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Zhao T, Zhang Q, Wen Q, Liu S, Niu Z, Qu Y, Wang Y, Ding Q, Wei P, Li L, Kong T, Fu P, Qian S, Wang K, Wu X, Zheng J. Characteristics of T-Cell Receptor Repertoire for Differential Response to Methotrexate Treatment for Rheumatoid Arthritis. Immunol Invest 2024; 53:1113-1124. [PMID: 39140790 DOI: 10.1080/08820139.2024.2381078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
BACKGROUND Methotrexate (MTX) serves as the initial treatment for rheumatoid arthritis (RA). However, a substantial proportion of RA patients, estimated between 30% and 50%, do not respond positively to MTX. While the T-cell receptor (TCR) is crucial for the immune response during RA, its role in differentiating MTX responsiveness has not been thoroughly investigated. METHODS This study used next-generation sequencing to analyze the TCR β-chain complementary determining region sequences in peripheral blood mononuclear cells obtained from RA patients before MTX treatment. This study aimed to compare the characteristics of the TCR repertoire between the MTX responder and non-responder groups. RESULTS The study identified a significant difference in the TRBV6-6 gene (p = .003) concerning MTX treatment response. Additionally, a significant difference was found in the number of "3" nucleotide deletions at the 5'Jdels site (p = .023) in the VDJ rearrangement. CONCLUSION These findings suggest distinct TCR repertoire characteristics between MTX responder and non-responder groups among RA patients. This discovery offers new insights into understanding the variable responses of RA patients to MTX therapy.
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MESH Headings
- Humans
- Arthritis, Rheumatoid/drug therapy
- Arthritis, Rheumatoid/immunology
- Arthritis, Rheumatoid/genetics
- Methotrexate/therapeutic use
- Male
- Female
- Middle Aged
- Antirheumatic Agents/therapeutic use
- Antirheumatic Agents/pharmacology
- Adult
- High-Throughput Nucleotide Sequencing
- Aged
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Treatment Outcome
- Complementarity Determining Regions/genetics
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
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Affiliation(s)
- Taowa Zhao
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Qian Zhang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Qinwen Wen
- Department of Rheumatology and Immunology, Ningbo First Hospital, Ningbo, China
| | - Shuyin Liu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Zitong Niu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Yang Qu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Yiting Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Qiaojiao Ding
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Pengyao Wei
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Lin Li
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Tong Kong
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Pan Fu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Sihua Qian
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Kaizhe Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Xiudi Wu
- Department of Rheumatology and Immunology, Ningbo First Hospital, Ningbo, China
| | - Jianping Zheng
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
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2
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Yue M, Li J, Li J, Hu T, Feng S, Cao J, Tang R, Wang P, Zhu F, Han L, Wu J, Cui X, Liu R. Comparative analysis of the immune repertoire between peripheral blood and bone marrow fluids in those infected by EBV and immunodeficiency: A retrospective case study. Medicine (Baltimore) 2024; 103:e39501. [PMID: 39312313 PMCID: PMC11419465 DOI: 10.1097/md.0000000000039501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/08/2024] [Indexed: 09/25/2024] Open
Abstract
High-throughput immune repertoire (IR) sequencing provides direct insight into the diversity of B cell receptor (BCR) and T cell receptor (TCR), with great potential to revolutionize the diagnosis, monitoring, and prevention of immune system-related disorders. In this study, multiplex PCR was applied to amplify the complementarity-determining regions of BCR and TCR, followed by comprehensive analysis by high-throughput sequencing. We compare the TCR (BCR) of bone marrow fluid (BMF) and peripheral blood (PB) samples from 17 patients in the Epstein-Barr and immunodeficiency groups, respectively. Our study shows that the diversity of the IR of blood samples is very similar to that of bone marrow samples statistically. However, the distributions of the monoclonal genes are significantly different in these 2 samples of most patients. This suggests that the BMFs can be replaced by the PB samples in diversity detection of IR to monitor the immune status of the body, while the detection of the BMFs is unreplaceable when the monoclonal change occurs. We used high-throughput sequencing to assess the TCR and BCR of the patients and provide a basis for the clinical analysis of PB and bone marrow samples and selection of disease diagnosis and monitoring methods.
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Affiliation(s)
- Mei Yue
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Juanjuan Li
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Junhui Li
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Tao Hu
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Shunqiao Feng
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Jing Cao
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Ruihong Tang
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | | | | | - Lu Han
- MyGenostics Inc, Beijing, China
| | - Jian Wu
- MyGenostics Inc, Beijing, China
| | - Xiaodai Cui
- Department of Key Laboratory, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Rong Liu
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
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3
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Chen L, Hu Y, Zheng B, Luo L, Su Z. Human TCR repertoire in cancer. Cancer Med 2024; 13:e70164. [PMID: 39240157 PMCID: PMC11378360 DOI: 10.1002/cam4.70164] [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: 05/06/2024] [Revised: 08/02/2024] [Accepted: 08/19/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND T cells, the "superstar" of the immune system, play a crucial role in antitumor immunity. T-cell receptors (TCR) are crucial molecules that enable T cells to identify antigens and start immunological responses. The body has evolved a unique method for rearrangement, resulting in a vast diversity of TCR repertoires. A healthy TCR repertoire is essential for the particular identification of antigens by T cells. METHODS In this article, we systematically summarized the TCR creation mechanisms and analysis methodologies, particularly focusing on the application of next-generation sequencing (NGS) technology. We explore the TCR repertoire in health and cancer, and discuss the implications of TCR repertoire analysis in understanding carcinogenesis, cancer progression, and treatment. RESULTS The TCR repertoire analysis has enormous potential for monitoring the emergence and progression of malignancies, as well as assessing therapy response and prognosis. The application of NGS has dramatically accelerated our comprehension of TCR diversity and its role in cancer immunity. CONCLUSIONS To substantiate the significance of TCR repertoires as biomarkers, more thorough and exhaustive research should be conducted. The TCR repertoire analysis, enabled by advanced sequencing technologies, is poised to become a crucial tool in the future of cancer diagnosis, monitoring, and therapy evaluation.
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Affiliation(s)
- Lin Chen
- Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yuan Hu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Anesthesia Nursing, West China Second University Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
| | - Bohao Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Limei Luo
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Zhenzhen Su
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
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Chen Y, Fu Q, Ma Y, Wang N, Yang J, Liang Q, Wang K, Gao L. Identification of the immune repertoire of γδ T-cell receptors in psoriasis. Immunol Cell Biol 2024; 102:570-577. [PMID: 38710590 DOI: 10.1111/imcb.12765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/18/2024] [Accepted: 04/14/2024] [Indexed: 05/08/2024]
Abstract
The γδ T cells are a subpopulation of T cells that are abundantly found in the skin and mucous membranes. Their reactivity to self-antigens and ability to secrete various cytokines make them a key component in psoriasis development. Although the correlation between the immune repertoire (IR) of γδ T-cell receptors and the occurrence and severity of psoriasis remains incompletely explored, high-throughput sequencing of γδ T cells has led to a deeper understanding of IR in psoriasis. This study investigated the differences between γδ T cells in patients with psoriasis and healthy controls. The γδ T cells were identified via immunofluorescence staining and a correlation analysis was performed according to the psoriasis area and severity index (PASI) scores. The IR sequencing method was used to detect IR in the γδ T-cell receptors. The findings demonstrated more skin γδ T cells in patients with psoriasis, which were positively correlated with the PASI score. There were subtle differences in most variable (V), diversity (D) and joining (J) gene segments and VJ/VDJ combination segments between patients with psoriasis and healthy controls. However, a higher diversity of complementarity-determining region 3 (CDR3) was observed in patients with psoriasis. In summary, the IR of skin γδ T cells was significantly altered in patients with psoriasis, and the diversity in the cell's CDR3 population is a promising biomarker for assessment of psoriasis severity.
