although both enriched CD4+ and CD8+ T cells showed TH1 and cytotoxic signatures. Furthermore, we identified a new subset of polyfunctional CD4+ T cells with CD1-restricted, TH1, and cytotoxic characteristics, and this subset might provide protective immunity against Mtb.
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Affiliation(s)
- Ming-Ming Shao
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Feng-Shuang Yi
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Zhong-Yin Huang
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Peng Peng
- Department of Respiratory and Critical Care Medicine, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, China
| | - Feng-Yao Wu
- Department of Tuberculosis, Nanning Fourth People’s Hospital, Nanning, China
| | - Huan-Zhong Shi
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Kan Zhai
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- *Correspondence: Kan Zhai,
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3
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Zhang J, Hu M, Wang B, Gao J, Wang L, Li L, Chen S, Cui B, Gu W, Wang W, Ning G. Comprehensive assessment of T-cell repertoire following autologous hematopoietic stem cell transplantation for treatment of type 1 diabetes using high-throughput sequencing. Pediatr Diabetes 2018; 19:1229-1237. [PMID: 30022578 DOI: 10.1111/pedi.12728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/17/2018] [Accepted: 07/09/2018] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE We aimed to investigate T-cell receptor (TCR) repertoires in type 1 diabetes (T1D) patients receiving autologous hematopoietic stem cell transplantation (AHSCT) treatment. METHODS High-throughput deep TCR beta (TCRB) chain sequencing was performed to assess millions of individual TCRs in five T1D patients receiving AHSCT treatment and another five patients receiving insulin treatment during 12 months of follow-up. RESULTS No significant changes in TCRB sequence reads, complementarity-determining region 3 (CDR3) sequences, or the usage of TCRB VJ gene-segments were observed at 12 months after AHSCT. Compared with the baseline, the usage of TCRB VJ gene-segments at 12 months decreased in the insulin treatment group (1836.4 ± 437.7 vs 2763.6 ± 390.6, P = 0.015), and the change rates were larger than those undergoing AHSCT (-0.62 ± 0.16 vs 0.06 ± 0.45, P = 0.002). Changes in the TCR repertoire were smaller after AHSCT than those with insulin treatment (P = 2.2*10-32 ). TCRBV 7-7/TCRBJ 2-5 was depleted after AHSCT while expanded with insulin treatment. TCRBV 12-4, TCRBV 10-3, TCRBV 12-3/TCRBJ 1-2 were expanded after AHSCT while ablated with insulin treatment. CONCLUSIONS We found that AHSCT is safe without reduction in the diversity of TCR repertoires and TCR repertoires tend to be more stable after AHSCT. Furthermore, these four candidate TCRBV/TCRBJ gene usages on CDR3 regions may act as therapeutic targets and biomarkers.
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Affiliation(s)
- Juanjuan Zhang
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Min Hu
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
| | - Bokai Wang
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Jie Gao
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Li Wang
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Li Li
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Sisi Chen
- Beijing Genomics Institute, Shenzhen, Guangdong, China
| | - Bin Cui
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Weiqiong Gu
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Weiqing Wang
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China
| | - Guang Ning
- Department of Endocrine and Metabolic diseases, Ruijin Hospital, Shanghai Jiao-Tong University, School of Medicine, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Shanghai, China.,Laboratory for Endocrine & Metabolic Diseases, Institute of Health Science, Shanghai JiaoTong University, School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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4
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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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5
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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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6
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Cheng C, Wang B, Gao L, Liu J, Chen X, Huang H, Zhao Z. Next generation sequencing reveals changes of the γδ T cell receptor repertoires in patients with pulmonary tuberculosis. Sci Rep 2018; 8:3956. [PMID: 29500378 PMCID: PMC5834497 DOI: 10.1038/s41598-018-22061-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/14/2018] [Indexed: 12/25/2022] Open
Abstract
Tuberculosis (TB) is a severe global threat to human health. The immune protection initiated by γδ T cells play an important role in mycobacterial infection. Vaccines for Mycobacterium tuberculosis (Mtb) based on γδ T cells provide a novel approach for TB control. In our previous studies, we found a preponderant complementarity-determining region 3 (CDR3) sequence of the γδ T cell receptor (TCR) in TB patients, and successfully identified a tuberculosis antigen that can effectively activate γδ T cells with a reverse genetic strategy. However, due to the throughput limitation of the method we used, the information we obtained about the γδ TCR repertoire and preponderant CDR3 sequences was limited. In this study, we introduced next generation sequencing (NGS) to study the γδ TCR CDR3 repertoires in TB patients. We found that the CDR3δ tended to be more polyclonal and CDR3γ tended to be longer in TB patients; the γδ T cells expressing CDR3 sequences using a Vγ9-JγP rearrangement expanded significantly during Mtb infection. We also identified new preponderant CDR3 sequences during Mtb infection. This study comprehensively characterized the γδ T cell receptor repertoire changes, and provides useful information for the development of new vaccines and adjuvants against TB.
