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Li Y, Li H, Huang W, Yu Q, Wang K, Xiong Y, Wang Q, Qin Y, Kuang X, Tang J. Single-cell RNA sequencing reveals the landscape of biomarker in allergic rhinitis patient undergoing intracervical lymphatic immunotherapy and related pan-cancer analysis. ENVIRONMENTAL TOXICOLOGY 2024; 39:2817-2829. [PMID: 38291708 DOI: 10.1002/tox.24151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 02/01/2024]
Abstract
INTRODUCTION Allergic rhinitis (AR) is one of the leading allergic diseases worldwide. Allergen immunotherapy (AIT) induces persistent specific allergen tolerance to achieve remission of the symptoms in AR patients. We creatively conducted the intra-cervical lymphatic immunotherapy (ICLIT) for AR patients. However, the underlying molecular mechanism of immune cell response of AIT in AR remains elusive. METHOD To investigate the transcriptome profile in AR patients who underwent ICLIT, we comprehensively investigated the transcriptional changes in B cells from peripheral blood mononuclear cells of AR patient by single-cell RNA sequencing. Immunoglobulins and relative key gene, which influences the B cell differentiation, was demonstrated. The biomarkers' association with different types of tumors was investigated. RESULTS Naive B cells, germinal center B cells, activated memory B cells, and memory B cells constituted the B cells subsets. The expression of IGHE, IGHGs, IGHA, IGHD, and IGHM from memory B cells was validated. Pseudotime analysis further indicated the dynamic change from the expression of the immunoglobulins in the memory B cells, suggesting that ITGB1 may contribute to the differentiation procedure of memory B cells. The cell-cell communication among these immune cells demonstrated the significantly enhanced CD23, BTLA signaling after ICLIT in AR patient. ITGB1 was upregulated in 13 tumors and downregulated in six others. High ITGB1 expression was linked to poor prognosis in eight types of tumors. ITGB1 expression showed correlations with tumor mutation burden, tissue purity, and microsatellite instability in different types of tumors. DISCUSSION ITGB1 was demonstrated as a potential biomarker for AR patients after ICLIT and is significant in identifying immune infiltration in tumor tissue and predicting tumor prognosis.
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Affiliation(s)
- Yin Li
- Department of Otolaryngology, The First People's Hospital of Foshan, Foshan, China
| | - Hao Li
- Department of Infectious Diseases, The First People's Hospital of Changde City, Xiangya School of Medicine, Central South University, Changde, China
| | - Weijun Huang
- Department of Ultrasound, The First People's Hospital of Foshan, Foshan, China
| | - Qingqing Yu
- Department of Otolaryngology, The First People's Hospital of Foshan, Foshan, China
| | - Kai Wang
- Department of Otolaryngology, The First People's Hospital of Foshan, Foshan, China
| | - Yu Xiong
- Department of Otolaryngology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qixing Wang
- Department of Otolaryngology, The First People's Hospital of Foshan, Foshan, China
| | - Yang Qin
- Department of Otolaryngology, The First People's Hospital of Foshan, Foshan, China
| | - Xiong Kuang
- Department of Otolaryngology, The First People's Hospital of Foshan, Foshan, China
| | - Jun Tang
- Department of Otolaryngology, The First People's Hospital of Foshan, Foshan, China
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Liu M, Bertolazzi G, Sridhar S, Lee RX, Jaynes P, Mulder K, Syn N, Hoppe MM, Fan S, Peng Y, Thng J, Chua R, Jayalakshmi, Batumalai Y, De Mel S, Poon L, Chan EHL, Lee J, Hue SSS, Chang ST, Chuang SS, Chandy KG, Ye X, Pan-Hammarström Q, Ginhoux F, Chee YL, Ng SB, Tripodo C, Jeyasekharan AD. Spatially-resolved transcriptomics reveal macrophage heterogeneity and prognostic significance in diffuse large B-cell lymphoma. Nat Commun 2024; 15:2113. [PMID: 38459052 PMCID: PMC10923916 DOI: 10.1038/s41467-024-46220-z] [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: 04/26/2023] [Accepted: 02/19/2024] [Indexed: 03/10/2024] Open
Abstract
Macrophages are abundant immune cells in the microenvironment of diffuse large B-cell lymphoma (DLBCL). Macrophage estimation by immunohistochemistry shows varying prognostic significance across studies in DLBCL, and does not provide a comprehensive analysis of macrophage subtypes. Here, using digital spatial profiling with whole transcriptome analysis of CD68+ cells, we characterize macrophages in distinct spatial niches of reactive lymphoid tissues (RLTs) and DLBCL. We reveal transcriptomic differences between macrophages within RLTs (light zone /dark zone, germinal center/ interfollicular), and between disease states (RLTs/ DLBCL), which we then use to generate six spatially-derived macrophage signatures (MacroSigs). We proceed to interrogate these MacroSigs in macrophage and DLBCL single-cell RNA-sequencing datasets, and in gene-expression data from multiple DLBCL cohorts. We show that specific MacroSigs are associated with cell-of-origin subtypes and overall survival in DLBCL. This study provides a spatially-resolved whole-transcriptome atlas of macrophages in reactive and malignant lymphoid tissues, showing biological and clinical significance.