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Affiliation(s)
- Yuting Chen
- Department of Dermatology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, China
| | - Quanze Fu
- Clinical Research Institute, The First Affiliated Hospital of Xiamen University, State Key Laboratory of Cellular Stress Biology, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yinjiang Ma
- Clinical Research Institute, The First Affiliated Hospital of Xiamen University, State Key Laboratory of Cellular Stress Biology, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Nan Wang
- Clinical Research Institute, The First Affiliated Hospital of Xiamen University, State Key Laboratory of Cellular Stress Biology, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Ji Yang
- Department of Dermatology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, China
- Department of Dermatology, Zhongshan Hospital Fudan University, Shanghai, China
| | - Qing Liang
- Clinical Research Institute, The First Affiliated Hospital of Xiamen University, State Key Laboratory of Cellular Stress Biology, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Kejia Wang
- Clinical Research Institute, The First Affiliated Hospital of Xiamen University, State Key Laboratory of Cellular Stress Biology, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Lujuan Gao
- Department of Dermatology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, Fujian, China
- Department of Dermatology, Zhongshan Hospital Fudan University, Shanghai, China
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5
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Xu S, Zhang Y, Yang Y, Dong K, Zhang H, Luo C, Liu SM. A m 6A regulators-related classifier for prognosis and tumor microenvironment characterization in hepatocellular carcinoma. Front Immunol 2024; 15:1374465. [PMID: 39119345 PMCID: PMC11306056 DOI: 10.3389/fimmu.2024.1374465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Background Increasing evidence have highlighted the biological significance of mRNA N6-methyladenosine (m6A) modification in regulating tumorigenicity and progression. However, the potential roles of m6A regulators in tumor microenvironment (TME) formation and immune cell infiltration in liver hepatocellular carcinoma (LIHC or HCC) requires further clarification. Method RNA sequencing data were obtained from TCGA-LIHC databases and ICGC-LIRI-JP databases. Consensus clustering algorithm was used to identify m6A regulators cluster subtypes. Weighted gene co-expression network analysis (WGCNA), LASSO regression, Random Forest (RF), and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) were applied to identify candidate biomarkers, and then a m6Arisk score model was constructed. The correlations of m6Arisk score with immunological characteristics (immunomodulators, cancer immunity cycles, tumor-infiltrating immune cells (TIICs), and immune checkpoints) were systematically evaluated. The effective performance of nomogram was evaluated using concordance index (C-index), calibration plots, decision curve analysis (DCA), and receiver operating characteristic curve (ROC). Results Two distinct m6A modification patterns were identified based on 23 m6A regulators, which were correlated with different clinical outcomes and biological functions. Based on the constructed m6Arisk score model, HCC patients can be divided into two distinct risk score subgroups. Further analysis indicated that the m6Arisk score showed excellent prognostic performance. Patients with a high m6Arisk score was significantly associated with poorer clinical outcome, lower drug sensitivity, and higher immune infiltration. Moreover, we developed a nomogram model by incorporating the m6Arisk score and clinicopathological features. The application of the m6Arisk score for the prognostic stratification of HCC has good clinical applicability and clinical net benefit. Conclusion Our findings reveal the crucial role of m6A modification patterns for predicting HCC TME status and prognosis, and highlight the good clinical applicability and net benefit of m6Arisk score in terms of prognosis, immunophenotype, and drug therapy in HCC patients.
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Affiliation(s)
- Shaohua Xu
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Yi Zhang
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ying Yang
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kexin Dong
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hanfei Zhang
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chunhua Luo
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Song-Mei Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
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Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP. An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. BMC Genomics 2023; 24:349. [PMID: 37365517 DOI: 10.1186/s12864-023-09424-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
T cell receptor repertoires can be profiled using next generation sequencing (NGS) to measure and monitor adaptive dynamical changes in response to disease and other perturbations. Genomic DNA-based bulk sequencing is cost-effective but necessitates multiplex target amplification using multiple primer pairs with highly variable amplification efficiencies. Here, we utilize an equimolar primer mixture and propose a single statistical normalization step that efficiently corrects for amplification bias post sequencing. Using samples analyzed by both our open protocol and a commercial solution, we show high concordance between bulk clonality metrics. This approach is an inexpensive and open-source alternative to commercial solutions.
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Affiliation(s)
- Burcu Gurun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- School of Medicine, Oregon Health and Science University, Portland, OR, USA.
| | - Wesley Horton
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Dhaarini Murugan
- Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Biqing Zhu
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Patrick Leyshock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Sushil Kumar
- Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Katelyn T Byrne
- Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert H Vonderheide
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Motomi Mori
- Department of Biostatistics, St. Jude's Children's Research Hospital, Memphis, TN, USA
| | - Paul T Spellman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Lisa M Coussens
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Terence P Speed
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
- School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, 3010, Australia.
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7
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Guo C, Tang Y, Li Q, Yang Z, Guo Y, Chen C, Zhang Y. Deciphering the immune heterogeneity dominated by natural killer cells with prognostic and therapeutic implications in hepatocellular carcinoma. Comput Biol Med 2023; 158:106872. [PMID: 37030269 DOI: 10.1016/j.compbiomed.2023.106872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/15/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023]
Abstract
Belonging to type 1 innate lymphoid cells (ILC1), natural killer (NK) cells play an important role not only in fighting microbial infections but also in anti-tumor response. Hepatocellular carcinoma (HCC) represents an inflammation-related malignancy and NK cells are enriched in the liver, making them an essential component of the HCC immune microenvironment. In this study, we performed single-cell RNA-sequencing (scRNA-seq) analysis to identify the NK cell marker genes (NKGs) and uncovered 80 prognosis-related ones by the TCGA-LIHC dataset. Based on prognostic NKGs, HCC patients were categorized into two subtypes with distinct clinical outcomes. Subsequently, we conducted LASSO-COX and stepwise regression analysis on prognostic NKGs to establish a five-gene (UBB, CIRBP, GZMH, NUDC, and NCL) prognostic signature-NKscore. Different mutation statuses of the two risk groups stratified by NKscore were comprehensively characterized. Besides, the established NKscore-integrated nomogram presented enhanced predictive performance. Single sample gene set enrichment analysis (ssGSEA) analysis was used to uncover the landscape of the tumor immune microenvironment (TIME) and the high-NKscore risk group was characterized with an immune-exhausted phenotype while the low-NKscore risk group held relatively strong anti-cancer immunity. T cell receptor (TCR) repertoire, tumor inflammation signature (TIS), and Immunophenoscore (IPS) analyses revealed differences in immunotherapy sensitivity between the two NKscore risk groups. Taken together, we developed a novel NK cell-related signature to predict the prognosis and immunotherapy efficacy for HCC patients.
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Affiliation(s)
- Chengbin Guo
- Faculty of Medicine, Macau University of Science and Technology, Tapai, Macau, 999078, China
| | - Yuqin Tang
- Clinical Bioinformatics Experimental Center, Henan Provincial People's Hospital, Zhengzhou University, 450003, Zhengzhou, China
| | - Qizhuo Li
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhao Yang
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuqi Guo
- Clinical Bioinformatics Experimental Center, Henan Provincial People's Hospital, Zhengzhou University, 450003, Zhengzhou, China.
| | - Chuanliang Chen
- Clinical Bioinformatics Experimental Center, Henan Provincial People's Hospital, Zhengzhou University, 450003, Zhengzhou, China.
| | - Yongqiang Zhang
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
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8
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Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP. An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. RESEARCH SQUARE 2023:rs.3.rs-2140339. [PMID: 36824803 PMCID: PMC9949261 DOI: 10.21203/rs.3.rs-2140339/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
T cell receptor repertoires can be profiled using next generation sequencing (NGS) to measure and monitor adaptive dynamical changes in response to disease and other perturbations. Genomic DNA-based bulk sequencing is cost-effective but necessitates multiplex target amplification using multiple primer pairs with highly variable amplification efficiencies. Here, we utilize an equimolar primer mixture and propose a single statistical normalization step that efficiently corrects for amplification bias post sequencing. Using samples analyzed by both our open protocol and a commercial solution, we show high concordance between bulk clonality metrics. This approach is an inexpensive and open-source alternative to commercial solutions.
