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Wang L, Zhou Y, Cui H, Zhuang X, Cheng C, Weng Y, Liu H, Wang S, Pan X, Cui Y, Zhang W. IGH repertoire analysis at scale: deciphering the complexity of B cell infiltration and migration in esophageal squamous cell carcinoma. Cancer Gene Ther 2024; 31:131-147. [PMID: 37985722 DOI: 10.1038/s41417-023-00689-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/10/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023]
Abstract
Tumor-infiltrating B-lineage cells have become predictors of prognosis and immunotherapy responses in various cancers. However, limited knowledge about their infiltration and migration patterns has hindered the understanding of their anti-tumor functions. Here, we examined the immunoglobulin heavy chain (IGH) repertoires in 496 multi-regional tumor, 107 normal tissue, and 48 metastatic lymph node samples obtained from 107 patients with esophageal squamous cell carcinoma (ESCC). Our study revealed higher IgG-type B-lineage cells infiltration in tumors than in healthy tissue, which was associated with improved patient outcomes. Genes such as ACTN1, COL6A5, and pathways like focal adhesion, which shapes the physical structure of tumors, could affect B-lineage cell infiltration. Notably, the IGH sequence was used as an identity-tag to monitor B cell migration, and their infiltration schema within the tumor were depicted based on our multi-regional tumor specimens. This analysis revealed an escalation in B cell clones overlapped between metastatic lymph nodes and tumors. Therefore, the Lymph Node Activation Index was defined, which could predict the outcomes of patients with lymph node metastasis. This research introduces a novel framework for probing B cell infiltration and migration within the tumor microenvironment using large-scale transcriptome data, while simultaneously providing fresh perspectives on B cell immunology within ESCC.
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Affiliation(s)
- Longlong Wang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Yong Zhou
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Heyang Cui
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Xuehan Zhuang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Chen Cheng
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Yongjia Weng
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Huijuan Liu
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Shubin Wang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Xinghua Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Yongping Cui
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China.
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, China.
| | - Weimin Zhang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China.
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
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2
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Lin G, Wang X, Ye H, Cao W. Radiomic Models Predict Tumor Microenvironment Using Artificial Intelligence-the Novel Biomarkers in Breast Cancer Immune Microenvironment. Technol Cancer Res Treat 2023; 22:15330338231218227. [PMID: 38111330 PMCID: PMC10734346 DOI: 10.1177/15330338231218227] [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: 09/12/2023] [Revised: 10/22/2023] [Accepted: 11/16/2023] [Indexed: 12/20/2023] Open
Abstract
Breast cancer is the most common malignancy in women, and some subtypes are associated with a poor prognosis with a lack of efficacious therapy. Moreover, immunotherapy and the use of other novel antibody‒drug conjugates have been rapidly incorporated into the standard management of advanced breast cancer. To extract more benefit from these therapies, clarifying and monitoring the tumor microenvironment (TME) status is critical, but this is difficult to accomplish based on conventional approaches. Radiomics is a method wherein radiological image features are comprehensively collected and assessed to build connections with disease diagnosis, prognosis, therapy efficacy, the TME, etc In recent years, studies focused on predicting the TME using radiomics have increasingly emerged, most of which demonstrate meaningful results and show better capability than conventional methods in some aspects. Beyond predicting tumor-infiltrating lymphocytes, immunophenotypes, cytokines, infiltrating inflammatory factors, and other stromal components, radiomic models have the potential to provide a completely new approach to deciphering the TME and facilitating tumor management by physicians.
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Affiliation(s)
- Guang Lin
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Xiaojia Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Hunan Ye
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Wenming Cao
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
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3
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Yang P, He Y, Qing P, Xu W, Xie D, Cazier J, Liu X, Varnai C, Zhou Y, Zhao Y, Tang H, Yin X, Liu Y. Application of T-cell receptor repertoire as a novel monitor in dynamic tracking and assessment: A cohort-study based on RA patients. J Cell Mol Med 2022; 26:6042-6055. [PMID: 36440548 PMCID: PMC9753462 DOI: 10.1111/jcmm.17623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/19/2022] [Accepted: 10/21/2022] [Indexed: 11/29/2022] Open
Abstract
T-cell receptor repertoire (TCRR) sequencing has been widely applied in many fields as a novel tool. This study explored characteristics of TCRR in detail with a cohort of 598 rheumatoid arthritis (RA) patients before and after anti-rheumatic treatments. We highlighted the abnormal TCRR distribution in RA characterized by decreased diversity and increased proportion of hyperexpanded clones (HECs), which was potentially attributed to skewed usage of global V/J segments but not a few certain ones. Enriched motifs analysis in RA community demonstrated the huge heterogeneity of CDR3 sequences, so that individual factors are strongly recommended to be taken into consideration when it comes to clinical application of TCRR. Disease-modifying antirheumatic drugs (DMARDs) can regulate immune system through recovery of TCRR richness to relieve symptoms. Remarkably, sensitive gene profile and advantageous gene profile were identified in this study as new biomarkers for different DMARDs regimens.