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Affiliation(s)
- Chaofei Cheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Bei Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.,Clinical Immunology Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Lei Gao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Jianmin Liu
- The Sixth People's Hospital of Zhengzhou, Zhengzhou, 450015, China
| | - Xinchun Chen
- Department of Pathogen Biology, School of Medicine, Shenzhen University, Shenzhen, 518002, China.
| | - He Huang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China. .,Clinical Immunology Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| | - Zhendong Zhao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China. .,Clinical Immunology Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China. .,CAMS-Oxford University International Center for Translational Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
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7
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Mai T, Takano A, Suzuki H, Hirose T, Mori T, Teramoto K, Kiyotani K, Nakamura Y, Daigo Y. Quantitative analysis and clonal characterization of T-cell receptor β repertoires in patients with advanced non-small cell lung cancer treated with cancer vaccine. Oncol Lett 2017; 14:283-292. [PMID: 28693166 DOI: 10.3892/ol.2017.6125] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 03/03/2017] [Indexed: 12/31/2022] Open
Abstract
With the development of cancer immunotherapy that may activate T cells, a practical and quantitative method to improve monitoring and/or prediction of immunological response of patients as a predictive biomarker is of importance. To examine possible biomarkers for a therapeutic cancer vaccine containing a mixture of three epitope peptides derived from cell division-associated 1, lymphocyte antigen 6 complex locus K and insulin-like growth factor-II mRNA-binding protein 3, T-cell receptor β (TCRβ) repertoires of blood samples from 24 patients with human leukocyte antigen-A*2402-positive non-small cell lung cancer were characterized prior to and following 8 weeks of the cancer vaccine treatment, by applying a next-generation sequencing method. It was identified that 14 patients with overall survival (OS) times of ≥12 months had significantly lower TCRβ diversity indexes in samples prior to treatment, compared with 10 patients who succumbed within 1 year (P=0.03). In addition, patients with a high level of activated CD8+ T cells that are defined by a high granzyme A/CD8 ratio had favorable OS rates (log-rank test, P=0.04). The TCRβ diversity index and immunogenic gene markers following vaccine administration may serve as predictive or monitoring biomarkers for cancer vaccine treatment.
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Affiliation(s)
- Tu Mai
- Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, IL 60637, USA.,Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Atsushi Takano
- Department of Medical Oncology, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan.,Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan
| | - Hiroyuki Suzuki
- Department of Regenerative Surgery, Fukushima Medical University, School of Medicine, Fukushima 960-1295, Japan
| | - Takashi Hirose
- Division of Respiratory Medicine and Allergology, Department of Internal Medicine, Showa University School of Medicine, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Takahiro Mori
- Tohoku Community Cancer Services Program, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8574, Japan
| | - Koji Teramoto
- Department of Medical Oncology, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan.,Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan
| | - Kazuma Kiyotani
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Yusuke Nakamura
- Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, IL 60637, USA.,Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.,Department of Surgery, University of Chicago, Chicago, IL 60637, USA
| | - Yataro Daigo
- Department of Medical Oncology, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan.,Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan
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8
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Parkhurst M, Gros A, Pasetto A, Prickett T, Crystal JS, Robbins P, Rosenberg SA. Isolation of T-Cell Receptors Specifically Reactive with Mutated Tumor-Associated Antigens from Tumor-Infiltrating Lymphocytes Based on CD137 Expression. Clin Cancer Res 2016; 23:2491-2505. [PMID: 27827318 DOI: 10.1158/1078-0432.ccr-16-2680] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/02/2016] [Accepted: 11/02/2016] [Indexed: 01/07/2023]
Abstract
Purpose: The adoptive transfer of lymphocytes genetically modified to express tumor reactive T-cell receptors (TCR) can mediate tumor regression. Some tumor-infiltrating lymphocytes (TIL) recognize somatic mutations expressed only in the patient's tumors, and evidence suggests that clinically effective TILs target tumor-specific neoantigens. Here we attempted to isolate neoantigen-reactive TCRs as a prelude to the treatment of patients with autologous T cells genetically modified to express such TCRs.Experimental Design: Mutations expressed by tumors were identified using whole-exome and RNA sequencing. Tandem minigene (TMG) constructs encoding 12-24 mutated gene products were synthesized, each encoding the mutated amino acid flanked by 12 amino acids of the normal protein sequence. TILs were cultured with autologous dendritic cells (DC) transfected with in vitro transcribed (IVT) mRNAs encoding TMGs and were evaluated for IFNγ secretion and CD137 expression. Neoantigen-reactive T cells were enriched from TILs by sorting for CD137+ CD8+ T cells and expanded in vitro Dominant TCR α and β chains were identified in the enriched populations using a combination of 5' rapid amplification of cDNA ends, deep sequencing of genomic DNA, PairSeq analysis, and single-cell RT-PCR analysis. Human PBL retrovirally transduced to express the TCRs were evaluated for recognition of relevant neoantigens.Results: We identified 27 TCRs from 6 patients that recognized 14 neoantigens expressed by autologous tumor cells.Conclusions: This strategy provides the means to generate T cells expressing neoantigen-reactive TCRs for use in future adoptive cell transfer immunotherapy trials for patients with cancer. Clin Cancer Res; 23(10); 2491-505. ©2016 AACR.
