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Goto M, Takahashi H, Yoshida R, Itamiya T, Nakano M, Nagafuchi Y, Harada H, Shimizu T, Maeda M, Kubota A, Toda T, Hatano H, Sugimori Y, Kawahata K, Yamamoto K, Shoda H, Ishigaki K, Ota M, Okamura T, Fujio K. Age-associated CD4 + T cells with B cell-promoting functions are regulated by ZEB2 in autoimmunity. Sci Immunol 2024; 9:eadk1643. [PMID: 38330141 DOI: 10.1126/sciimmunol.adk1643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
Aging is a significant risk factor for autoimmunity, and many autoimmune diseases tend to onset during adulthood. We conducted an extensive analysis of CD4+ T cell subsets from 354 patients with autoimmune disease and healthy controls via flow cytometry and bulk RNA sequencing. As a result, we identified a distinct CXCR3midCD4+ effector memory T cell subset that expands with age, which we designated "age-associated T helper (THA) cells." THA cells exhibited both a cytotoxic phenotype and B cell helper functions, and these features were regulated by the transcription factor ZEB2. Consistent with the highly skewed T cell receptor usage of THA cells, gene expression in THA cells from patients with systemic lupus erythematosus reflected disease activity and was affected by treatment with a calcineurin inhibitor. Moreover, analysis of single-cell RNA sequencing data revealed that THA cells infiltrate damaged organs in patients with autoimmune diseases. Together, our characterization of THA cells may facilitate improved understanding of the relationship between aging and autoimmune diseases.
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Affiliation(s)
- Manaka Goto
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Hideyuki Takahashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Takahiro Itamiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Hiroaki Harada
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Toshiaki Shimizu
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Meiko Maeda
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Akatsuki Kubota
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yusuke Sugimori
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kimito Kawahata
- Department of Rheumatology and Allergology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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2
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Ota M, Hirao S, Uchimura K. Lower TB notification rates in later life in the same birth cohort, Japan, 1950-2020. Int J Tuberc Lung Dis 2024; 28:157-159. [PMID: 38454190 DOI: 10.5588/ijtld.23.0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024] Open
Affiliation(s)
- M Ota
- Division of Technical Assistance to Tuberculosis Programmes, and
| | - S Hirao
- Division of Technical Assistance to Tuberculosis Programmes, and
| | - K Uchimura
- Division of Epidemiology and Clinical Research, Research Institute of Tuberculosis, Tokyo, Japan
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3
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Yuuki H, Itamiya T, Nagafuchi Y, Ota M, Fujio K. B cell receptor repertoire abnormalities in autoimmune disease. Front Immunol 2024; 15:1326823. [PMID: 38361948 PMCID: PMC10867955 DOI: 10.3389/fimmu.2024.1326823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
B cells play a crucial role in the immune response and contribute to various autoimmune diseases. Recent studies have revealed abnormalities in the B cell receptor (BCR) repertoire of patients with autoimmune diseases, with distinct features observed among different diseases and B cell subsets. Classically, BCR repertoire was used as an identifier of distinct antigen-specific clonotypes, but the recent advancement of analyzing large-scale repertoire has enabled us to use it as a tool for characterizing cellular biology. In this review, we provide an overview of the BCR repertoire in autoimmune diseases incorporating insights from our latest research findings. In systemic lupus erythematosus (SLE), we observed a significant skew in the usage of VDJ genes, particularly in CD27+IgD+ unswitched memory B cells and plasmablasts. Notably, autoreactive clones within unswitched memory B cells were found to be increased and strongly associated with disease activity, underscoring the clinical significance of this subset. Similarly, various abnormalities in the BCR repertoire have been reported in other autoimmune diseases such as rheumatoid arthritis. Thus, BCR repertoire analysis holds potential for enhancing our understanding of the underlying mechanisms involved in autoimmune diseases. Moreover, it has the potential to predict treatment effects and identify therapeutic targets in autoimmune diseases.
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Affiliation(s)
- Hayato Yuuki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahiro Itamiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Schmidt R, Ward CC, Dajani R, Armour-Garb Z, Ota M, Allain V, Hernandez R, Layeghi M, Xing G, Goudy L, Dorovskyi D, Wang C, Chen YY, Ye CJ, Shy BR, Gilbert LA, Eyquem J, Pritchard JK, Dodgson SE, Marson A. Base-editing mutagenesis maps alleles to tune human T cell functions. Nature 2024; 625:805-812. [PMID: 38093011 DOI: 10.1038/s41586-023-06835-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
CRISPR-enabled screening is a powerful tool for the discovery of genes that control T cell function and has nominated candidate targets for immunotherapies1-6. However, new approaches are required to probe specific nucleotide sequences within key genes. Systematic mutagenesis in primary human T cells could reveal alleles that tune specific phenotypes. DNA base editors are powerful tools for introducing targeted mutations with high efficiency7,8. Here we develop a large-scale base-editing mutagenesis platform with the goal of pinpointing nucleotides that encode amino acid residues that tune primary human T cell activation responses. We generated a library of around 117,000 single guide RNA molecules targeting base editors to protein-coding sites across 385 genes implicated in T cell function and systematically identified protein domains and specific amino acid residues that regulate T cell activation and cytokine production. We found a broad spectrum of alleles with variants encoding critical residues in proteins including PIK3CD, VAV1, LCP2, PLCG1 and DGKZ, including both gain-of-function and loss-of-function mutations. We validated the functional effects of many alleles and further demonstrated that base-editing hits could positively and negatively tune T cell cytotoxic function. Finally, higher-resolution screening using a base editor with relaxed protospacer-adjacent motif requirements9 (NG versus NGG) revealed specific structural domains and protein-protein interaction sites that can be targeted to tune T cell functions. Base-editing screens in primary immune cells thus provide biochemical insights with the potential to accelerate immunotherapy design.
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Affiliation(s)
- Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.
| | - Carl C Ward
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
| | - Rama Dajani
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Zev Armour-Garb
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Mineto Ota
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Vincent Allain
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Université Paris Cité, INSERM UMR976, Hôpital Saint-Louis, Paris, France
| | - Rosmely Hernandez
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Madeline Layeghi
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Galen Xing
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Laine Goudy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Dmytro Dorovskyi
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charlotte Wang
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Yan Yi Chen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R Shy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, USA
- Arc Institute, Palo Alto, CA, USA
| | - Justin Eyquem
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Stacie E Dodgson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
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5
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Nakajima S, Tsuchiya H, Ota M, Ogawa M, Yamada S, Yoshida R, Maeda J, Shirai H, Kasai T, Hirose J, Ninagawa K, Fujieda Y, Iwasaki T, Aizaki Y, Kajiyama H, Matsushita M, Kawakami E, Tamura N, Mimura T, Ohmura K, Morinobu A, Atsumi T, Tanaka Y, Takeuchi T, Tanaka S, Okamura T, Fujio K. Synovial Tissue Heterogeneity in Japanese Patients With Rheumatoid Arthritis Elucidated Using a Cell-Type Deconvolution Approach. Arthritis Rheumatol 2023; 75:2130-2136. [PMID: 37390361 DOI: 10.1002/art.42642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/26/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
OBJECTIVE Recent advances in single-cell RNA sequencing technology have improved our understanding of the immunological landscape of rheumatoid arthritis (RA). We aimed to stratify the synovium from East Asian patients with RA by immune cell compositions and gain insight into the inflammatory drivers of each synovial phenotype. METHODS Synovial tissues were obtained from East Asian patients in Japan with RA (n = 41) undergoing articular surgery. The cellular composition was quantified by a deconvolution approach using a public single-cell-based reference. Inflammatory pathway activity was calculated by gene set variation analysis, and chromatin accessibility was evaluated using assay of transposase accessible chromatin-sequencing. RESULTS We stratified RA synovium into three distinct subtypes based on the hierarchical clustering of cellular composition data. One subtype was characterized by abundant HLA-DRAhigh synovial fibroblasts, autoimmune-associated B cells, GZMK+ GZMB+ CD8+ T cells, interleukin (IL)1-β+ monocytes, and plasmablasts. In addition, tumor necrosis factor (TNF)-α, interferons (IFNs), and IL-6 signaling were highly activated in this subtype, and the expression of various chemokines was significantly enhanced. Moreover, we found an open chromatin region overlapping with RA risk locus rs9405192 near the IRF4 gene, suggesting the genetic background influences the development of this inflammatory synovial state. The other two subtypes were characterized by increased IFNs and IL-6 signaling, and expression of molecules associated with degeneration, respectively. CONCLUSION This study adds insights into the synovial heterogeneity in East Asian patients and shows a promising link with predominant inflammatory signals. Evaluating the site of inflammation has the potential to lead to appropriate drug selection that matches the individual pathology.
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Affiliation(s)
- Sotaro Nakajima
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruka Tsuchiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology and Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Megumi Ogawa
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Saeko Yamada
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Junko Maeda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Harumi Shirai
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Taro Kasai
- Department of Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Hirose
- Department of Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keita Ninagawa
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Yuichiro Fujieda
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Takeshi Iwasaki
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshimi Aizaki
- Department of Rheumatology and Applied Immunology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Hiroshi Kajiyama
- Department of Rheumatology and Applied Immunology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Masakazu Matsushita
- Department of Internal Medicine and Rheumatology, Juntendo University School of Medicine, Tokyo, Japan
| | - Eiryo Kawakami
- Department of Artificial Intelligence Medicine, Chiba University Graduate School of Medicine, Chiba, Japan and Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Yokohama, Japan
| | - Naoto Tamura
- Department of Internal Medicine and Rheumatology, Juntendo University School of Medicine, Tokyo, Japan
| | - Toshihide Mimura
- Department of Rheumatology and Applied Immunology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akio Morinobu
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tatsuya Atsumi
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Fukuoka, Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Sakae Tanaka
- Department of Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomohisa Okamura
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Ota M, Nakano M, Nagafuchi Y, Kobayashi S, Hatano H, Yoshida R, Akutsu Y, Itamiya T, Ban N, Tsuchida Y, Shoda H, Yamamoto K, Ishigaki K, Okamura T, Fujio K. Multimodal repertoire analysis unveils B cell biology in immune-mediated diseases. Ann Rheum Dis 2023; 82:1455-1463. [PMID: 37468219 DOI: 10.1136/ard-2023-224421] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023]
Abstract
OBJECTIVES Despite the involvement of B cells in the pathogenesis of immune-mediated diseases (IMDs), biological mechanisms underlying their function are scarcely understood. To overcome this gap, here we constructed and investigated a large-scale repertoire catalogue of five B cell subsets of patients with IMDs. METHODS We mapped B cell receptor regions from RNA sequencing data of sorted B cell subsets. Our dataset consisted of 595 donors under IMDs and health. We characterised the repertoire features from various aspects, including their association with immune cell transcriptomes and clinical features and their response to belimumab treatment. RESULTS Heavy-chain complementarity-determining region 3 (CDR-H3) length among naïve B cells was shortened among autoimmune diseases. Strong negative correlation between interferon signature strength and CDR-H3 length was observed in naïve B cells and suggested the role for interferon in premature B cell development. VDJ gene usage was skewed especially in plasmablasts and unswitched-memory B cells of patients with systemic lupus erythematosus (SLE). We developed a scoring system to quantify this skewing, and it positively correlated with peripheral helper T cell transcriptomic signatures and negatively correlated with the amount of somatic hyper mutations in plasmablasts, suggesting the association of extrafollicular pathway. Further, this skewing led to high usage of IGHV4-34 gene with 9G4 idiotypes in unswitched-memory B cells, which showed a prominent positive correlation with disease activity in SLE. Gene usage skewing in unswitched-memory B cells was ameliorated after belimumab treatment. CONCLUSIONS Our multimodal repertoire analysis enabled us the system-level understanding of B cell abnormality in diseases.
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Affiliation(s)
- Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Satomi Kobayashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Yuko Akutsu
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Takahiro Itamiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Nobuhiro Ban
- Research Division, Chugai Pharmaceutical Co Ltd, Yokohama, Japan
| | - Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
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7
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Weinstock JS, Arce MM, Freimer JW, Ota M, Marson A, Battle A, Pritchard JK. Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease. bioRxiv 2023:2023.09.17.557749. [PMID: 37745614 PMCID: PMC10516010 DOI: 10.1101/2023.09.17.557749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The effects of genetic variation on complex traits act mainly through changes in gene regulation. Although many genetic variants have been linked to target genes in cis, the trans-regulatory cascade mediating their effects remains largely uncharacterized. Mapping trans-regulators based on natural genetic variation, including eQTL mapping, has been challenging due to small effects. Experimental perturbation approaches offer a complementary and powerful approach to mapping trans-regulators. We used CRISPR knockouts of 84 genes in primary CD4+ T cells to perturb an immune cell gene network, targeting both inborn error of immunity (IEI) disease transcription factors (TFs) and background TFs matched in constraint and expression level, but without a known immune disease association. We developed a novel Bayesian structure learning method called Linear Latent Causal Bayes (LLCB) to estimate the gene regulatory network from perturbation data and observed 211 directed edges among the genes which could not be detected in existing CD4+ trans-eQTL data. We used LLCB to characterize the differences between the IEI and background TFs, finding that the gene groups were highly interconnected, but that IEI TFs were much more likely to regulate immune cell specific pathways and immune GWAS genes. We further characterized nine coherent gene programs based on downstream effects of the TFs and linked these modules to regulation of GWAS genes, finding that canonical JAK-STAT family members are regulated by KMT2A, a global epigenetic regulator. These analyses reveal the trans-regulatory cascade from upstream epigenetic regulator to intermediate TFs to downstream effector cytokines and elucidate the logic linking immune GWAS genes to key signaling pathways.
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Affiliation(s)
- Joshua S. Weinstock
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
- Department of Genetics, Stanford University, Stanford, CA
| | - Maya M. Arce
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Jacob W. Freimer
- Department of Genetics, Stanford University, Stanford, CA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA
| | - Mineto Ota
- Department of Genetics, Stanford University, Stanford, CA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, 94143
- Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, 94129
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94143
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94158
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD
- Department of Computer Science, Johns Hopkins University, Baltimore, MD
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University, Stanford, CA
- Department of Biology, Stanford University, Stanford, CA
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8
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Inoue M, Nagafuchi Y, Ota M, Tsuchiya H, Tateishi S, Kanda H, Fujio K. Carriers of HLA-DRB1*04:05 have a better clinical response to abatacept in rheumatoid arthritis. Sci Rep 2023; 13:15250. [PMID: 37709837 PMCID: PMC10502099 DOI: 10.1038/s41598-023-42324-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/08/2023] [Indexed: 09/16/2023] Open
Abstract
HLA-DRB1 shared epitope risk alleles are the strongest genetic risk factors for rheumatoid arthritis (RA) and potential biomarkers for treatment response to biological disease-modifying antirheumatic drugs (bDMARDs). This study aimed to investigate the association between treatment response and individual HLA-DRB1 alleles in RA patients receiving different bDMARDs. We recruited 106 patients with active RA who had started abatacept, tocilizumab, or TNF inhibitors as a first-line bDMARDs. We examined the relationship between Simplified Disease Activity Index (SDAI) improvement at 3 months and HLA-DRB1 allele carriage. The results revealed that the HLA-DRB1*04:05 allele, a shared-epitope allele, was significantly associated with better SDAI improvement only after abatacept treatment (SDAI improvement 28.5% without the allele vs 59.8% with allele, p = 0.003). However, no significant association was found with other treatments. Both multivariate linear regression and mediation analysis confirmed that the HLA-DRB1*04:05 allele was independently associated with abatacept treatment response, regardless of anti-CCP antibody titers. The study concluded that in patients with RA receiving their first-line bDMARD treatment, carrying the HLA-DRB1*04:05 allele was associated with better SDAI improvement specifically in abatacept-treated patients. These disease-risk HLA alleles have the potential to serve as genomic biomarkers for predicting treatment response with co-stimulation blockage therapy.
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Affiliation(s)
- Mariko Inoue
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
- Clinical Research Promotion Center, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Haruka Tsuchiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Shoko Tateishi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hiroko Kanda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
- Immune-Mediated Diseases Therapy Center, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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9
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Mamedov MR, Vedova S, Freimer JW, Sahu AD, Ramesh A, Arce MM, Meringa AD, Ota M, Chen PA, Hanspers K, Nguyen VQ, Takeshima KA, Rios AC, Pritchard JK, Kuball J, Sebestyen Z, Adams EJ, Marson A. CRISPR screens decode cancer cell pathways that trigger γδ T cell detection. Nature 2023; 621:188-195. [PMID: 37648854 PMCID: PMC11003766 DOI: 10.1038/s41586-023-06482-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/26/2023] [Indexed: 09/01/2023]
Abstract
γδ T cells are potent anticancer effectors with the potential to target tumours broadly, independent of patient-specific neoantigens or human leukocyte antigen background1-5. γδ T cells can sense conserved cell stress signals prevalent in transformed cells2,3, although the mechanisms behind the targeting of stressed target cells remain poorly characterized. Vγ9Vδ2 T cells-the most abundant subset of human γδ T cells4-recognize a protein complex containing butyrophilin 2A1 (BTN2A1) and BTN3A1 (refs. 6-8), a widely expressed cell surface protein that is activated by phosphoantigens abundantly produced by tumour cells. Here we combined genome-wide CRISPR screens in target cancer cells to identify pathways that regulate γδ T cell killing and BTN3A cell surface expression. The screens showed previously unappreciated multilayered regulation of BTN3A abundance on the cell surface and triggering of γδ T cells through transcription, post-translational modifications and membrane trafficking. In addition, diverse genetic perturbations and inhibitors disrupting metabolic pathways in the cancer cells, particularly ATP-producing processes, were found to alter BTN3A levels. This induction of both BTN3A and BTN2A1 during metabolic crises is dependent on AMP-activated protein kinase (AMPK). Finally, small-molecule activation of AMPK in a cell line model and in patient-derived tumour organoids led to increased expression of the BTN2A1-BTN3A complex and increased Vγ9Vδ2 T cell receptor-mediated killing. This AMPK-dependent mechanism of metabolic stress-induced ligand upregulation deepens our understanding of γδ T cell stress surveillance and suggests new avenues available to enhance γδ T cell anticancer activity.
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Affiliation(s)
- Murad R. Mamedov
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Shane Vedova
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob W. Freimer
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Avinash Das Sahu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Amrita Ramesh
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Maya M. Arce
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Angelo D. Meringa
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Mineto Ota
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Peixin Amy Chen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kristina Hanspers
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Vinh Q. Nguyen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | | | - Anne C. Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Jürgen Kuball
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Hematology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Zsolt Sebestyen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Erin J. Adams
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
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10
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Natsumoto B, Shoda H, Nagafuchi Y, Ota M, Okumura T, Horie Y, Okamura T, Yamamoto K, Tsuji M, Otsu M, Taniguchi H, Fujio K. Functional evaluation of rare OASL variants by analysis of SLE patient-derived iPSCs. J Autoimmun 2023; 139:103085. [PMID: 37354689 DOI: 10.1016/j.jaut.2023.103085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023]
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is a chronic systemic autoimmune disease characterized by genetic heterogeneity and an interferon (IFN) signature. The overall landscapes of the heritability of SLE remains unclear. OBJECTIVES To identify and elucidate the biological functions of rare variants underlying SLE, we conducted analyses of patient-derived induced pluripotent stem cells (iPSCs) in combination with genetic analysis. METHODS Two familial SLE patient- and two healthy donor (HD)-derived iPSCs were established. Type 1 IFN-secreting dendritic cells (DCs) were differentiated from iPSCs. Genetic analyses of SLE-iPSCs, and 117 SLE patients and 107 HDs in the ImmuNexUT database were performed independently. Genome editing of the variants on iPSCs was performed with the CRISPR/Cas9 system. RESULTS Type 1 IFN secretion was significantly increased in DCs differentiated from SLE-iPSCs compared to HD-iPSCs. Genetic analyses revealed a rare variant in the 2'-5'-Oligoadenylate Synthetase Like (OASL) shared between SLE-iPSCs and another independent SLE patient, and significant accumulation of OASL variants among SLE patients (HD 0.93%, SLE 6.84%, OR 8.387) in the database. Genome editing of mutated OASL 202Q to wild-type 202 R or wild-type OASL 202 R to mutated 202Q resulted in reduced or enhanced Type 1 IFN secretion of DCs. Three other OASL variants (R60W, T261S and A447V) accumulated in SLE patients had also capacities to enhance Type 1 IFN secretion in response to dsRNA. CONCLUSIONS We established a patient-derived iPSC-based strategy to investigate the linkage of genotype and phenotype in autoimmune diseases. Detailed case-based investigations using patient-derived iPSCs provide information to unveil the heritability of the pathogenesis of autoimmune diseases.
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Affiliation(s)
- Bunki Natsumoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan.
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan.
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Takashi Okumura
- Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Yumi Horie
- Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Motonori Tsuji
- Institute of Molecular Function, Misato-shi Saitama, 341-0037, Japan
| | - Makoto Otsu
- Department of Transfusion and Cell Transplantation, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara Kanagawa, 252-0374, Japan
| | - Hideki Taniguchi
- Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8654, Japan.
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11
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Iwamoto M, Aoki C, Ota M, Minami E, Yoshiyama A, Tanaka M, Sakane J, Ikari A, Tominaga T, Takai S, Oku H, Kimura K, Lee SW. P198 Identification of sentinel lymph nodes using the near infrared light camera system LIGHTVISION®. Breast 2023. [DOI: 10.1016/s0960-9776(23)00316-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
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12
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Yamada S, Nagafuchi Y, Wang M, Ota M, Hatano H, Takeshima Y, Okubo M, Kobayashi S, Sugimori Y, Masahiro N, Yoshida R, Hanata N, Suwa Y, Tsuchida Y, Iwasaki Y, Sumitomo S, Kubo K, Shimane K, Setoguchi K, Azuma T, Kanda H, Shoda H, Zhang X, Yamamoto K, Ishigaki K, Okamura T, Fujio K. Immunomics analysis of rheumatoid arthritis identified precursor dendritic cells as a key cell subset of treatment resistance. Ann Rheum Dis 2023; 82:809-819. [PMID: 36918189 DOI: 10.1136/ard-2022-223645] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023]
Abstract
OBJECTIVES Little is known about the immunology underlying variable treatment response in rheumatoid arthritis (RA). We performed large-scale transcriptome analyses of peripheral blood immune cell subsets to identify immune cells that predict treatment resistance. METHODS We isolated 18 peripheral blood immune cell subsets of 55 patients with RA requiring addition of new treatment and 39 healthy controls, and performed RNA sequencing. Transcriptome changes in RA and treatment effects were systematically characterised. Association between immune cell gene modules and treatment resistance was evaluated. We validated predictive value of identified parameters for treatment resistance using quantitative PCR (qPCR) and mass cytometric analysis cohorts. We also characterised the identified population by synovial single cell RNA-sequencing analysis. RESULTS Immune cells of patients with RA were characterised by enhanced interferon and IL6-JAK-STAT3 signalling that demonstrate partial normalisation after treatment. A gene expression module of plasmacytoid dendritic cells (pDC) reflecting the expansion of dendritic cell precursors (pre-DC) exhibited strongest association with treatment resistance. Type I interferon signalling was negatively correlated to pre-DC gene expression. qPCR and mass cytometric analysis in independent cohorts validated that the pre-DC associated gene expression and the proportion of pre-DC were significantly higher before treatment in treatment-resistant patients. A cluster of synovial DCs showed both features of pre-DC and pro-inflammatory conventional DC2s. CONCLUSIONS An increase in pre-DC in peripheral blood predicted RA treatment resistance. Pre-DC could have pathophysiological relevance to RA treatment response.
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Affiliation(s)
- Saeko Yamada
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan .,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Min Wang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.,Laboratory for Human Immunogenetics, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Yusuke Takeshima
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Mai Okubo
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Satomi Kobayashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.,Department of Medicine and Rheumatology, Tokyo Metropolitan Geriatric Hospital, Tokyo, Japan
| | - Yusuke Sugimori
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.,Department of Rheumatology, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Nakano Masahiro
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.,Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Norio Hanata
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Yuichi Suwa
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Yukiko Iwasaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Shuji Sumitomo
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Kanae Kubo
- Department of Medicine and Rheumatology, Tokyo Metropolitan Geriatric Hospital, Tokyo, Japan
| | - Kenichi Shimane
- Department of Rheumatology, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Keigo Setoguchi
- Allergy and Immunological Diseases, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | | | - Hiroko Kanda
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.,Immune-Mediated Diseases Therapy Center, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
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Hayashi K, Tanaka Y, Tsuda T, Nomura A, Fujino N, Furusho H, Sakai N, Iwata Y, Usui S, Sakata K, Kato T, Tada H, Kusayama T, Usuda K, Kawashiri MA, Passman RS, Wada T, Yamagishi M, Takamura M, Fujino N, Nohara A, Kawashiri MA, Hayashi K, Sakata K, Yoshimuta T, Konno T, Funada A, Tada H, Nakanishi C, Hodatsu A, Mori M, Tsuda T, Teramoto R, Nagata Y, Nomura A, Shimojima M, Yoshida S, Yoshida T, Hachiya S, Tamura Y, Kashihara Y, Kobayashi T, Shibayama J, Inaba S, Matsubara T, Yasuda T, Miwa K, Inoue M, Fujita T, Yakuta Y, Aburao T, Matsui T, Higashi K, Koga T, Hikishima K, Namura M, Horita Y, Ikeda M, Terai H, Gamou T, Tama N, Kimura R, Tsujimoto D, Nakahashi T, Ueda K, Ino H, Higashikata T, Kaneda T, Takata M, Yamamoto R, Yoshikawa T, Ohira M, Suematsu T, Tagawa S, Inoue T, Okada H, Kita Y, Fujita C, Ukawa N, Inoguchi Y, Ito Y, Araki T, Oe K, Minamoto M, Yokawa J, Tanaka Y, Mori K, Taguchi T, Kaku B, Katsuda S, Hirase H, Haraki T, Fujioka K, Terada K, Ichise T, Maekawa N, Higashi M, Okeie K, Kiyama M, Ota M, Todo Y, Aoyama T, Yamaguchi M, Noji Y, Mabuchi T, Yagi M, Niwa S, Takashima Y, Murai K, Nishikawa T, Mizuno S, Ohsato K, Misawa K, Kokado H, Michishita I, Iwaki T, Nozue T, Katoh H, Nakashima K, Ito S, Yamagishi M. Correction: Characterization of baseline clinical factors associated with incident worsening kidney function in patients with non-valvular atrial fibrillation: the Hokuriku-Plus AF Registry. Heart Vessels 2023; 38:412. [PMID: 36508013 DOI: 10.1007/s00380-022-02218-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Kenshi Hayashi
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan.
| | - Yoshihiro Tanaka
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan.,Center for Arrhythmia Research, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Toyonobu Tsuda
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Akihiro Nomura
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Noboru Fujino
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Hiroshi Furusho
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan.,Department of Cardiology, Ishikawa Prefectural Central Hospital, 2-1, Kuratsuki-higashi, Kanazawa, Japan
| | - Norihiko Sakai
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, Japan
| | - Yasunori Iwata
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, Japan
| | - Soichiro Usui
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Kenji Sakata
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Takeshi Kato
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Hayato Tada
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Takashi Kusayama
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Keisuke Usuda
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Masa-Aki Kawashiri
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Rod S Passman
- Center for Arrhythmia Research, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Takashi Wada
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, Japan
| | - Masakazu Yamagishi
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan.,Osaka University of Human Sciences, Settsu, Osaka, Japan
| | - Masayuki Takamura
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
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Iwasaki Y, Takeshima Y, Nakano M, Okubo M, Ota M, Suzuki A, Kochi Y, Okamura T, Endo T, Miki I, Sakurada K, Yamamoto K, Fujio K. Combined plasma metabolomic and transcriptomic analysis identify histidine as a biomarker and potential contributor in SLE pathogenesis. Rheumatology (Oxford) 2023; 62:905-913. [PMID: 35689621 DOI: 10.1093/rheumatology/keac338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVES To investigate metabolite alterations in the plasma of SLE patients to identify novel biomarkers and provide insight into SLE pathogenesis. METHODS Patients with SLE (n = 41, discovery cohort and n = 37, replication cohort), healthy controls (n = 30 and n = 29) and patients with RA (n = 19, disease control) were recruited. Metabolic profiles of the plasma samples were analysed using liquid chromatography-time-of-flight mass spectrometry and capillary electrophoresis-time-of-flight mass spectrometry. Transcriptome data was analysed using RNA-sequencing for 18 immune cell subsets. The importance of histidine (His) in plasmablast differentiation was investigated by using mouse splenic B cells. RESULTS We demonstrate that a specific amino acid combination including His can effectively distinguish between SLE patients and healthy controls. Random forest and partial least squares-discriminant analysis identified His as an effective classifier for SLE patients. A decrease in His plasma levels correlated with damage accrual independent of prednisolone dosage and type I IFN signature. The oxidative phosphorylation signature in plasmablasts negatively correlated with His levels. We also showed that plasmablast differentiation induced by innate immune signals was dependent on His. CONCLUSIONS Plasma His levels are a potential biomarker for SLE patients and are associated with damage accrual. Our data suggest the importance of His as a pathogenic metabolite in SLE pathogenesis.
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Affiliation(s)
- Yukiko Iwasaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo.,Department of Palliative Medicine.,Department of Rheumatology and Applied Immunology, Faculty of Medicine, Saitama Medical University, Saitama
| | - Yusuke Takeshima
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo.,Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama
| | - Mai Okubo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama.,Department of Genomic Function and Diversity, Tokyo Medical and Dental University, Tokyo
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo
| | - Takaho Endo
- Medical Sciences Innovation Hub Program, Cluster for Science, Technology and Innovation Hub, RIKEN, Yokohama
| | - Ichiro Miki
- Medical Sciences Innovation Hub Program, Cluster for Science, Technology and Innovation Hub, RIKEN, Yokohama
| | - Kazuhiro Sakurada
- Medical Sciences Innovation Hub Program, Cluster for Science, Technology and Innovation Hub, RIKEN, Yokohama.,Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine Graduate School of Medicine, Tokyo, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo
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15
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Sugimori Y, Iwasaki Y, Takeshima Y, Okubo M, Kobayashi S, Hatano H, Yamada S, Nakano M, Yoshida R, Ota M, Tsuchida Y, Nagafuchi Y, Shimane K, Yoshida K, Kurosaka D, Sumitomo S, Shoda H, Yamamoto K, Okamura T, Fujio K. Transcriptome Profiling of Immune Cell Types in Peripheral Blood Reveals Common and Specific Pathways Involved in the Pathogenesis of Myositis-Specific Antibody-Positive Inflammatory Myopathies. ACR Open Rheumatol 2023; 5:93-102. [PMID: 36651871 PMCID: PMC9926062 DOI: 10.1002/acr2.11521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/10/2022] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE Idiopathic inflammatory myopathies (IIM) demonstrate characteristic clinical phenotypes depending on the myositis-specific antibody (MSAs) present. We aimed to identify common or MSA-specific immunological pathways in different immune cell types from peripheral blood by transcriptome analysis. METHODS We recruited 33 patients with IIM who were separated into the following groups: 15 patients with active disease at onset and 18 with inactive disease under treatment. All patients were positive for MSAs: anti-melanoma differentiation-associated gene 5 (MDA5) antibody (Ab) in 10 patients, anti-Mi-2 Ab in 7, and anti-aminoacyl-transfer RNA synthetase (ARS) Ab in 16. The patients were compared with 33 healthy controls. Twenty-four immune cell types sorted from peripheral blood were analyzed by flow cytometry, RNA sequencing, and differentially expressed gene analysis combined with pathway analysis. RESULTS The frequencies of memory B cell types were significantly decreased in active patients, and the frequency of plasmablasts was prominently increased in active patients with anti-MDA5 Ab in comparison with healthy controls. The expression of type I interferon (IFN)-stimulated genes of all immune cell types was increased in the active, but not inactive, patients. Endoplasmic reticulum stress-related genes in all IIM memory B cells and oxidative phosphorylation-related genes in inactive IIM double negative B cells were also increased, suggesting prominent B cell activation in IIM. Furthermore, active patients with anti-MDA5 Ab, anti-Mi-2 Ab, or anti-ARS Ab were distinguished by IFN-stimulated and oxidative phosphorylation-related gene expression in plasmablasts. CONCLUSION Unique gene expression patterns in patients with IIM with different disease activity levels and MSA types suggest different pathophysiologies. Especially, B cells may contribute to common and MSA-specific immunological pathways in IIM.
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Affiliation(s)
- Yusuke Sugimori
- The University of Tokyo and Tokyo Metropolitan Bokutoh HospitalTokyoJapan
| | - Yukiko Iwasaki
- The University of Tokyo, Tokyo, Japan, and Saitama Medical UniversitySaitamaJapan
| | | | | | | | | | | | | | | | | | | | | | | | - Ken Yoshida
- The Jikei University School of MedicineTokyoJapan
| | | | | | | | - Kazuhiko Yamamoto
- University of Tokyo, Japan, and RIKEN Center for Integrative Medical SciencesYokohamaJapan
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16
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Daka S, Matsuoka Y, Ota M, Hirao S, Phiri A. Causes of pre-treatment loss to follow-up in patients with TB. Public Health Action 2022; 12:148-152. [PMID: 36561903 PMCID: PMC9716822 DOI: 10.5588/pha.22.0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 12/04/2022] Open
Abstract
SETTING Five urban TB diagnostic centres in Lusaka, Zambia. OBJECTIVE To determine the proportion of bacteriologically confirmed pre-treatment lost to follow-up (LTFU) patients with TB found at the study settings in 2020. DESIGN This was a retrospective cohort study in which the TB laboratory and treatment registers at the study sites were cross-matched. RESULTS A total of 1,085 bacteriologically confirmed patients with TB were found in the laboratory TB registers at the study settings. Of these, 809 (74.6%) were males, whereas 8 (0.7%) were children, 1,005 (92.6%) were diagnosed using Xpert, 78 (7.2%) by microscopy. A total of 91 (8.4%, 95% CI 6.8-10.2) were determined to be pre-treatment LTFU. Those who had very low (14.0%, 95% CI 8.5-21.2) and low (11.8%, 95% CI 8.4-16.0) results on Xpert were respectively 3.1 (95% CI 1.6-6.0) and 2.6 (95% CI 1.4-4.8) times more likely to become pre-treatment LTFU than those who had medium (4.5%, 95% CI 2.5-7.4) results. The proportions of pre-treatment LTFU varied among the study sites from 0.7% to 16.1%. CONCLUSION Health facilities should strive to account for every patient with TB, with particular attention to those who are bacteriologically confirmed.
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Affiliation(s)
- S. Daka
- Japan Anti-Tuberculosis Association, Lusaka, Zambia
| | - Y. Matsuoka
- Japan Anti-Tuberculosis Association, Lusaka, Zambia
| | - M. Ota
- Research Institute of Tuberculosis, Tokyo, Japan
| | - S. Hirao
- Research Institute of Tuberculosis, Tokyo, Japan
| | - A. Phiri
- Ministry of Health, Lusaka District Health Office, Lusaka, Zambia
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17
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Urakawa M, Yasukawa A, Hoshino Y, Ota M, Hatamoto H, Hirao S, Zama T, Nagata Y, Yoshiyama T. TB-related technical enquiries received in Japan, 2017-2019. Public Health Action 2022; 12:206-209. [PMID: 36561899 PMCID: PMC9716821 DOI: 10.5588/pha.22.0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/03/2022] [Indexed: 12/05/2022] Open
Abstract
SETTING Japan, an intermediate TB burden country. OBJECTIVE To review TB-related technical enquiries received at the Research Institute of Tuberculosis, Japan, from January 2017 to December 2019. DESIGN This was a cohort study. RESULTS A total of 2,197 enquiries were analysed. On average, 61.0 enquiries/month (range: 42-81) were received. The enquiry rates were highest for the Yamanashi (4.65/100,000 population) and Ishikawa (4.55) Prefectures, and lowest in the Yamagata (0.46) and Tochigi (0.56) Prefectures. The main organisations the enquirers belonged to were local governments (n = 1,585, 72.1%) and healthcare facilities (n = 307, 14.0%). The enquirers were medical doctors (n = 391, 17.8%), nurses (n = 1,207, 54.9%), other healthcare professionals (n = 57, 2.6%), the general public (n = 168, 7.6%) and others/unknown (n = 374, 17.0%). The most frequent enquiries were about TB diagnosis and treatment (n = 501, 22.8%), including laboratory diagnosis (n = 88, 4.0%), TB treatment in general (n = 93, 4.2%) and management of comorbidities (n = 86, 3.9%), followed by contact investigations (n = 385, 17.5%) and TB in foreigners (n = 344, 15.7%). CONCLUSION As the most frequent enquiries were about diagnosis and treatment of TB, the health ministry of Japan should maintain a few specialised TB institutions with TB physicians to provide technical assistance.
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Affiliation(s)
- M. Urakawa
- Research Institute of Tuberculosis, Tokyo, Japan
| | - A. Yasukawa
- Research Institute of Tuberculosis, Tokyo, Japan
| | - Y. Hoshino
- Research Institute of Tuberculosis, Tokyo, Japan
| | - M. Ota
- Research Institute of Tuberculosis, Tokyo, Japan
| | - H. Hatamoto
- Research Institute of Tuberculosis, Tokyo, Japan
| | - S. Hirao
- Research Institute of Tuberculosis, Tokyo, Japan
| | - T. Zama
- Research Institute of Tuberculosis, Tokyo, Japan
| | - Y. Nagata
- Research Institute of Tuberculosis, Tokyo, Japan
| | - T. Yoshiyama
- Research Institute of Tuberculosis, Tokyo, Japan
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18
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Nagafuchi Y, Ota M, Hatano H, Inoue M, Kobayashi S, Okubo M, Sugimori Y, Nakano M, Yamada S, Yoshida R, Tsuchida Y, Iwasaki Y, Shoda H, Okada Y, Yamamoto K, Ishigaki K, Okamura T, Fujio K. Control of naive and effector CD4 T cell receptor repertoires by rheumatoid-arthritis-risk HLA alleles. J Autoimmun 2022; 133:102907. [PMID: 36126366 DOI: 10.1016/j.jaut.2022.102907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Human Leukocyte Antigen (HLA) alleles regulate susceptibility to rheumatoid arthritis (RA) and immune-mediated diseases. This study aims to elucidate the impact of HLA alleles to T cell subsets. METHODS We performed genome-wide and HLA allele association analysis for T cell receptor (TCR) beta chain repertoire in 13 purified T cell subsets from the ImmuNexUT database, consisting of 407 donors with ten immune-mediated diseases and healthy controls. RESULTS HLA class II alleles were associated with TRBV gene usage and the public clones of CD4 T cells, while HLA class I alleles were associated with CD8 T cells. RA-risk and immune-mediated diseases-risk HLA alleles were associated with TRBV gene usage of naive and effector CD4 T cell subsets and public clones accumulating in Th17. Clonal diversity was independent of HLA alleles and was correlated with transcriptome changes that reflect TCR signaling. CONCLUSION This study revealed in vivo evidence that both HLA alleles and environmental factors shape naive and effector TCR repertoires in RA and immune-mediated diseases patients.
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Affiliation(s)
- Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mariko Inoue
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satomi Kobayashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mai Okubo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Sugimori
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saeko Yamada
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukiko Iwasaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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19
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Hanata N, Ota M, Tsuchida Y, Nagafuchi Y, Okamura T, Shoda H, Fujio K. Serum extracellular traps associate with the activation of myeloid cells in SLE patients with the low level of anti-DNA antibodies. Sci Rep 2022; 12:18397. [PMID: 36319843 PMCID: PMC9626644 DOI: 10.1038/s41598-022-23076-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/25/2022] [Indexed: 11/05/2022] Open
Abstract
Neutrophil extracellular traps (NETs) are involved in systemic lupus erythematosus (SLE). We sought to cluster SLE patients based on serum NET levels. Serum NET levels were higher in SLE patients than healthy controls. Frequencies of pleuritis and myositis were increased in patients with high serum NET levels. Serum NET levels negatively correlated with anti-double stranded DNA (anti-dsDNA) antibody titers and C1q-binding immune complexes, but positively correlated with C-reactive protein (CRP) and monocyte counts. Neutrophil transcriptome analysis demonstrated no difference in NET-associated signatures, irrespective of serum NET levels, suggesting anti-dsDNA antibody-mediated clearance of NETs. In serum, NET levels were significantly correlated with myeloid cell-derived inflammatory molecules. Serum NET-based cluster analysis revealed 3 groups of patients based on serum NET and CRP levels, anti-dsDNA antibody titers, and monocyte count. Monocytes were consistently activated following NET-containing immune complex (NET-IC) stimulation. In conclusion, SLE patients with high serum NET levels had lower anti-dsDNA antibody titers and higher inflammatory responses. NET-IC-stimulated monocytes might associate with an inflammatory response characterized by elevated CRP levels. These findings can apply to precision medicine, as inflammatory processes, rather than antibody-dependent processes, can be targeted in specific subpopulations of SLE patients.
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Affiliation(s)
- Norio Hanata
- grid.26999.3d0000 0001 2151 536XDepartment of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mineto Ota
- grid.26999.3d0000 0001 2151 536XDepartment of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yumi Tsuchida
- grid.26999.3d0000 0001 2151 536XDepartment of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuo Nagafuchi
- grid.26999.3d0000 0001 2151 536XDepartment of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomohisa Okamura
- grid.26999.3d0000 0001 2151 536XDepartment of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hirofumi Shoda
- grid.26999.3d0000 0001 2151 536XDepartment of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- grid.26999.3d0000 0001 2151 536XDepartment of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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20
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Sakai K, Moritaka T, Morita T, Tomita K, Minami T, Nishimoto T, Egashira S, Ota M, Sakawa Y, Ozaki N, Kodama R, Kojima T, Takezaki T, Yamazaki R, Tanaka SJ, Aihara K, Koenig M, Albertazzi B, Mabey P, Woolsey N, Matsukiyo S, Takabe H, Hoshino M, Kuramitsu Y. Author Correction: Direct observations of pure electron outflow in magnetic reconnection. Sci Rep 2022; 12:16501. [PMID: 36192592 PMCID: PMC9530177 DOI: 10.1038/s41598-022-21220-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- K Sakai
- Graduate School of Engineering, Osaka University, 2‑1 Yamadaoka, Suita, Osaka, 565‑0871, Japan. .,Institute of Laser Engineering, Osaka University, 2‑6 Yamadaoka, Suita, Osaka, 565‑0871, Japan.
| | - T Moritaka
- Department of Helical Plasma Research, National Institute for Fusion Science, Toki, 509‑5292, Japan
| | - T Morita
- Faculty of Engineering Sciences, Kyushu University, 6‑1 Kasuga‑Koen, Kasuga, Fukuoka, 816‑8580, Japan
| | - K Tomita
- Division of Quantum Science and Engineering, Graduate School of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita‑ku, Sapporo, Hokkaido, 060‑8628, Japan
| | - T Minami
- Graduate School of Engineering, Osaka University, 2‑1 Yamadaoka, Suita, Osaka, 565‑0871, Japan.,Institute of Laser Engineering, Osaka University, 2‑6 Yamadaoka, Suita, Osaka, 565‑0871, Japan
| | - T Nishimoto
- Graduate School of Engineering, Osaka University, 2‑1 Yamadaoka, Suita, Osaka, 565‑0871, Japan.,Institute of Laser Engineering, Osaka University, 2‑6 Yamadaoka, Suita, Osaka, 565‑0871, Japan
| | - S Egashira
- Institute of Laser Engineering, Osaka University, 2‑6 Yamadaoka, Suita, Osaka, 565‑0871, Japan
| | - M Ota
- Institute of Laser Engineering, Osaka University, 2‑6 Yamadaoka, Suita, Osaka, 565‑0871, Japan
| | - Y Sakawa
- Institute of Laser Engineering, Osaka University, 2‑6 Yamadaoka, Suita, Osaka, 565‑0871, Japan
| | - N Ozaki
- Graduate School of Engineering, Osaka University, 2‑1 Yamadaoka, Suita, Osaka, 565‑0871, Japan.,Institute of Laser Engineering, Osaka University, 2‑6 Yamadaoka, Suita, Osaka, 565‑0871, Japan
| | - R Kodama
- Graduate School of Engineering, Osaka University, 2‑1 Yamadaoka, Suita, Osaka, 565‑0871, Japan.,Institute of Laser Engineering, Osaka University, 2‑6 Yamadaoka, Suita, Osaka, 565‑0871, Japan
| | - T Kojima
- Faculty of Engineering Sciences, Kyushu University, 6‑1 Kasuga‑Koen, Kasuga, Fukuoka, 816‑8580, Japan
| | - T Takezaki
- Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama, 930‑8555, Japan
| | - R Yamazaki
- Institute of Laser Engineering, Osaka University, 2‑6 Yamadaoka, Suita, Osaka, 565‑0871, Japan.,Department of Physical Sciences, Aoyama Gakuin University, 5‑10‑1 Fuchinobe, Sagamihara, Kanagawa, 252‑5258, Japan
| | - S J Tanaka
- Graduate School of Engineering, Osaka University, 2‑1 Yamadaoka, Suita, Osaka, 565‑0871, Japan.,Department of Physical Sciences, Aoyama Gakuin University, 5‑10‑1 Fuchinobe, Sagamihara, Kanagawa, 252‑5258, Japan
| | - K Aihara
- Department of Physical Sciences, Aoyama Gakuin University, 5‑10‑1 Fuchinobe, Sagamihara, Kanagawa, 252‑5258, Japan
| | - M Koenig
- LULI-CNRS, CEA, Sorbonne Universités, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau Cedex, France
| | - B Albertazzi
- LULI-CNRS, CEA, Sorbonne Universités, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau Cedex, France
| | - P Mabey
- LULI-CNRS, CEA, Sorbonne Universités, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau Cedex, France
| | - N Woolsey
- Department of Physics, York Plasma Institute, University of York, York, YO10 5DD, UK
| | - S Matsukiyo
- Faculty of Engineering Sciences, Kyushu University, 6‑1 Kasuga‑Koen, Kasuga, Fukuoka, 816‑8580, Japan
| | - H Takabe
- Leung Center for Cosmology and Particle Astrophysics, National Taiwan University, Taipei, 10617, Taiwan
| | - M Hoshino
- Department of Earth and Planetary Science, University of Tokyo, 7‑3‑1 Hongo, Bunkyo, Tokyo, 113‑0033, Japan
| | - Y Kuramitsu
- Graduate School of Engineering, Osaka University, 2‑1 Yamadaoka, Suita, Osaka, 565‑0871, Japan. .,Institute of Laser Engineering, Osaka University, 2‑6 Yamadaoka, Suita, Osaka, 565‑0871, Japan.
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21
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Tsuchida Y, Shoda H, Nakano M, Ota M, Okamura T, Yamamoto K, Kurano M, Yatomi Y, Fujio K, Sawada T. Autotaxin is a potential link between genetic risk factors and immunological disturbances of plasmacytoid dendritic cells in systematic lupus erythematosus. Lupus 2022; 31:1578-1585. [PMID: 36134766 DOI: 10.1177/09612033221128494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND The importance of autotaxin, an enzyme that catalyzes lysophospholipid production, has recently been recognized in various diseases, including cancer and autoimmune diseases. Herein, we examined the role of autotaxin in systemic lupus erythematosus (SLE), utilizing data from ImmuNexUT, a comprehensive database consisting of transcriptome data and expression quantitative trait locus (eQTL) data of immune cells from patients with immune-mediated disorders. METHODS Serum autotaxin concentrations in patients with SLE and healthy controls (HCs) were compared. The transcriptome data of patients with SLE and age- and sex-matched HCs were obtained from ImmuNexUT. The expression of ENPP2, the gene encoding autotaxin, was examined in peripheral blood immune cells. Next, weighted gene correlation network analysis (WGCNA) was performed to identify genes with expression patterns similar to ENPP2. The ImmuNexUT eQTL database and public epigenomic databases were used to infer the relationship between autotaxin and pathogenesis of SLE. RESULTS Autotaxin levels were elevated in the serum of patients with SLE compared to HCs. Furthermore, the expression of ENPP2 was higher in plasmacytoid dendritic cells (pDCs) than in other immune cell subsets, and its expression was elevated in pDCs of patients with SLE compared to HCs. In WGCNA, ENPP2 belonged to a module that correlated with disease activity. This module was enriched in interferon-associated genes and included genes whose expression was influenced by single-nucleotide polymorphisms associated with SLE, suggesting that it is a key module connecting genetic risk factors of SLE with disease pathogenesis. Analysis utilizing the ImmuNexUT eQTL database and public epigenomic databases suggested that the increased expression of ENPP2 in pDCs from patients with SLE may be caused by increased expression of interferon-associated genes and increased binding of STAT3 complexes to the regulatory region of ENPP2. CONCLUSIONS Autotaxin may play a critical role in connecting genetic risk factors of SLE to disease pathogenesis in pDCs.
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Affiliation(s)
- Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, 13143The University of Tokyo, Tokyo, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, 13143The University of Tokyo, Tokyo, Japan
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, 13143The University of Tokyo, Tokyo, Japan.,Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, 13143The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, 13143The University of Tokyo, Tokyo, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, 13143The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, 13143The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, 13143The University of Tokyo, Tokyo, Japan.,Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Makoto Kurano
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, 13143The University of Tokyo, Tokyo, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, 13143The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, 13143The University of Tokyo, Tokyo, Japan
| | - Tetsuji Sawada
- Department of Rheumatology, 38548Tokyo Medical University Hospital, Tokyo, Japan
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22
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Takii Y, Mizusawa J, Kanemitsu Y, Komori K, Shiozawa M, Ohue M, Ikeda S, Takiguchi N, Kobatake T, Ike H, Sato T, Tomita N, Ota M, Sunami E, Hamaguchi T, Shida D, Katayama H, Shimada Y, Fukuda H. 414P Long-term follow-up of the randomized trial of the conventional technique versus the no-touch isolation technique for primary tumor resection in patients with colon cancer ( JCOG1006). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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23
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Nakano M, Ota M, Takeshima Y, Iwasaki Y, Hatano H, Nagafuchi Y, Itamiya T, Maeda J, Yoshida R, Yamada S, Nishiwaki A, Takahashi H, Takahashi H, Akutsu Y, Kusuda T, Suetsugu H, Liu L, Kim K, Yin X, Bang SY, Cui Y, Lee HS, Shoda H, Zhang X, Bae SC, Terao C, Yamamoto K, Okamura T, Ishigaki K, Fujio K. Distinct transcriptome architectures underlying lupus establishment and exacerbation. Cell 2022; 185:3375-3389.e21. [PMID: 35998627 DOI: 10.1016/j.cell.2022.07.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/19/2022] [Accepted: 07/22/2022] [Indexed: 12/13/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease involving multiple immune cells. To elucidate SLE pathogenesis, it is essential to understand the dysregulated gene expression pattern linked to various clinical statuses with a high cellular resolution. Here, we conducted a large-scale transcriptome study with 6,386 RNA sequencing data covering 27 immune cell types from 136 SLE and 89 healthy donors. We profiled two distinct cell-type-specific transcriptomic signatures: disease-state and disease-activity signatures, reflecting disease establishment and exacerbation, respectively. We then identified candidate biological processes unique to each signature. This study suggested the clinical value of disease-activity signatures, which were associated with organ involvement and therapeutic responses. However, disease-activity signatures were less enriched around SLE risk variants than disease-state signatures, suggesting that current genetic studies may not well capture clinically vital biology. Together, we identified comprehensive gene signatures of SLE, which will provide essential foundations for future genomic and genetic studies.
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Affiliation(s)
- Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Yusuke Takeshima
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Yukiko Iwasaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Takahiro Itamiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Junko Maeda
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Saeko Yamada
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Aya Nishiwaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Haruka Takahashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Hideyuki Takahashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Yuko Akutsu
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Takeshi Kusuda
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroyuki Suetsugu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Department of Orthopaedic Surgery, Hamanomachi hospital, Fukuoka 810-8539, Japan
| | - Lu Liu
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui 230032, China; Institute of Dermatology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul 02447, South Korea; Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, South Korea
| | - Xianyong Yin
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui 230032, China; Institute of Dermatology, Anhui Medical University, Hefei, Anhui 230032, China; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Human Phenome Institute, Fudan University, Shanghai 201203, China
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 04763, South Korea; Hanyang University Institute of Bioscience and Biotechnology & Hanyang University Institute for Rheumatology Research, Seoul 04763, South Korea
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 04763, South Korea; Hanyang University Institute of Bioscience and Biotechnology & Hanyang University Institute for Rheumatology Research, Seoul 04763, South Korea
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Xuejun Zhang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui 230032, China; Institute of Dermatology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 04763, South Korea; Hanyang University Institute of Bioscience and Biotechnology & Hanyang University Institute for Rheumatology Research, Seoul 04763, South Korea
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Clinical Research Center, Shizuoka General Hospital, Shizuoka 420-8527, Japan; The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8529, Japan
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Kazuyoshi Ishigaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan.
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24
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Tsukumo SI, Subramani PG, Seija N, Tabata M, Maekawa Y, Mori Y, Ishifune C, Itoh Y, Ota M, Fujio K, Di Noia JM, Yasutomo K. AFF3, a susceptibility factor for autoimmune diseases, is a molecular facilitator of immunoglobulin class switch recombination. Sci Adv 2022; 8:eabq0008. [PMID: 36001653 PMCID: PMC9401627 DOI: 10.1126/sciadv.abq0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Immunoglobulin class switch recombination (CSR) plays critical roles in controlling infections and inflammatory tissue injuries. Here, we show that AFF3, a candidate gene for both rheumatoid arthritis and type 1 diabetes, is a molecular facilitator of CSR with an isotype preference. Aff3-deficient mice exhibit low serum levels of immunoglobulins, predominantly immunoglobulin G2c (IgG2c) followed by IgG1 and IgG3 but not IgM. Furthermore, Aff3-deficient mice show weak resistance to Plasmodium yoelii infection, confirming that Aff3 modulates immunity to this pathogen. Mechanistically, the AFF3 protein binds to the IgM and IgG1 switch regions via a C-terminal domain, and Aff3 deficiency reduces the binding of AID to the switch regions less efficiently. One AFF3 risk allele for rheumatoid arthritis is associated with high mRNA expression of AFF3, IGHG2, and IGHA2 in human B cells. These findings demonstrate that AFF3 directly regulates CSR by facilitating the recruitment of AID to the switch regions.
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Affiliation(s)
- Shin-ichi Tsukumo
- Department of Immunology and Parasitology, Graduate School of Medicine, Tokushima University, Tokushima, Japan
- Department of Interdisciplinary Research on Medicine and Photonics, Institute of Post-LED Photonics, Tokushima University, Tokushima, Japan
| | - Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Department of Medicine and Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Noé Seija
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Mizuho Tabata
- Department of Parasitology and Infectious Diseases, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yoichi Maekawa
- Department of Parasitology and Infectious Diseases, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yuya Mori
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Shiga, Japan
| | - Chieko Ishifune
- Department of Immunology and Parasitology, Graduate School of Medicine, Tokushima University, Tokushima, Japan
| | - Yasushi Itoh
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Shiga, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Javier M. Di Noia
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Department of Medicine and Division of Experimental Medicine, McGill University, Montréal, QC, Canada
- Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Koji Yasutomo
- Department of Immunology and Parasitology, Graduate School of Medicine, Tokushima University, Tokushima, Japan
- Department of Interdisciplinary Research on Medicine and Photonics, Institute of Post-LED Photonics, Tokushima University, Tokushima, Japan
- The Research Cluster Program on Immunological Diseases, Tokushima University, Tokushima, Japan
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25
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Okubo M, Sumitomo S, Tsuchida Y, Nagafuchi Y, Takeshima Y, Yanaoka H, Shirai H, Kobayashi S, Sugimori Y, Maeda J, Hatano H, Iwasaki Y, Shoda H, Okamura T, Yamamoto K, Ota M, Fujio K. Transcriptome analysis of immune cells from Behçet's syndrome patients: the importance of IL-17-producing cells and antigen-presenting cells in the pathogenesis of Behçet's syndrome. Arthritis Res Ther 2022; 24:186. [PMID: 35941595 PMCID: PMC9358821 DOI: 10.1186/s13075-022-02867-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 07/15/2022] [Indexed: 11/18/2022] Open
Abstract
Background Behçet’s syndrome (BS) is an immune-mediated disease characterized by recurrent oral ulcers, genital ulcers, uveitis, and skin symptoms. HLA-B51, as well as other genetic polymorphisms, has been reported to be associated with BS; however, the pathogenesis of BS and its relationship to genetic risk factors still remain unclear. To address these points, we performed immunophenotyping and transcriptome analysis of immune cells from BS patients and healthy donors. Methods ImmuNexUT is a comprehensive database consisting of RNA sequencing data and eQTL database of immune cell subsets from patients with immune-mediated diseases and healthy donors, and flow cytometry data and transcriptome data from 23 BS patients and 28 healthy donors from the ImmuNexUT study were utilized for this study. Differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify genes associated with BS and clinical features of BS. eQTL database was used to assess the relationship between genetic risk factors of BS with those genes. Results The frequency of Th17 cells was increased in BS patients, and transcriptome analysis of Th17 cells suggested the activation of the NFκB pathway in Th17 cells of BS patients. Next, WGCNA was used to group genes into modules with similar expression patterns in each subset. Modules of antigen-presenting cells were associated with BS, and pathway analysis suggested the activation of antigen-presenting cells of BS patients. Further examination of genes in BS-associated modules indicated that the expression of YBX3, a member of a plasmacytoid dendritic cell (pDC) gene module associated with BS, is influenced by a BS risk polymorphism, rs2617170, in pDCs, suggesting that YBX3 may be a key molecule connecting genetic risk factors of BS with disease pathogenesis. Furthermore, pathway analysis of modules associated with HLA-B51 indicated that the association of IL-17-associated pathways in memory CD8+ T cells with HLA-B51; therefore, IL-17-producing CD8+ T cells, Tc17 cells, may play a critical role in BS. Conclusions Various cells including CD4+ T cells, CD8+ T cells, and antigen-presenting cells are important in the pathogenesis of BS. Tc17 cells and YBX3 may be potential therapeutic targets in BS. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-022-02867-x.
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Affiliation(s)
- Mai Okubo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Shuji Sumitomo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yusuke Takeshima
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Haruyuki Yanaoka
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Harumi Shirai
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Satomi Kobayashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yusuke Sugimori
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Junko Maeda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yukiko Iwasaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.,Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
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26
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Matsukiyo S, Yamazaki R, Morita T, Tomita K, Kuramitsu Y, Sano T, Tanaka SJ, Takezaki T, Isayama S, Higuchi T, Murakami H, Horie Y, Katsuki N, Hatsuyama R, Edamoto M, Nishioka H, Takagi M, Kojima T, Tomita S, Ishizaka N, Kakuchi S, Sei S, Sugiyama K, Aihara K, Kambayashi S, Ota M, Egashira S, Izumi T, Minami T, Nakagawa Y, Sakai K, Iwamoto M, Ozaki N, Sakawa Y. High-power laser experiment on developing supercritical shock propagating in homogeneously magnetized plasma of ambient gas origin. Phys Rev E 2022; 106:025205. [PMID: 36109929 DOI: 10.1103/physreve.106.025205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
A developing supercritical collisionless shock propagating in a homogeneously magnetized plasma of ambient gas origin having higher uniformity than the previous experiments is formed by using high-power laser experiment. The ambient plasma is not contaminated by the plasma produced in the early time after the laser shot. While the observed developing shock does not have stationary downstream structure, it possesses some characteristics of a magnetized supercritical shock, which are supported by a one-dimensional full particle-in-cell simulation taking the effect of finite time of laser-target interaction into account.
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Affiliation(s)
- S Matsukiyo
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- International Research Center for Space and Planetary Environmental Science, Kyushu University, Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
- Institute of Laser Engineering, Osaka University, 2-6, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - R Yamazaki
- Department of Physical Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
- Institute of Laser Engineering, Osaka University, 2-6, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - T Morita
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - K Tomita
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Division of Quantum Science and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Y Kuramitsu
- Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - T Sano
- Institute of Laser Engineering, Osaka University, 2-6, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - S J Tanaka
- Department of Physical Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
- Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - T Takezaki
- Faculty of Engineering, University of Toyama, 3190, Gofuku, Toyama 930-8555, Japan
- Department of Creative Engineering, National Institute of Technology, Kitakyushu College, 5-20-1 Shii, Kokuraminamiku, Kitakyushu, Fukuoka 802-0985, Japan
| | - S Isayama
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- International Research Center for Space and Planetary Environmental Science, Kyushu University, Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
| | - T Higuchi
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - H Murakami
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - Y Horie
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - N Katsuki
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - R Hatsuyama
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - M Edamoto
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - H Nishioka
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - M Takagi
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - T Kojima
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - S Tomita
- Astronomical Institute, Tohoku University, 6-3 Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8578, Japan
| | - N Ishizaka
- Department of Physical Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - S Kakuchi
- Department of Physical Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - S Sei
- Department of Physical Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - K Sugiyama
- Department of Physical Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - K Aihara
- Department of Physical Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - S Kambayashi
- Department of Physical Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - M Ota
- Graduate School of Science, Osaka University, 1-1 Machikane-yama, Toyonaka, Osaka 560-0043, Japan
| | - S Egashira
- Graduate School of Science, Osaka University, 1-1 Machikane-yama, Toyonaka, Osaka 560-0043, Japan
| | - T Izumi
- Graduate School of Science, Osaka University, 1-1 Machikane-yama, Toyonaka, Osaka 560-0043, Japan
| | - T Minami
- Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Y Nakagawa
- Graduate School of Science, Osaka University, 1-1 Machikane-yama, Toyonaka, Osaka 560-0043, Japan
| | - K Sakai
- Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - M Iwamoto
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Department of Earth and Planetary Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - N Ozaki
- Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Y Sakawa
- Institute of Laser Engineering, Osaka University, 2-6, Yamadaoka, Suita, Osaka 565-0871, Japan
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Sakai K, Moritaka T, Morita T, Tomita K, Minami T, Nishimoto T, Egashira S, Ota M, Sakawa Y, Ozaki N, Kodama R, Kojima T, Takezaki T, Yamazaki R, Tanaka SJ, Aihara K, Koenig M, Albertazzi B, Mabey P, Woolsey N, Matsukiyo S, Takabe H, Hoshino M, Kuramitsu Y. Direct observations of pure electron outflow in magnetic reconnection. Sci Rep 2022; 12:10921. [PMID: 35773286 PMCID: PMC9247195 DOI: 10.1038/s41598-022-14582-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/09/2022] [Indexed: 11/25/2022] Open
Abstract
Magnetic reconnection is a universal process in space, astrophysical, and laboratory plasmas. It alters magnetic field topology and results in energy release to the plasma. Here we report the experimental results of a pure electron outflow in magnetic reconnection, which is not accompanied with ion flows. By controlling an applied magnetic field in a laser produced plasma, we have constructed an experiment that magnetizes the electrons but not the ions. This allows us to isolate the electron dynamics from the ions. Collective Thomson scattering measurements reveal the electron Alfvénic outflow without ion outflow. The resultant plasmoid and whistler waves are observed with the magnetic induction probe measurements. We observe the unique features of electron-scale magnetic reconnection simultaneously in laser produced plasmas, including global structures, local plasma parameters, magnetic field, and waves.
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Affiliation(s)
- K Sakai
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - T Moritaka
- Department of Helical Plasma Research, National Institute for Fusion Science, Toki, 509-5292, Japan
| | - T Morita
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka, 816-8580, Japan
| | - K Tomita
- Division of Quantum Science and Engineering, Graduate School of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - T Minami
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - T Nishimoto
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - S Egashira
- Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - M Ota
- Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Y Sakawa
- Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - N Ozaki
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - R Kodama
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - T Kojima
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka, 816-8580, Japan
| | - T Takezaki
- Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama, 930-8555, Japan
| | - R Yamazaki
- Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa, 252-5258, Japan
| | - S J Tanaka
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa, 252-5258, Japan
| | - K Aihara
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa, 252-5258, Japan
| | - M Koenig
- LULI-CNRS, CEA, Sorbonne Universités, École Polytechnique, Institut Polytechnique de Paris, F-91120, Palaiseau cedex, France
| | - B Albertazzi
- LULI-CNRS, CEA, Sorbonne Universités, École Polytechnique, Institut Polytechnique de Paris, F-91120, Palaiseau cedex, France
| | - P Mabey
- LULI-CNRS, CEA, Sorbonne Universités, École Polytechnique, Institut Polytechnique de Paris, F-91120, Palaiseau cedex, France
| | - N Woolsey
- Department of Physics, York Plasma Institute, University of York, York, YO10 5DD, UK
| | - S Matsukiyo
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka, 816-8580, Japan
| | - H Takabe
- Leung Center for Cosmology and Particle Astrophysics, National Taiwan University, Taipei, 10617, Taiwan
| | - M Hoshino
- Department of Earth and Planetary Science, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Y Kuramitsu
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Nakano M, Ota M, Takeshima Y, Iwasaki Y, Hatano H, Nagafuchi Y, Kim K, Bang SY, Lee HS, Shoda H, Zhang X, Bae SC, Terao C, Yamamoto K, Okamura T, Ishigaki K, Fujio K. OP0110 CELL-TYPE-SPECIFIC TRANSCRIPTOME ARCHITECTURE UNDERLYING THE ESTABLISHMENT AND EXACERBATION OF SYSTEMIC LUPUS ERYTHEMATOSUS. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.1684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundSystemic lupus erythematosus (SLE) is a complex autoimmune disease with unknown etiology involving multiple immune cells and has diverse clinical phenotypes. This heterogeneous nature has hampered a better understanding of SLE pathogenesis and the development of effective therapeutic agents. While recent single-cell RNA sequencing studies of SLE identified several important cell subpopulations, they were limited by sparse expression information at single-cell level and small sample sizes.ObjectivesThis study aimed to elucidate the dysregulated gene expression pattern linked to multiple clinical statuses of SLE with a fine cellular resolution and higher sensitivity. We also attempted to resolve a complex interaction between risk variants and the transcriptome dysregulation seen in SLE patients.MethodsWe conducted a large-scale bulk transcriptome study of 6,386 RNA-sequencing data including 27 purified immune cell types in peripheral blood from 136 SLE and 89 healthy donors in the Immune Cell Gene Expression Atlas from the University of Tokyo (ImmuNexUT) cohort1. At enrollment, SLE patients had diverse clinical manifestations (disease activity, organ involvement and treatment profiles) and 22 patients were re-evaluated after belimumab treatment.ResultsWe first profiled two distinct cell-type-specific transcriptomic signatures: disease-state and disease-activity signatures, reflecting disease establishment and exacerbation, respectively.After confirming the high replicability of both signatures in independent cohorts, we identified candidates of biological processes unique to each signature: e.g., upregulated E2F transcriptional activity in Th1, CD8+ memory T-lineage and NK cells, and dynamic increase of IL21 and CXCL13 in Th1 cells in an active phase of SLE. Pathway analysis highlighted the importance of immunometabolic process for SLE (e.g., oxidative phosphorylation) in cell-type-specific resolution.Moreover, we demonstrated cell-type-specific contributions to diverse organ involvement, e.g., Th1 for mucocutaneous, monocyte-lineage cells for musculoskeletal, neutrophil-lineage cells for renal activity, respectively.We also observed the strong associations of disease-activity signatures with treatment effect: (i) belimumab suppressed activity signatures from B-lineage cells, especially in good responders and (ii) mycophenolate mofetil substantially suppressed activity signatures from plasmablast, Th1, and central memory CD8 cells.However, through stratified LD score regression using large-scale SLE-GWASs, we revealed that disease-activity signatures were less enriched around SLE risk variants than disease-state signatures. Consistent with this result, the directions of SLE risk alleles’ expression quantitative trait locus (eQTL) effects were significantly concordant with the directions of disease-state signatures, but not with those of activity signatures. These findings suggested that the current genetic case-control studies may not well capture clinically vital biology linked to drug target discovery for SLE. Meanwhile, we also detected some examples of activity signatures that might contribute to the disease risk by modulating risk allele’s eQTL effects.Figure 1.ConclusionWe identified comprehensive gene signatures reflecting the establishment and exacerbation of SLE, which provide essential foundations for future genomic, genetic, and clinical studies.References[1]Ota, M. et al. Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases. Cell 2021;184:3006-21.e17.AcknowledgementsThis study was supported by Chugai Pharmaceutical Co., Ltd., Tokyo, Japan; the Ministry of Education, Culture, Sports; and the Japan Agency for Medical Research and Development (AMED) (JP21tm0424221 and JP21zf0127004).Disclosure of InterestsMasahiro Nakano: None declared, Mineto Ota Grant/research support from: Mineto Ota belongs to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Yusuke Takeshima Grant/research support from: Yusuke Takeshima belonged to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Yukiko Iwasaki: None declared, Hiroaki Hatano: None declared, Yasuo Nagafuchi Grant/research support from: Yasuo Nagafuchi belongs to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Kwangwoo Kim: None declared, So-Young Bang: None declared, Hye Soon Lee: None declared, Hirofumi Shoda: None declared, Xuejun Zhang: None declared, Sang-Cheol Bae: None declared, Chikashi Terao: None declared, Kazuhiko Yamamoto: None declared, Tomohisa Okamura Grant/research support from: Tomohisa Okamura belongs to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Kazuyoshi Ishigaki: None declared, Keishi Fujio Speakers bureau: Keishi Fujio receives speaker fees from Chugai Pharmaceutical., Consultant of: Keishi Fujio receives consulting honoraria from Chugai Pharmaceutical., Grant/research support from: Keishi Fujio receives research support from Chugai Pharmaceutical.
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Ishikawa K, Sasaki H, Ogushi Y, Niikura A, Ota T, Ichimura Y, Hashimoto Y, Kurokawa I, Sugishita H, Tanifuji S, Yamagishi M, Shimoyama H, Ota M, Oshinomi K, Hayashi K, Morita J, Shichijo T, Fukagai T, Sugawara S. Lipid abnormality, current diabetes and age affect erectile hardness ∼ An analysis of data from complete medical checkups performed at a single hospital in Japan. J Sex Med 2022. [DOI: 10.1016/j.jsxm.2022.03.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Yamagishi M, Sasaki H, Ogushi Y, Niikura A, Ota T, Ichimura Y, Hashimoto Y, Sugishita H, Kurokawa I, Tanifuji S, Imamura Y, Shimoyama H, Ota M, Ishikawa K, Hayashi K, Fukagai T. A study of erectile dysfunction in men 40 years of age or younger. J Sex Med 2022. [DOI: 10.1016/j.jsxm.2022.03.422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Shimoyama H, Sasaki H, Ogushi Y, Niikura A, Ota T, Ichimura Y, Hshimoto Y, Kurokawa I, Sugishita H, Tanifuji S, Yamagishi M, Imamura Y, Ota M, Ishikawa K, Hayashi K. Clinical analysis on the pharmaceutical formulation of VIAGRA OD Film. J Sex Med 2022. [DOI: 10.1016/j.jsxm.2022.03.434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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32
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Takeshima Y, Iwasaki Y, Nakano M, Narushima Y, Ota M, Nagafuchi Y, Sumitomo S, Okamura T, Elkon K, Ishigaki K, Suzuki A, Kochi Y, Yamamoto K, Fujio K. Immune cell multiomics analysis reveals contribution of oxidative phosphorylation to B-cell functions and organ damage of lupus. Ann Rheum Dis 2022; 81:845-853. [PMID: 35236659 DOI: 10.1136/annrheumdis-2021-221464] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/09/2022] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disease. While the long-term prognosis has greatly improved, better long-term survival is still necessary. The type I interferon (IFN) signature, a prominent feature of SLE, is not an ideal therapeutic target or outcome predictor. To explore immunological pathways in SLE more precisely, we performed transcriptomic, epigenomic and genomic analyses using 19 immune cell subsets from peripheral blood. METHODS We sorted 19 immune cell subsets and identified the mRNA expression profiles and genetic polymorphisms in 107 patients with SLE and 92 healthy controls. Combined differentially expressed genes and expression quantitative trait loci analysis was conducted to find key driver genes in SLE pathogenesis. RESULTS We found transcriptomic, epigenetic and genetic importance of oxidative phosphorylation (OXPHOS)/mitochondrial dysfunction in SLE memory B cells. Particularly, we identified an OXPHOS-regulating gene, PRDX6 (peroxiredoxin 6), as a key driver in SLE B cells. Prdx6-deficient B cells showed upregulated mitochondrial respiration as well as antibody production. We revealed OXPHOS signature was associated with type I IFN signalling-related genes (ISRGs) signature in SLE memory B cells. Furthermore, the gene sets related to innate immune signalling among ISRGs presented correlation with OXPHOS and these two signatures showed associations with SLE organ damage as well as specific clinical phenotypes. CONCLUSION This work elucidated the potential prognostic marker for SLE. Since OXPHOS consists of the electron transport chain, a functional unit in mitochondria, these findings suggest the importance of mitochondrial dysfunction as a key immunological pathway involved in SLE.
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Affiliation(s)
- Yusuke Takeshima
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, The University of Tokyo, Tokyo, Japan
| | - Yukiko Iwasaki
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan .,Department of Palliative Medicine, Saitama Medical University, Saitama, Japan
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan
| | - Yuta Narushima
- Research Division, Chugai Pharmaceutical Co Ltd, Kamakura, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, The University of Tokyo, Tokyo, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, The University of Tokyo, Tokyo, Japan
| | - Shuji Sumitomo
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, The University of Tokyo, Tokyo, Japan
| | - Keith Elkon
- Division of Rheumatology, University of Washington, Seattle, Washington, USA
| | - Kazuyoshi Ishigaki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, Riken Yokohama Institute, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, Riken Yokohama Institute, Yokohama, Japan
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, Riken Yokohama Institute, Yokohama, Japan.,Department of Genomic Function and Diversity, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, Riken Yokohama Institute, Yokohama, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, The University of Tokyo, Tokyo, Japan
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Yamazaki R, Matsukiyo S, Morita T, Tanaka SJ, Umeda T, Aihara K, Edamoto M, Egashira S, Hatsuyama R, Higuchi T, Hihara T, Horie Y, Hoshino M, Ishii A, Ishizaka N, Itadani Y, Izumi T, Kambayashi S, Kakuchi S, Katsuki N, Kawamura R, Kawamura Y, Kisaka S, Kojima T, Konuma A, Kumar R, Minami T, Miyata I, Moritaka T, Murakami Y, Nagashima K, Nakagawa Y, Nishimoto T, Nishioka Y, Ohira Y, Ohnishi N, Ota M, Ozaki N, Sano T, Sakai K, Sei S, Shiota J, Shoji Y, Sugiyama K, Suzuki D, Takagi M, Toda H, Tomita S, Tomiya S, Yoneda H, Takezaki T, Tomita K, Kuramitsu Y, Sakawa Y. High-power laser experiment forming a supercritical collisionless shock in a magnetized uniform plasma at rest. Phys Rev E 2022; 105:025203. [PMID: 35291161 DOI: 10.1103/physreve.105.025203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
We present an experimental method to generate quasiperpendicular supercritical magnetized collisionless shocks. In our experiment, ambient nitrogen (N) plasma is at rest and well magnetized, and it has uniform mass density. The plasma is pushed by laser-driven ablation aluminum (Al) plasma. Streaked optical pyrometry and spatially resolved laser collective Thomson scattering clarify structures of plasma density and temperatures, which are compared with one-dimensional particle-in-cell simulations. It is indicated that just after the laser irradiation, the Al plasma is magnetized by a self-generated Biermann battery field, and the plasma slaps the incident N plasma. The compressed external field in the N plasma reflects N ions, leading to counterstreaming magnetized N flows. Namely, we identify the edge of the reflected N ions. Such interacting plasmas form a magnetized collisionless shock.
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Affiliation(s)
- R Yamazaki
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
- Institute of Laser Engineering, Osaka University, 2-6, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - S Matsukiyo
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - T Morita
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
| | - S J Tanaka
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - T Umeda
- Institute for Space-Earth Environmental Research, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - K Aihara
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - M Edamoto
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga 816-8580, Japan
| | - S Egashira
- Graduate School of Science, Osaka University, 1-1 Machikane-yama, Toyonaka, Osaka 560-0043, Japan
| | - R Hatsuyama
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga 816-8580, Japan
| | - T Higuchi
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga 816-8580, Japan
| | - T Hihara
- Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Y Horie
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga 816-8580, Japan
| | - M Hoshino
- Department of Earth and Planetary Science, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - A Ishii
- Max Planck Institute for Gravitational Physics (Albert Einstein Institute), Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - N Ishizaka
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - Y Itadani
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga 816-8580, Japan
| | - T Izumi
- Graduate School of Science, Osaka University, 1-1 Machikane-yama, Toyonaka, Osaka 560-0043, Japan
| | - S Kambayashi
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - S Kakuchi
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - N Katsuki
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga 816-8580, Japan
| | - R Kawamura
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - Y Kawamura
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - S Kisaka
- Department of Physical Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - T Kojima
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga 816-8580, Japan
| | - A Konuma
- Institute for Laser Science, University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - R Kumar
- Graduate School of Science, Osaka University, 1-1 Machikane-yama, Toyonaka, Osaka 560-0043, Japan
| | - T Minami
- Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - I Miyata
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - T Moritaka
- Fundamental Physics Simulation Research Division, National Institute for Fusion Science, 322-6 Oroshi-cho, Toki 509-5292, Japan
| | - Y Murakami
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga 816-8580, Japan
| | - K Nagashima
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga 816-8580, Japan
| | - Y Nakagawa
- Graduate School of Science, Osaka University, 1-1 Machikane-yama, Toyonaka, Osaka 560-0043, Japan
| | - T Nishimoto
- School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Y Nishioka
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga 816-8580, Japan
| | - Y Ohira
- Department of Earth and Planetary Science, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - N Ohnishi
- Department of Aerospace Engineering, Tohoku University, 6-6 Aramaki Aza Aoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - M Ota
- Graduate School of Science, Osaka University, 1-1 Machikane-yama, Toyonaka, Osaka 560-0043, Japan
| | - N Ozaki
- Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - T Sano
- Institute of Laser Engineering, Osaka University, 2-6, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - K Sakai
- Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - S Sei
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - J Shiota
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - Y Shoji
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - K Sugiyama
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - D Suzuki
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - M Takagi
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga 816-8580, Japan
| | - H Toda
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - S Tomita
- Astronomical Institute, Tohoku University, 6-3 Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8578, Japan
| | - S Tomiya
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 252-5258, Japan
| | - H Yoneda
- Institute for Laser Science, University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - T Takezaki
- Department of Creative Engineering, National Institute of Technology, Kitakyushu College, 5-20-1 Shii, Kokuraminamiku, Kitakyushu, Fukuoka 802-0985, Japan
- Faculty of Engineering, University of Toyama, 3190, Gofuku, Toyama 930-8555, Japan
| | - K Tomita
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Division of Quantum Science and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Y Kuramitsu
- Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Y Sakawa
- Institute of Laser Engineering, Osaka University, 2-6, Yamadaoka, Suita, Osaka 565-0871, Japan
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Kobayashi S, Nagafuchi Y, Okubo M, Sugimori Y, Hatano H, Yamada S, Nakano M, Yoshida R, Takeshima Y, Ota M, Tsuchida Y, Iwasaki Y, Setoguchi K, Kubo K, Okamura T, Yamamoto K, Shoda H, Fujio K. Dysregulation of the gene signature of effector regulatory T cells in the early phase of systemic sclerosis. Rheumatology (Oxford) 2022; 61:4163-4174. [PMID: 35040949 DOI: 10.1093/rheumatology/keac031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/11/2022] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES We evaluated flow-cytometric and transcriptome features of peripheral blood immune cells from early-phase (disease duration < 5 years) systemic sclerosis (SSc) in comparison to late-phase SSc. METHODS Fifty Japanese patients with SSc (12 early SSc cases and 38 late SSc cases) and 50 age- and sex-matched healthy controls were enrolled. A comparison of flow-cytometric subset proportions and RNA-sequencing of 24 peripheral blood immune cell subsets was performed. We evaluated differentially expressed genes (DEGs), characterized the co-expressed gene modules, and estimated the composition of subpopulations by deconvolution based on single-cell RNA-sequencing data. As a disease control, idiopathic inflammatory myositis (IIM) patients were also evaluated. RESULTS Analyzing the data from early and late SSc, Fraction II effector regulatory T cell (Fr. II eTreg) genes showed a remarkable differential gene expression, which was enriched for genes related to oxidative phosphorylation. Although the flow-cytometric proportion of Fr. II eTregs was not changed in early SSc, deconvolution indicated expansion of the activated subpopulation. Co-expressed gene modules of Fr. II eTregs demonstrated enrichment of the DEGs of early SSc and correlation with the proportion of the activated subpopulation. These results suggested that DEGs in Fr. II eTregs from patients with early SSc were closely associated with the increased proportion of the activated subpopulation. Similar dysregulation of Fr. II eTregs was also observed in data from patients with early IIM. CONCLUSIONS RNA-seq of immune cells indicated the dysregulation of Fr. II eTregs in early SSc with increased proportion of the activated subpopulation.
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Affiliation(s)
- Satomi Kobayashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo.,Department of Medicine and Rheumatology, Tokyo Metropolitan Geriatric Hospital, Japan. 35-2 Sakaechou, Itabashi-ku, 173-0015, Japan, Tokyo, Tokyo
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Mai Okubo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Yusuke Sugimori
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Saeko Yamada
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Yusuke Takeshima
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Yukiko Iwasaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Keigo Setoguchi
- Department of Rheumatology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Japan. 3-18-22 Honkomagome, Bunkyo-ku, 113-8677, Japan, Tokyo, Tokyo
| | - Kanae Kubo
- Department of Medicine and Rheumatology, Tokyo Metropolitan Geriatric Hospital, Japan. 35-2 Sakaechou, Itabashi-ku, 173-0015, Japan, Tokyo, Tokyo
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo.,Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Japan. 1-7-22 Suehiro-cho, Tsurumi-ku, Kanagawa, 230-0045, Japan, Yokohama, Yokohama
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
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Abstract
Recent innovation in high-throughput sequencing technologies has drastically empowered the scientific research. Consequently, now, it is possible to capture comprehensive profiles of samples at multiple levels including genome, epigenome, and transcriptome at a time. Applying these kinds of rich information to clinical settings is of great social significance. For some traits such as cardiovascular diseases, attempts to apply omics datasets in clinical practice for the prediction of the disease risk have already shown promising results, although still under way for immune-mediated diseases. Multiple studies have tried to predict treatment response in immune-mediated diseases using genomic, transcriptomic, or clinical information, showing various possible indicators. For better prediction of treatment response or disease outcome in immune-mediated diseases, combining multi-layer information together may increase the power. In addition, in order to efficiently pick up meaningful information from the massive data, high-quality annotation of genomic functions is also crucial. In this review, we discuss the achievement so far and the future direction of multi-omics approach to immune-mediated diseases.
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Affiliation(s)
- Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan. .,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
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36
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Ota M, Nagafuchi Y, Hatano H, Ishigaki K, Terao C, Takeshima Y, Yanaoka H, Kobayashi S, Okubo M, Shirai H, Sugimori Y, Maeda J, Nakano M, Yamada S, Yoshida R, Tsuchiya H, Tsuchida Y, Akizuki S, Yoshifuji H, Ohmura K, Mimori T, Yoshida K, Kurosaka D, Okada M, Setoguchi K, Kaneko H, Ban N, Yabuki N, Matsuki K, Mutoh H, Oyama S, Okazaki M, Tsunoda H, Iwasaki Y, Sumitomo S, Shoda H, Kochi Y, Okada Y, Yamamoto K, Okamura T, Fujio K. Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases. Cell 2021; 184:3006-3021.e17. [PMID: 33930287 DOI: 10.1016/j.cell.2021.03.056] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/25/2021] [Accepted: 03/28/2021] [Indexed: 02/07/2023]
Abstract
Genetic studies have revealed many variant loci that are associated with immune-mediated diseases. To elucidate the disease pathogenesis, it is essential to understand the function of these variants, especially under disease-associated conditions. Here, we performed a large-scale immune cell gene-expression analysis, together with whole-genome sequence analysis. Our dataset consists of 28 distinct immune cell subsets from 337 patients diagnosed with 10 categories of immune-mediated diseases and 79 healthy volunteers. Our dataset captured distinctive gene-expression profiles across immune cell types and diseases. Expression quantitative trait loci (eQTL) analysis revealed dynamic variations of eQTL effects in the context of immunological conditions, as well as cell types. These cell-type-specific and context-dependent eQTLs showed significant enrichment in immune disease-associated genetic variants, and they implicated the disease-relevant cell types, genes, and environment. This atlas deepens our understanding of the immunogenetic functions of disease-associated variants under in vivo disease conditions.
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Affiliation(s)
- Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yusuke Takeshima
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Haruyuki Yanaoka
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Satomi Kobayashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Mai Okubo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Harumi Shirai
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yusuke Sugimori
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Junko Maeda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Saeko Yamada
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Haruka Tsuchiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shuji Akizuki
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Hajime Yoshifuji
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Ken Yoshida
- Division of Rheumatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Daitaro Kurosaka
- Division of Rheumatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Masato Okada
- Immuno-Rheumatology Center, St. Luke's International Hospital, Tokyo 104-8560, Japan
| | - Keigo Setoguchi
- Division of Collagen Disease, Department of Medicine, Tokyo Metropolitan Komagome Hospital, Tokyo 113-0021, Japan
| | - Hiroshi Kaneko
- Division of Rheumatic Diseases, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Nobuhiro Ban
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa 247-8530, Japan
| | - Nami Yabuki
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa 247-8530, Japan
| | - Kosuke Matsuki
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa 247-8530, Japan
| | - Hironori Mutoh
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa 247-8530, Japan
| | - Sohei Oyama
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa 247-8530, Japan
| | - Makoto Okazaki
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa 247-8530, Japan
| | - Hiroyuki Tsunoda
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa 247-8530, Japan
| | - Yukiko Iwasaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shuji Sumitomo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tomohisa Okamura
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
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Ota M, Hoshino Y, Hirao S. Analysis of 605 tuberculosis outbreaks in Japan, 1993-2015: time, place and transmission site. Epidemiol Infect 2021; 149:e85. [PMID: 33745484 PMCID: PMC8080251 DOI: 10.1017/s0950268821000625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/03/2021] [Accepted: 03/17/2021] [Indexed: 11/06/2022] Open
Abstract
Since 1993, reports on tuberculosis (TB) outbreaks have been collected in Japan; however, there has never been an overall analysis of these TB outbreaks. We aim to provide one here. The TB outbreak data were obtained from the Ministry of Health, Labour and Welfare and are described in terms of time, place and transmission site. The average number of TB cases and latent tuberculosis infection (LTBI) were compared by the transmission site. Some 605 TB outbreaks with 3491 TB cases were reported in 1993-2015 with an increasing trend (r = 0.45), during which time 728 777 TB cases were reported nationwide. On an average, TB outbreaks occurred more often in April to May (5.5 outbreaks per 2 months) than in December to January (3.4). The most common transmission sites were workplaces (n = 255), followed by health facilities (n = 144), schools (n = 60) and welfare facilities (n = 48). Psychiatric hospitals and nursing homes had the highest average number of TB cases per outbreak (8.5 each), whereas schools and prisons had the highest numbers of LTBI cases (29.1 and 38.9, respectively). Countries, particularly those that have resources to investigate TB outbreaks, should collect and analyse findings of TB outbreaks, as it informs surveillance systems and eventually strengthens general health systems.
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Affiliation(s)
- M. Ota
- Research Institute of Tuberculosis, Tokyo, Japan
| | - Y. Hoshino
- Research Institute of Tuberculosis, Tokyo, Japan
| | - S. Hirao
- Research Institute of Tuberculosis, Tokyo, Japan
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38
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Daka S, Matsuoka Y, Ota M, Hirao S, Phiri A. Re-evaluated treatment outcomes of bacteriologically positive TB patients registered at a clinic in Lusaka, Zambia in 2018. Public Health Action 2021; 11:22-25. [PMID: 33777717 DOI: 10.5588/pha.20.0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/05/2021] [Indexed: 11/10/2022] Open
Abstract
SETTING An urban TB diagnostic centre in Lusaka, Zambia. OBJECTIVE To re-evaluate treatment outcomes of all bacteriologically confirmed TB patients registered in 2018. DESIGN This was a retrospective cohort study on TB patients. Treatment outcomes of patients who were transferred out were retrieved. RESULTS A total of 182 patients were registered, 26 of whom had missing documents; these were excluded from the study. Of the remaining 156 patients who were reviewed, 86 (55.1%) were correctly evaluated by the centre, 35 (22.4%) were incorrectly evaluated and 35 (22.4%) were 'transferred out' (not evaluated). As a result of this review, the number of evaluated patients increased from 86 (55.1%) to 150 (96.2%). The cure and treatment success rates rose from 43.6% and 44.2%, respectively, to 57.7% and 73.1%, respectively. Of note, 14 of the 35 patients who were initially declared 'transferred out' did not actually reach their treatment facilities and ended up being lost to follow-up. CONCLUSION This study shows that it is possible to evaluate almost all TB patients. Re-evaluation of treatment outcomes of TB patients revealed the problems in the TB services that need to be improved in the future.
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Affiliation(s)
- S Daka
- Japan Anti-Tuberculosis Association, Lusaka, Zambia
| | - Y Matsuoka
- Japan Anti-Tuberculosis Association, Lusaka, Zambia
| | - M Ota
- Research Institute of Tuberculosis, Tokyo, Japan
| | - S Hirao
- Research Institute of Tuberculosis, Tokyo, Japan
| | - A Phiri
- Ministry of Health, Lusaka District Health Office, Lusaka, Zambia
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Abstract
BACKGROUND Rheumatoid arthritis (RA) is an autoimmune disease characterized by tumor-like hyperplasia and inflammation of the synovium, which causes synovial cell invasion into the bone and cartilage. In RA pathogenesis, various molecules in effector cells (i.e., immune cells and mesenchymal cells) are dysregulated by genetic and environmental factors. Synovial fibroblasts (SFs), the most abundant resident mesenchymal cells in the synovium, are the major local effectors of the destructive joint inflammation and exert their effects through the pathogenic production of molecules such as interleukin-6. MAIN BODY To date, more than 100 RA susceptibility loci have been identified in genome-wide association studies (GWASs), and finding novel therapeutic targets utilizing genome analysis is considered a promising approach because some candidate causal genes identified by GWASs have previously been established as therapeutic targets. For further exploration of RA-responsible cells and cell type-specific therapeutic targets, integrated analysis (or functional genome analysis) of the genome and intermediate traits (e.g., transcriptome and epigenome) is crucial. CONCLUSION This review builds on the existing knowledge regarding the epigenomic abnormalities in RASFs and discusses the recent advances in single-cell analysis, highlighting the prospects of SFs as targets for safer and more effective therapies against RA.
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Affiliation(s)
- Haruka Tsuchiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.
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40
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Affiliation(s)
- M Ota
- Department of Dermatology, Chitose City Hospital, Chitose, Japan
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41
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Tonegawa R, Miyamoto K, Ueda N, Nakajima K, Wada M, Yamagata K, Ishibashi K, Inoue Y, Noda T, Nagase S, Ota M, Aiba T, Nakajima T, Fukuda T, Kusano K. Ventricular tachycardia in cardiac sarcoidosis -prognosis, characterization of ventricular substrates and outcomes of treatment-. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.2141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The prognosis, the underlying substrate and clinical outcomes of treatment are unclear in patients with cardiac sarcoidosis (CS)-related ventricular tachycardia (VT).
Objective
This study investigated the prognosis and the relationship between electroanatomical mapping (EAM) and imaging findings in patients with CS-related VT.
Methods
A total of 203 CS patients (Age 68.1±11.6 years, 87 males) were enrolled at two tertiary care medical centers between 2000 and 2018. All met the 2016 Japanese Circulation Society guidelines for diagnosis of CS. They were followed for a composite of major adverse cardiac events (MACE) including cardiac death, heart transplantation, unscheduled hospitalization for heart failure, and life-threatening ventricular arrhythmias. Distribution of late gadolinium enhancement (LGE) on cardiac MRI (CMR) and/or an abnormal myocardial 18F-fluorodeoxyglucose (FDG) uptake on positron emission tomography at diagnosis were examined. The relationship between EAM and the image findings were also analyzed in patients with radiofrequency ablation (RFA) for VT.
Results
During a median follow-up of 53 months, 87 of the 203 patients (43%) experienced a MACE. Baseline factors associated with MACE were presence of sustained VT (HR, 2.43, 95% CI 1.54–3.85, P<0.001), left ventricular ejection fraction below 50% (HR, 1.95 95% CI 1.07–3.56, P=0.029), and abnormal myocardial FDG uptake (HR, 2.42 95% CI 1.04–5.61, P=0.039). Overall, 69 of the 203 patients (34%) experienced sustained VT. Abnormal myocardial FDG uptake was significantly more prevalent in patients with VT than in those without (92.7% vs. 78.5%, P=0.02). A total of 25 patients (9.9%) required RFA for CS-related VT (Age 64.0±8.7 years, 12 males, 1.32±0.56 RFAs per patient). Abnormal electrocardiograms (EGM) were observed in 22 of the 25 patients (88%). LGE was more frequent than abnormal FDG uptake in areas with an abnormal EGM (77% vs. 41%; P=0.002). Over a mean follow-up period of 67-months, 13 of the 25 patients with RFA (52%) remained free of VT episodes (Figure). VT recurred in nine of the 12 patients with RFA and in 17 of the 47 patients without RFA, but was suppressed by intensive pharmacologic therapy such as the combined use of amiodarone and sotalol. In patients with CS-related VT, survival without experiencing a MACE did not differ in participants with or without RFA.
Conclusions
In our 203 CS patients, sustained VT and abnormal FDG uptake were associated with worse cardiac outcomes. The prevalence of abnormal FDG uptake was significantly higher in patients with CS-related VT, LGE on CMR was more frequent within localized areas of an abnormal EGM, suggesting that both scar itself and the associated inflammation were involved in the pathogenesis of CS-related VT. Successful RFA of CS-related VT is still challenging, and recurrence is common. Preprocedural CMR can be useful in detecting abnormal EGMs that are potential targets for substrate ablation.
Funding Acknowledgement
Type of funding source: None
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Affiliation(s)
- R Tonegawa
- National Cerebral and Cardiovascular Center, Department of Cardiovascular Medicine, Suita, Kumamoto University, Department of Advanced Cardiovascular Medicine, Kumamoto, Japan
| | - K Miyamoto
- National Cerebral & Cardiovascular Center, Division of arrhythmia, Department of Cardiovascular Medicine, Suita, Japan
| | - N Ueda
- National Cerebral & Cardiovascular Center, Division of arrhythmia, Department of Cardiovascular Medicine, Suita, Japan
| | - K Nakajima
- National Cerebral & Cardiovascular Center, Division of arrhythmia, Department of Cardiovascular Medicine, Suita, Japan
| | - M Wada
- National Cerebral & Cardiovascular Center, Division of arrhythmia, Department of Cardiovascular Medicine, Suita, Japan
| | - K Yamagata
- National Cerebral & Cardiovascular Center, Division of arrhythmia, Department of Cardiovascular Medicine, Suita, Japan
| | - K Ishibashi
- National Cerebral & Cardiovascular Center, Division of arrhythmia, Department of Cardiovascular Medicine, Suita, Japan
| | - Y Inoue
- National Cerebral & Cardiovascular Center, Division of arrhythmia, Department of Cardiovascular Medicine, Suita, Japan
| | - T Noda
- National Cerebral & Cardiovascular Center, Division of arrhythmia, Department of Cardiovascular Medicine, Suita, Japan
| | - S Nagase
- National Cerebral & Cardiovascular Center, Division of arrhythmia, Department of Cardiovascular Medicine, Suita, Japan
| | - M Ota
- National Cerebral & Cardiovascular Center, Department of Radiology, Suita, Japan
| | - T Aiba
- National Cerebral & Cardiovascular Center, Division of arrhythmia, Department of Cardiovascular Medicine, Suita, Japan
| | - T Nakajima
- Saitama Cardiovascular and Respiratory Center, Department of Cardiology, Kumagaya, Japan
| | - T Fukuda
- National Cerebral & Cardiovascular Center, Department of Radiology, Suita, Japan
| | - K.F Kusano
- National Cerebral and Cardiovascular Center, Department of Cardiovascular Medicine, Suita, Kumamoto University, Department of Advanced Cardiovascular Medicine, Kumamoto, Japan
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Tsuchiya H, Ota M, Sumitomo S, Ishigaki K, Suzuki A, Sakata T, Tsuchida Y, Inui H, Hirose J, Kochi Y, Kadono Y, Shirahige K, Tanaka S, Yamamoto K, Fujio K. Parsing multiomics landscape of activated synovial fibroblasts highlights drug targets linked to genetic risk of rheumatoid arthritis. Ann Rheum Dis 2020; 80:440-450. [PMID: 33139312 DOI: 10.1136/annrheumdis-2020-218189] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/26/2022]
Abstract
OBJECTIVES Synovial fibroblasts (SFs) are one of the major components of the inflamed synovium in rheumatoid arthritis (RA). We aimed to gain insight into the pathogenic mechanisms of SFs through elucidating the genetic contribution to molecular regulatory networks under inflammatory condition. METHODS SFs from RA and osteoarthritis (OA) patients (n=30 each) were stimulated with eight different cytokines (interferon (IFN)-α, IFN-γ, tumour necrosis factor-α, interleukin (IL)-1β, IL-6/sIL-6R, IL-17, transforming growth factor-β1, IL-18) or a combination of all 8 (8-mix). Peripheral blood mononuclear cells were fractioned into five immune cell subsets (CD4+ T cells, CD8+ T cells, B cells, natural killer (NK) cells, monocytes). Integrative analyses including mRNA expression, histone modifications (H3K27ac, H3K4me1, H3K4me3), three-dimensional (3D) genome architecture and genetic variations of single nucleotide polymorphisms (SNPs) were performed. RESULTS Unstimulated RASFs differed markedly from OASFs in the transcriptome and epigenome. Meanwhile, most of the responses to stimulations were shared between the diseases. Activated SFs expressed pathogenic genes, including CD40 whose induction by IFN-γ was significantly affected by an RA risk SNP (rs6074022). On chromatin remodelling in activated SFs, RA risk loci were enriched in clusters of enhancers (super-enhancers; SEs) induced by synergistic proinflammatory cytokines. An RA risk SNP (rs28411362), located in an SE under synergistically acting cytokines, formed 3D contact with the promoter of metal-regulatory transcription factor-1 (MTF1) gene, whose binding motif showed significant enrichment in stimulation specific-SEs. Consistently, inhibition of MTF1 suppressed cytokine and chemokine production from SFs and ameliorated mice model of arthritis. CONCLUSIONS Our findings established the dynamic landscape of activated SFs and yielded potential therapeutic targets associated with genetic risk of RA.
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Affiliation(s)
- Haruka Tsuchiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shuji Sumitomo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuyoshi Ishigaki
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Toyonori Sakata
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Inui
- Department of Orthopaedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Hirose
- Department of Orthopaedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuho Kadono
- Department of Orthopaedic Surgery, Saitama Medical University, Saitama, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Sakae Tanaka
- Department of Orthopaedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Chino S, Mochizuki Y, Toyosaki E, Ota M, Mizuma K, Nohara T, Sawai A, Shinke T. Utility of transcranial color flow imaging for detecting high risk morphology of patent foramen ovale in patients with cerebral infarction. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.2443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Micro-bubble test by using transcranial color flow imaging (TCCFI) is important as a screening evaluation for diagnosis of paradoxical cerebral embolism which requires the proof of right to left shunt at atrial septum. In addition, high risk features of patent foramen ovale (PFO) that may allow thrombus to easily pass through the PFO itself were previously reported. However, little is known about the association between the degrees on micro-bubble test by TCCFI and the features of high risk PFO.
Purpose
Our aim is to clarify the relationship between the degree of micro-bubble test in TCCFI and the morphology of PFO from transesophageal echocardiography (TEE).
Methods
Seventy-seven patients in whom cardiogenic embolism was strongly suspected by neurologists in Showa University from April to December in 2019 were retrospectively studied. 55 patients underwent both TCCFI and TEE with sufficient Valsalva stress. TCCFI grade of micro-bubble test was classified into 3 groups (A: none, B: small, and C: massive), in which signified “none” is no sign of micro-embolic signals (MES) within 30 seconds, “small” is 1 or more MES, and “massive” is so much MES look like a curtain (Figure). Evaluated high risk characteristics of PFO for cerebral embolism as previously reported were as follows; (1) tunnel height, (2) tunnel length, (3) total excursion distance into right and left atrium, (4) existence of Eustachian valve or Chiari network, (6) angle of PFO from inferior vena cava (7) large shunt (20 or more micro-bubbles).
Results
Of all TCCFI-positive patients (n=32; Group B=19, Group C=13) with cerebral embolism, PFOs were detected in 23 patients in TEE. Therefore, the sensitivity and specificity of TCCFI to PFO were 87% and 63% (AUC=0.75, p<0.001, respectively). Interestingly, all 13 patients (Group C) had manifest PFOs. Moreover, group C include 2 patients with platypnea orthodeoxia syndrome in which hypoxia in the sitting position becomes apparent. Among PFO-positive patients, tunnel height, length, total excursion distance into right and left atrium, and large shunt in TEE were significantly larger in Group C than Group B (p<0.05).
Conclusions
Micro-bubble test by using TCCFI may have screening advantages in predicting paradoxical cerebral embolism, high-risk morphology of PFO, and platypnea orthodeoxia syndrome.
Figure 1
Funding Acknowledgement
Type of funding source: None
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Affiliation(s)
- S Chino
- Showa University Hospital, Tokyo, Japan
| | | | | | - M Ota
- Showa University Hospital, Tokyo, Japan
| | - K Mizuma
- Showa University Hospital, Tokyo, Japan
| | - T Nohara
- Showa University Hospital, Tokyo, Japan
| | - A Sawai
- Showa University Hospital, Tokyo, Japan
| | - T Shinke
- Showa University Hospital, Tokyo, Japan
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Kobayashi S, Nagafuchi Y, Okubo M, Sugimori Y, Shirai H, Hatano H, Junko M, Yanaoka H, Takeshima Y, Ota M, Iwasaki Y, Sumitomo S, Okamura T, Yamamoto K, Shoda H, Fujio K. Integrated bulk and single-cell RNA-sequencing identified disease-relevant monocytes and a gene network module underlying systemic sclerosis. J Autoimmun 2020; 116:102547. [PMID: 33039247 DOI: 10.1016/j.jaut.2020.102547] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 09/15/2020] [Accepted: 09/25/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Immunological disturbances have been reported in systemic sclerosis (SSc). This study assessed the transcriptome disturbances in immune cell subsets in SSc and characterized a disease-related gene network module and immune cell cluster at single cell resolution. METHODS Twenty-one Japanese SSc patients were enrolled and compared with 13 age- and sex-matched healthy controls (HC). Nineteen peripheral blood immune cell subsets were sorted by flow cytometry and bulk RNA-seq analysis was performed for each. Differential expression and pathway analyses were conducted. Iterative weighted gene correlation network analysis (iWGCNA) of each subset revealed clustered co-expressed gene network modules. Random forest analysis prioritized a disease-related gene module. Single cell RNA-seq analysis of 878 monocytes was integrated with bulk RNA-seq analysis and with a public database for single cell RNA-seq analysis of SSc patients. RESULTS Inflammatory pathway genes were differentially expressed in widespread immune cell subsets of SSc. An inflammatory gene module from CD16+ monocytes, which included KLF10, PLAUR, JUNB and JUND, showed the greatest discrimination between SSc and HC. One of the clusters of SSc monocytes identified by single-cell RNA-seq analysis characteristically expressed these inflammatory co-expressed genes and was similar to lung infiltrating FCN1hi monocytes expressing IL1B. CONCLUSIONS Our integrated analysis of bulk and single cell RNA-seq analysis identified an inflammatory gene module and a cluster of monocytes that are relevant to SSc pathophysiology. They could serve as candidate novel therapeutic targets in SSc.
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Affiliation(s)
- Satomi Kobayashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Mai Okubo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Yusuke Sugimori
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Harumi Shirai
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Maeda Junko
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Haruyuki Yanaoka
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan; Immuno-Rheumatology Center, St. Luke's International Hospital, St. Luke's International University, 9-1 Akashi-cho, Chuo-ku, Tokyo, 104-8560, Japan.
| | - Yusuke Takeshima
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Yukiko Iwasaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Shuji Sumitomo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan; Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan; Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
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Ota M, Kanauchi Y, Mizushima T. PGI8 Facility Size-Based Diagnostic Patterns of the Crohn's Disease-Associated Perianal Fistula Using an Employer-Based Health Insurance Claims Database in JAPAN. Value Health Reg Issues 2020. [DOI: 10.1016/j.vhri.2020.07.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ono M, Oh A, Ota M, Miyaguchi Y, Ueda H, Kinai E. PRO12 Investigation of Consistency of Haemophilia a Care in JAPAN: A Claims-Based Cohort Study. Value Health Reg Issues 2020. [DOI: 10.1016/j.vhri.2020.07.507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Iwasaki Y, Takeshima Y, Nakano M, Ota M, Nagafuchi Y, Suzuki A, Kochi Y, Okamura T, Endo T, Miki I, Sakurada K, Yamamoto K, Fujio K. THU0225 INTEGRATIVE PLASMA METABOLOME AND TRANSCRIPTOME ANALYSIS REVEALED THE IMPORTANCE OF HISTIDINE HOMEOSTASIS IN SLE PATHOGENESIS WITH POTENTIAL FOR IMPROVED SLE PATIENTS STRATIFICATION. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background:Recently, immunometabolism has gathered attention of many immunologists. It has been widely recognized that metabolic reprogramming in each immune cell brings different effects on different cells and is important for regulating their functions. Along with the progress of statistical genetics, serum metabolites were shown to be under genetic regulations1). Metabolic changes are now considered not only to be mere phenotypes of cells but also to be key factors for controlling immune cell differentiation, proliferation and function through regulating gene expressions eventually. Although genome-wide association studies have brought deep insights into SLE pathogenesis, the precise pathway from genome to metabolome has been largely unknown, and vice versa.Objectives:The aim of this study is to investigate metabolomic regulation in SLE in relation to gene expressions by integrating plasma metabolome data and transcriptome data.Methods:We collected plasma samples from patients with SLE (n=57) who met the 1997 American College of Rheumatology criteria for SLE. Gender- and age-matched healthy controls (HCs) (n=56) were recruited. Metabolic profiles focusing on 39 amino acids were analyzed with liquid chromatography (LC)-mass spectrometry. Transcriptome data of SLE patients were obtained from our RNA-sequencing data of each immune cell subset (total 19 subsets). Whole-genome sequencing was also performed.Results:Our previous experiment showed that about 160 peaks were detected from comprehensive LC-TOFMS and amino acids were useful for distinguishing SLE patients from HCs. Both partial least squares discriminant analysis (PLS-DA) and random forest, a machine learning algorithm, revealed the importance of histidine (His), one of the essential amino acids, to classify SLE patients from HCs, whose plasma level was lower in SLE patients. In addition, inverse correlation between His level and titer of ds-DNA as well as damage index (SDI) was detected. His level was correlated neither with PSL dosage nor with type I interferon (IFN) signature. Receiver operating characteristic (ROC) analysis showed the best predictability for SLE with the combination of specific amino acids including His. Our transcriptome analysis has revealed the significance of oxidative phosphorylation (OXPHOS) in B cells for SLE pathogenesis. Interestingly, OXPHOS signature was inversely correlated with His level in SLE B cells.Conclusion:His may be an important factor for SLE pathogenesis especially in B cells independently from IFN signal. SLC15A4, a transporter of His on lysosome, is one of the SLE GWAS SNPs and has been reported to play an important role in IFN production in B cells through regulation of TLR7/9 activation 2). We also identified that SLE patients with risk allele of SLC15A4 had tendency to show higher plasma His level, indicating His homeostasis could become a novel treatment target for SLE. Moreover, the inverse correlation of His level to SDI as well as OXPHOS signature suggests that His might play a key role for promoting organ damages in SLE.References:[1]Nat Genet.2017;49:568. 2)Immunity. 2014;41:375. 3)Semin Arthritis Rheum.2019;48:1142Disclosure of Interests: :Yukiko Iwasaki: None declared, Yusuke Takeshima: None declared, Masahiro Nakano: None declared, Mineto Ota: None declared, Yasuo Nagafuchi: None declared, Akari Suzuki: None declared, Yuta Kochi: None declared, Tomohisa Okamura: None declared, Takaho Endo: None declared, Ichiro Miki: None declared, Kazuhiro Sakurada: None declared, Kazuhiko Yamamoto Grant/research support from: Astellas, BMS, MitsubishiTanabe, Pfizer, Ayumi, Takeda, Chugai, Eisai, Taisho Toyama, UCB, and ImmunoFuture, Keishi Fujio Grant/research support from: Astellas, BMS, MitsubishiTanabe, Pfizer, Ayumi, Takeda, Chugai, Eisai, Taisho Toyama, Eli Lilly, Sanofi, and UCB
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Hori H, Matsuo J, Teraishi T, Sasayama D, Kawamoto Y, Kinoshita Y, Ota M, Hattori K, Kunugi H. Moderating effect of schizotypy on the relationship between smoking and neurocognition. Eur Psychiatry 2020. [DOI: 10.1016/j.eurpsy.2012.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
AbstractPurposeSmoking rates in schizotypic individuals are shown to be elevated, as in patients with schizophrenia, although findings on the association of smoking with different symptomatology of schizotypy have been mixed. Moreover, possible moderating effects of schizotypy on the relationship between smoking and cognition have not been well documented.Subjects and methodsThe Schizotypal Personality Questionnaire (SPQ) and the full version of the Wechsler Memory Scale-Revised (WMS-R) were administered to 501 healthy adults. Subjects were divided into smokers (n = 85) and non-smokers (n = 416) based on the presence/absence of current smoking.ResultsThe analysis of covariance (ANCOVA) on the three factor scores as well as the total score of the SPQ, controlling for age and gender, revealed that cognitive-perceptual factor was significantly associated with an increased rate of smoking (P = 0.048). The ANCOVA on the WMS-R indices, with smoking group as a fixed factor and age, gender and total SPQ score as covariates, revealed that the schizotypy-by-smoking interaction was significant for attention/working memory (P = 0.029).Discussion and conclusionPositive schizotypy may be associated with more smoking. Schizotypy and smoking could interact with each other to negatively affect attention/working memory.
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Chilembo M, Oguri S, Matsuoka Y, Ota M, Musiankuni P, Kabungo J. Pre-treatment lost to follow-up tuberculosis patients, Chongwe, Zambia, 2017: a retrospective cohort study. Public Health Action 2020; 10:21-26. [PMID: 32368520 DOI: 10.5588/pha.19.0059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/19/2019] [Indexed: 11/10/2022] Open
Abstract
Setting Four tuberculosis (TB) diagnostic health facilities of the Chongwe District, Zambia. Objective To determine the frequency of bacteriologically confirmed TB patients lost to follow-up (LTFU) before treatment from January to December 2017. Design This is a retrospective cohort study involving the review of TB registers. Information on presumptive TB patients who tested positive either by smear microscopy or Xpert® MTB/RIF assay was extracted from the laboratory TB registers of the TB diagnostic facilities and cross-matched with the TB treatment registers of TB treatment facilities. Results Two hundred and seventeen bacteriologically confirmed TB patients were found in the laboratory TB registers. Of these, 145 (67%) were males and seven (3%) were children; 177 (81%) patients were diagnosed using Xpert, while the remaining 40 (19%) were diagnosed using sputum smear microscopy. A total of 71 (33%) were not linked to treatment. Those diagnosed using smear microscopy were 2.5 times (95% CI 1.1-5.3) more likely to be LTFU before treatment than those diagnosed using Xpert. Conclusion About one third of TB patients who were not linked to treatment could potentially extend the duration of bacilli transmission in their communities. National TB control programmes should consider including LTFU patients before treatment in routine monitoring and evaluation.
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Affiliation(s)
- M Chilembo
- Japan Anti-Tuberculosis Association, Lusaka, Zambia
| | - S Oguri
- Japan Anti-Tuberculosis Association, Lusaka, Zambia
| | - Y Matsuoka
- Japan Anti-Tuberculosis Association, Lusaka, Zambia
| | - M Ota
- Research Institute of Tuberculosis, Tokyo, Japan
| | - P Musiankuni
- Chongwe District Health Office, Ministry of Health, Chongwe, Zambia
| | - J Kabungo
- Chongwe District Health Office, Ministry of Health, Chongwe, Zambia
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50
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Tsukamoto S, Fujita S, Ota M, Mizusawa J, Shida D, Kanemitsu Y, Ito M, Shiomi A, Komori K, Ohue M, Akazai Y, Shiozawa M, Yamaguchi T, Bando H, Tsuchida A, Okamura S, Akagi Y, Takiguchi N, Saida Y, Akasu T, Moriya Y. Long-term follow-up of the randomized trial of mesorectal excision with or without lateral lymph node dissection in rectal cancer (JCOG0212). Br J Surg 2020; 107:586-594. [PMID: 32162301 DOI: 10.1002/bjs.11513] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/29/2019] [Accepted: 12/18/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Japan Clinical Oncology Group (JCOG) 0212 (ClinicalTrials.gov NCT00190541) was a non-inferiority phase III trial of patients with clinical stage II-III rectal cancer without lateral pelvic lymph node enlargement. The trial compared mesorectal excision (ME) with ME and lateral lymph node dissection (LLND), with a primary endpoint of recurrence-free survival (RFS). The planned primary analysis at 5 years failed to confirm the non-inferiority of ME alone compared with ME and LLND. The present study aimed to compare ME alone and ME with LLND using long-term follow-up data from JCOG0212. METHODS Patients with clinical stage II-III rectal cancer below the peritoneal reflection and no lateral pelvic lymph node enlargement were included in this study. After surgeons confirmed R0 resection by ME, patients were randomized to receive ME alone or ME with LLND. The primary endpoint was RFS. RESULTS A total of 701 patients from 33 institutions were assigned to ME with LLND (351) or ME alone (350) between June 2003 and August 2010. The 7-year RFS rate was 71.1 per cent for ME with LLND and 70·7 per cent for ME alone (hazard ratio (HR) 1·09, 95 per cent c.i. 0·84 to 1·42; non-inferiority P = 0·064). Subgroup analysis showed improved RFS among patients with clinical stage III disease who underwent ME with LLND compared with ME alone (HR 1·49, 1·02 to 2·17). CONCLUSION Long-term follow-up data did not support the non-inferiority of ME alone compared with ME and LLND. ME with LLND is recommended for patients with clinical stage III disease, whereas LLND could be omitted in those with clinical stage II tumours.
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Affiliation(s)
- S Tsukamoto
- Department of Colorectal Surgery, Tokyo Medical University Hospital, Tokyo, Japan
| | - S Fujita
- Department of Surgery, Tochigi Cancer Centre, Tochigi, Japan
| | - M Ota
- Department of Surgery, Yokohama City University Medical Centre, Kanagawa, Japan
| | - J Mizusawa
- Japan Clinical Oncology Group Data Centre and Operations Office, National Cancer Centre Hospital, Tokyo Medical University Hospital, Tokyo, Japan
| | - D Shida
- Department of Colorectal Surgery, Tokyo Medical University Hospital, Tokyo, Japan
| | - Y Kanemitsu
- Department of Colorectal Surgery, Tokyo Medical University Hospital, Tokyo, Japan
| | - M Ito
- Colorectal Surgery Division, National Cancer Centre Hospital East, Chiba, