1
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Ma J, Wu Y, Ma L, Yang X, Zhang T, Song G, Li T, Gao K, Shen X, Lin J, Chen Y, Liu X, Fu Y, Gu X, Chen Z, Jiang S, Rao D, Pan J, Zhang S, Zhou J, Huang C, Shi S, Fan J, Guo G, Zhang X, Gao Q. A blueprint for tumor-infiltrating B cells across human cancers. Science 2024; 384:eadj4857. [PMID: 38696569 DOI: 10.1126/science.adj4857] [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: 07/02/2023] [Accepted: 03/06/2024] [Indexed: 05/04/2024]
Abstract
B lymphocytes are essential mediators of humoral immunity and play multiple roles in human cancer. To decode the functions of tumor-infiltrating B cells, we generated a B cell blueprint encompassing single-cell transcriptome, B cell-receptor repertoire, and chromatin accessibility data across 20 different cancer types (477 samples, 269 patients). B cells harbored extraordinary heterogeneity and comprised 15 subsets, which could be grouped into two independent developmental paths (extrafollicular versus germinal center). Tumor types grouped into the extrafollicular pathway were linked with worse clinical outcomes and resistance to immunotherapy. The dysfunctional extrafollicular program was associated with glutamine-derived metabolites through epigenetic-metabolic cross-talk, which promoted a T cell-driven immunosuppressive program. These data suggest an intratumor B cell balance between extrafollicular and germinal-center responses and suggest that humoral immunity could possibly be harnessed for B cell-targeting immunotherapy.
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Affiliation(s)
- Jiaqiang Ma
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yingcheng Wu
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xupeng Yang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Tiancheng Zhang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guohe Song
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Teng Li
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke Gao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xia Shen
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Lin
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yamin Chen
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoshan Liu
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xixi Gu
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zechuan Chen
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shan Jiang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dongning Rao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiaomeng Pan
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shu Zhang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chen Huang
- Department of Gastrointestinal Surgery, Shanghai General Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200080, China
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaoming Zhang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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2
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Sammut SJ, Galson JD, Minter R, Sun B, Chin SF, De Mattos-Arruda L, Finch DK, Schätzle S, Dias J, Rueda OM, Seoane J, Osbourn J, Caldas C, Bashford-Rogers RJM. Predictability of B cell clonal persistence and immunosurveillance in breast cancer. Nat Immunol 2024; 25:916-924. [PMID: 38698238 PMCID: PMC11065701 DOI: 10.1038/s41590-024-01821-0] [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: 02/20/2024] [Accepted: 03/15/2024] [Indexed: 05/05/2024]
Abstract
B cells and T cells are important components of the adaptive immune system and mediate anticancer immunity. The T cell landscape in cancer is well characterized, but the contribution of B cells to anticancer immunosurveillance is less well explored. Here we show an integrative analysis of the B cell and T cell receptor repertoire from individuals with metastatic breast cancer and individuals with early breast cancer during neoadjuvant therapy. Using immune receptor, RNA and whole-exome sequencing, we show that both B cell and T cell responses seem to coevolve with the metastatic cancer genomes and mirror tumor mutational and neoantigen architecture. B cell clones associated with metastatic immunosurveillance and temporal persistence were more expanded and distinct from site-specific clones. B cell clonal immunosurveillance and temporal persistence are predictable from the clonal structure, with higher-centrality B cell antigen receptors more likely to be detected across multiple metastases or across time. This predictability was generalizable across other immune-mediated disorders. This work lays a foundation for prioritizing antibody sequences for therapeutic targeting in cancer.
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MESH Headings
- Humans
- Female
- Breast Neoplasms/immunology
- B-Lymphocytes/immunology
- Immunologic Surveillance
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, B-Cell/metabolism
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- T-Lymphocytes/immunology
- Monitoring, Immunologic
- Exome Sequencing
- Antigens, Neoplasm/immunology
- Neoplasm Metastasis
- Clone Cells
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Affiliation(s)
- Stephen-John Sammut
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
- The Royal Marsden Hospital NHS Foundation Trust, London, UK.
| | | | | | - Bo Sun
- Wellcome Centre for Human Genetics, Oxford, UK
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Leticia De Mattos-Arruda
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | | | | | | | - Oscar M Rueda
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Institució Catalana de Recerca i Estudis Avançats (ICREA), Universitat Autònoma de Barcelona (UAB), CIBERONC, Barcelona, Spain
| | | | - Carlos Caldas
- School of Clinical Medicine, University of Cambridge, Cambridge, UK.
| | - Rachael J M Bashford-Rogers
- Wellcome Centre for Human Genetics, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
- Oxford Cancer Centre, Oxford, UK.
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3
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Tuulasvaara A, Kurdo G, Martola J, Laakso SM. Cervical lymph node diameter reflects disease progression in multiple sclerosis. Mult Scler Relat Disord 2024; 84:105496. [PMID: 38354443 DOI: 10.1016/j.msard.2024.105496] [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: 10/13/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Multiple sclerosis (MS) is an autoimmune disease against the central nervous system (CNS), where B cells activate in the deep cervical lymph nodes (CLNs) before migrating to the CNS. CLN diameter in head magnetic resonance imaging (MRI) is an unexplored possible biomarker for disease activity. METHODS We measured CLN axial diameter from head MRIs of patients with active stable relapsing-remitting MS (a-RRMS-stable, n = 26), highly active stable RRMS (ha-RRMS-stable, n = 23), RRMS patients directly after a relapse (RRMS-relapse, n = 64) and follow-up MRIs from the same patients (r-RRMS-follow-up, n = 26). MRIs of primary headache syndrome patients (n = 38) served as a control group. We evaluated the correlation between CLN diameter and clinical data. RESULTS Increases in EDSS in approximately 2 year-follow up after imaging was connected to smaller CLN diameter at imaging (correlation coefficient -0.305, p = 0.009). In a regression model, age did not show a significant effect to CLN diameter in MS patients. Enlarged CLNs of over 10 mm diameter were more common in patients with shorter disease duration (p = 0.013). The largest CLN axial diameter in RRMS-relapse group was smaller than in the control group (p = 0.005), whereas MS subgroups of the study did not differ in CLN diameter. CONCLUSIONS CLN diameter appears to reflect disease duration and disease progression in MS, in line with compartmentalization of immunological activity to the CNS in time. Decrease in CLN diameter was seen also during relapse. CLN axial diameter in MRI shows promise as a feasible biomarker for assessing MS disease activity.
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Affiliation(s)
- Anni Tuulasvaara
- Department of Neurology, Brain Center, Helsinki University Hospital, Helsinki, Finland; Department of Neurosciences, Clinicum, University of Helsinki, Helsinki, Finland
| | - Goran Kurdo
- Medical Imaging Center, Helsinki University Hospital, Helsinki, Finland
| | - Juha Martola
- Medical Imaging Center, Helsinki University Hospital, Helsinki, Finland
| | - Sini M Laakso
- Department of Neurology, Brain Center, Helsinki University Hospital, Helsinki, Finland; Department of Neurosciences, Clinicum, University of Helsinki, Helsinki, Finland; Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.
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4
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Peres A, Klein V, Frankel B, Lees W, Polak P, Meehan M, Rocha A, Correia Lopes J, Yaari G. Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data. Brief Bioinform 2024; 25:bbae221. [PMID: 38752856 PMCID: PMC11097599 DOI: 10.1093/bib/bbae221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/06/2024] [Accepted: 04/18/2024] [Indexed: 05/19/2024] Open
Abstract
Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency, reproducibility, and collaboration in AIRR-seq data analysis, serving as a model for handling and documenting bioinformatics pipelines in other research domains.
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Affiliation(s)
- Ayelet Peres
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university, 5290002 Ramat Gan, Israel
| | - Vered Klein
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university, 5290002 Ramat Gan, Israel
| | - Boaz Frankel
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university, 5290002 Ramat Gan, Israel
| | - William Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
- INESC TEC – Institute for Systems and Computer Engineering, Technology and Science Porto, Portugal
| | - Pazit Polak
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university, 5290002 Ramat Gan, Israel
| | - Mark Meehan
- INESC TEC – Institute for Systems and Computer Engineering, Technology and Science Porto, Portugal
| | - Artur Rocha
- INESC TEC – Institute for Systems and Computer Engineering, Technology and Science Porto, Portugal
| | - João Correia Lopes
- INESC TEC – Institute for Systems and Computer Engineering, Technology and Science Porto, Portugal
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university, 5290002 Ramat Gan, Israel
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5
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Martinovic T, Vidicevic S, Ciric D, Bumbasirevic V, Stanojevic Z, Tasic J, Petricevic S, Isakovic A, Martinovic VC, Drndarevic N, Trajkovic V, Kravic-Stevovic T. The presence of Mott cells in the lymph nodes of rats with experimental autoimmune encephalomyelitis. Histochem Cell Biol 2024; 161:287-295. [PMID: 37952208 DOI: 10.1007/s00418-023-02252-y] [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] [Accepted: 10/25/2023] [Indexed: 11/14/2023]
Abstract
Mott cells are plasma cells that have multiple spherical Russell bodies packed in their cytoplasm. Russell bodies are dilated endoplasmic reticulum cisternae filled with aggregates of immunoglobulins that are neither secreted nor degraded. Mott cells were observed in our study by light and electron microscope in the lymph nodes of rats with experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. Mott cells were detected on hematoxylin and eosin (HE)-stained lymph node sections as vacuolated cells with eccentrically positioned nuclei and large number of faint blue spherical inclusions in the cytoplasm. Electron microscopic investigation revealed the presence of Russell bodies of the "medusa" form inside Mott cells in lymph node ultra-thin sections of EAE animals. Mott cells expressed the plasma cell marker CD138 and either kappa or lambda immunoglobulin light chains, indicating their origin from polyclonally activated B cells. Finally, Mott cells were associated with active EAE, as they were not found in the lymph nodes of EAE-resistant Albino Oxford rats. The presence of Russell bodies implies an excessive production of immunoglobulins in EAE, thus further emphasizing the role of B cells, and among them Mott cells, in the pathogenesis of this animal model of multiple sclerosis.
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Affiliation(s)
- Tamara Martinovic
- Institute of Histology and Embryology, Faculty of Medicine, University of Belgrade, Višegradska 26, 11000, Belgrade, Serbia
| | - Sasenka Vidicevic
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Darko Ciric
- Institute of Histology and Embryology, Faculty of Medicine, University of Belgrade, Višegradska 26, 11000, Belgrade, Serbia.
| | - Vladimir Bumbasirevic
- Institute of Histology and Embryology, Faculty of Medicine, University of Belgrade, Višegradska 26, 11000, Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Zeljka Stanojevic
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jelena Tasic
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Sasa Petricevic
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Isakovic
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | | | - Vladimir Trajkovic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Tamara Kravic-Stevovic
- Institute of Histology and Embryology, Faculty of Medicine, University of Belgrade, Višegradska 26, 11000, Belgrade, Serbia
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6
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Tieck MP, Vasilenko N, Ruschil C, Kowarik MC. Peripheral memory B cells in multiple sclerosis vs. double negative B cells in neuromyelitis optica spectrum disorder: disease driving B cell subsets during CNS inflammation. Front Cell Neurosci 2024; 18:1337339. [PMID: 38385147 PMCID: PMC10879280 DOI: 10.3389/fncel.2024.1337339] [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: 11/12/2023] [Accepted: 01/16/2024] [Indexed: 02/23/2024] Open
Abstract
B cells are fundamental players in the pathophysiology of autoimmune diseases of the central nervous system, such as multiple sclerosis (MS) and neuromyelitis optica spectrum disorder (NMOSD). A deeper understanding of disease-specific B cell functions has led to the differentiation of both diseases and the development of different treatment strategies. While NMOSD is strongly associated with pathogenic anti-AQP4 IgG antibodies and proinflammatory cytokine pathways, no valid autoantibodies have been identified in MS yet, apart from certain antigen targets that require further evaluation. Although both diseases can be effectively treated with B cell depleting therapies, there are distinct differences in the peripheral B cell subsets that influence CNS inflammation. An increased peripheral blood double negative B cells (DN B cells) and plasmablast populations has been demonstrated in NMOSD, but not consistently in MS patients. Furthermore, DN B cells are also elevated in rheumatic diseases and other autoimmune entities such as myasthenia gravis and Guillain-Barré syndrome, providing indirect evidence for a possible involvement of DN B cells in other autoantibody-mediated diseases. In MS, the peripheral memory B cell pool is affected by many treatments, providing indirect evidence for the involvement of memory B cells in MS pathophysiology. Moreover, it must be considered that an important effector function of B cells in MS may be the presentation of antigens to peripheral immune cells, including T cells, since B cells have been shown to be able to recirculate in the periphery after encountering CNS antigens. In conclusion, there are clear differences in the composition of B cell populations in MS and NMOSD and treatment strategies differ, with the exception of broad B cell depletion. This review provides a detailed overview of the role of different B cell subsets in MS and NMOSD and their implications for treatment options. Specifically targeting DN B cells and plasmablasts in NMOSD as opposed to memory B cells in MS may result in more precise B cell therapies for both diseases.