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Affiliation(s)
- Peiqing Yang
- Department of Rheumatology, West China HospitalSichuan UniversityChengduChina
| | - Yijing He
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine CenterWest China Hospital, Sichuan UniversityChengduChina,Laboratory of Nervous System Disease and Brain Functions, Clinical Research InstituteThe Affiliated Hospital of Southwest Medical UniversityLuzhouChina
| | - Pingying Qing
- Department of Rheumatology, West China HospitalSichuan UniversityChengduChina
| | - Wangdong Xu
- Department of Rheumatology, West China HospitalSichuan UniversityChengduChina,Department of Evidence‐Based MedicineSchool of Public Health, Southwest Medical UniversityLuzhouChina
| | - Dan Xie
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine CenterWest China Hospital, Sichuan UniversityChengduChina
| | | | - Xiao Liu
- BGI‐Shenzhen and Shenzhen Key Laboratory of Transomics BiotechnologiesBGI‐ShenzhenShenzhenChina
| | - Csilla Varnai
- Center for Computational BiologyUniversity of BirminghamBirminghamUK
| | - Yi Zhou
- Department of Medical Affairs, West China HospitalSichuan UniversityChengduChina
| | - Yi Zhao
- Department of Rheumatology, West China HospitalSichuan UniversityChengduChina
| | - Huairong Tang
- Health Management CenterWest China Hospital of Sichuan UniversityChengduChina
| | | | - Yi Liu
- Department of Rheumatology, West China HospitalSichuan UniversityChengduChina
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4
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Zheng B, Yang Y, Chen L, Wu M, Zhou S. B-Cell Receptor Repertoire Sequencing: Deeper Digging into the Mechanisms and Clinical Aspects of Immune-mediated Diseases. iScience 2022; 25:105002. [PMID: 36157582 PMCID: PMC9494237 DOI: 10.1016/j.isci.2022.105002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
B cells play an essential role in adaptive immunity and are intimately correlated with pleiotropic immune-mediated diseases. Each B cell occupies a unique B cell receptor (BCR), and all BCRs throughout our body form “BCR repertoire.” With the development of sequencing technology and coupled bioinformatics, accumulating evidence indicates that BCR repertoire largely varies under physiological and pathological conditions. Therefore, comprehensive grasp of BCR repertoire will provide new insights into the pathogenesis of immune-mediated diseases and help exploit efficient diagnostic and treatment strategies. In this review, we start with an overview of BCR repertoire and related sequencing technologies and summarize their current applications in immune-mediated diseases. We also underscore the challenges of this emerging field and propose promising future directions in advancing BCR repertoire exploration.
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Affiliation(s)
- Bohao Zheng
- Wuxi School of Medicine, Jiangnan University, Wuxi, P. R. China
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Yuqing Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Lin Chen
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Mengrui Wu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
- Corresponding author
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5
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Wang Z, Cheng Z, Lu S, Chard Dunmall LS, Wang J, Guo Y, Wang Y. Characterization of the Intra-tumoral B Cell Immunoglobulin Repertoire Is of Prognostic Value for Esophageal Squamous Cell Carcinoma. Front Immunol 2022; 13:896627. [PMID: 35812448 PMCID: PMC9257635 DOI: 10.3389/fimmu.2022.896627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
Esophageal Squamous Cell carcinomas (ESCC) is a highly heterogeneous malignancy that is among the leading cause of cancer-related death worldwide. B cells play pivotal roles in the immune defense system and cancer progression and regression, yet the repertoire of tumor infiltrating B cells (TIBs) and its association with clinical outcome remains unexplored in ESCC. Here we collected bulk RNA-seq sequencing data from 119 ESCC tumors and matched adjacent normal samples to delineate the B cell repertoire. We found that ESCC is more heavily infiltrated by B cells and plasma cells compared to activated T cells. The immunoglobulin heavy chain variable region (IGHV) gene usage was remarkably biased and IGHV3-74 was under-represented in ESCC tumors. The TIBs showed a more oligoclonal profile along with widespread clonal expansion and IgG subclass switch events (CSRs). Survival analysis revealed several unexpected associations between tumor infiltrating B cells and prognosis. Higher levels of immunoglobulin expression (IGH), CD138 expression, IGH to MS4A1 ratio, CSR events and clone diversity are all associated with better survival. Notably, we found that the abundance of CD20-negative IgG2-producing plasma cells has a strong positive effect on overall survival with a hazard ratio (HR) of 0.40 (log-rank p: 0.002). Combing molecular subtyping, the IgG2-producing plasma cells could stratify high-risk patients more accurately with a HR of 0.253 (log-rank p: 0.0006). The direct link between protective B cell populations and ESCC prognosis provides biomarkers for high-risk patient selection and holds great promise for developing strategies for immunotherapy targeting B cells in ESCC patients.