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9
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Gao B, Wang Y, Li C, Lu S. Estrogen-related genes influence immune cell infiltration and immunotherapy response in Hepatocellular Carcinoma. Front Immunol 2023; 14:1114717. [PMID: 36814910 PMCID: PMC9939443 DOI: 10.3389/fimmu.2023.1114717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/25/2023] [Indexed: 02/08/2023] Open
Abstract
Background Immunotherapy has been the first-line treatment option in advanced Hepatocellular Carcinoma(HCC); but now, there are no established molecular markers that can predict immunotherapy response. Estrogen has a crucial role in the development of a variety of liver illnesses, including liver fibrosis, Nonalcoholic fatty liver disease (NAFLD), and HCC. Nonetheless, the significance of estrogen-related genes in HCC immunotherapy and the underlying molecular mechanisms are not yet fully understood. Method In this study, we constructed a novel estrogen-related gene prognostic signature (ERGPS) by analyzing bulk RNA sequencing data from 365 HCC patients. Based on the median risk score, we divided 365 HCC patients into low- and high-risk groups. Tumor mutation burden (TMB), Microsatellite instability (MSI), T cell receptor (TCR) richness, B cell receptor (BCR) richness, single-nucleotide variants (SNV) Neoantigens, Cancer Testicular Antigens (CTA) scores, and Tumour Immune Dysfunction and Exclusion (TIDE) scores were used to evaluate the magnitude of immunotherapy response. Multiple external datasets validate the validity and robustness of the prognostic signature. Real-time quantitative polymerase chain reaction (qRT-PCR) was used to validate estrogen-related gene overexpression in HCC tissue samples. Results ERGPS is an independent risk factor affecting the prognosis of HCC patients and is superior to other clinical variables in predicting patient survival and immunotherapy response. Multiple independent external datasets confirmed the superior predictive efficacy of the prognostic signature. The prognostic signature was positively correlated with TMB score, MSI score, TCR richness, BCR richness, SNV Neoantigens score, CTA score, expression levels of immune checkpoint-related genes, and TIDE score. Patients with HCC in the high-risk group identified by the prognostic signature were likely to be more responsive to immunotherapy and more suitable for immunotherapy. qRT-PCR confirmed that estrogen-related genes of the construct signature were highly expressed in HCC tumor tissues. Conclusion Estrogen-related genes are overexpressed in HCC tissues. Our novel prognostic signature can accurately predict not only the prognosis but also the immunotherapy response of HCC patients. In the future, prognostic signatures will be a useful tool for clinicians to screen patients with HCC who are suitable for immunotherapy.
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Affiliation(s)
- Biao Gao
- Nankai University School of Medicine, Nankai University, Tianjin, China,Faculty of Hepato-Pancreato-Biliary Surgery, Chinese PLA General Hospital, Beijing, China
| | - Yafei Wang
- Nankai University School of Medicine, Nankai University, Tianjin, China,Faculty of Hepato-Pancreato-Biliary Surgery, Chinese PLA General Hospital, Beijing, China
| | - Chonghui Li
- Faculty of Hepato-Pancreato-Biliary Surgery, Chinese PLA General Hospital, Beijing, China,Institute of Hepatobiliary Surgery, Chinese PLA General Hospital, Beijing, China,*Correspondence: Chonghui Li, ; Shichun Lu,
| | - Shichun Lu
- Faculty of Hepato-Pancreato-Biliary Surgery, Chinese PLA General Hospital, Beijing, China,Institute of Hepatobiliary Surgery, Chinese PLA General Hospital, Beijing, China,*Correspondence: Chonghui Li, ; Shichun Lu,
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10
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Qi H, Xue JB, Lai DY, Li A, Tao SC. Current advances in antibody-based serum biomarker studies: From protein microarray to phage display. Proteomics Clin Appl 2022; 16:e2100098. [PMID: 36071670 DOI: 10.1002/prca.202100098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 08/16/2022] [Accepted: 09/05/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE This review aims to summarize the technological advances in the field of antibody-based biomarker studies by proteome microarray and phage display. In addition, the possible development directions of this field are also discussed. EXPERIMENTAL DESIGN We have focused on the antibody profiling by proteome microarray and phage display, including the technological advances, the tools/resources constructed, and the characteristics of both platforms. RESULTS With the help of tools/resources and technological advances in proteome microarray and phage display, the efficiency of profiling antibody-based biomarkers in serum samples has been greatly improved. CONCLUSIONS In the past few years, proteome microarray and phage display, especially the latter one, have already demonstrated their capacity and efficiency for biomarker identification. In the near future, we believe that more antibody-based biomarkers could be identified, and some of them could eventually be developed into real clinical applications.
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Affiliation(s)
- Huan Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Jun-Biao Xue
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Dan-Yun Lai
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Ang Li
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
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11
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Gao H, Yu L, Yan F, Zheng Y, Huang H, Zhuang X, Zeng Y. Landscape of B Cell Receptor Repertoires in COVID-19 Patients Revealed Through CDR3 Sequencing of Immunoglobulin Heavy and Light Chains. Immunol Invest 2022; 51:1994-2008. [PMID: 35797435 DOI: 10.1080/08820139.2022.2092407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The outbreak and persistence of coronavirus disease 2019 (COVID-19) threaten human health. B cells play a vital role in fighting the infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite many studies on the immune responses in COVID-19 patients, it is still unclear how B cell receptor (BCR) constituents, including immunoglobulin heavy (IGHs) and light chains (IGLs), respond to SARS-CoV-2 in patients with varying symptoms. In this study, we conducted complementarity-determining region 3 (CDR3) sequencing of BCR IGHs and IGLs from the peripheral blood of COVID-19 patients and healthy donors. The results showed significantly reduced clonal diversity, more expanded clones, and longer CDR3 lengths of IGH and IGL in COVID-19 patients than those in healthy individuals. The IGLs had a much higher percentage of VJ skew usage (47.83% IGLV and 42.86% IGLJ were significantly regulated) than the IGHs (12.09% IGHV and 0% IGHJ) between the healthy individuals and patients, which indicated the importance of BCR light chains. Furthermore, we found a largely expanded IGLV3-25 gene cluster mostly pairing with IGLJ1 and ILGJ2 in COVID-19 patients and a newly identified upregulated IGLJ1 gene and IGLJ2+IGLV13-21 recombination, both of which are potential sources of SARS-CoV-2-targeting antibodies. Our findings on specific immune B-cell signatures associated with COVID-19 have clinical implications for vaccine and biomarker development for disease diagnosis.
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Affiliation(s)
- Hongzhi Gao
- Central Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.,Department of Respiratory Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Liying Yu
- Central Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Furong Yan
- Central Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Youxian Zheng
- Department of Microbiology, Quanzhou Municipal Center for Disease Control and Prevention, Fujian Province, Quanzhou, China
| | - Hongbo Huang
- Department of Pulmonary and Critical Care Medicine, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xibin Zhuang
- Department of Pulmonary and Critical Care Medicine, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian Province, China
| | - Yiming Zeng
- Department of Respiratory Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
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12
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Song P, Li W, Guo L, Ying J, Gao S, He J. Identification and Validation of a Novel Signature Based on NK Cell Marker Genes to Predict Prognosis and Immunotherapy Response in Lung Adenocarcinoma by Integrated Analysis of Single-Cell and Bulk RNA-Sequencing. Front Immunol 2022; 13:850745. [PMID: 35757748 PMCID: PMC9231585 DOI: 10.3389/fimmu.2022.850745] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Natural killer (NK) cells, the effectors of the innate immune system, have a remarkable influence on cancer prognosis and immunotherapy. In this study, a total of 1,816 samples from nine independent cohorts in public datasets were enrolled. We first conducted a comprehensive analysis of single-cell RNA-sequencing data of lung adenocarcinoma (LUAD) from the Gene Expression Omnibus (GEO) database and determined 189 NK cell marker genes. Subsequently, we developed a seven-gene prognostic signature based on NK cell marker genes in the TCGA LUAD cohort, which stratified patients into high-risk and low-risk groups. The predictive power of the signature was well verified in different clinical subgroups and GEO cohorts. With a multivariate analysis, the signature was identified as an independent prognostic factor. Low-risk patients had higher immune cell infiltration states, especially CD8+ T cells and follicular helper T cells. There existed a negative association between inflammatory activities and risk score, and the richness and diversity of the T-cell receptor (TCR) repertoire was higher in the low-risk groups. Importantly, analysis of an independent immunotherapy cohort (IMvigor210) revealed that low-risk patients had better immunotherapy responses and prognosis than high-risk patients. Collectively, our study developed a novel signature based on NK cell marker genes, which had a potent capability to predict the prognosis and immunotherapy response of LUAD patients.