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Affiliation(s)
| | | | | | - M. C. Kowarik
- Department of Neurology and Stroke, Center for Neurology, and Hertie-Institute for Clinical Brain Research Eberhard-Karls University of Tübingen, Tübingen, Germany
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7
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Wang Q, Feng D, Jia S, Lu Q, Zhao M. B-Cell Receptor Repertoire: Recent Advances in Autoimmune Diseases. Clin Rev Allergy Immunol 2024; 66:76-98. [PMID: 38459209 DOI: 10.1007/s12016-024-08984-6] [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] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
In the field of contemporary medicine, autoimmune diseases (AIDs) are a prevalent and debilitating group of illnesses. However, they present extensive and profound challenges in terms of etiology, pathogenesis, and treatment. A major reason for this is the elusive pathophysiological mechanisms driving disease onset. Increasing evidence suggests the indispensable role of B cells in the pathogenesis of autoimmune diseases. Interestingly, B-cell receptor (BCR) repertoires in autoimmune diseases display a distinct skewing that can provide insights into disease pathogenesis. Over the past few years, advances in high-throughput sequencing have provided powerful tools for analyzing B-cell repertoire to understand the mechanisms during the period of B-cell immune response. In this paper, we have provided an overview of the mechanisms and analytical methods for generating BCR repertoire diversity and summarize the latest research progress on BCR repertoire in autoimmune diseases, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), primary Sjögren's syndrome (pSS), multiple sclerosis (MS), and type 1 diabetes (T1D). Overall, B-cell repertoire analysis is a potent tool to understand the involvement of B cells in autoimmune diseases, facilitating the creation of innovative therapeutic strategies targeting specific B-cell clones or subsets.
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Affiliation(s)
- Qian Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Delong Feng
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Sujie Jia
- Department of Pharmacy, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China.
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
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8
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Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee NY, Jensen C, Ladd D, Hanssen F, Heumos S, Yaari G, Kowarik MC, Nahnsen S, Kleinstein SH. nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576147. [PMID: 38293151 PMCID: PMC10827190 DOI: 10.1101/2024.01.18.576147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets. nf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core/airrflow). Detailed documentation and example results are available on the nf-core website at (https://nf-co.re/airrflow).
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9
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Chang H, Ashlock DA, Graether SP, Keller SM. Anchor Clustering for million-scale immune repertoire sequencing data. BMC Bioinformatics 2024; 25:42. [PMID: 38273275 PMCID: PMC10809746 DOI: 10.1186/s12859-024-05659-z] [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: 06/19/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The clustering of immune repertoire data is challenging due to the computational cost associated with a very large number of pairwise sequence comparisons. To overcome this limitation, we developed Anchor Clustering, an unsupervised clustering method designed to identify similar sequences from millions of antigen receptor gene sequences. First, a Point Packing algorithm is used to identify a set of maximally spaced anchor sequences. Then, the genetic distance of the remaining sequences to all anchor sequences is calculated and transformed into distance vectors. Finally, distance vectors are clustered using unsupervised clustering. This process is repeated iteratively until the resulting clusters are small enough so that pairwise distance comparisons can be performed. RESULTS Our results demonstrate that Anchor Clustering is faster than existing pairwise comparison clustering methods while providing similar clustering quality. With its flexible, memory-saving strategy, Anchor Clustering is capable of clustering millions of antigen receptor gene sequences in just a few minutes. CONCLUSIONS This method enables the meta-analysis of immune-repertoire data from different studies and could contribute to a more comprehensive understanding of the immune repertoire data space.
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Affiliation(s)
- Haiyang Chang
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Daniel A Ashlock
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Stefan M Keller
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.
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10
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Aspden JW, Murphy MA, Kashlan RD, Xiong Y, Poznansky MC, Sîrbulescu RF. Intruders or protectors - the multifaceted role of B cells in CNS disorders. Front Cell Neurosci 2024; 17:1329823. [PMID: 38269112 PMCID: PMC10806081 DOI: 10.3389/fncel.2023.1329823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
B lymphocytes are immune cells studied predominantly in the context of peripheral humoral immune responses against pathogens. Evidence has been accumulating in recent years on the diversity of immunomodulatory functions that B cells undertake, with particular relevance for pathologies of the central nervous system (CNS). This review summarizes current knowledge on B cell populations, localization, infiltration mechanisms, and function in the CNS and associated tissues. Acute and chronic neurodegenerative pathologies are examined in order to explore the complex, and sometimes conflicting, effects that B cells can have in each context, with implications for disease progression and treatment outcomes. Additional factors such as aging modulate the proportions and function of B cell subpopulations over time and are also discussed in the context of neuroinflammatory response and disease susceptibility. A better understanding of the multifactorial role of B cell populations in the CNS may ultimately lead to innovative therapeutic strategies for a variety of neurological conditions.
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Affiliation(s)
- James W. Aspden
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Matthew A. Murphy
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Rommi D. Kashlan
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Yueyue Xiong
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Mark C. Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Ruxandra F. Sîrbulescu
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
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11
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Hoehn KB, Kleinstein SH. B cell phylogenetics in the single cell era. Trends Immunol 2024; 45:62-74. [PMID: 38151443 PMCID: PMC10872299 DOI: 10.1016/j.it.2023.11.004] [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: 10/26/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/29/2023]
Abstract
The widespread availability of single-cell RNA sequencing (scRNA-seq) has led to the development of new methods for understanding immune responses. Single-cell transcriptome data can now be paired with B cell receptor (BCR) sequences. However, RNA from BCRs cannot be analyzed like most other genes because BCRs are genetically diverse within individuals. In humans, BCRs are shaped through recombination followed by mutation and selection for antigen binding. As these processes co-occur with cell division, B cells can be studied using phylogenetic trees representing the mutations within a clone. B cell trees can link experimental timepoints, tissues, or cellular subtypes. Here, we review the current state and potential of how B cell phylogenetics can be combined with single-cell data to understand immune responses.
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Affiliation(s)
- Kenneth B Hoehn
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
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12
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Xu C, Zhang T, Wang H, Zhu L, Ruan Y, Huang Z, Wang J, Zhu H, Huang C, Pan M. Integrative single-cell analysis reveals distinct adaptive immune signatures in the cutaneous lesions of pemphigus. J Autoimmun 2024; 142:103128. [PMID: 37939532 DOI: 10.1016/j.jaut.2023.103128] [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: 07/03/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023]
Abstract
Pemphigus, an autoimmune bullous disease affecting the skin and mucosal membranes, is primarily driven by anti-desmoglein (Dsg) autoantibodies. However, the underlying immune mechanisms of this disease remain largely elusive. Here, we compile an unbiased atlas of immune cells in pemphigus cutaneous lesions at single-cell resolution. We reveal clonally expanded antibody-secreting cells (ASCs) that exhibit variable hypermutation and accumulation of IgG4 class-switching in their immunoglobulin genes. Importantly, pathogenic Dsg-specific ASCs are localized within pemphigus lesions and can evolve from both Dsg-autoreactive and non-binding precursors. We observe an altered distribution of CD4+ T cell subsets within pemphigus lesions, including an imbalance of Th17/Th2 cells. Significantly, we identify a distinct subpopulation of Th17 cells expressing CXCL13 and IL-21 within pemphigus lesions, implying its pivotal role in B cell recruitment and local production of autoantibodies. Furthermore, we characterize multiple clonally expanded CD8+ subpopulations, including effector GMZB+ and GMZK+ subsets with augmented cytotoxic activities, within pemphigus lesions. Chemokine-receptor mapping uncovers cell-type-specific signaling programs involved in the recruitment of T/B cells within pemphigus lesions. Our findings significantly contribute to advancing the understanding of the heterogeneous immune microenvironment and the pathogenesis of pemphigus cutaneous lesions, thereby providing valuable insights for potential therapeutic interventions in this disease.
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Affiliation(s)
- Chuqiao Xu
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianyu Zhang
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Biliary Tract Disease Research, Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hailun Wang
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Zhu
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Ruan
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zixuan Huang
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingying Wang
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haiqin Zhu
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chuanxin Huang
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Biliary Tract Disease Research, Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Meng Pan
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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13
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Haebe S, Day G, Czerwinski DK, Sathe A, Grimes SM, Chen T, Long SR, Martin B, Ozawa MG, Ji HP, Shree T, Levy R. Follicular lymphoma evolves with a surmountable dependency on acquired glycosylation motifs in the B-cell receptor. Blood 2023; 142:2296-2304. [PMID: 37683139 PMCID: PMC10797552 DOI: 10.1182/blood.2023020360] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
ABSTRACT An early event in the genesis of follicular lymphoma (FL) is the acquisition of new glycosylation motifs in the B-cell receptor (BCR) due to gene rearrangement and/or somatic hypermutation. These N-linked glycosylation motifs (N-motifs) contain mannose-terminated glycans and can interact with lectins in the tumor microenvironment, activating the tumor BCR pathway. N-motifs are stable during FL evolution, suggesting that FL tumor cells are dependent on them for their survival. Here, we investigated the dynamics and potential impact of N-motif prevalence in FL at the single-cell level across distinct tumor sites and over time in 17 patients. Although most patients had acquired at least 1 N-motif as an early event, we also found (1) cases without N-motifs in the heavy or light chains at any tumor site or time point and (2) cases with discordant N-motif patterns across different tumor sites. Inferring phylogenetic trees of the patients with discordant patterns, we observed that both N-motif-positive and N-motif-negative tumor subclones could be selected and expanded during tumor evolution. Comparing N-motif-positive with N-motif-negative tumor cells within a patient revealed higher expression of genes involved in the BCR pathway and inflammatory response, whereas tumor cells without N-motifs had higher activity of pathways involved in energy metabolism. In conclusion, although acquired N-motifs likely support FL pathogenesis through antigen-independent BCR signaling in most patients with FL, N-motif-negative tumor cells can also be selected and expanded and may depend more heavily on altered metabolism for competitive survival.
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Affiliation(s)
- Sarah Haebe
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Grady Day
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Debra K. Czerwinski
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Anuja Sathe
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Susan M. Grimes
- Stanford Genome Technology Center, Stanford University, Stanford, CA
| | - Tianqi Chen
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Steven R. Long
- Department of Pathology, University of California, San Francisco, CA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Brock Martin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Michael G. Ozawa
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Hanlee P. Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Tanaya Shree
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Ronald Levy
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
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14
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van Noort JM, Baker D, Kipp M, Amor S. The pathogenesis of multiple sclerosis: a series of unfortunate events. Clin Exp Immunol 2023; 214:1-17. [PMID: 37410892 PMCID: PMC10711360 DOI: 10.1093/cei/uxad075] [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: 05/21/2023] [Revised: 06/10/2023] [Accepted: 07/04/2023] [Indexed: 07/08/2023] Open
Abstract
Multiple sclerosis (MS) is characterized by the chronic inflammatory destruction of myelinated axons in the central nervous system. Several ideas have been put forward to clarify the roles of the peripheral immune system and neurodegenerative events in such destruction. Yet, none of the resulting models appears to be consistent with all the experimental evidence. They also do not answer the question of why MS is exclusively seen in humans, how Epstein-Barr virus contributes to its development but does not immediately trigger it, and why optic neuritis is such a frequent early manifestation in MS. Here we describe a scenario for the development of MS that unifies existing experimental evidence as well as answers the above questions. We propose that all manifestations of MS are caused by a series of unfortunate events that usually unfold over a longer period of time after a primary EBV infection and involve periodic weakening of the blood-brain barrier, antibody-mediated CNS disturbances, accumulation of the oligodendrocyte stress protein αB-crystallin and self-sustaining inflammatory damage.