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Affiliation(s)
- Min Liu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Radiation Oncology, Chongqing University Cancer Hospital, Chongqing, PR China
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
| | - Giorgio Bertolazzi
- Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Shruti Sridhar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Rui Xue Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Kevin Mulder
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Nicholas Syn
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biomedical Informatics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michal Marek Hoppe
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shuangyi Fan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yanfen Peng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jocelyn Thng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Reiya Chua
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
| | - Jayalakshmi
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
| | - Yogeshini Batumalai
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
| | - Sanjay De Mel
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Limei Poon
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Esther Hian Li Chan
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joanne Lee
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Susan Swee-Shan Hue
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sheng-Tsung Chang
- Department of Pathology, Chi-Mei Medical Center, Tainan City, Taiwan, ROC
| | - Shih-Sung Chuang
- Department of Pathology, Chi-Mei Medical Center, Tainan City, Taiwan, ROC
| | - K George Chandy
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Xiaofei Ye
- Kindstar Global Precision Medicine Institute, Wuhan, PR China
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Yen Lin Chee
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Siok-Bian Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
- Histopathology Unit, Institute of Molecular Oncology Foundation (IFOM) ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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Coupland SE, Du MQ, Ferry JA, de Jong D, Khoury JD, Leoncini L, Naresh KN, Ott G, Siebert R, Xerri L. The fifth edition of the WHO classification of mature B-cell neoplasms: open questions for research. J Pathol 2024; 262:255-270. [PMID: 38180354 DOI: 10.1002/path.6246] [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: 10/04/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024]
Abstract
The fifth edition of the World Health Organization Classification of Haematolymphoid Tumours (WHO-HAEM5) is the product of an evidence-based evolution of the revised fourth edition with wide multidisciplinary consultation. Nonetheless, while every classification incorporates scientific advances and aims to improve upon the prior version, medical knowledge remains incomplete and individual neoplasms may not be easily subclassified in a given scheme. Thus, optimal classification requires ongoing study, and there are certain aspects of some entities and subtypes that require further refinements. In this review, we highlight a selection of these challenging areas to prompt more research investigations. These include (1) a 'placeholder term' of splenic B-cell lymphoma/leukaemia with prominent nucleoli (SBLPN) to accommodate many of the splenic lymphomas previously classified as hairy cell leukaemia variant and B-prolymphocytic leukaemia, a clear new start to define their pathobiology; (2) how best to classify BCL2 rearrangement negative follicular lymphoma including those with BCL6 rearrangement, integrating the emerging new knowledge on various germinal centre B-cell subsets; (3) what is the spectrum of non-IG gene partners of MYC translocation in diffuse large B-cell lymphoma/high-grade B-cell lymphoma and how they impact MYC expression and clinical outcome; how best to investigate this in a routine clinical setting; and (4) how best to define high-grade B-cell lymphoma not otherwise specified and high-grade B-cell lymphoma with 11q aberrations to distinguish them from their mimics and characterise their molecular pathogenetic mechanism. Addressing these questions would provide more robust evidence to better define these entities/subtypes, improve their diagnosis and/or prognostic stratification, leading to better patient care. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sarah E Coupland
- Liverpool Clinical Laboratories, Liverpool University Hospitals Foundation Trust, Liverpool, UK
| | - Ming-Qing Du
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Judith A Ferry
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daphne de Jong
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joseph D Khoury
- Department of Pathology, Microbiology and Immunology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lorenzo Leoncini
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Kikkeri N Naresh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Luc Xerri