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Affiliation(s)
- Peng Song
- 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, China
| | - Wenbin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- 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, China
| | - Jie He
- 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, China
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13
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Hirschhorn D, Betof Warner A, Maniyar R, Chow A, Mangarin LM, Cohen AD, Hamadene L, Rizzuto GA, Budhu S, Suek N, Liu C, Houghton AN, Merghoub T, Wolchok JD. Cyclophosphamide enhances the antitumor potency of GITR engagement by increasing oligoclonal cytotoxic T cell fitness. JCI Insight 2021; 6:151035. [PMID: 34676831 PMCID: PMC8564916 DOI: 10.1172/jci.insight.151035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/02/2021] [Indexed: 01/22/2023] Open
Abstract
Only a subset of cancer patients responds to checkpoint blockade inhibition in the clinic. Strategies to overcome resistance are promising areas of investigation. Targeting glucocorticoid-induced tumor necrosis factor receptor-related protein (GITR) has shown efficacy in preclinical models, but GITR engagement is ineffective in controlling advanced, poorly immunogenic tumors, such as B16 melanoma, and has not yielded benefit in clinical trials. The alkylating agent cyclophosphamide (CTX) depletes regulatory T cells (Tregs), expands tumor-specific effector T cells (Teffs) via homeostatic proliferation, and induces immunogenic cell death. GITR agonism has an inhibitory effect on Tregs and activates Teffs. We therefore hypothesized that CTX and GITR agonism would promote effective antitumor immunity. Here we show that the combination of CTX and GITR agonism controlled tumor growth in clinically relevant mouse models. Mechanistically, we show that the combination therapy caused tumor cell death, clonal expansion of highly active CD8+ T cells, and depletion of Tregs by activation-induced cell death. Control of tumor growth was associated with the presence of an expanded population of highly activated, tumor-infiltrating, oligoclonal CD8+ T cells that led to a diminished TCR repertoire. Our studies show that the combination of CTX and GITR agonism is a rational chemoimmunotherapeutic approach that warrants further clinical investigation.
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Affiliation(s)
- Daniel Hirschhorn
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Allison Betof Warner
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
| | - Rachana Maniyar
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Andrew Chow
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
| | - Levi Mb Mangarin
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Adam D Cohen
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and
| | - Linda Hamadene
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Gabrielle A Rizzuto
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Sadna Budhu
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Nathan Suek
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Cailian Liu
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Alan N Houghton
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Taha Merghoub
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
| | - Jedd D Wolchok
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
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14
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Granadier D, Iovino L, Kinsella S, Dudakov JA. Dynamics of thymus function and T cell receptor repertoire breadth in health and disease. Semin Immunopathol 2021; 43:119-134. [PMID: 33608819 PMCID: PMC7894242 DOI: 10.1007/s00281-021-00840-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/12/2021] [Indexed: 12/26/2022]
Abstract
T cell recognition of unknown antigens relies on the tremendous diversity of the T cell receptor (TCR) repertoire; generation of which can only occur in the thymus. TCR repertoire breadth is thus critical for not only coordinating the adaptive response against pathogens but also for mounting a response against malignancies. However, thymic function is exquisitely sensitive to negative stimuli, which can come in the form of acute insult, such as that caused by stress, infection, or common cancer therapies; or chronic damage such as the progressive decline in thymic function with age. Whether it be prolonged T cell deficiency after hematopoietic cell transplantation (HCT) or constriction in the breadth of the peripheral TCR repertoire with age; these insults result in poor adaptive immune responses. In this review, we will discuss the importance of thymic function for generation of the TCR repertoire and how acute and chronic thymic damage influences immune health. We will also discuss methods that are used to measure thymic function in patients and strategies that have been developed to boost thymic function.
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Affiliation(s)
- David Granadier
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Department of Molecular and Cellular Biology, University of Washington, Seattle, WA, USA
| | - Lorenzo Iovino
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sinéad Kinsella
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jarrod A Dudakov
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
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15
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Lian YF, Xu Y, Gu YR, Bi YH, Liao CH, Zhao MX, Liao XL, Wang ZH, Wu HK, Huang YH. Distinct T-cell receptor profiles associated with hepatitis B e antigen seroconversion during entecavir treatment. Liver Int 2020; 40:2672-2684. [PMID: 32564486 DOI: 10.1111/liv.14566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/18/2020] [Accepted: 06/07/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS T-cell receptor (TCR) repertoire is ambiguously changed in chronic hepatitis B (CHB) patients during antivirus therapy. We tried to assess TCR repertoire dynamics and its clinical significance upon HBeAg seroconversion in CHB patients. METHODS Twenty CHB patients undergoing 1-year entecavir (ETV) treatment were enrolled, including 10 complete response (CR) vs 10 non-complete response (NCR) patients based on HBeAg seroconversion at week 48. The TCRβ complementarity-determining region 3 (CDR3) of peripheral CD4+ and CD8+ T cells at weeks 0, 12 and 48 was analyzed by unbiased high-throughput sequencing. The TCR repertoire profiles and their correlations with serological parameters were analyzed. RESULTS The diversity of TCRβ repertoires was decreasing in CR patients but increasing in NCR patients. The distribution pattern of TCR repertoires stratified according to clonotype frequencies changed in the opposite direction between CR and NCR patients. Narrow amounts of newly appearing clonotypes in CR patients experienced a more intensive and robust expansion and this phenomenon could occur as early as week 12 for the CD4+ subset but later at week 48 for the CD8+ subset. There existed some CR-exclusive clonotypes with a relatively low but increasing frequency at week 48. The number of unique TCRβ clonotypes was positively correlated with the ALT or HBV DNA level in CR patients but showed no or negative correlation in NCR patients. CONCLUSION Distinct TCR profiles contribute to predicting HBeAg seroconversion in CHB patients during ETV treatment and certain TCRβ CDR3 motif may be utilized for CHB immunotherapy in the future.