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Affiliation(s)
- Johannes M van Noort
- Department of Pathology, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands
| | - David Baker
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Markus Kipp
- Institute of Anatomy, Rostock University Medical Center, Rostock, Germany
| | - Sandra Amor
- Department of Pathology, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Institute of Anatomy, Rostock University Medical Center, Rostock, Germany
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15
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Groß-Albenhausen E, Weier A, Velten M, Heider T, Chunder R, Kuerten S. Immune monitoring of SARS-CoV-2-specific T cell and B cell responses in patients with multiple sclerosis treated with ocrelizumab. Front Immunol 2023; 14:1254128. [PMID: 37841269 PMCID: PMC10569464 DOI: 10.3389/fimmu.2023.1254128] [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: 07/06/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction Since the development of the coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), there has been significant interest in determining the effectiveness of SARS-CoV-2 vaccines in patients under immunomodulatory or immunosuppressive therapies. The aim of this study was to evaluate the impact of ocrelizumab, a monoclonal anti-CD20 antibody, on SARS-CoV-2-specific T cell and B cell responses in patients with relapsing-remitting multiple sclerosis (RRMS). Methods To this end, peripheral blood mononuclear cells (PBMCs) were isolated from n = 23 patients with RRMS. Of these patients, n = 17 were tested before (time point t0) and one month after (time point t1) their first dose of ocrelizumab. In addition, we studied n = 9 RRMS patients that got infected with SARS-CoV-2 over the course of ocrelizumab therapy (time point t2). PBMCs were also isolated from n = 19 age- and gender-matched healthy controls (HCs) after vaccination or infection with SARS-CoV-2, respectively. Interferon-γ (IFN-γ)/interleukin-2 (IL-2) and granzyme B (GzB)/perforin (PFN) double-color enzyme-linked immunospot (ELISPOT) assays or single-color ELISPOT assays were performed to measure SARS-CoV-2 antigen-specific T cell and B cell responses. Anti-viral antibody titers were quantified in the serum by chemiluminescence immunoassay. Results Our data indicate a significant difference in the SARS-CoV-2 specific IFN-γ (P = 0.0119) and PFN (P = 0.0005) secreting T cell compartment in the MS cohort at t0 compared to HCs. Following the first dose of ocrelizumab treatment, a significant decrease in the number of SARS-CoV-2 spike protein-specific B cells was observed (P = 0.0012). Infection with SARS-CoV-2 in MS patients under ocrelizumab therapy did not significantly alter their existing immune response against the virus. Kaplan-Meier survival analysis suggested that the spike S1 protein-specific immunoglobulin (Ig)G response might be a key parameter for predicting the probability of (re)infection with SARS-CoV-2. Discussion Our results call for a critical discussion regarding appropriate vaccination intervals and potential biomarkers for the prediction of (re)infection with SARS-CoV-2 in patients with MS receiving ocrelizumab. Unique identifier DRKS00029110; URL: http://apps.who.int/trialsearch/.
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Affiliation(s)
- Elina Groß-Albenhausen
- Institute of Neuroanatomy, Faculty of Medicine, University of Bonn and University Hospital Bonn, Bonn, Germany
| | - Alicia Weier
- Institute of Neuroanatomy, Faculty of Medicine, University of Bonn and University Hospital Bonn, Bonn, Germany
| | - Markus Velten
- Department of Anesthesiology and Intensive Care Medicine, University Medical Center Bonn, Bonn, Germany
| | - Thorsten Heider
- Clinic for Neurology, Klinikum St. Marien Amberg, Amberg, Germany
| | - Rittika Chunder
- Institute of Neuroanatomy, Faculty of Medicine, University of Bonn and University Hospital Bonn, Bonn, Germany
| | - Stefanie Kuerten
- Institute of Neuroanatomy, Faculty of Medicine, University of Bonn and University Hospital Bonn, Bonn, Germany
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16
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Yang H, Qin Q, Wang M, Yin Y, Li R, Tang Y. Crosstalk between peripheral immunity and central nervous system in Alzheimer's disease. Cell Immunol 2023; 391-392:104743. [PMID: 37451918 DOI: 10.1016/j.cellimm.2023.104743] [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: 06/28/2022] [Revised: 06/18/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
The significance of peripheral immunity in the pathogenesis and progression of Alzheimer's diseases (AD) has been recognized. Brain-infiltrated peripheral immune components transporting across the blood-brain barrier (BBB) may reshape the central immune environment. However, mechanisms of how these components open the BBB for AD occurrence and development and correlations between peripheral and central immunity have not been fully explored. Herein, we formulate a hypothesis whereby peripheral immunity as a critical factor allows AD to progress. Peripheral central immune cell crosstalk is associated with early AD pathology and related risk factors. The damaged BBB permits peripheral immune cells to enter the central immune system to deprive its immune privilege promoting the progression toward developing AD. This review summarizes the influences of risk factors on peripheral immunity, alongside their functions, highlighting the concept of peripheral and central immunity as an integrated system in AD pathogenesis, which has received scant attention before.
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Affiliation(s)
- Hanchen Yang
- Innovation Center for Neurological Disorders, Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Qi Qin
- Innovation Center for Neurological Disorders, Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Meng Wang
- Innovation Center for Neurological Disorders, Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Yunsi Yin
- Innovation Center for Neurological Disorders, Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Ruiyang Li
- Innovation Center for Neurological Disorders, Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Yi Tang
- Innovation Center for Neurological Disorders, Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China; Neurodegenerative Laboratory of Ministry of Education of the People's Republic of China, Beijing Key Laboratory of Geriatric Cognitive Disorders, Beijing, China.
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17
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Laaker C, Baenen C, Kovács KG, Sandor M, Fabry Z. Immune cells as messengers from the CNS to the periphery: the role of the meningeal lymphatic system in immune cell migration from the CNS. Front Immunol 2023; 14:1233908. [PMID: 37662908 PMCID: PMC10471710 DOI: 10.3389/fimmu.2023.1233908] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
In recent decades there has been a large focus on understanding the mechanisms of peripheral immune cell infiltration into the central nervous system (CNS) in neuroinflammatory diseases. This intense research led to several immunomodulatory therapies to attempt to regulate immune cell infiltration at the blood brain barrier (BBB), the choroid plexus (ChP) epithelium, and the glial barrier. The fate of these infiltrating immune cells depends on both the neuroinflammatory environment and their type-specific interactions with innate cells of the CNS. Although the fate of the majority of tissue infiltrating immune cells is death, a percentage of these cells could become tissue resident immune cells. Additionally, key populations of immune cells can possess the ability to "drain" out of the CNS and act as messengers reporting signals from the CNS toward peripheral lymphatics. Recent data supports that the meningeal lymphatic system is involved not just in fluid homeostatic functions in the CNS but also in facilitating immune cell migration, most notably dendritic cell migration from the CNS to the meningeal borders and to the draining cervical lymph nodes. Similar to the peripheral sites, draining immune cells from the CNS during neuroinflammation have the potential to coordinate immunity in the lymph nodes and thus influence disease. Here in this review, we will evaluate evidence of immune cell drainage from the brain via the meningeal lymphatics and establish the importance of this in animal models and humans. We will discuss how targeting immune cells at sites like the meningeal lymphatics could provide a new mechanism to better provide treatment for a variety of neurological conditions.
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Affiliation(s)
- Collin Laaker
- Neuroscience Training Program, University of Wisconsin Madison, Madison, WI, United States
| | - Cameron Baenen
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI, United States
| | - Kristóf G. Kovács
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI, United States
| | - Matyas Sandor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI, United States
| | - Zsuzsanna Fabry
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI, United States
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18
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Jeusset L, Abdollahi N, Verny T, Armand M, De Septenville A, Davi F, Bernardes JS. ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors. NAR Genom Bioinform 2023; 5:lqad064. [PMID: 37388820 PMCID: PMC10304752 DOI: 10.1093/nargab/lqad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/25/2023] [Accepted: 06/26/2023] [Indexed: 07/01/2023] Open
Abstract
High throughput sequencing of adaptive immune receptor repertoire (AIRR-seq) has provided numerous human immunoglobulin (IG) sequences allowing specific B cell receptor (BCR) studies such as the antigen-driven evolution of antibodies (soluble forms of the membrane-bound IG part of the BCR). AIRR-seq data allows researchers to examine intraclonal differences caused primarily by somatic hypermutations in IG genes and affinity maturation. Exploring this essential adaptive immunity process could help elucidate the generation of antibodies with high affinity or broadly neutralizing activities. Retracing their evolutionary history could also clarify how vaccines or pathogen exposition drive the humoral immune response, and unravel the clonal architecture of B cell tumors. Computational methods are necessary for large-scale analysis of AIRR-seq properties. However, there is no efficient and interactive tool for analyzing intraclonal diversity, permitting users to explore adaptive immune receptor repertoires in biological and clinical applications. Here we present ViCloD, a web server for large-scale visual analysis of repertoire clonality and intraclonal diversity. ViCloD uses preprocessed data in the format defined by the Adaptive Immune Receptor Repertoire (AIRR) Community. Then, it performs clonal grouping and evolutionary analyses, producing a collection of useful plots for clonal lineage inspection. The web server presents diverse functionalities, including repertoire navigation, clonal abundance analysis, and intraclonal evolutionary tree reconstruction. Users can download the analyzed data in different table formats and save the generated plots as images. ViCloD is a simple, versatile, and user-friendly tool that can help researchers and clinicians to analyze B cell intraclonal diversity. Moreover, its pipeline is optimized to process hundreds of thousands of sequences within a few minutes, allowing an efficient investigation of large and complex repertoires.
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Affiliation(s)
- Lucile Jeusset
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Paris, France
| | - Nika Abdollahi
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- IMGT, the international ImMunoGeneTics Information System, CNRS, Institute of Human Genetics, Montpellier University, France
| | - Thibaud Verny
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- Ecole des Mines ParisTech, Paris, France
| | - Marine Armand
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Paris, France
| | | | - Frédéric Davi
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Paris, France
| | - Juliana Silva Bernardes
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
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19
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Pelissier A, Luo S, Stratigopoulou M, Guikema JEJ, Rodríguez Martínez M. Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires. Front Immunol 2023; 14:1123968. [PMID: 37138881 PMCID: PMC10150052 DOI: 10.3389/fimmu.2023.1123968] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/13/2023] [Indexed: 05/05/2023] Open
Abstract
The adaptive immune system has the extraordinary ability to produce a broad range of immunoglobulins that can bind a wide variety of antigens. During adaptive immune responses, activated B cells duplicate and undergo somatic hypermutation in their B-cell receptor (BCR) genes, resulting in clonal families of diversified B cells that can be related back to a common ancestor. Advances in high-throughput sequencing technologies have enabled the high-throughput characterization of B-cell repertoires, however, the accurate identification of clonally related BCR sequences remains a major challenge. In this study, we compare three different clone identification methods on both simulated and experimental data, and investigate their impact on the characterization of B-cell diversity. We observe that different methods lead to different clonal definitions, which affects the quantification of clonal diversity in repertoire data. Our analyses show that direct comparisons between clonal clusterings and clonal diversity of different repertoires should be avoided if different clone identification methods were used to define the clones. Despite this variability, the diversity indices inferred from the repertoires' clonal characterization across samples show similar patterns of variation regardless of the clonal identification method used. We find the Shannon entropy to be the most robust in terms of the variability of diversity rank across samples. Our analysis also suggests that the traditional germline gene alignment-based method for clonal identification remains the most accurate when the complete information about the sequence is known, but that alignment-free methods may be preferred for shorter sequencing read lengths. We make our implementation freely available as a Python library cdiversity.