- Institut Paoli-Calmettes, CRCM and Aix-Marseille University, Marseille, France
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4
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Yu Y, Dong L, Dong C, Zhang X. Validation of a Proteomic-Based Prognostic Model for Breast Cancer and Immunological Analysis. Int J Genomics 2023; 2023:1738750. [PMID: 38145160 PMCID: PMC10748720 DOI: 10.1155/2023/1738750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/07/2023] [Accepted: 11/25/2023] [Indexed: 12/26/2023] Open
Abstract
Breast cancer (BC) has emerged as an extremely destructive malignancy, causing significant harm to female patients and society at large. Proteomic research holds great promise for early diagnosis and treatment of diseases, and the integration of proteomics with genomics can offer valuable assistance in the early diagnosis, treatment, and improved prognosis of BC patients. In this study, we downloaded breast cancer protein expression data from The Cancer Genome Atlas (TCGA) and combined proteomics with genomics to construct a proteomic-based prognostic model for BC. This model consists of nine proteins (HEREGULIN, IDO, PEA15, MERIT40_pS29, CIITA, AKT2, CD171 DVL3, and CABL9). The accuracy of the model in predicting the survival prognosis of BC patients was further validated through risk curve analysis, survival curve analysis, and independent prognostic analysis. We further confirmed the impact of differential expression of these nine key proteins on overall survival in BC patients, and the differential expression of the key proteins and their encoding genes was validated using immunohistochemical staining. Enrichment analysis revealed functional associations primarily related to PPAR signaling pathway, steroid hormone metabolism, chemokine signaling pathway, DNA conformation changes, immunoglobulin production, and immunoglobulin complex in the high- and low-risk groups. Immune infiltration analysis revealed differential expression of immune cells between the high- and low-risk groups, providing a theoretical basis for subsequent immunotherapy. The model constructed in this study can predict the survival of BC patients, and the identified key proteins may serve as biomarkers to aid in the early diagnosis of BC. Enrichment analysis and immune infiltration analysis provide a necessary theoretical basis for further exploration of the molecular mechanisms and subsequent immunotherapy.
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Affiliation(s)
- Yunlin Yu
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang 443000, China
| | - Linhuan Dong
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang 443000, China
| | - Changjun Dong
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang 443000, China
| | - Xianlin Zhang
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang 443000, China
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5
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Playoust E, Remark R, Vivier E, Milpied P. Germinal center-dependent and -independent immune responses of tumor-infiltrating B cells in human cancers. Cell Mol Immunol 2023; 20:1040-1050. [PMID: 37419983 PMCID: PMC10468534 DOI: 10.1038/s41423-023-01060-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 06/14/2023] [Indexed: 07/09/2023] Open
Abstract
B cells play essential roles in immunity, mainly through the production of high affinity plasma cells (PCs) and memory B (Bmem) cells. The affinity maturation and differentiation of B cells rely on the integration of B-cell receptor (BCR) intrinsic and extrinsic signals provided by antigen binding and the microenvironment, respectively. In recent years, tumor infiltrating B (TIL-B) cells and PCs (TIL-PCs) have been revealed as important players in antitumor responses in human cancers, but their interplay and dynamics remain largely unknown. In lymphoid organs, B-cell responses involve both germinal center (GC)-dependent and GC-independent pathways for Bmem cell and PC production. Affinity maturation of BCR repertoires occurs in GC reactions with specific spatiotemporal dynamics of signal integration by B cells. In general, the reactivation of high-affinity Bmem cells by antigens triggers GC-independent production of large numbers of PC without BCR rediversification. Understanding B-cell dynamics in immune responses requires the integration of multiple tools and readouts such as single-cell phenotyping and RNA-seq, in situ analyses, BCR repertoire analysis, BCR specificity and affinity assays, and functional tests. Here, we review how those tools have recently been applied to study TIL-B cells and TIL-PC in different types of solid tumors. We assessed the published evidence for different models of TIL-B-cell dynamics involving GC-dependent or GC-independent local responses and the resulting production of antigen-specific PCs. Altogether, we highlight the need for more integrative B-cell immunology studies to rationally investigate TIL-B cells as a leverage for antitumor therapies.