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Affiliation(s)
- Zhizhong Wang
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Zhenguo Cheng
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shuangshuang Lu
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Louisa S. Chard Dunmall
- Centre for Biomarkers Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jun Wang
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Yongjun Guo
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Yaohe Wang, ; Yongjun Guo,
| | - Yaohe Wang
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Centre for Biomarkers Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- *Correspondence: Yaohe Wang, ; Yongjun Guo,
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6
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van Duijvenvoorde M, Derks S, Bahce I, Leemans CR, van de Ven R, Fransen MF. Comparison of the tumor microenvironments of squamous cell carcinoma at different anatomical locations within the upper aerodigestive tract in relation to response to ICI therapy. Clin Transl Immunology 2022; 11:e1363. [PMID: 35035956 PMCID: PMC8747970 DOI: 10.1002/cti2.1363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022] Open
Abstract
Immunotherapy with immune checkpoint inhibitors (ICI) has improved treatment outcomes in many cancer types and has focused attention on cancer immunity and the role of the tumor microenvironment (TME). Studies into efficacy of immunotherapy and TME are generally restricted to tumors in one anatomical location, while the histological type may have substantial influence on the contexture of the TME, perhaps more so than anatomical location, and subsequently to the response to immunotherapy. This review aims to focus on the TME in ICI‐treated tumors of the same histological type, namely carcinogen‐induced squamous cell carcinoma developing within the aerodigestive tract, at three locations, i.e. head and neck (HNSCC), esophagus (ESCC) and lung (LUSC).
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Affiliation(s)
- Maurice van Duijvenvoorde
- Department of Pulmonary Diseases Amsterdam UMC, location VUmc Cancer Center Amsterdam and Amsterdam Institute for Infection and Immunity Amsterdam The Netherlands.,Department of Otolaryngology Head and Neck Surgery Amsterdam UMC, location VUmc Cancer Center Amsterdam and Amsterdam Institute for Infection and Immunity Amsterdam The Netherlands
| | - Sarah Derks
- Department of Medical Oncology Amsterdam UMC, location VUmc Cancer Center Amsterdam and Amsterdam Institute for Infection and Immunity Amsterdam The Netherlands.,Oncode Institute Utrecht The Netherlands
| | - Idris Bahce
- Department of Pulmonary Diseases Amsterdam UMC, location VUmc Cancer Center Amsterdam and Amsterdam Institute for Infection and Immunity Amsterdam The Netherlands
| | - C René Leemans
- Department of Otolaryngology Head and Neck Surgery Amsterdam UMC, location VUmc Cancer Center Amsterdam and Amsterdam Institute for Infection and Immunity Amsterdam The Netherlands
| | - Rieneke van de Ven
- Department of Otolaryngology Head and Neck Surgery Amsterdam UMC, location VUmc Cancer Center Amsterdam and Amsterdam Institute for Infection and Immunity Amsterdam The Netherlands
| | - Marieke F Fransen
- Department of Pulmonary Diseases Amsterdam UMC, location VUmc Cancer Center Amsterdam and Amsterdam Institute for Infection and Immunity Amsterdam The Netherlands
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7
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Zhang C, Tan Q, Li S, Shen L, Zhang J, Liu Y, Yang W, Lu Z. Induction of EBV latent membrane protein-2A (LMP2A)-specific T cells and construction of individualized TCR-engineered T cells for EBV-associated malignancies. J Immunother Cancer 2021; 9:jitc-2021-002516. [PMID: 34210819 PMCID: PMC8252876 DOI: 10.1136/jitc-2021-002516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2021] [Indexed: 12/05/2022] Open
Abstract
Background Latent membrane protein-2A (LMP2A)-specific TCR-engineered T cells could be a promising treatment approach to Epstein–Barr virus-associated malignancies. However, previous studies mainly reported LMP2A-reactive TCRs only focusing on specific HLA subtypes and corresponding epitopes, and thus, they were only suitable for patients with specific HLA. Methods Due to hugely varied HLA subtypes and presented LMP2A epitopes in different individuals, our study attempted to develop an individualized approach, based on the weekly in vitro stimulation of peripheral T cells for 2 weeks with autologous dendritic cells (DCs) pulsed with a pool of LMP2A peptides covering LMP2A whole protein and combination analysis of high throughput TCRβ sequencing of prestimulated and poststimulated T cells and single-cell TCR sequencing of poststimulated T cells, and to identify LMP2A-specific TCRs of which poststimulated frequencies significantly increased than corresponding prestimulated frequencies. Results Following this approach, multiple LMP2A-reactive TCRs were identified, optimized and cloned into lentiviral vector, and then transduced into peripheral T cells. These engineerd T cells were demonstrated to specifically recognize the LMP2A presented by autologous DCs and lymphoblastoid cell lines in vitro and in vivo. Conclusions This approach provides an efficient procedure to isolate individualized LMP2A-specific TCRs for basic and translational research, as well as for clinical applications.