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Affiliation(s)
- Aurelien Pelissier
- IBM Research Europe, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Siyuan Luo
- IBM Research Europe, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Maria Stratigopoulou
- Department of Pathology, Amsterdam University Medical Centers, location AMC, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, Netherlands
| | - Jeroen E. J. Guikema
- Department of Pathology, Amsterdam University Medical Centers, location AMC, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, Netherlands
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20
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Ortega-Hernandez OD, Martínez-Cáceres EM, Presas-Rodríguez S, Ramo-Tello C. Epstein-Barr Virus and Multiple Sclerosis: A Convoluted Interaction and the Opportunity to Unravel Predictive Biomarkers. Int J Mol Sci 2023; 24:ijms24087407. [PMID: 37108566 PMCID: PMC10138841 DOI: 10.3390/ijms24087407] [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: 01/14/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Since the early 1980s, Epstein-Barr virus (EBV) infection has been described as one of the main risk factors for developing multiple sclerosis (MS), and recently, new epidemiological evidence has reinforced this premise. EBV seroconversion precedes almost 99% of the new cases of MS and likely predates the first clinical symptoms. The molecular mechanisms of this association are complex and may involve different immunological routes, perhaps all running in parallel (i.e., molecular mimicry, the bystander damage theory, abnormal cytokine networks, and coinfection of EBV with retroviruses, among others). However, despite the large amount of evidence available on these topics, the ultimate role of EBV in the pathogenesis of MS is not fully understood. For instance, it is unclear why after EBV infection some individuals develop MS while others evolve to lymphoproliferative disorders or systemic autoimmune diseases. In this regard, recent studies suggest that the virus may exert epigenetic control over MS susceptibility genes by means of specific virulence factors. Such genetic manipulation has been described in virally-infected memory B cells from patients with MS and are thought to be the main source of autoreactive immune responses. Yet, the role of EBV infection in the natural history of MS and in the initiation of neurodegeneration is even less clear. In this narrative review, we will discuss the available evidence on these topics and the possibility of harnessing such immunological alterations to uncover predictive biomarkers for the onset of MS and perhaps facilitate prognostication of the clinical course.
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Affiliation(s)
- Oscar-Danilo Ortega-Hernandez
- Multiple Sclerosis Unit, Department of Neurosciences, Hospital Universitari Germans Trias i Pujol-IGTP, 08916 Badalona, Spain
| | - Eva M Martínez-Cáceres
- Department of Immunology, Hospital Universitari Germans Trias i Pujol-IGTP, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Silvia Presas-Rodríguez
- Multiple Sclerosis Unit, Department of Neurosciences, Hospital Universitari Germans Trias i Pujol-IGTP, 08916 Badalona, Spain
| | - Cristina Ramo-Tello
- Multiple Sclerosis Unit, Department of Neurosciences, Hospital Universitari Germans Trias i Pujol-IGTP, 08916 Badalona, Spain
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21
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Castellani G, Croese T, Peralta Ramos JM, Schwartz M. Transforming the understanding of brain immunity. Science 2023; 380:eabo7649. [PMID: 37023203 DOI: 10.1126/science.abo7649] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Contemporary studies have completely changed the view of brain immunity from envisioning the brain as isolated and inaccessible to peripheral immune cells to an organ in close physical and functional communication with the immune system for its maintenance, function, and repair. Circulating immune cells reside in special niches in the brain's borders, the choroid plexus, meninges, and perivascular spaces, from which they patrol and sense the brain in a remote manner. These niches, together with the meningeal lymphatic system and skull microchannels, provide multiple routes of interaction between the brain and the immune system, in addition to the blood vasculature. In this Review, we describe current ideas about brain immunity and their implications for brain aging, diseases, and immune-based therapeutic approaches.
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Affiliation(s)
- Giulia Castellani
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tommaso Croese
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Michal Schwartz
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
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22
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Geladaris A, Häusser-Kinzel S, Pretzsch R, Nissimov N, Lehmann-Horn K, Häusler D, Weber MS. IL-10-providing B cells govern pro-inflammatory activity of macrophages and microglia in CNS autoimmunity. Acta Neuropathol 2023; 145:461-477. [PMID: 36854993 PMCID: PMC10020302 DOI: 10.1007/s00401-023-02552-6] [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: 12/05/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 03/02/2023]
Abstract
B cells contribute to chronic inflammatory conditions as source of antibody-secreting plasma cells and as antigen-presenting cells activating T cells, making anti-CD20-mediated B cell depletion a widely used therapeutic option. B cells or B cell subsets may, however, exert regulatory effects, while to date, the immunological and/or clinical impact of these observations remained unclear. We found that in multiple sclerosis (MS) patients, B cells contain regulatory features and that their removal enhanced activity of monocytes. Using a co-culture system, we identified B cell-provided interleukin (IL)-10 as key factor in controlling pro-inflammatory activity of peripheral myeloid cells as well as microglia. Depleting B cells via anti-CD20 in a mouse model of MS unleashed the activity of myeloid cells and microglia and accelerated disease severity; in contrast, adoptive transfer of IL-10-providing B cells restored in vivo control of central nervous system (CNS) macrophages and microglia and reversed clinical exacerbation. These findings suggest that B cells exert meaningful regulatory properties, which should be considered when designing novel B cell-directed agents.
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Affiliation(s)
- Anastasia Geladaris
- Institute of Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
- Fraunhofer-Institute for Translational Medicine and Pharmacology ITMP, Göttingen, Germany
| | - Silke Häusser-Kinzel
- Institute of Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Roxanne Pretzsch
- Institute of Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
- Department of Neurology, University Medical Centre Göttingen, Göttingen, Germany
| | - Nitzan Nissimov
- Institute of Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
- Department of Neurosurgery, Charité-Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Klaus Lehmann-Horn
- Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Darius Häusler
- Institute of Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
- Fraunhofer-Institute for Translational Medicine and Pharmacology ITMP, Göttingen, Germany
| | - Martin S Weber
- Institute of Neuropathology, University Medical Centre Göttingen, Göttingen, Germany.
- Fraunhofer-Institute for Translational Medicine and Pharmacology ITMP, Göttingen, Germany.
- Department of Neurology, University Medical Centre Göttingen, Göttingen, Germany.
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23
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Aloisi F, Giovannoni G, Salvetti M. Epstein-Barr virus as a cause of multiple sclerosis: opportunities for prevention and therapy. Lancet Neurol 2023; 22:338-349. [PMID: 36764322 DOI: 10.1016/s1474-4422(22)00471-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 02/10/2023]
Abstract
Multiple sclerosis is a chronic inflammatory disease of the CNS that results from the interplay between heritable and environmental factors. Mounting evidence from different fields of research supports the pivotal role of the Epstein-Barr virus (EBV) in the development of multiple sclerosis. However, translating this knowledge into clinically actionable information requires a better understanding of the mechanisms linking EBV to pathophysiology. Ongoing research is trying to clarify whether EBV causes neuroinflammation via autoimmunity or antiviral immunity, and if the interaction of EBV with genetic susceptibility to multiple sclerosis can explain why a ubiquitous virus promotes immune dysfunction in susceptible individuals. If EBV also has a role in driving disease activity, the characterisation of this role will help diagnosis, prognosis, and treatment in people with multiple sclerosis. Ongoing clinical trials targeting EBV and new anti-EBV vaccines provide hope for future treatments and preventive interventions.
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Affiliation(s)
- Francesca Aloisi
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy.
| | - Gavin Giovannoni
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine and Blizard Institute, Queen Mary University, London, UK
| | - Marco Salvetti
- Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy; IRCCS Neuromed, Pozzilli, Italy
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24
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Sun Y, Yu H, Guan Y. Glia Connect Inflammation and Neurodegeneration in Multiple Sclerosis. Neurosci Bull 2023; 39:466-478. [PMID: 36853544 PMCID: PMC10043151 DOI: 10.1007/s12264-023-01034-9] [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: 06/27/2022] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
Multiple sclerosis (MS) is regarded as a chronic inflammatory disease that leads to demyelination and eventually to neurodegeneration. Activation of innate immune cells and other inflammatory cells in the brain and spinal cord of people with MS has been well described. However, with the innovation of technology in glial cell research, we have a deep understanding of the mechanisms of glial cells connecting inflammation and neurodegeneration in MS. In this review, we focus on the role of glial cells, including microglia, astrocytes, and oligodendrocytes, in the pathogenesis of MS. We mainly focus on the connection between glial cells and immune cells in the process of axonal damage and demyelinating neuron loss.
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Affiliation(s)
- Ye Sun
- Department of Neurology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Haojun Yu
- Department of Neurology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yangtai Guan
- Department of Neurology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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25
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Bogers L, Engelenburg HJ, Janssen M, Unger PPA, Melief MJ, Wierenga-Wolf AF, Hsiao CC, Mason MRJ, Hamann J, van Langelaar J, Smolders J, van Luijn MM. Selective emergence of antibody-secreting cells in the multiple sclerosis brain. EBioMedicine 2023; 89:104465. [PMID: 36796230 PMCID: PMC9958261 DOI: 10.1016/j.ebiom.2023.104465] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Although distinct brain-homing B cells have been identified in multiple sclerosis (MS), it is unknown how these further evolve to contribute to local pathology. We explored B-cell maturation in the central nervous system (CNS) of MS patients and determined their association with immunoglobulin (Ig) production, T-cell presence, and lesion formation. METHODS Ex vivo flow cytometry was performed on post-mortem blood, cerebrospinal fluid (CSF), meninges and white matter from 28 MS and 10 control brain donors to characterize B cells and antibody-secreting cells (ASCs). MS brain tissue sections were analysed with immunostainings and microarrays. IgG index and CSF oligoclonal bands were measured with nephelometry, isoelectric focusing, and immunoblotting. Blood-derived B cells were cocultured under T follicular helper-like conditions to evaluate their ASC-differentiating capacity in vitro. FINDINGS ASC versus B-cell ratios were increased in post-mortem CNS compartments of MS but not control donors. Local presence of ASCs associated with a mature CD45low phenotype, focal MS lesional activity, lesional Ig gene expression, and CSF IgG levels as well as clonality. In vitro B-cell maturation into ASCs did not differ between MS and control donors. Notably, lesional CD4+ memory T cells positively correlated with ASC presence, reflected by local interplay with T cells. INTERPRETATION These findings provide evidence that local B cells at least in late-stage MS preferentially mature into ASCs, which are largely responsible for intrathecal and local Ig production. This is especially seen in active MS white matter lesions and likely depends on the interaction with CD4+ memory T cells. FUNDING Stichting MS Research (19-1057 MS; 20-490f MS), National MS Fonds (OZ2018-003).
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Affiliation(s)
- Laurens Bogers
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Hendrik J Engelenburg
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, The Netherlands
| | - Malou Janssen
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands; Department of Neurology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Peter-Paul A Unger
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Marie-José Melief
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Annet F Wierenga-Wolf
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Cheng-Chih Hsiao
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, The Netherlands
| | - Matthew R J Mason
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, The Netherlands
| | - Jörg Hamann
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, The Netherlands; Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, 1007 MB, Amsterdam, The Netherlands
| | - Jamie van Langelaar
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Joost Smolders
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands; Neuroimmunology Research Group, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, The Netherlands; Department of Neurology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Marvin M van Luijn
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands.
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26
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Abstract
Multiple sclerosis (MS) is regarded as a chronic inflammatory disease that leads to demyelination and eventually to neurodegeneration. Activation of innate immune cells and other inflammatory cells in the brain and spinal cord of people with MS has been well described. However, with the innovation of technology in glial cell research, we have a deep understanding of the mechanisms of glial cells connecting inflammation and neurodegeneration in MS. In this review, we focus on the role of glial cells, including microglia, astrocytes, and oligodendrocytes, in the pathogenesis of MS. We mainly focus on the connection between glial cells and immune cells in the process of axonal damage and demyelinating neuron loss.
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27
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Safra M, Werner L, Peres A, Polak P, Salamon N, Schvimer M, Weiss B, Barshack I, Shouval DS, Yaari G. A somatic hypermutation-based machine learning model stratifies individuals with Crohn's disease and controls. Genome Res 2023; 33:71-79. [PMID: 36526432 PMCID: PMC9977146 DOI: 10.1101/gr.276683.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
Crohn's disease (CD) is a chronic relapsing-remitting inflammatory disorder of the gastrointestinal tract that is characterized by altered innate and adaptive immune function. Although massively parallel sequencing studies of the T cell receptor repertoire identified oligoclonal expansion of unique clones, much less is known about the B cell receptor (BCR) repertoire in CD. Here, we present a novel BCR repertoire sequencing data set from ileal biopsies from pediatric patients with CD and controls, and identify CD-specific somatic hypermutation (SHM) patterns, revealed by a machine learning (ML) algorithm trained on BCR repertoire sequences. Moreover, ML classification of a different data set from blood samples of adults with CD versus controls identified that V gene usage, clusters, or mutation frequencies yielded excellent results in classifying the disease (F1 > 90%). In summary, we show that an ML algorithm enables the classification of CD based on unique BCR repertoire features with high accuracy.