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Affiliation(s)
- Yi-Fan Lian
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ying Xu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yu-Rong Gu
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yan-Hua Bi
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chun-Hong Liao
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Miao-Xian Zhao
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xia-Lin Liao
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhan-Hui Wang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hong-Kai Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yue-Hua Huang
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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16
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Feng J, Fan S, Sun Y, Zhang Z, Ren H, Li W, Cui L, Peng B, Ren X, Zhang W, Guan H, Wang J. Study of B Cell Repertoire in Patients With Anti-N-Methyl-D-Aspartate Receptor Encephalitis. Front Immunol 2020; 11:1539. [PMID: 32849520 PMCID: PMC7403192 DOI: 10.3389/fimmu.2020.01539] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/11/2020] [Indexed: 12/11/2022] Open
Abstract
Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is the most common antibody-mediated encephalitis. There are several studies on B cell repertoire of anti-NMDAR encephalitis in Caucasians. Here, the cerebrospinal fluid (CSF) samples of 12 Chinese patients with first-episode anti-NMDAR encephalitis were collected to investigate the B cell receptor (BCR) binding to NMDAR by single cell amplification of BCR and Sanger sequencing. BCR data of healthy persons, and of patients with anti-leucine-rich glioma inactivated 1 (anti-LGI1) encephalitis, multiple sclerosis (MS), and neuromyelitis optica spectrum disorder (NMOSD) from the public databases were used as control. A heavy chain common clone IGHV1-18*04,IGHD1-26*01/ IGHD2-2*03/IGHD2-8*01, IGHJ3*02_(CDR3) ARVGSKYGFETFDI was found in 11 of 12 enrolled patients but not in the comparison data set. In addition, 4 shared clonotypes were found among these patients, and three of them contained the common clone. This study also revealed that the antibody gene family usage preference between patients and healthy controls were different, while they had similar antibody mutation rate. Our findings may have potential clinical implications for the diagnosis of anti-NMDAR encephalitis.
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Affiliation(s)
- Jingjing Feng
- CAS Key Laboratory of Mental Health, Institute of Psychology, Beijing, China.,Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Siyuan Fan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yinwei Sun
- CAS Key Laboratory of Mental Health, Institute of Psychology, Beijing, China.,Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | | | - Haitao Ren
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenhan Li
- Oumeng V Medical Laboratory, Hangzhou, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Peng
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaotun Ren
- Department of Neurology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Weihua Zhang
- Department of Neurology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Hongzhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Wang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Beijing, China.,Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
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17
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Ni Q, Zhang J, Zheng Z, Chen G, Christian L, Grönholm J, Yu H, Zhou D, Zhuang Y, Li QJ, Wan Y. VisTCR: An Interactive Software for T Cell Repertoire Sequencing Data Analysis. Front Genet 2020; 11:771. [PMID: 32849789 PMCID: PMC7416706 DOI: 10.3389/fgene.2020.00771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 06/29/2020] [Indexed: 11/13/2022] Open
Abstract
Recent progress in high throughput sequencing technologies has provided an opportunity to probe T cell receptor (TCR) repertoire, bringing about an explosion of TCR sequencing data and analysis tools. For easier and more heuristic analysis TCR sequencing data, we developed a client-based HTML program (VisTCR). It has a data storage module and a data analysis module that integrate multiple cutting-edge analysis algorithms in a hierarchical fashion. Researchers can group and re-group samples for different analysis purposes by customized "Experiment Design File." Moreover, the VisTCR provides a user-friendly interactive interface, by all the TCR analysis methods and visualization results can be accessed and saved as tables or graphs in the process of analysis. The source code is freely available at https://github.com/qingshanni/VisTCR.
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Affiliation(s)
- Qingshan Ni
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Jianyang Zhang
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | | | - Gang Chen
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Laura Christian
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Juha Grönholm
- Molecular Development of the Immune System Section, NIAID Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Haili Yu
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Daxue Zhou
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Yuan Zhuang
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Qi-Jing Li
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Ying Wan
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
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18
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Abstract
Tumor immunology is undergoing a renaissance due to the recent profound clinical successes of tumor immunotherapy. These advances have coincided with an exponential growth in the development of -omics technologies. Armed with these technologies and their associated computational and modeling toolsets, systems biologists have turned their attention to tumor immunology in an effort to understand the precise nature and consequences of interactions between tumors and the immune system. Such interactions are inherently multivariate, spanning multiple time and size scales, cell types, and organ systems, rendering systems biology approaches particularly amenable to their interrogation. While in its infancy, the field of 'Cancer Systems Immunology' has already influenced our understanding of tumor immunology and immunotherapy. As the field matures, studies will move beyond descriptive characterizations toward functional investigations of the emergent behavior that govern tumor-immune responses. Thus, Cancer Systems Immunology holds incredible promise to advance our ability to fight this disease.
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Affiliation(s)
| | - Edgar G Engleman
- Department of Pathology, Stanford University School of MedicineStanfordUnited States
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of MedicineStanfordUnited States
- Stanford Cancer Institute, Stanford UniversityStanfordUnited States
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19
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A new risk model comprising genes highly correlated with CD133 identifies different tumor-immune microenvironment subtypes impacting prognosis in hepatocellular carcinoma. Aging (Albany NY) 2020; 12:12234-12250. [PMID: 32564007 PMCID: PMC7343494 DOI: 10.18632/aging.103409] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/25/2020] [Indexed: 12/13/2022]
Abstract
The existence of cancer stem cells (CSCs), marked by CD133, is the primary cause of death in hepatocellular carcinoma (HCC). Here, we generated a new risk model comprising the signatures of four genes highly correlated with CD133 (CD133(hi)) that help improve survival in HCC. Three datasets were used to identify the differential CD133(hi) genes by comparing sorted CD133+ liver CSCs and CD133- differentiated counterparts. Univariate analysis was used to screen significantly differential CD133(hi) genes associated with overall survival in the training dataset, which were used for risk model construction. High-risk patients were strongly associated with poor survival by Kaplan-Meier survival analysis in both the training and validation datasets. Clinical stratification analyses further demonstrated that the risk factors acted as independent factors and that high-risk patients were characterized by more aggressive cancer features. Functional enrichment analyses performed by gene set enrichment analysis (GSEA) and the Database for Annotation, Visualization and Integrated Discovery (DAVID) revealed that high-risk patients showed the disturbance of immune hepatic homeostasis involving aberrant immune cells, including macrophages and T and B cells, and an abnormal inflammatory response including the IL6/Jak/STAT3 pathway and TNF signaling pathway. In conclusion, our constructed CD133(hi) gene risk model provides a resource for understanding the role of CD133+ CSCs in the progression of HCC in terms of tumor-immune interactions.
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20
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Hu HT, Luo LH, Tian YT. Immune repertoire of digestive system tumors. Shijie Huaren Xiaohua Zazhi 2020; 28:335-340. [DOI: 10.11569/wcjd.v28.i9.335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Immune repertoire refers to the sum of T cells and B cells with functional diversity in the circulatory system of one individual at any given time. Immune repertoire sequencing aims to study T and B lymphocytes, evaluate the diversity of the immune system, and dig deeper into the relationship between immune repertoire and diseases, using multiple polymerase chain reaction or rapid amplification of 5' cDNA ends to amplify the complementary determining regions that determine the diversity of B cell receptors or T cell receptors as well as high-throughput sequencing and data analysis. Recently, immune repertoire has been widely studied in the identification of biomarkers and therapeutic targets, efficacy monitoring, and prognosis analysis in cancer. This paper reviews the progress in the research of immune repertoire of digestive system tumors.
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Affiliation(s)
- Hai-Tao Hu
- Department of Pancreatic and Gastric Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Li-Hua Luo
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong Province, China
| | - Yan-Tao Tian
- Department of Pancreatic and Gastric Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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21
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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: 6] [Impact Index Per Article: 1.2] [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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22
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Busch S, Talamini M, Brenner S, Abdulazim A, Hänggi D, Neumaier M, Seiz-Rosenhagen M, Fuchs T. Circulating monocytes and tumor-associated macrophages express recombined immunoglobulins in glioblastoma patients. Clin Transl Med 2019; 8:18. [PMID: 31155685 PMCID: PMC6545295 DOI: 10.1186/s40169-019-0235-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/17/2019] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Glioblastoma is the most common and malignant brain tumor in adults. Glioblastoma is usually fatal 12-15 months after diagnosis and the current possibilities in therapy are mostly only palliative. Therefore, new forms of diagnosis and therapy are urgently needed. Since tumor-associated macrophages are key players in tumor progression and survival there is large potential in investigating their immunological characteristics in glioblastoma patients. Recent evidence shows the expression of variable immunoglobulins and TCRαβ in subpopulations of monocytes, in vitro polarized macrophages and macrophages in the tumor microenvironment. We set out to investigate the immunoglobulin sequences of circulating monocytes and tumor-associated macrophages from glioblastoma patients to evaluate their potential as novel diagnostic or therapeutic targets. RESULTS We routinely find consistent expression of immunoglobulins in tumor-associated macrophages (TAM) and circulating monocytes from all glioblastoma patients analyzed in this study. However, the immunoglobulin repertoires of circulating monocytes and TAM are generally more restricted compared to B cells. Furthermore, the immunoglobulin expression in the macrophage populations negatively correlates with the tumor volume. Interestingly, the comparison of somatic mutations, V-chain usage, CDR3-length and the distribution of used heavy chain genes on the locus of chromosome 14 of the immunoglobulins from myeloid to B cells revealed virtually no differences. CONCLUSIONS The investigation of the immunoglobulin repertoires from TAM and circulating monocytes in glioblastoma-patients revealed a negative correlation to the tumor volume, which could not be detected in the immunoglobulin repertoires of the patients' B lymphocytes. Furthermore, the immunoglobulin repertoires of monocytes were more diverse than the repertoires of the macrophages in the tumor microenvironment from the same patients suggesting a tumor-specific immune response which could be advantageous for the use as diagnostic or therapeutic target.
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Affiliation(s)
- Svenja Busch
- Institute for Clinical Chemistry, Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Marina Talamini
- Institute for Clinical Chemistry, Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Steffen Brenner
- Department of Neurosurgery, University Hospital Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Amr Abdulazim
- Department of Neurosurgery, University Hospital Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Daniel Hänggi
- Department of Neurosurgery, University Hospital Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry, Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Marcel Seiz-Rosenhagen
- Department of Neurosurgery, University Hospital Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Tina Fuchs
- Institute for Clinical Chemistry, Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
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23
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Ren L, Leisegang M, Deng B, Matsuda T, Kiyotani K, Kato T, Harada M, Park JH, Saloura V, Seiwert T, Vokes E, Agrawal N, Nakamura Y. Identification of neoantigen-specific T cells and their targets: implications for immunotherapy of head and neck squamous cell carcinoma. Oncoimmunology 2019; 8:e1568813. [PMID: 30906664 PMCID: PMC6422382 DOI: 10.1080/2162402x.2019.1568813] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/23/2018] [Accepted: 11/02/2018] [Indexed: 01/04/2023] Open
Abstract
To develop a practically applicable method for T-cell receptor (TCR)-engineered T cell immunotherapy targeting neoantigens, we have been attempting to identify neoantigen-specific T cell receptors (TCRs) and establish TCR-engineered T cells in a 3-4-month period. In this study, we report the characterization of T cell repertoires in tumor microenvironment (TME) and identification of neoantigen-specific TCRs after stimulation of patient-derived T cells. We screened 15 potential neoantigen peptides and successfully identified two CD8+HLA-dextramer+ T cells, which recognized MAGOHBG17A and ZCCHC14P368L. All three dominant TCR clonotypes from MAGOHBG17A-HLA dextramer-sorted CD8+ T cells were also found in T cells in TME, while none of dominant TCR clonotypes from ZCCHC14P368L-HLA dextramer-sorted CD8+ T cells was found in the corresponding TME. The most dominant TCRA/TCRB pairs for these two neoantigens were cloned into HLA-matched healthy donors' T lymphocytes to generate TCR-engineered T cells. The functional assay showed MAGOHBG17A TCR-engineered T cells could be significantly activated in a mutation-specific, HLA-restricted and peptide-dose-dependent manner while ZCCHC14P368L TCR-engineered T cells could not. Our data showed neoantigen-reactive T cell clonotypes that were identified in the patient's peripheral blood could be present in the corresponding TME and might be good TCRs targeting neoantigens.
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Affiliation(s)
- Lili Ren
- Department of Medicine, The University of Chicago, Chicago, IL, USA.,Cytotherapy Laboratory, Shenzhen People's Hospital (The second Clinical Medical College of Jinan University), Shenzhen, China
| | - Matthias Leisegang
- Institute of Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Boya Deng
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Tatsuo Matsuda
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Kazuma Kiyotani
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Taigo Kato
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Makiko Harada
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Jae-Hyun Park
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | | | - Tanguy Seiwert
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Everett Vokes
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Nishant Agrawal
- Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Yusuke Nakamura
- Department of Medicine, The University of Chicago, Chicago, IL, USA.,Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Surgery, The University of Chicago, Chicago, IL, USA
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24
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Cui JH, Lin KR, Yuan SH, Jin YB, Chen XP, Su XK, Jiang J, Pan YM, Mao SL, Mao XF, Luo W. TCR Repertoire as a Novel Indicator for Immune Monitoring and Prognosis Assessment of Patients With Cervical Cancer. Front Immunol 2018; 9:2729. [PMID: 30524447 PMCID: PMC6262070 DOI: 10.3389/fimmu.2018.02729] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 11/05/2018] [Indexed: 01/22/2023] Open
Abstract
There is increasing evidence that deep sequencing-based T cell repertoire can sever as a biomarker of immune response in cancer patients; however, the characteristics of T cell repertoire including diversity and similarity, as well as its prognostic significance in patients with cervical cancer (CC) remain unknown. In this study, we applied a high throughput T cell receptor (TCR) sequencing method to characterize the T cell repertoires of peripheral blood samples from 25 CC patients, 30 cervical intraepithelial neoplasia (CIN) patients and 20 healthy women for understanding the immune alterations during the cervix carcinogenesis. In addition, we also explored the signatures of TCR repertoires in the cervical tumor tissues and paired sentinel lymph nodes from 16 CC patients and their potential value in predicting the prognosis of patients. Our results revealed that the diversity of circulating TCR repertoire gradually decreased during the cervix carcinogenesis and progression, but the circulating TCR repertoires in CC patients were more similar to CIN patients than healthy women. Interestingly, several clonotypes uniquely detected in CC patients tended to share similar CDR3 motifs, which differed from those observed in CIN patients. In addition, the TCR repertoire diversity in sentinel lymphatic nodes from CC patients was higher than in tumor tissues. More importantly, less clonotypes in TCR repertoire of sentinel lymphatic node was associated with the poor prognosis of the patients. Overall, our findings suggested that TCR repertoire might be a potential indicator of immune monitoring and a biomarker for predicting the prognosis of CC patients. Although functional studies of T cell populations are clearly required, this study have expanded our understanding of T cell immunity during the development of CC and provided an experimental basis for further studies on its pathogenesis and immunotherapy.
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Affiliation(s)
- Jin-Huan Cui
- Clinical Research Institute, The First People's Hospital of FoShan (Affiliated FoShan Hospital of Sun Yat-sen University), Foshan, China
| | - Kai-Rong Lin
- Clinical Research Institute, The First People's Hospital of FoShan (Affiliated FoShan Hospital of Sun Yat-sen University), Foshan, China
| | - Song-Hua Yuan
- Department of Gynecology, The First People's Hospital of FoShan (Affiliated FoShan Hospital of Sun Yat-sen University), Foshan, China
| | - Ya-Bin Jin
- Clinical Research Institute, The First People's Hospital of FoShan (Affiliated FoShan Hospital of Sun Yat-sen University), Foshan, China
| | - Xiang-Ping Chen
- Clinical Research Institute, The First People's Hospital of FoShan (Affiliated FoShan Hospital of Sun Yat-sen University), Foshan, China
| | - Xi-Kang Su
- Department of Clinical Laboratory, The First People's Hospital of FoShan (Affiliated FoShan Hospital of Sun Yat-sen University), Foshan, China
| | - Jun Jiang
- Department of Abdominothoracic Radiotherapy, The First People's Hospital of FoShan (Affiliated FoShan Hospital of Sun Yat-sen University), Foshan, China
| | - Ying-Ming Pan
- Clinical Research Institute, The First People's Hospital of FoShan (Affiliated FoShan Hospital of Sun Yat-sen University), Foshan, China
| | - Shao-Long Mao
- Clinical Research Institute, The First People's Hospital of FoShan (Affiliated FoShan Hospital of Sun Yat-sen University), Foshan, China
| | - Xiao-Fan Mao
- Clinical Research Institute, The First People's Hospital of FoShan (Affiliated FoShan Hospital of Sun Yat-sen University), Foshan, China
| | - Wei Luo
- Clinical Research Institute, The First People's Hospital of FoShan (Affiliated FoShan Hospital of Sun Yat-sen University), Foshan, China
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25
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Ou M, Zheng F, Zhang X, Liu S, Tang D, Zhu P, Qiu J, Dai Y. Integrated analysis of B‑cell and T‑cell receptors by high‑throughput sequencing reveals conserved repertoires in IgA nephropathy. Mol Med Rep 2018; 17:7027-7036. [PMID: 29568935 PMCID: PMC5928659 DOI: 10.3892/mmr.2018.8793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/01/2018] [Indexed: 01/12/2023] Open
Abstract
Immunoglobulin A nephropathy (IgAN) is a type of glomerular disorder associated with immune dysregulation, and understanding B‑/T‑cell receptors (BCRs/TCRs) may be valuable for the development of specific immunotherapeutic interventions. In the present study, B and T cells were isolated from IgAN patients and healthy controls, and the composition of the BCR/TCR complementarity‑determining region (CDR)3 was analyzed by multiplex polymerase chain reaction, high‑throughput sequencing and bioinformatics. The present results revealed that the BCR/TCR CDR3 clones were expressed at very low frequencies, and the composition of clone types in patients with IgAN was skewed; the majority of clones were unique, and only 12 BCR and 228 TCR CDR3 clones were public ones, of which 16 were expressed at a significantly higher frequency in patients with IgAN (P<0.001). There were also certain conserved amino acid residues between unique clones or groups, and the residues GMDV, EQY and EQF were recurring only in the IgAN group. In addition, some VDJ gene recombinations indicated great variation between groups, including 4 high‑frequency VDJ gene recombinations in the IgAN patients (P<0.001). Immune repertoires provide novel information, and conserved BCR/TCR CDR3 clones and VDJ gene recombinations with great variation may be potential therapeutic targets for IgAN patients.
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Affiliation(s)
- Minglin Ou
- Clinical Medical Research Center of Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Fengping Zheng
- Clinical Medical Research Center of Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Xinzhou Zhang
- Clinical Medical Research Center of Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Song Liu
- Clinical Medical Research Center of Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Donge Tang
- Clinical Medical Research Center of Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Peng Zhu
- Lab Center of Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, P.R. China
| | - Jingjun Qiu
- Lab Center of Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, P.R. China
| | - Yong Dai
- Clinical Medical Research Center of Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
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26
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Jiang Q, Liu Y, Xu B, Zheng W, Xiang X, Tang X, Dong H, Chen Y, Wang C, Deng G, Mao Q, Shang X, Wu Y. Analysis of T cell receptor repertoire in monozygotic twins concordant and discordant for chronic hepatitis B infection. Biochem Biophys Res Commun 2018; 497:153-159. [PMID: 29438710 DOI: 10.1016/j.bbrc.2018.02.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 02/05/2018] [Indexed: 12/12/2022]
Abstract
Due to their identical inheritance and shared surroundings, identical twins have been the recommended group for studying the susceptibility and prognosis of diseases. Here, CD8+ T cell receptor beta (TCRβ) chains were analyzed by high-throughput sequencing in three pairs of healthy identical twins and chronic hepatitis B patients. The data showed a high level of similarity in the TCR repertoire of each pair in terms of average TCR Vβ segment expression and frequency of the complementary determining region 3 (CDR3) pattern and skewed or oligoclonal clonotypes. Notably, the level of similarity in TCR Vβ expression between the twins appeared to be independent of the consistency or inconsistency of chronic HBV infection, although the detailed CDR3 pattern and frequency were related to disease prognosis. There were more immunodominant clonotypes in patients with HBV antigen seroconversion, which showed an increased abundance. These immunodominant clonotypes may be used as favorable prognostic biomarkers and potential targets for immunotherapy. Thus, delineating the CD8+ T cell repertoire of identical twins with concordant chronic viral infections provides a promising means to screen protective TCR genes for immunotherapy.
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Affiliation(s)
- Qiong Jiang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Yao Liu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Baoyan Xu
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Wenhong Zheng
- Department of Health, Third Military Medical University, Chongqing 400038, PR China
| | - Xiaomei Xiang
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Xiaoqin Tang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Hui Dong
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Yongwen Chen
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Chenhui Wang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Guohong Deng
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Qing Mao
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Xiaoyun Shang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China.
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China.
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27
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Rosati E, Dowds CM, Liaskou E, Henriksen EKK, Karlsen TH, Franke A. Overview of methodologies for T-cell receptor repertoire analysis. BMC Biotechnol 2017; 17:61. [PMID: 28693542 PMCID: PMC5504616 DOI: 10.1186/s12896-017-0379-9] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/26/2017] [Indexed: 12/13/2022] Open
Abstract
Background The T-cell receptor (TCR), located on the surface of T cells, is responsible for the recognition of the antigen-major histocompatibility complex, leading to the initiation of an inflammatory response. Analysing the TCR repertoire may help to gain a better understanding of the immune system features and of the aetiology and progression of diseases, in particular those with unknown antigenic triggers. The extreme diversity of the TCR repertoire represents a major analytical challenge; this has led to the development of specialized methods which aim to characterize the TCR repertoire in-depth. Currently, next generation sequencing based technologies are most widely employed for the high-throughput analysis of the immune cell repertoire. Results Here, we report on the latest methodological advancements in the field by describing and comparing the available tools; from the choice of the starting material and library preparation method, to the sequencing technologies and data analysis. Finally, we provide a practical example and our own experience by reporting some exemplary results from a small internal benchmark study, where current approaches from the literature and the market are employed and compared. Conclusions Several valid methods for clonotype identification and TCR repertoire analysis exist, however, a gold standard method for the field has not yet been identified. Depending on the purpose of the scientific study, some approaches may be more suitable than others. Finally, due to possible method specific biases, scientists must be careful when comparing results obtained using different methods. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0379-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - C Marie Dowds
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - Evaggelia Liaskou
- Centre for Liver Research and NIHR Birmingham Liver Biomedical Research Unit, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Eva Kristine Klemsdal Henriksen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany.
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28
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Yang J, Yan D, Guo R, Chen J, Li Y, Fan J, Fu X, Yao X, Diao H, Li L. Predictive value of serum ALT and T-cell receptor beta variable chain for HBeAg seroconversion in chronic hepatitis B patients during tenofovir treatment. Medicine (Baltimore) 2017; 96:e6242. [PMID: 28272219 PMCID: PMC5348167 DOI: 10.1097/md.0000000000006242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Effective antiviral therapy plays a key role in slowing the progression of chronic hepatitis B (CHB). Identification of serum indices, including hepatitis B e antigen (HBeAg) expression and seroconversion, will facilitate evaluation of the efficacy of antiviral therapy in HBeAg-positive CHB patients. The biochemical, serological, virological parameters, and the frequency of circulating CD4CD25 regulatory T cell (Treg) in 32 patients were measured at baseline and every 12 weeks during 96 weeks of tenofovir disoproxil fumarate (TDF) treatment. The relationship between the hepatitis B virus (HBV) deoxyribonucleic acid (DNA) and Treg and alanine aminotransferase (ALT) levels was analyzed, respectively. The molecular profiles of T-cell receptor beta variable chain (TRBV) were determined using gene melting spectral pattern. For the seroconverted 12 patients, ALT declined to normal levels by week 24 and remained at this level in subsequent treatment; moreover, the predictive cutoff value of ALT for HBeAg seroconversion (SC) was 41.5 U/L at week 24. The positive correlation between HBV DNA and Treg and ALT was significant in SC patients, but not in non-SC patients. Six TRBV families (BV3, BV11, BV12, BV14, BV20, and BV24) were predominantly expressed in SC patients at baseline. The decline of ALT could be used to predict HBeAg seroconversion for CHB patients during TDF treatment. In addition, the profile of Tregs and TRBVs may be associated with HBeAg seroconversion and could also be a potential indicator for predicting HBeAg SC and treatment outcome for CHB patients.
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Affiliation(s)
- Jiezuan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou
| | - Dong Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou
| | - Renyong Guo
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou
| | - Jiajia Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou
| | - Yongtao Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou
| | - Jun Fan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou
| | - Xuyan Fu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou
| | - Xinsheng Yao
- Department of immunology, Zunyi Medical Univesity, Zunyi, China
| | - Hongyan Diao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou
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29
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Bouquet J, Gardy JL, Brown S, Pfeil J, Miller RR, Morshed M, Avina-Zubieta A, Shojania K, McCabe M, Parker S, Uyaguari M, Federman S, Tang P, Steiner T, Otterstater M, Holt R, Moore R, Chiu CY, Patrick DM. RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease. Clin Infect Dis 2017; 64:476-481. [PMID: 28172519 PMCID: PMC5850034 DOI: 10.1093/cid/ciw767] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/27/2016] [Indexed: 01/09/2023] Open
Abstract
Background Chronic fatigue syndrome (CFS) remains poorly understood. Although infections are speculated to trigger the syndrome, a specific infectious agent and underlying pathophysiological mechanism remain elusive. In a previous study, we described similar clinical phenotypes in CFS patients and alternatively diagnosed chronic Lyme syndrome (ADCLS) patients—individuals diagnosed with Lyme disease by testing from private Lyme specialty laboratories but who test negative by reference 2-tiered serologic analysis. Methods Here, we performed blinded RNA-seq analysis of whole blood collected from 25 adults diagnosed with CFS and 13 ADCLS patients, comparing these cases to 25 matched controls and 11 patients with well-controlled systemic lupus erythematosus (SLE). Samples were collected at patient enrollment and not during acute symptom flares. RNA-seq data were used to study host gene expression, B-cell/T-cell receptor profiles (BCR/TCR), and potential viral infections. Results No differentially expressed genes (DEGs) were found to be significant when CFS or ADCLS cases were compared to controls. Forty-two DEGs were found when SLE cases were compared to controls, consistent with activation of interferon signaling pathways associated with SLE disease. BCR/TCR repertoire analysis did not show significant differences between CFS and controls or ADCLS and controls. Finally, viral sequences corresponding to anelloviruses, human pegivirus 1, herpesviruses, and papillomaviruses were detected in RNA-seq data, but proportions were similar (P = .73) across all genus-level taxonomic categories. Conclusions Our observations do not support a theory of transcriptionally mediated immune cell dysregulation in CFS and ADCLS, at least outside of periods of acute symptom flares.
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Affiliation(s)
- Jerome Bouquet
- Department of Laboratory Medicine, University of California, San Francisco, USA
| | - Jennifer L Gardy
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Scott Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Jacob Pfeil
- Department of Laboratory Medicine, University of California, San Francisco, USA
| | - Ruth R Miller
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Muhammad Morshed
- British Columbia Centre for Disease Control Public Health Laboratory, 655 W 12th Ave., Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, Vancouver, British Columbia, Canada
| | - Antonio Avina-Zubieta
- Department of Medicine, Division of Rheumatology, University of British Columbia, Vancouver, BC, Canada
| | - Kam Shojania
- Department of Medicine, Division of Rheumatology, University of British Columbia, Vancouver, BC, Canada
| | - Mark McCabe
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Shoshana Parker
- Centre for Health Evaluation Outcome Sciences, Vancouver, Canada
| | - Miguel Uyaguari
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, USA
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Centre, Doha, Qatar
| | - Ted Steiner
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, Canada
| | - Michael Otterstater
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Rob Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, USA
| | - David M Patrick
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
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30
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Liu S, Hou XL, Sui WG, Lu QJ, Hu YL, Dai Y. Direct measurement of B-cell receptor repertoire's composition and variation in systemic lupus erythematosus. Genes Immun 2017; 18:22-27. [PMID: 28053320 DOI: 10.1038/gene.2016.45] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/30/2016] [Accepted: 11/01/2016] [Indexed: 01/11/2023]
Abstract
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that is known to be associated with polyclonal B-cell hyper-reactivity. B-cell receptor (BCR) has a central role in B-cell development, activation, survival and apoptosis, and thus is a critical component of the regulation of both protective and autoreactive B cells. In this study, we applied multiplex PCR and Illumina high-throughput sequencing to study the composition and variation of the BCRs in peripheral blood mononuclear cells from SLE patients and healthy donors (NC). We found that SLE group displayed significantly shorter CDR3 average length (14.86±0.76aa vs 15.70±0.43aa), more arginine percentage of CDR3 amino acids (7.57±0.20% vs 7.32±0.19%) and poorer immunological diversity than the healthy ones. CDR3 sequence YGMDV present in all SLE samples may provide more information in generating more effective B-cell targeted diagnosis/therapies strategies.
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Affiliation(s)
- S Liu
- Department of Clinical Medical Research, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - X L Hou
- Nephrology Department of Guilin 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, China
| | - W G Sui
- Nephrology Department of Guilin 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, China
| | - Q J Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, China
| | - Y L Hu
- Department of Cancer Research, Shenzhen University, Shenzhen, China.,Department of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Y Dai
- Department of Clinical Medical Research, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
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31
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Chen Y, Xu Y, Zhao M, Liu Y, Gong M, Xie C, Wu H, Wang Z. High-throughput T cell receptor sequencing reveals distinct repertoires between tumor and adjacent non-tumor tissues in HBV-associated HCC. Oncoimmunology 2016; 5:e1219010. [PMID: 27853640 DOI: 10.1080/2162402x.2016.1219010] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/16/2016] [Accepted: 07/26/2016] [Indexed: 12/17/2022] Open
Abstract
T lymphocytes, which recognize antigen peptides through specific T cell receptors (TCRs), play an important role in the human adaptive immune response. TCR diversity is closely associated with host immune response and cancer prognosis. Although tumor-infiltrating T lymphocytes have implications for tumor prognosis, few studies have performed a detailed characterization of TCR diversity in both tumor and non-tumor tissues in hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC). Here, we performed high-throughput sequencing of the TCRβ chain complementarity determining region 3 (CDR3) of liver-infiltrating T cells from 48 HBV-associated HCC patients. A significantly higher average number of CDR3 aa clonotypes (2259 vs. 1324, p < 0.001), and significantly higher TCR diversity (Gini coefficient, p < 0.001; Simpson index, p < 0.01; Shannon entropy, p < 0.001) were observed in tumor tissues compared with adjacent non-tumor tissues. The ratio of highly expanded clones (HECs) was significantly higher in non-tumor tissues than in tumor tissues when the HEC threshold was defined as 2% or greater (p < 0.05). Our analysis of the median Morisita-Horn index indicated weak TCR repertoire similarity between tumor and matched non-tumor tissues. The median number of shared clones in tumor tissue and matched non-tumor tissue from each patient was 360.5, representing 5.1-15.8% (10.6 ± 0.4%) of all clones in each patient. We observed extensive heterogeneity of T lymphocytes in tumors and higher HEC ratios in adjacent non-tumor tissues of HCC patients. The differential T cell repertoires in tumor and non-tumor tissues suggest a distinct T cell immune microenvironment in patients with HBV-associated HCC.
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Affiliation(s)
- Yunqing Chen
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Ying Xu
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Miaoxian Zhao
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Yu Liu
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Mingxing Gong
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Cantao Xie
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Hongkai Wu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University , Guangzhou, China
| | - Zhanhui Wang
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University , Guangzhou, China
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