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Affiliation(s)
- Chaoting Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Qin Tan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shance Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Luyan Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jingtao Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ying Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Wenjun Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China .,Key Laboratory of Fertility Preservation and Maintenance, School of Basic Medicine and the General Hospital, Ningxia Medical University, Yinchuan, China
| | - Zheming Lu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
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8
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Yuzhakova DV, Volchkova LN, Pogorelyy MV, Serebrovskaya EO, Shagina IA, Bryushkova EA, Nakonechnaya TO, Izosimova AV, Zavyalova DS, Karabut MM, Izraelson M, Samoylenko IV, Zagainov VE, Chudakov DM, Zagaynova EV, Sharonov GV. Measuring Intratumoral Heterogeneity of Immune Repertoires. Front Oncol 2020; 10:512. [PMID: 32457825 PMCID: PMC7227437 DOI: 10.3389/fonc.2020.00512] [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: 12/04/2019] [Accepted: 03/23/2020] [Indexed: 12/22/2022] Open
Abstract
There is considerable clinical and fundamental value in measuring the clonal heterogeneity of T and B cell expansions in tumors and tumor-associated lymphoid structures—along with the associated heterogeneity of the tumor neoantigen landscape—but such analyses remain challenging to perform. Here, we propose a straightforward approach to analyze the heterogeneity of immune repertoires between different tissue sections in a quantitative and controlled way, based on a beta-binomial noise model trained on control replicates obtained at the level of single-cell suspensions. This approach allows to identify local clonal expansions with high accuracy. We reveal in situ proliferation of clonal T cells in a mouse model of melanoma, and analyze heterogeneity of immunoglobulin repertoires between sections of a metastatically-infiltrated lymph node in human melanoma and primary human colon tumor. On the latter example, we demonstrate the importance of training the noise model on datasets with depth and content that is comparable to the samples being studied. Altogether, we describe here the crucial basic instrumentarium needed to facilitate proper experimental setup planning in the rapidly evolving field of intratumoral immune repertoires, from the wet lab to bioinformatics analysis.
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Affiliation(s)
- Diana Vladimirovna Yuzhakova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Lilia N Volchkova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Mikhail Valerievich Pogorelyy
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina O Serebrovskaya
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Irina A Shagina
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina A Bryushkova
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Department of Molecular Biology, Moscow State University, Moscow, Russia
| | - Tatiana O Nakonechnaya
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anna V Izosimova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Daria S Zavyalova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Maria M Karabut
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Mark Izraelson
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Igor V Samoylenko
- Oncodermatology Department, N. N. Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Vladimir E Zagainov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Volga District Medical Centre Under Federal Medical and Biological Agency, Nizhny Novgorod, Russia
| | - Dmitriy M Chudakov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Adaptive Immunity Group, Central European Institute of Technology, Masaryk University, Brno, Czechia.,MiLaboratory LLC, Skolkovo Innovation Centre, Moscow, Russia
| | - Elena V Zagaynova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - George Vladimirovich Sharonov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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9
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Lin L, Lin DC. Biological Significance of Tumor Heterogeneity in Esophageal Squamous Cell Carcinoma. Cancers (Basel) 2019; 11:cancers11081156. [PMID: 31409002 PMCID: PMC6721624 DOI: 10.3390/cancers11081156] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common and aggressive malignancy, with hitherto dismal clinical outcome. Genomic analyses of patient samples reveal a complex heterogeneous landscape for ESCC, which presents in both intertumor and intratumor forms, manifests at both genomic and epigenomic levels, and contributes significantly to tumor evolution, drug resistance, and metastasis. Here, we review the important molecular characteristics underlying ESCC heterogeneity, with an emphasis on genomic aberrations and their functional contribution to cancer evolutionary trajectories. We further discuss how novel experimental tools, including single-cell sequencing and three-dimensional organoids, may advance our understanding of tumor heterogeneity. Lastly, we suggest that deciphering the mechanisms governing tumor heterogeneity holds the potential to developing precision therapeutics for ESCC patients.
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Affiliation(s)
- Lehang Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen University, Guangzhou 510120, China
| | - De-Chen Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen University, Guangzhou 510120, China.
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