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Affiliation(s)
- Modi Safra
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Lael Werner
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petah Tikva 4920235, Israel;,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ayelet Peres
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Pazit Polak
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Naomi Salamon
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Michael Schvimer
- Institute of Pathology, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Batia Weiss
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;,Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Iris Barshack
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;,Institute of Pathology, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Dror S. Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petah Tikva 4920235, Israel;,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gur Yaari
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
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28
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Dirks J, Andres O, Paul L, Manukjan G, Schulze H, Morbach H. IgD shapes the pre-immune naïve B cell compartment in humans. Front Immunol 2023; 14:1096019. [PMID: 36776874 PMCID: PMC9908586 DOI: 10.3389/fimmu.2023.1096019] [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: 11/11/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
B cell maturation and immunoglobulin (Ig) repertoire selection are governed by expression of a functional B cell receptor (BCR). Naïve B cells co-express their BCR as IgM and IgD isotype. However, the role of the additionally expressed IgD on naïve B cells is not known. Here we assessed the impact of IgD on naïve B cell maturation and Ig repertoire selection in 8 individuals from 3 different families with heterozygous loss-of-function or loss-of expression mutations in IGHD. Although naïve B cells from these individuals expressed IgM on their surface, the IGHD variant in heterozygous state entailed a chimeric situation by allelic exclusion with almost half of the naïve B cell population lacking surface IgD expression. Flow cytometric analyses revealed a distinct phenotype of IgD-negative naïve B cells with decreased expression of CD19, CD20 and CD21 as well as lower BAFF-R and integrin-β7 expression. IgD-negative B cells were less responsive in vitro after engaging the IgM-BCR, TLR7/9 or CD40 pathway. Additionally, a selective disadvantage of IgD-negative B cells within the T2 transitional and mature naïve B cell compartment as well as reduced frequencies of IgMlo/- B cells within the mature naïve B cell compartment lacking IgD were evident. RNA-Ig-seq of bulk sorted B cell populations showed an altered selection of distinct VH segments in the IgD-negative mature naïve B cell population. We conclude that IgD expression on human naïve B cells is redundant for generation of naïve B cells in general, but further shapes the naive B cell compartment starting from T2 transitional B cells. Our observations suggest an unexpected role of IgD expression to be critical for selection of distinct Ig VH segments into the pre-immune Ig repertoire and for the survival of IgMlo/- naïve B cells known to be enriched in poly-/autoreactive B cell clones.
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Affiliation(s)
- Johannes Dirks
- Pediatric Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Oliver Andres
- Pediatric Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Luisa Paul
- Pediatric Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany.,Department of Pediatrics I, University Hospital Essen, University of Duisburg Essen, Essen, Germany
| | - Georgi Manukjan
- Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg, Germany
| | - Harald Schulze
- Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg, Germany
| | - Henner Morbach
- Pediatric Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
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29
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Katoh H, Komura D, Furuya G, Ishikawa S. Immune repertoire profiling for disease pathobiology. Pathol Int 2023; 73:1-11. [PMID: 36342353 PMCID: PMC10099665 DOI: 10.1111/pin.13284] [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: 05/24/2022] [Revised: 09/20/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Lymphocytes consist of highly heterogeneous populations, each expressing a specific cell surface receptor corresponding to a particular antigen. Lymphocytes are both the cause and regulator of various diseases, including autoimmune/allergic diseases, lifestyle diseases, neurodegenerative diseases, and cancers. Recently, immune repertoire sequencing has attracted much attention because it helps obtain global profiles of the immune receptor sequences of infiltrating T and B cells in specimens. Immune repertoire sequencing not only helps deepen our understanding of the molecular mechanisms of immune-related pathology but also assists in discovering novel therapeutic modalities for diseases, thereby shedding colorful light on otherwise tiny monotonous cells when observed under a microscope. In this review article, we introduce and detail the background and methodology of immune repertoire sequencing and summarize recent scientific achievements in association with human diseases. Future perspectives on this genetic technique in the field of histopathological research will also be discussed.
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Affiliation(s)
- Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Genta Furuya
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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30
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Ruschil C, Gabernet G, Kemmerer CL, Jarboui MA, Klose F, Poli S, Ziemann U, Nahnsen S, Kowarik MC. Cladribine treatment specifically affects peripheral blood memory B cell clones and clonal expansion in multiple sclerosis patients. Front Immunol 2023; 14:1133967. [PMID: 36960053 PMCID: PMC10028280 DOI: 10.3389/fimmu.2023.1133967] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/13/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction B cells are acknowledged as crucial players in the pathogenesis of multiple sclerosis (MS). Several disease modifying drugs including cladribine have been shown to exert differential effects on peripheral blood B cell subsets. However, little is known regarding functional changes within the peripheral B cell populations. In this study, we obtained a detailed picture of B cell repertoire changes under cladribine treatment on a combined immunoglobulin (Ig) transcriptome and proteome level. Methods We performed next-generation sequencing of Ig heavy chain (IGH) transcripts and Ig mass spectrometry in cladribine-treated patients with relapsing-remitting multiple sclerosis (n = 8) at baseline and after 6 and 12 months of treatment in order to generate Ig transcriptome and Ig peptide libraries. Ig peptides were overlapped with the corresponding IGH transcriptome in order to analyze B cell clones on a combined transcriptome and proteome level. Results The analysis of peripheral blood B cell percentages pointed towards a significant decrease of memory B cells and an increase of naive B cells following cladribine therapy. While basic IGH repertoire parameters (e.g. variable heavy chain family usage and Ig subclasses) were only slightly affected by cladribine treatment, a significantly decreased number of clones and significantly lower diversity in the memory subset was noticeable at 6 months following treatment which was sustained at 12 months. When looking at B-cell clones comprising sequences from the different time-points, clones spanning between all three time-points were significantly more frequent than clones including sequences from two time-points. Furthermore, Ig proteome analyses showed that Ig transcriptome specific peptides could mostly be equally aligned to all three time-points pointing towards a proportion of B-cell clones that are maintained during treatment. Discussion Our findings suggest that peripheral B cell related treatment effects of cladribine tablets might be exerted through a reduction of possibly disease relevant clones in the memory B cell subset without disrupting the overall clonal composition of B cells. Our results -at least partially- might explain the relatively mild side effects regarding infections and the sustained immune response after vaccinations during treatment. However, exact disease driving B cell subsets and their effects remain unknown and should be addressed in future studies.
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Affiliation(s)
- Christoph Ruschil
- Department of Neurology and Stroke, Center for Neurology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Hertie-Institute for Clinical Brain Research, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Gisela Gabernet
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Constanze Louisa Kemmerer
- Hertie-Institute for Clinical Brain Research, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Mohamed Ali Jarboui
- Core Facility for Medical Bioanalytics (CFMB), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Franziska Klose
- Core Facility for Medical Bioanalytics (CFMB), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Sven Poli
- Department of Neurology and Stroke, Center for Neurology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Hertie-Institute for Clinical Brain Research, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Ulf Ziemann
- Department of Neurology and Stroke, Center for Neurology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Hertie-Institute for Clinical Brain Research, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Markus Christian Kowarik
- Department of Neurology and Stroke, Center for Neurology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Hertie-Institute for Clinical Brain Research, Eberhard Karls University of Tübingen, Tübingen, Germany
- *Correspondence: Markus Christian Kowarik,
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31
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Vakrakou AG, Paschalidis N, Pavlos E, Giannouli C, Karathanasis D, Tsipota X, Velonakis G, Stadelmann-Nessler C, Evangelopoulos ME, Stefanis L, Kilidireas C. Specific myeloid signatures in peripheral blood differentiate active and rare clinical phenotypes of multiple sclerosis. Front Immunol 2023; 14:1071623. [PMID: 36761741 PMCID: PMC9905713 DOI: 10.3389/fimmu.2023.1071623] [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: 10/16/2022] [Accepted: 01/03/2023] [Indexed: 01/26/2023] Open
Abstract
Current understanding of Multiple Sclerosis (MS) pathophysiology implicates perturbations in adaptive cellular immune responses, predominantly T cells, in Relapsing-Remitting forms (RRMS). Nevertheless, from a clinical perspective MS is a heterogeneous disease reflecting the heterogeneity of involved biological systems. This complexity requires advanced analysis tools at the single-cell level to discover biomarkers for better patient-group stratification. We designed a novel 44-parameter mass cytometry panel to interrogate predominantly the role of effector and regulatory subpopulations of peripheral blood myeloid subsets along with B and T-cells (excluding granulocytes) in MS, assessing three different patient cohorts: RRMS, PPMS (Primary Progressive) and Tumefactive MS patients (TMS) (n=10, 8, 14 respectively). We further subgrouped our cohort into inactive or active disease stages to capture the early underlying events in disease pathophysiology. Peripheral blood analysis showed that TMS cases belonged to the spectrum of RRMS, whereas PPMS cases displayed different features. In particular, TMS patients during a relapse stage were characterized by a specific subset of CD11c+CD14+ CD33+, CD192+, CD172+-myeloid cells with an alternative phenotype of monocyte-derived macrophages (high arginase-1, CD38, HLA-DR-low and endogenous TNF-a production). Moreover, TMS patients in relapse displayed a selective CD4 T-cell lymphopenia of cells with a Th2-like polarised phenotype. PPMS patients did not display substantial differences from healthy controls, apart from a trend toward higher expansion of NK cell subsets. Importantly, we found that myeloid cell populations are reshaped under effective disease-modifying therapy predominantly with glatiramer acetate and to a lesser extent with anti-CD20, suggesting that the identified cell signature represents a specific therapeutic target in TMS. The expanded myeloid signature in TMS patients was also confirmed by flow cytometry. Serum neurofilament light-chain levels confirmed the correlation of this myeloid cell signature with indices of axonal injury. More in-depth analysis of myeloid subsets revealed an increase of a subset of highly cytolytic and terminally differentiated NK cells in PPMS patients with leptomeningeal enhancement (active-PPMS), compared to those without (inactive-PPMS). We have identified previously uncharacterized subsets of circulating myeloid cells and shown them to correlate with distinct disease forms of MS as well as with specific disease states (relapse/remission).
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Affiliation(s)
- Aigli G Vakrakou
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece.,Department of Neuropathology, University of Göttingen Medical Center, Göttingen, Germany
| | - Nikolaos Paschalidis
- Mass Cytometry-CyTOF Laboratory, Center for Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Eleftherios Pavlos
- Center for Clinical Research, Experimental Surgery and Translational Research Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Division of Basic Sciences, University of Crete Medical School, Heraklion, Greece
| | - Christina Giannouli
- Center for Clinical Research, Experimental Surgery and Translational Research Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Dimitris Karathanasis
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Xristina Tsipota
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Velonakis
- Research Unit of Radiology, 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Maria-Eleftheria Evangelopoulos
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Leonidas Stefanis
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Constantinos Kilidireas
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece.,Department of Neurology, Henry Dunant Hospital Center, Athens, Greece
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Blazso P, Csomos K, Tipton CM, Ujhazi B, Walter JE. Lineage Reconstruction of In Vitro Identified Antigen-Specific Autoreactive B Cells from Adaptive Immune Receptor Repertoires. Int J Mol Sci 2022; 24:ijms24010225. [PMID: 36613668 PMCID: PMC9820449 DOI: 10.3390/ijms24010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
The emergence, survival, growth and maintenance of autoreactive (AR) B-cell clones, the hallmark of humoral autoimmunity, leave their footprints in B-cell receptor repertoires. Collecting IgH sequences related to polyreactive (PR) ones from adaptive immune receptor repertoire (AIRR) datasets make the reconstruction and analysis of PR/AR B-cell lineages possible. We developed a computational approach, named ImmChainTracer, to extract members and to visualize clonal relationships of such B-cell lineages. Our approach was successfully applied on the IgH repertoires of patients suffering from monogenic hypomorphic RAG1 and 2 deficiency (pRD) or polygenic systemic lupus erythematosus (SLE) autoimmune diseases to identify relatives of AR IgH sequences and to track their fate in AIRRs. Signs of clonal expansion, affinity maturation and class-switching events in PR/AR and non-PR/AR B-cell lineages were revealed. An extension of our method towards B-cell expansion caused by any trigger (e.g., infection, vaccination or antibody development) may provide deeper insight into antigen specific B-lymphogenesis.
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Affiliation(s)
- Peter Blazso
- Department of Pediatrics, University of Szeged, 6720 Szeged, Hungary
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
- Correspondence: (P.B.); (J.E.W.)
| | - Krisztian Csomos
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Christopher M. Tipton
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, GA 30322, USA
| | - Boglarka Ujhazi
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Jolan E. Walter
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
- Division of Allergy and Immunology, Massachusetts General Hospital for Children, Boston, MA 02114, USA
- Correspondence: (P.B.); (J.E.W.)
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Waly D, Muthupandian A, Fan CW, Anzinger H, Magor BG. Immunoglobulin VDJ repertoires reveal hallmarks of germinal centers in unique cell clusters isolated from zebrafish ( Danio rerio) lymphoid tissues. Front Immunol 2022; 13:1058877. [PMID: 36569890 PMCID: PMC9772432 DOI: 10.3389/fimmu.2022.1058877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/03/2022] [Indexed: 12/13/2022] Open
Abstract
DNA mutagenesis during antibody affinity maturation has potentially oncogenic or autoimmune outcomes if not tightly controlled as it is in mammalian germinal centers. Cold blooded vertebrates lack germinal centers, yet have a functional Ig gene mutator enzyme, Aicda. In fish there are clusters of Aicda+ cells encircled by pigmented 'melano-macrophages' and we test the hypothesis that these clusters are functionally analogous to germinal centers. Sequenced IgH VDJ repertoire libraries from individual isolated clusters showed evidence of B-cell clonal expansion and VDJ somatic hypermutation. Construction of Ig clonal lineage trees revealed that unlike surrounding lymphoid tissue, each cluster is dominated by a few B-cell VDJ clonotypes having hundreds of mutated variants. Recruitment of B-cells to the clusters appears to be ongoing, as there are additional Ig clones having smaller lineages. Finally, we show evidence for positive selection for replacement mutations in regions encoding the antigen contact loops, but not in the framework regions, consistent with functional antibody modification. Melano-macrophages appear to trap the Ag used for post-mutation B-cell selection, performing a role analogous to the follicular dendritic cells of mammalian germinal centers. These findings provide insights into the evolution of the affinity maturation process, the improvement of fish vaccines and possibly also the workings of atypical ectopic germinal centers generated in several human diseases.
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Affiliation(s)
- Doaa Waly
- *Correspondence: Brad G. Magor, ; Doaa Waly,
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Zhang C, Bzikadze AV, Safonova Y, Mirarab S. A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods. Front Immunol 2022; 13:1014439. [PMID: 36618367 PMCID: PMC9815712 DOI: 10.3389/fimmu.2022.1014439] [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: 08/08/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Affinity maturation (AM) of B cells through somatic hypermutations (SHMs) enables the immune system to evolve to recognize diverse pathogens. The accumulation of SHMs leads to the formation of clonal lineages of antibody-secreting b cells that have evolved from a common naïve B cell. Advances in high-throughput sequencing have enabled deep scans of B cell receptor repertoires, paving the way for reconstructing clonal trees. However, it is not clear if clonal trees, which capture microevolutionary time scales, can be reconstructed using traditional phylogenetic reconstruction methods with adequate accuracy. In fact, several clonal tree reconstruction methods have been developed to fix supposed shortcomings of phylogenetic methods. Nevertheless, no consensus has been reached regarding the relative accuracy of these methods, partially because evaluation is challenging. Benchmarking the performance of existing methods and developing better methods would both benefit from realistic models of clonal lineage evolution specifically designed for emulating B cell evolution. In this paper, we propose a model for modeling B cell clonal lineage evolution and use this model to benchmark several existing clonal tree reconstruction methods. Our model, designed to be extensible, has several features: by evolving the clonal tree and sequences simultaneously, it allows modeling selective pressure due to changes in affinity binding; it enables scalable simulations of large numbers of cells; it enables several rounds of infection by an evolving pathogen; and, it models building of memory. In addition, we also suggest a set of metrics for comparing clonal trees and measuring their properties. Our results show that while maximum likelihood phylogenetic reconstruction methods can fail to capture key features of clonal tree expansion if applied naively, a simple post-processing of their results, where short branches are contracted, leads to inferences that are better than alternative methods.
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Affiliation(s)
- Chao Zhang
- Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, United States
| | - Andrey V. Bzikadze
- Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, United States
| | - Yana Safonova
- Computer Science and Engineering Department, University of California, San Diego, San Diego, CA, United States
| | - Siavash Mirarab
- Electrical and Computer Engineering Department, University of California, San Diego, San Diego, CA, United States,*Correspondence: Siavash Mirarab,
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Attfield KE, Jensen LT, Kaufmann M, Friese MA, Fugger L. The immunology of multiple sclerosis. Nat Rev Immunol 2022; 22:734-750. [PMID: 35508809 DOI: 10.1038/s41577-022-00718-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 12/11/2022]
Abstract
Our incomplete understanding of the causes and pathways involved in the onset and progression of multiple sclerosis (MS) limits our ability to effectively treat this complex neurological disease. Recent studies explore the role of immune cells at different stages of MS and how they interact with cells of the central nervous system (CNS). The findings presented here begin to question the exclusivity of an antigen-specific cause and highlight how seemingly distinct immune cell types can share common functions that drive disease. Innovative techniques further expose new disease-associated immune cell populations and reinforce how environmental context is critical to their phenotype and subsequent role in disease. Importantly, the differentiation of immune cells into a pathogenic state is potentially reversible through therapeutic manipulation. As such, understanding the mechanisms that provide plasticity to causal cell types is likely key to uncoupling these disease processes and may identify novel therapeutic targets that replace the need for cell ablation.
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Affiliation(s)
- Kathrine E Attfield
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Oxford University Hospitals, University of Oxford, Oxford, UK
| | - Lise Torp Jensen
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Max Kaufmann
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Manuel A Friese
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Oxford University Hospitals, University of Oxford, Oxford, UK.
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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Liu XY, Li J, Zhang Y, Fan L, Xia Y, Wu Y, Chen J, Zhao X, Gao Q, Xu B, Nie C, Li Z, Tong A, Wang W, Cai J. Kidney microbiota dysbiosis contributes to the development of hypertension. Gut Microbes 2022; 14:2143220. [PMID: 36369946 PMCID: PMC9662196 DOI: 10.1080/19490976.2022.2143220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Gut microbiota dysbiosis promotes metabolic syndromes (e.g., hypertension); however, the patterns that drive hypertensive pathology and could be targeted for therapeutic intervention are unclear. We hypothesized that gut microbes might translocate to the kidney to trigger hypertension. We aimed to uncover their method of colonization, and thereby how to maintain blood pressure homeostasis. Using combined approaches based on fluorescence in situ hybridization (FISH) and immunofluorescence staining, electron microscopy analysis, bacterial cultures, species identification, and RNA-sequencing-based meta-transcriptomics, we first demonstrated the presence of bacteria within the kidney of spontaneously hypertensive rats (SHRs) and its normotensive counterpart, Wistar-Kyoto rats (WKYs), and patients with hypertension. Translocated renal bacteria were coated with secretory IgA (sIgA) or remained dormant in the L-form. Klebsiella pneumoniae (K.pn) was identified in the kidneys of germ-free (GF) mice following intestinal transplantation, which suggested an influx of gut bacteria into the kidneys. Renal bacterial taxa and their function are associated with hypertension. Hypertensive hosts showed increased richness in the pathobionts of their kidneys, which were partly derived from the gastrointestinal tract. We also demonstrated the indispensable role of bacterial IgA proteases in the translocation of live microbes. Furthermore, Tartary buckwheat dietary intervention reduced blood pressure and modulated the core renal flora-host ecosystem to near-normal states. Taken together, the unique patterns of viable and dormant bacteria in the kidney provide insight into the pathogenesis of non-communicable chronic diseases and cardiometabolic diseases (e.g., hypertension), and may lead to potential novel microbiota-targeted dietary therapies.
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Affiliation(s)
- Xin-Yu Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China,CONTACT Xin-Yu Liu State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Li
- Hypertension Center, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Heart Center & Beijing Key Laboratory of Hypertension, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yamei Zhang
- Clinical Genetics Laboratory, Affiliated Hospital &Clinical Medical College of Chengdu University, Chengdu, P.R. China,School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Luyun Fan
- Hypertension Center, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanli Xia
- Clinical Genetics Laboratory, Affiliated Hospital &Clinical Medical College of Chengdu University, Chengdu, P.R. China,School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yongyang Wu
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, China
| | - Junru Chen
- Reproductive and Genetic Hospital of CITIC‐Xiangya, Changsha, China
| | - Xinyu Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qiannan Gao
- Hypertension Center, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bing Xu
- Department of Proctology, University of Chinese Academy of Sciences-Shenzhen Hospital (Guang Ming), Shenzhen, China
| | - Chunlai Nie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Zhengyu Li
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Aiping Tong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wenjie Wang
- Hypertension Center, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun Cai
- Hypertension Center, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Jun Cai Hypertension Center, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
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37
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von Niederhäusern V, Ruder J, Ghraichy M, Jelcic I, Müller AM, Schanz U, Martin R, Trück J. B-Cell Reconstitution After Autologous Hematopoietic Stem Cell Transplantation in Multiple Sclerosis. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2022; 9:9/6/e200027. [PMID: 36229189 PMCID: PMC9562041 DOI: 10.1212/nxi.0000000000200027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/25/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND AND OBJECTIVES Autologous hematopoietic stem cell transplantation (aHSCT) is increasingly used to treat aggressive forms of multiple sclerosis (MS). This procedure is believed to result in an immune reset and restoration of a self-tolerant immune system. Immune reconstitution has been extensively studied for T cells, but only to a limited extent for B cells. As increasing evidence suggests an important role of B cells in MS pathogenesis, we sought here to better understand reconstitution and the extent of renewal of the B-cell system after aHSCT in MS. METHODS Using longitudinal multidimensional flow cytometry and immunoglobulin heavy chain (IgH) repertoire sequencing following aHSCT with BCNU + Etoposide + Ara-C + Melphalan anti-thymocyte globulin, we analyzed the B-cell compartment in a cohort of 20 patients with MS in defined intervals before and up to 1 year after aHSCT and compared these findings with data from healthy controls. RESULTS Total B-cell numbers recovered within 3 months and increased above normal levels 1 year after transplantation, successively shifting from a predominantly transitional to a naive immune phenotype. Memory subpopulations recovered slowly and remained below normal levels with reduced repertoire diversity 1 year after transplantation. Isotype subclass analysis revealed a proportional shift toward IgG1-expressing cells and a reduction in IgG2 cells. Mutation analysis of IgH sequences showed that highly mutated memory B cells and plasma cells may transiently survive conditioning while the analysis of sequence cluster overlap, variable (IGHV) and joining (IGHJ) gene usage and repertoire diversity suggested a renewal of the late posttransplant repertoire. In patients with early cytomegalovirus reactivation, reconstitution of naive and memory B cells was delayed. DISCUSSION Our detailed characterization of B-cell reconstitution after aHSCT in MS indicates a reduced reactivation potential of memory B cells up to 1 year after transplantation, which may leave patients susceptible to infection, but may also be an important aspect of its mechanism of action.
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Affiliation(s)
- Valentin von Niederhäusern
- From the Division of Immunology and Children's Research Center (V.N., M.G., J.T.), University Children's Hospital Zurich, University of Zurich; Neuroimmunology and MS Research Section (J.R., I.J., R.M.), Department of Neurology, University Hospital Zurich, University of Zurich; and Department of Medical Oncology and Hematology (A.M.M., U.S.), University Hospital Zurich
| | - Josefine Ruder
- From the Division of Immunology and Children's Research Center (V.N., M.G., J.T.), University Children's Hospital Zurich, University of Zurich; Neuroimmunology and MS Research Section (J.R., I.J., R.M.), Department of Neurology, University Hospital Zurich, University of Zurich; and Department of Medical Oncology and Hematology (A.M.M., U.S.), University Hospital Zurich
| | - Marie Ghraichy
- From the Division of Immunology and Children's Research Center (V.N., M.G., J.T.), University Children's Hospital Zurich, University of Zurich; Neuroimmunology and MS Research Section (J.R., I.J., R.M.), Department of Neurology, University Hospital Zurich, University of Zurich; and Department of Medical Oncology and Hematology (A.M.M., U.S.), University Hospital Zurich
| | - Ilijas Jelcic
- From the Division of Immunology and Children's Research Center (V.N., M.G., J.T.), University Children's Hospital Zurich, University of Zurich; Neuroimmunology and MS Research Section (J.R., I.J., R.M.), Department of Neurology, University Hospital Zurich, University of Zurich; and Department of Medical Oncology and Hematology (A.M.M., U.S.), University Hospital Zurich
| | - Antonia Maria Müller
- From the Division of Immunology and Children's Research Center (V.N., M.G., J.T.), University Children's Hospital Zurich, University of Zurich; Neuroimmunology and MS Research Section (J.R., I.J., R.M.), Department of Neurology, University Hospital Zurich, University of Zurich; and Department of Medical Oncology and Hematology (A.M.M., U.S.), University Hospital Zurich
| | - Urs Schanz
- From the Division of Immunology and Children's Research Center (V.N., M.G., J.T.), University Children's Hospital Zurich, University of Zurich; Neuroimmunology and MS Research Section (J.R., I.J., R.M.), Department of Neurology, University Hospital Zurich, University of Zurich; and Department of Medical Oncology and Hematology (A.M.M., U.S.), University Hospital Zurich
| | - Roland Martin
- From the Division of Immunology and Children's Research Center (V.N., M.G., J.T.), University Children's Hospital Zurich, University of Zurich; Neuroimmunology and MS Research Section (J.R., I.J., R.M.), Department of Neurology, University Hospital Zurich, University of Zurich; and Department of Medical Oncology and Hematology (A.M.M., U.S.), University Hospital Zurich
| | - Johannes Trück
- From the Division of Immunology and Children's Research Center (V.N., M.G., J.T.), University Children's Hospital Zurich, University of Zurich; Neuroimmunology and MS Research Section (J.R., I.J., R.M.), Department of Neurology, University Hospital Zurich, University of Zurich; and Department of Medical Oncology and Hematology (A.M.M., U.S.), University Hospital Zurich.
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Han G, Deng Q, Marques-Piubelli ML, Dai E, Dang M, Ma MCJ, Li X, Yang H, Henderson J, Kudryashova O, Meerson M, Isaev S, Kotlov N, Nomie KJ, Bagaev A, Parra ER, Solis Soto LM, Parmar S, Hagemeister FB, Ahmed S, Iyer SP, Samaniego F, Steiner R, Fayad L, Lee H, Fowler NH, Flowers CR, Strati P, Westin JR, Neelapu SS, Nastoupil LJ, Vega F, Wang L, Green MR. Follicular Lymphoma Microenvironment Characteristics Associated with Tumor Cell Mutations and MHC Class II Expression. Blood Cancer Discov 2022; 3:428-443. [PMID: 35687817 PMCID: PMC9894575 DOI: 10.1158/2643-3230.bcd-21-0075] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/02/2021] [Accepted: 06/03/2022] [Indexed: 01/01/2023] Open
Abstract
Follicular lymphoma (FL) is a B-cell malignancy with a complex tumor microenvironment that is rich in nonmalignant immune cells. We applied single-cell RNA sequencing to characterize the diverse tumor and immune cell populations of FL and identified major phenotypic subsets of FL T cells, including a cytotoxic CD4 T-cell population. We characterized four major FL subtypes with differential representation or relative depletion of distinct T-cell subsets. By integrating exome sequencing, we observed that somatic mutations are associated with, but not definitive for, reduced MHC expression on FL cells. In turn, expression of MHCII genes by FL cells was associated with significant differences in the proportions and targetable immunophenotypic characteristics of T cells. This provides a classification framework of the FL microenvironment in association with FL genotypes and MHC expression, and informs different potential immunotherapeutic strategies based upon tumor cell MHCII expression. SIGNIFICANCE We have characterized the FL-infiltrating T cells, identified cytotoxic CD4 T cells as an important component that is associated with tumor cell-intrinsic characteristics, and identified sets of targetable immune checkpoints on T cells that differed from FLs with normal versus low MHC expression. See related commentary by Melnick, p. 374. This article is highlighted in the In This Issue feature, p. 369.
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Affiliation(s)
- Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qing Deng
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Enyu Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Man Chun John Ma
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xubin Li
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Haopeng Yang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jared Henderson
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | | | | | | | - Edwin R. Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa M. Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Simrit Parmar
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Fredrick B. Hagemeister
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sairah Ahmed
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Swaminathan P. Iyer
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Felipe Samaniego
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Raphael Steiner
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luis Fayad
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hun Lee
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nathan H. Fowler
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
- BostonGene Corporation, Waltham, Massachusetts
| | - Christopher R. Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paolo Strati
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason R. Westin
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sattva S. Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Loretta J. Nastoupil
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Francisco Vega
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael R. Green
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
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39
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Zaragoza-Infante L, Junet V, Pechlivanis N, Fragkouli SC, Amprachamian S, Koletsa T, Chatzidimitriou A, Papaioannou M, Stamatopoulos K, Agathangelidis A, Psomopoulos F. IgIDivA: immunoglobulin intraclonal diversification analysis. Brief Bioinform 2022; 23:6679272. [PMID: 36044248 PMCID: PMC9487589 DOI: 10.1093/bib/bbac349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/14/2022] Open
Abstract
Intraclonal diversification (ID) within the immunoglobulin (IG) genes expressed by B cell clones arises due to ongoing somatic hypermutation (SHM) in a context of continuous interactions with antigen(s). Defining the nature and order of appearance of SHMs in the IG genes can assist in improved understanding of the ID process, shedding light into the ontogeny and evolution of B cell clones in health and disease. Such endeavor is empowered thanks to the introduction of high-throughput sequencing in the study of IG gene repertoires. However, few existing tools allow the identification, quantification and characterization of SHMs related to ID, all of which have limitations in their analysis, highlighting the need for developing a purpose-built tool for the comprehensive analysis of the ID process. In this work, we present the immunoglobulin intraclonal diversification analysis (IgIDivA) tool, a novel methodology for the in-depth qualitative and quantitative analysis of the ID process from high-throughput sequencing data. IgIDivA identifies and characterizes SHMs that occur within the variable domain of the rearranged IG genes and studies in detail the connections between identified SHMs, establishing mutational pathways. Moreover, it combines established and new graph-based metrics for the objective determination of ID level, combined with statistical analysis for the comparison of ID level features for different groups of samples. Of importance, IgIDivA also provides detailed visualizations of ID through the generation of purpose-built graph networks. Beyond the method design, IgIDivA has been also implemented as an R Shiny web application. IgIDivA is freely available at https://bio.tools/igidiva
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Affiliation(s)
- Laura Zaragoza-Infante
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Hematology Unit, 1st Dept of Internal Medicine, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki
| | - Valentin Junet
- Anaxomics Biotech SL, Barcelona, Spain.,Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Nikos Pechlivanis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | | | - Serovpe Amprachamian
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | | | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Maria Papaioannou
- Hematology Unit, 1st Dept of Internal Medicine, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
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40
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Weber CR, Rubio T, Wang L, Zhang W, Robert PA, Akbar R, Snapkov I, Wu J, Kuijjer ML, Tarazona S, Conesa A, Sandve GK, Liu X, Reddy ST, Greiff V. Reference-based comparison of adaptive immune receptor repertoires. CELL REPORTS METHODS 2022; 2:100269. [PMID: 36046619 PMCID: PMC9421535 DOI: 10.1016/j.crmeth.2022.100269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 04/01/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022]
Abstract
B and T cell receptor (immune) repertoires can represent an individual's immune history. While current repertoire analysis methods aim to discriminate between health and disease states, they are typically based on only a limited number of parameters. Here, we introduce immuneREF: a quantitative multidimensional measure of adaptive immune repertoire (and transcriptome) similarity that allows interpretation of immune repertoire variation by relying on both repertoire features and cross-referencing of simulated and experimental datasets. To quantify immune repertoire similarity landscapes across health and disease, we applied immuneREF to >2,400 datasets from individuals with varying immune states (healthy, [autoimmune] disease, and infection). We discovered, in contrast to the current paradigm, that blood-derived immune repertoires of healthy and diseased individuals are highly similar for certain immune states, suggesting that repertoire changes to immune perturbations are less pronounced than previously thought. In conclusion, immuneREF enables the population-wide study of adaptive immune response similarity across immune states.
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Affiliation(s)
- Cédric R. Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Teresa Rubio
- Laboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, Spain
| | - Longlong Wang
- BGI-Shenzhen, Shenzhen, China
- BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Philippe A. Robert
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Igor Snapkov
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | | | - Marieke L. Kuijjer
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sonia Tarazona
- Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, Valencia, Spain
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council, Valencia, Spain
| | - Geir K. Sandve
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
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41
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Abstract
The central nervous system (CNS) has been viewed as an immunologically privileged site, but emerging works are uncovering a large array of neuroimmune interactions primarily occurring at its borders. CNS barriers sites host diverse population of both innate and adaptive immune cells capable of, directly and indirectly, influence the function of the residing cells of the brain parenchyma. These structures are only starting to reveal their role in controlling brain function under normal and pathological conditions and represent an underexplored therapeutic target for the treatment of brain disorders. This review will highlight the development of the CNS barriers to host neuro-immune interactions and emphasize their newly described roles in neurodevelopmental, neurological, and neurodegenerative disorders, particularly for the meninges.
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Affiliation(s)
- Natalie M Frederick
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Gabriel A Tavares
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Antoine Louveau
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Molecular Medicine, Cleveland Clinic College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Kent University, Neurosciences, School of Biomedical Sciences, Cleveland, Ohio, USA
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42
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Bierhansl L, Hartung HP, Aktas O, Ruck T, Roden M, Meuth SG. Thinking outside the box: non-canonical targets in multiple sclerosis. Nat Rev Drug Discov 2022; 21:578-600. [PMID: 35668103 PMCID: PMC9169033 DOI: 10.1038/s41573-022-00477-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2022] [Indexed: 12/11/2022]
Abstract
Multiple sclerosis (MS) is an immune-mediated disease of the central nervous system that causes demyelination, axonal degeneration and astrogliosis, resulting in progressive neurological disability. Fuelled by an evolving understanding of MS immunopathogenesis, the range of available immunotherapies for clinical use has expanded over the past two decades. However, MS remains an incurable disease and even targeted immunotherapies often fail to control insidious disease progression, indicating the need for new and exceptional therapeutic options beyond the established immunological landscape. In this Review, we highlight such non-canonical targets in preclinical MS research with a focus on five highly promising areas: oligodendrocytes; the blood-brain barrier; metabolites and cellular metabolism; the coagulation system; and tolerance induction. Recent findings in these areas may guide the field towards novel targets for future therapeutic approaches in MS.
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Affiliation(s)
- Laura Bierhansl
- Department of Neurology, Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Hans-Peter Hartung
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Orhan Aktas
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tobias Ruck
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- German Center of Diabetes Research, Partner Düsseldorf, Neuherberg, Germany
| | - Sven G Meuth
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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43
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Relevance of Pathogenetic Mechanisms to Clinical Effectiveness of B-Cell-Depleting Monoclonal Antibodies in Multiple Sclerosis. J Clin Med 2022; 11:jcm11154288. [PMID: 35893382 PMCID: PMC9332715 DOI: 10.3390/jcm11154288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
Evidence of the effectiveness of B-cell-depleting monoclonal antibodies (mAbs) in multiple sclerosis (MS) prompted a partial revisitation of the pathogenetic paradigm of the disease, which was, so far, considered a T-cell-mediated autoimmune disorder. Mechanisms underlying the efficacy of B-cell-depleting mAbs in MS are still unknown. However, they likely involve the impairment of pleiotropic B-cell functions different from antibody secretion, such as their role as antigen-presenting cells during both the primary immune response in the periphery and the secondary response within the central nervous system (CNS). A potential impact of B-cell-depleting mAbs on inflammation compartmentalised within the CNS was also suggested, but little is known about the mechanism underlying this latter phenomenon as no definite evidence was provided so far on the ability of mAbs to cross the blood–brain barrier and reliable biomarkers of compartmentalised inflammation are lacking. The present paper briefly summarises the immunopathogenesis of MS with a focus on onset of autoimmunity and compartmentalisation of the immune response; mechanisms mediating B-cell depletion and underlying the effectiveness of B-cell-depleting mAbs are also discussed.
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44
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Gao YH, Zhang Y, Guo YX, Wang JQ, Gao MY, Zhao ZH, Gao R, Sun YN, Wang LB, Li X. Treatment with anacardic acid modulates dendritic cell activation and alleviates the disease development of autoimmune neuroinflammation in mice. Biochem Biophys Res Commun 2022; 613:34-40. [DOI: 10.1016/j.bbrc.2022.04.115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/25/2022] [Indexed: 12/17/2022]
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45
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Basic principles of neuroimmunology. Semin Immunopathol 2022; 44:685-695. [PMID: 35732977 DOI: 10.1007/s00281-022-00951-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/08/2022] [Indexed: 01/20/2023]
Abstract
The brain is an immune-privileged organ such that immune cell infiltration is highly regulated and better tolerating the introduction of antigen to reduce risk of harmful inflammation. Thus, the composition and the nature of the immune response is fundamentally different in the brain where avoiding immunopathology is prioritized compared to other peripheral organs. While the principle of immune privilege in the central nervous system (CNS) still holds true, the role of the immune system in the CNS has been revisited over the recent years. This redefining of immune privilege in the brain is a result of the recent re-discovery of the extensive CNS meningeal lymphatic system and the identification of resident T cells in the brain, meningeal layers, and its surrounding cerebrospinal fluid (CSF) in both humans and rodents. While neuro-immune interactions have been classically studied in the context of neuroinflammatory disease, recent works have also elucidated unconventional roles of immune-derived cytokines in neurological function, highlighting the many implications and potential of neuro-immune interactions. As a result, the study of neuro-immune interactions is becoming increasingly important in understanding both CNS homeostasis and disease. Here, we review the anatomically distinct immune compartments within the brain, the known mechanisms of leukocyte trafficking and infiltration into the CNS and unique transcriptional and functional characteristics of CNS-resident immune cells.
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46
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Boziki M, Bakirtzis C, Sintila SA, Kesidou E, Gounari E, Ioakimidou A, Tsavdaridou V, Skoura L, Fylaktou A, Nikolaidou V, Stangou M, Nikolaidis I, Giantzi V, Karafoulidou E, Theotokis P, Grigoriadis N. Ocrelizumab in Patients with Active Primary Progressive Multiple Sclerosis: Clinical Outcomes and Immune Markers of Treatment Response. Cells 2022; 11:cells11121959. [PMID: 35741088 PMCID: PMC9222195 DOI: 10.3390/cells11121959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/04/2023] Open
Abstract
Ocrelizumab is a B-cell-depleting monoclonal antibody approved for the treatment of relapsing-remitting multiple sclerosis (RRMS) and active primary progressive MS (aPPMS). This prospective, uncontrolled, open-label, observational study aimed to assess the efficacy of ocrelizumab in patients with aPPMS and to dissect the clinical, radiological and laboratory attributes of treatment response. In total, 22 patients with aPPMS followed for 24 months were included. The primary efficacy outcome was the proportion of patients with optimal response at 24 months, defined as patients free of relapses, free of confirmed disability accumulation (CDA) and free of T1 Gd-enhancing lesions and new/enlarging T2 lesions on the brain and cervical MRI. In total, 14 (63.6%) patients and 13 patients (59.1%) were classified as responders at 12 and 24 months, respectively. Time exhibited a significant effect on mean absolute and normalized gray matter cerebellar volume (F = 4.342, p = 0.23 and F = 4.279, p = 0.024, respectively). Responders at 24 months exhibited reduced peripheral blood ((%) of CD19+ cells) plasmablasts compared to non-responders at the 6-month point estimate (7.69 ± 4.4 vs. 22.66 ± 7.19, respectively, p = 0.043). Response to ocrelizumab was linked to lower total and gray matter cerebellar volume loss over time. Reduced plasmablast depletion was linked for the first time to sub-optimal response to ocrelizumab in aPPMS.
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Affiliation(s)
- Marina Boziki
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Christos Bakirtzis
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Styliani-Aggeliki Sintila
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Evangelia Kesidou
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Evdoxia Gounari
- Microbiology Laboratory, Department of Immunology, AHEPA University Hospital, 54636 Thessaloniki, Greece; (E.G.); (A.I.); (V.T.); (L.S.)
| | - Aliki Ioakimidou
- Microbiology Laboratory, Department of Immunology, AHEPA University Hospital, 54636 Thessaloniki, Greece; (E.G.); (A.I.); (V.T.); (L.S.)
| | - Vasiliki Tsavdaridou
- Microbiology Laboratory, Department of Immunology, AHEPA University Hospital, 54636 Thessaloniki, Greece; (E.G.); (A.I.); (V.T.); (L.S.)
| | - Lemonia Skoura
- Microbiology Laboratory, Department of Immunology, AHEPA University Hospital, 54636 Thessaloniki, Greece; (E.G.); (A.I.); (V.T.); (L.S.)
| | - Asimina Fylaktou
- National Peripheral Histocompatibility Center, Immunology Department, Hippokration General Hospital, 54642 Thessaloniki, Greece; (A.F.); (V.N.)
| | - Vasiliki Nikolaidou
- National Peripheral Histocompatibility Center, Immunology Department, Hippokration General Hospital, 54642 Thessaloniki, Greece; (A.F.); (V.N.)
| | - Maria Stangou
- Department of Nephrology, Medical School, Aristotle University of Thessaloniki, Hippokration Hospital, 54642 Thessaloniki, Greece;
| | - Ioannis Nikolaidis
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Virginia Giantzi
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Eleni Karafoulidou
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Paschalis Theotokis
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Nikolaos Grigoriadis
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
- Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
- Correspondence:
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47
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Gilboa A, Hope R, Ben Simon S, Polak P, Koren O, Yaari G. Ontogeny of the B Cell Receptor Repertoire and Microbiome in Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2713-2725. [PMID: 35623663 DOI: 10.4049/jimmunol.2100955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
The immune system matures throughout childhood to achieve full functionality in protecting our bodies against threats. The immune system has a strong reciprocal symbiosis with the host bacterial population and the two systems co-develop, shaping each other. Despite their fundamental role in health physiology, the ontogeny of these systems is poorly characterized. In this study, we investigated the development of the BCR repertoire by analyzing high-throughput sequencing of their receptors in several time points of young C57BL/6J mice. In parallel, we explored the development of the gut microbiome. We discovered that the gut IgA repertoires change from birth to adolescence, including an increase in CDR3 lengths and somatic hypermutation levels. This contrasts with the spleen IgM repertoires that remain stable and distinct from the IgA repertoires in the gut. We also discovered that large clones that germinate in the gut are initially confined to a specific gut compartment, then expand to nearby compartments and later on expand also to the spleen and remain there. Finally, we explored the associations between diversity indices of the B cell repertoires and the microbiome, as well as associations between bacterial and BCR clusters. Our results shed light on the ontogeny of the adaptive immune system and the microbiome, providing a baseline for future research.
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Affiliation(s)
- Amit Gilboa
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel; and
| | - Ronen Hope
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Shira Ben Simon
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Pazit Polak
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel; and
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Gur Yaari
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel;
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel; and
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48
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Worth AN, Palmer VL, Schabla NM, Perry GA, Fraser-Philbin AN, Swanson PC. Receptor editing constrains development of phosphatidyl choline-specific B cells in V H12-transgenic mice. Cell Rep 2022; 39:110899. [PMID: 35705027 DOI: 10.1016/j.celrep.2022.110899] [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: 03/05/2021] [Revised: 03/22/2022] [Accepted: 05/10/2022] [Indexed: 11/03/2022] Open
Abstract
B1 B cells reactive to phosphatidyl choline (PtC) exhibit restricted immunoglobulin heavy chain (HC) and light chain (LC) combinations, exemplified by VH12/Vκ4/5H. Two checkpoints are thought to focus PtC+ B cell maturation in VH12-transgenic mice (VH12 mice): V-J rearrangements encoding a "permissive" LC capable of VH12 HC pairing are selected first, followed by positive selection based on PtC binding, often requiring LC receptor editing to salvage PtC- B cells and acquire PtC reactivity. However, evidence obtained from breeding VH12 mice to editing-defective dnRAG1 mice and analyzing LC sequences from PtC+ and PtC- B cell subsets instead suggests that receptor editing functions after initial positive selection to remove PtC+ B cells in VH12 mice. This offers a mechanism to constrain natural, polyreactive B cells to limit their frequency. Sequencing also reveals occasional in-frame hybrid LC genes, reminiscent of type 2 gene replacement, that, testing suggests, arise via a recombination-activating gene (RAG)-independent mechanism.
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Affiliation(s)
- Alexandra N Worth
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Victoria L Palmer
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - N Max Schabla
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; Shoreline Biosciences, San Diego, CA 92121, USA
| | - Greg A Perry
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Anna N Fraser-Philbin
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Patrick C Swanson
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA.
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49
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Breaching Brain Barriers: B Cell Migration in Multiple Sclerosis. Biomolecules 2022; 12:biom12060800. [PMID: 35740925 PMCID: PMC9221446 DOI: 10.3390/biom12060800] [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: 05/05/2022] [Revised: 06/03/2022] [Accepted: 06/05/2022] [Indexed: 12/25/2022] Open
Abstract
Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS) known for the manifestation of demyelinated lesions throughout the CNS, leading to neurodegeneration. To date, not all pathological mechanisms that drive disease progression are known, but the clinical benefits of anti-CD20 therapies have put B cells in the spotlight of MS research. Besides their pathological effects in the periphery in MS, B cells gain access to the CNS where they can contribute to disease pathogenesis. Specifically, B cells accumulate in perivascular infiltrates in the brain parenchyma and the subarachnoid spaces of the meninges, but are virtually absent from the choroid plexus. Hence, the possible migration of B cells over the blood-brain-, blood-meningeal-, and blood-cerebrospinal fluid (CSF) barriers appears to be a crucial step to understanding B cell-mediated pathology. To gain more insight into the molecular mechanisms that regulate B cell trafficking into the brain, we here provide a comprehensive overview of the different CNS barriers in health and in MS and how they translate into different routes for B cell migration. In addition, we review the mechanisms of action of diverse therapies that deplete peripheral B cells and/or block B cell migration into the CNS. Importantly, this review shows that studying the different routes of how B cells enter the inflamed CNS should be the next step to understanding this disease.
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Thomas AM, Yang E, Smith MD, Chu C, Calabresi PA, Glunde K, van Zijl PCM, Bulte JWM. CEST MRI and MALDI imaging reveal metabolic alterations in the cervical lymph nodes of EAE mice. J Neuroinflammation 2022; 19:130. [PMID: 35659311 PMCID: PMC9164344 DOI: 10.1186/s12974-022-02493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 05/15/2022] [Indexed: 11/10/2022] Open
Abstract
Background Multiple sclerosis (MS) is a neurodegenerative disease, wherein aberrant immune cells target myelin-ensheathed nerves. Conventional magnetic resonance imaging (MRI) can be performed to monitor damage to the central nervous system that results from previous inflammation; however, these imaging biomarkers are not necessarily indicative of active, progressive stages of the disease. The immune cells responsible for MS are first activated and sensitized to myelin in lymph nodes (LNs). Here, we present a new strategy for monitoring active disease activity in MS, chemical exchange saturation transfer (CEST) MRI of LNs. Methods and results We studied the potential utility of conventional (T2-weighted) and CEST MRI to monitor changes in these LNs during disease progression in an experimental autoimmune encephalomyelitis (EAE) model. We found CEST signal changes corresponded temporally with disease activity. CEST signals at the 3.2 ppm frequency during the active stage of EAE correlated significantly with the cellular (flow cytometry) and metabolic (mass spectrometry imaging) composition of the LNs, as well as immune cell infiltration into brain and spinal cord tissue. Correlating primary metabolites as identified by matrix-assisted laser desorption/ionization (MALDI) imaging included alanine, lactate, leucine, malate, and phenylalanine. Conclusions Taken together, we demonstrate the utility of CEST MRI signal changes in superficial cervical LNs as a complementary imaging biomarker for monitoring disease activity in MS. CEST MRI biomarkers corresponded to disease activity, correlated with immune activation (surface markers, antigen-stimulated proliferation), and correlated with LN metabolite levels. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-022-02493-z.
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Affiliation(s)
- Aline M Thomas
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, Johns Hopkins University School of Medicine, MD, 21205, Baltimore, USA.,Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ethan Yang
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, Johns Hopkins University School of Medicine, MD, 21205, Baltimore, USA
| | - Matthew D Smith
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chengyan Chu
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, Johns Hopkins University School of Medicine, MD, 21205, Baltimore, USA.,Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter A Calabresi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kristine Glunde
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, Johns Hopkins University School of Medicine, MD, 21205, Baltimore, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter C M van Zijl
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, Johns Hopkins University School of Medicine, MD, 21205, Baltimore, USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Jeff W M Bulte
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, Johns Hopkins University School of Medicine, MD, 21205, Baltimore, USA. .,Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA. .,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Chemical and Biomolecular Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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