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Affiliation(s)
| | - Alena Gros
- NIH/NCI Surgery Branch, Bethesda, Maryland
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9
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Fozza C, Barraqueddu F, Corda G, Contini S, Virdis P, Dore F, Bonfigli S, Longinotti M. Study of the T-cell receptor repertoire by CDR3 spectratyping. J Immunol Methods 2016; 440:1-11. [PMID: 27823906 DOI: 10.1016/j.jim.2016.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 09/26/2016] [Accepted: 11/02/2016] [Indexed: 11/28/2022]
Abstract
The T-cell receptor (TCR) is the key player within the so called immunological synapse and the analysis of its repertoire offers a picture of both versatility and wideness of the whole immune T-cell compartment. Among the different approaches applied to its study the so-called spectratyping identifies the pattern of the third complementarity determining region (CDR3) length distribution in each one of the beta variable (TRBV) subfamilies encoded by the corresponding genes. This technique consists in a CDR3 fragment analysis through capillary electrophoresis, performed after cell separation, RNA extraction and reverse transcriptase PCR. This review will run through the most relevant studies which have tried to dissect the TCR repertoire usage in patients with different immune-mediated and infective diseases as well as solid or haematologic malignancies.
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Affiliation(s)
- Claudio Fozza
- Hematology, Department of Clinical and Experimental Medicine, University of Sassari, Viale San Pietro 12, 07100 Sassari, Italy.
| | - Francesca Barraqueddu
- Hematology, Department of Clinical and Experimental Medicine, University of Sassari, Viale San Pietro 12, 07100 Sassari, Italy
| | - Giovanna Corda
- Hematology, Department of Clinical and Experimental Medicine, University of Sassari, Viale San Pietro 12, 07100 Sassari, Italy
| | - Salvatore Contini
- Hematology, Department of Clinical and Experimental Medicine, University of Sassari, Viale San Pietro 12, 07100 Sassari, Italy
| | - Patrizia Virdis
- Hematology, Department of Clinical and Experimental Medicine, University of Sassari, Viale San Pietro 12, 07100 Sassari, Italy
| | - Fausto Dore
- Hematology, Department of Clinical and Experimental Medicine, University of Sassari, Viale San Pietro 12, 07100 Sassari, Italy
| | - Silvana Bonfigli
- Hematology, Department of Clinical and Experimental Medicine, University of Sassari, Viale San Pietro 12, 07100 Sassari, Italy
| | - Maurizio Longinotti
- Hematology, Department of Clinical and Experimental Medicine, University of Sassari, Viale San Pietro 12, 07100 Sassari, Italy
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Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates. Proteomes 2016; 4:proteomes4010011. [PMID: 28248221 PMCID: PMC5217363 DOI: 10.3390/proteomes4010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/05/2016] [Accepted: 03/01/2016] [Indexed: 01/20/2023] Open
Abstract
Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control.
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Jarvela JR, Tuscano L, Lee H, Silver RF. Pulmonary responses to pathogen-specific antigens in latent Mycobacterium tuberculosis infection. Tuberculosis (Edinb) 2015; 96:158-64. [PMID: 26732045 DOI: 10.1016/j.tube.2015.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/10/2015] [Indexed: 10/22/2022]
Abstract
In this study, we used ELISPOT to quantify frequencies of bronchoalveolar lavage (BAL) and peripheral blood T cells capable of producing IFNγ in response to PPD, antigen 85B, and Mtb-specific antigens CFP-10 and ESAT-6 in individuals with latent tuberculosis infection (LTBI) and Mtb-naïve controls. Compared to peripheral blood, BAL cells of LTBI subjects displayed significant enrichment for T cells responding to PPD, antigen 85B, and CFP-10, but not to ESAT-6. Baseline BAL cells of LTBI subjects displayed significant production of Mig (CXCL9) in response to PPD, antigen 85B, and CFP-10 as well. These findings suggest that enrichment for Mtb-specific T cells within BAL is not unique to active pulmonary tuberculosis and may, to the contrary, contribute to protection from re-infection in Mtb immune individuals.
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Affiliation(s)
- Jessica R Jarvela
- Division of Pulmonary, Critical Care and Sleep Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Division of Pulmonary, Critical Care and Sleep Medicine, Louis Stokes Cleveland Department of Veterans' Affairs Medical Center, Cleveland, OH, USA
| | - Lori Tuscano
- Division of Pulmonary, Critical Care and Sleep Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Division of Pulmonary, Critical Care and Sleep Medicine, Louis Stokes Cleveland Department of Veterans' Affairs Medical Center, Cleveland, OH, USA
| | - Hung Lee
- Division of Pulmonary, Critical Care and Sleep Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Division of Pulmonary, Critical Care and Sleep Medicine, Louis Stokes Cleveland Department of Veterans' Affairs Medical Center, Cleveland, OH, USA
| | - Richard F Silver
- Division of Pulmonary, Critical Care and Sleep Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Division of Pulmonary, Critical Care and Sleep Medicine, University Hospitals Case Medical Center, Cleveland, OH, USA; Division of Pulmonary, Critical Care and Sleep Medicine, Louis Stokes Cleveland Department of Veterans' Affairs Medical Center, Cleveland, OH, USA.
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Weinberger J, Jimenez-Heredia R, Schaller S, Suessner S, Sunzenauer J, Reindl-Schwaighofer R, Weiss R, Winkler S, Gabriel C, Danzer M, Oberbauer R. Immune Repertoire Profiling Reveals that Clonally Expanded B and T Cells Infiltrating Diseased Human Kidneys Can Also Be Tracked in Blood. PLoS One 2015; 10:e0143125. [PMID: 26600245 PMCID: PMC4658119 DOI: 10.1371/journal.pone.0143125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 10/30/2015] [Indexed: 12/28/2022] Open
Abstract
Recent advances in high-throughput sequencing allow for the competitive analysis of the human B and T cell immune repertoire. In this study we compared Immunoglobulin and T cell receptor repertoires of lymphocytes found in kidney and blood samples of 10 patients with various renal diseases based on next-generation sequencing data. We used Biomed-2 primer panels and ImmunExplorer software to sequence, analyze and compare complementarity determining regions and V-(D)-J elements. While generally an individual's renal receptor repertoire is different from the repertoire present in blood, 94% (30/32) of the lymphocytes with clonal expansion in kidney can also be traced in blood however, not all of these clonotypes are equally abundant. Summarizing the data of all analyzed patients, 68% of highly expanded T cell clonotypes and 30% of the highly expanded B cell clonotypes that have infiltrated the kidney can be found amongst the five most abundant clonotypes in blood. In addition, complementarity determining region 3 sequences of the immunoglobulin heavy chains are on average more diverse than T cell receptor beta chains. Immune repertoire analysis of tissue infiltrating B and T cells adds new approaches to the assessment of adaptive immune response in kidney diseases. Our data suggest that expanded clonotypes in the tissues might be traceable in blood samples in the course of treatment or the natural history of the disease.
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Affiliation(s)
- Johannes Weinberger
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Raul Jimenez-Heredia
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Susanne Schaller
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria
| | - Susanne Suessner
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Judith Sunzenauer
- Department of Internal Medicine III, KH Elisabethinen, Linz, Austria
- Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Roman Reindl-Schwaighofer
- Department of Internal Medicine III, KH Elisabethinen, Linz, Austria
- Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Richard Weiss
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Stephan Winkler
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria
| | - Christian Gabriel
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Martin Danzer
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
- * E-mail: (MD); (RO)
| | - Rainer Oberbauer
- Department of Internal Medicine III, KH Elisabethinen, Linz, Austria
- Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
- * E-mail: (MD); (RO)
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