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Affiliation(s)
- Eve Playoust
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | | | - Eric Vivier
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
- Innate Pharma, Marseille, France
| | - Pierre Milpied
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France.
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6
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Verrier L. Focus on the 9th Annual Seminar organized by the Canceropôle Provence-Alpes-Côte-d'Azur: Highlights of the event. Bull Cancer 2023:S0007-4551(23)00196-0. [PMID: 37150732 DOI: 10.1016/j.bulcan.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023]
Abstract
The 9th Annual Seminar of the Canceropôle Provence-Alpes-Côte-d'Azur took place on July, 5th-6th 2022 in Saint-Raphaël, south of France. Annual meeting of the regional scientific community working in the field of cancer research, this seminar brings together a large and diverse audience, with 285 people attending in 2022: PhD students, postdocs, PIs (Principal Investigators) and senior researchers, clinicians, patient associations, funding partners of the Canceropôle. This document reviews the major scientific results presented and key moments of the event.
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Affiliation(s)
- Laure Verrier
- Canceropôle Provence-Alpes-Côte-d'Azur, 27, boulevard Jean-Moulin, 13005 Marseille, France.
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7
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García-Valiente R, Merino Tejero E, Stratigopoulou M, Balashova D, Jongejan A, Lashgari D, Pélissier A, Caniels TG, Claireaux MAF, Musters A, van Gils MJ, Rodríguez Martínez M, de Vries N, Meyer-Hermann M, Guikema JEJ, Hoefsloot H, van Kampen AHC. Understanding repertoire sequencing data through a multiscale computational model of the germinal center. NPJ Syst Biol Appl 2023; 9:8. [PMID: 36927990 PMCID: PMC10019394 DOI: 10.1038/s41540-023-00271-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Sequencing of B-cell and T-cell immune receptor repertoires helps us to understand the adaptive immune response, although it only provides information about the clonotypes (lineages) and their frequencies and not about, for example, their affinity or antigen (Ag) specificity. To further characterize the identified clones, usually with special attention to the particularly abundant ones (dominant), additional time-consuming or expensive experiments are generally required. Here, we present an extension of a multiscale model of the germinal center (GC) that we previously developed to gain more insight in B-cell repertoires. We compare the extent that these simulated repertoires deviate from experimental repertoires established from single GCs, blood, or tissue. Our simulations show that there is a limited correlation between clonal abundance and affinity and that there is large affinity variability among same-ancestor (same-clone) subclones. Our simulations suggest that low-abundance clones and subclones, might also be of interest since they may have high affinity for the Ag. We show that the fraction of plasma cells (PCs) with high B-cell receptor (BcR) mRNA content in the GC does not significantly affect the number of dominant clones derived from single GCs by sequencing BcR mRNAs. Results from these simulations guide data interpretation and the design of follow-up experiments.
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Affiliation(s)
- Rodrigo García-Valiente
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Elena Merino Tejero
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Maria Stratigopoulou
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
| | - Daria Balashova
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Danial Lashgari
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Aurélien Pélissier
- IBM Research Zurich, 8803, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Tom G Caniels
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Mathieu A F Claireaux
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Anne Musters
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Marit J van Gils
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | | | - Niek de Vries
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Michael Meyer-Hermann
- Department for Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jeroen E J Guikema
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Pathology, Lymphoma and Myeloma Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Huub Hoefsloot
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Antoine H C van Kampen
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands.
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands.
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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8
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Han J, Masserey S, Shlesinger D, Kuhn R, Papadopoulou C, Agrafiotis A, Kreiner V, Dizerens R, Hong KL, Weber C, Greiff V, Oxenius A, Reddy ST, Yermanos A. Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes. BIOINFORMATICS ADVANCES 2022; 2:vbac062. [PMID: 36699357 PMCID: PMC9710610 DOI: 10.1093/bioadv/vbac062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/31/2022] [Accepted: 08/26/2022] [Indexed: 02/01/2023]
Abstract
Motivation Single-cell sequencing now enables the recovery of full-length immune receptor repertoires [B cell receptor (BCR) and T cell receptor (TCR) repertoires], in addition to gene expression information. The feature-rich datasets produced from such experiments require extensive and diverse computational analyses, each of which can significantly influence the downstream immunological interpretations, such as clonal selection and expansion. Simulations produce validated standard datasets, where the underlying generative model can be precisely defined and furthermore perturbed to investigate specific questions of interest. Currently, there is no tool that can be used to simulate single-cell datasets incorporating immune receptor repertoires and gene expression. Results We developed Echidna, an R package that simulates immune receptors and transcriptomes at single-cell resolution with user-tunable parameters controlling a wide range of features such as clonal expansion, germline gene usage, somatic hypermutation, transcriptional phenotypes and spatial location. Echidna can additionally simulate time-resolved B cell evolution, producing mutational networks with complex selection histories incorporating class-switching and B cell subtype information. We demonstrated the benchmarking potential of Echidna by simulating clonal lineages and comparing the known simulated networks with those inferred from only the BCR sequences as input. Finally, we simulated immune repertoire information onto existing spatial transcriptomic experiments, thereby generating novel datasets that could be used to develop and integrate methods to profile clonal selection in a spatially resolved manner. Together, Echidna provides a framework that can incorporate experimental data to simulate single-cell immune repertoires to aid software development and bioinformatic benchmarking of clonotyping, phylogenetics, transcriptomics and machine learning strategies. Availability and implementation The R package and code used in this manuscript can be found at github.com/alexyermanos/echidna and also in the R package Platypus (Yermanos et al., 2021). Installation instructions and the vignette for Echidna is described in the Platypus Computational Ecosystem (https://alexyermanos.github.io/Platypus/index.html). Publicly available data and corresponding sample accession numbers can be found in Supplementary Tables S2 and S3. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Solène Masserey
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Danielle Shlesinger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Raphael Kuhn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Chrysa Papadopoulou
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Andreas Agrafiotis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Victor Kreiner
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Raphael Dizerens
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Cédric Weber
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo 0450, Norway
| | - Annette Oxenius
- Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
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9
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Loeffler-Wirth H, Kreuz M, Schmidt M, Ott G, Siebert R, Binder H. Classifying Germinal Center Derived Lymphomas-Navigate a Complex Transcriptional Landscape. Cancers (Basel) 2022; 14:3434. [PMID: 35884496 PMCID: PMC9321060 DOI: 10.3390/cancers14143434] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Classification of lymphoid neoplasms is based mainly on histologic, immunologic, and (rarer) genetic features. It has been supplemented by gene expression profiling (GEP) in the last decade. Despite the considerable success, particularly in associating lymphoma subtypes with specific transcriptional programs and classifier signatures of up- or downregulated genes, competing molecular classifiers were often proposed in the literature by different groups for the same classification tasks to distinguish, e.g., BL versus DLBCL or different DLBCL subtypes. Moreover, rarer sub-entities such as MYC and BCL2 "double hit lymphomas" (DHL), IRF4-rearranged large cell lymphoma (IRF4-LCL), and Burkitt-like lymphomas with 11q aberration pattern (mnBLL-11q) attracted interest while their relatedness regarding the major classes is still unclear in many respects. We explored the transcriptional landscape of 873 lymphomas referring to a wide spectrum of subtypes by applying self-organizing maps (SOM) machine learning. The landscape reveals a continuum of transcriptional states activated in the different subtypes without clear-cut borderlines between them and preventing their unambiguous classification. These states show striking parallels with single cell gene expression of the active germinal center (GC), which is characterized by the cyclic progression of B-cells. The expression patterns along the GC trajectory are discriminative for distinguishing different lymphoma subtypes. We show that the rare subtypes take intermediate positions between BL, DLBCL, and FL as considered by the 5th edition of the WHO classification of haemato-lymphoid tumors in 2022. Classifier gene signatures extracted from these states as modules of coregulated genes are competitive with literature classifiers. They provide functional-defined classifiers with the option of consenting redundant classifiers from the literature. We discuss alternative classification schemes of different granularity and functional impact as possible avenues toward personalization and improved diagnostics of GC-derived lymphomas.
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Affiliation(s)
- Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics, University Leipzig (IZBI), 04107 Leipzig, Germany; (H.L.-W.); (M.S.)
| | - Markus Kreuz
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), 04103 Leipzig, Germany;
| | - Maria Schmidt
- Interdisciplinary Centre for Bioinformatics, University Leipzig (IZBI), 04107 Leipzig, Germany; (H.L.-W.); (M.S.)
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany;
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89073 Ulm, Germany;
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, University Leipzig (IZBI), 04107 Leipzig, Germany; (H.L.-W.); (M.S.)
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10
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Corinaldesi C, Holmes AB, Shen Q, Grunstein E, Pasqualucci L, Dalla-Favera R, Basso K. Tracking Immunoglobulin Repertoire and Transcriptomic Changes in Germinal Center B Cells by Single-Cell Analysis. Front Immunol 2022; 12:818758. [PMID: 35095922 PMCID: PMC8789751 DOI: 10.3389/fimmu.2021.818758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
In response to T-cell-dependent antigens, mature B cells in the secondary lymphoid organs are stimulated to form germinal centers (GCs), which are histological structures deputed to antibody affinity maturation, a process associated with immunoglobulin gene editing by somatic hypermutation (SHM) and class switch recombination (CSR). GC B cells are heterogeneous and transition across multiple stages before being eliminated by apoptosis or committing to post-GC differentiation as memory B cells or plasma cells. In order to explore the dynamics of SHM and CSR during the GC reaction, we identified GC subpopulations by single-cell (sc) transcriptomics and analyzed the load of immunoglobulin variable (V) region mutations as well as the isotype class distribution in each subpopulation. The results showed that the large majority of GC B cells display a quantitatively similar mutational load in the V regions and analogous IGH isotype class distribution, except for the precursors of memory B cells (PreM) and plasma cells (PBL). PreM showed a bimodal pattern with about half of the cells displaying high V region germline identity and enrichment for unswitched IGH, while the rest of the cells carried a mutational load similar to the bulk of GC B cells and showed a switched isotype. PBL displayed a bias toward expression of IGHG and higher V region germline identity compared to the bulk of GC B cells. Genes implicated in SHM and CSR were significantly induced in specific GC subpopulations, consistent with the occurrence of SHM in dark zone cells and suggesting that CSR can occur within the GC.
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Affiliation(s)
| | - Antony B. Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
| | - Qiong Shen
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
| | - Eli Grunstein
- Department of Otolaringology Head and Neck Surgery, Columbia University, New York, NY, United States
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
- Department of Microbiology and Immunology, Columbia University, New York, NY, United States
- Department of Genetics and Development, Columbia University, New York, NY, United States
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
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11
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Unraveling B cell trajectories at single cell resolution. Trends Immunol 2022; 43:210-229. [DOI: 10.1016/j.it.2022.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/31/2022]
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12
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Pae J, Jacobsen JT, Victora GD. Imaging the different timescales of germinal center selection. Immunol Rev 2021; 306:234-243. [PMID: 34825386 DOI: 10.1111/imr.13039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/06/2021] [Indexed: 12/16/2022]
Abstract
Germinal centers (GCs) are the site of antibody affinity maturation, a fundamental immunological process that increases the potency of antibodies and thereby their ability to protect against infection. GC biology is highly dynamic in both time and space, making it ideally suited for intravital imaging. Using multiphoton laser scanning microscopy (MPLSM), the field has gained insight into the molecular, cellular, and structural changes and movements that coordinate affinity maturation in real time in their native environment. On the other hand, several limitations of MPLSM have had to be overcome to allow full appreciation of GC events taking place across different timescales. Here, we review the technical advances afforded by intravital imaging and their contributions to our understanding of GC biology.
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Affiliation(s)
- Juhee Pae
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, USA
| | - Johanne T Jacobsen
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, USA
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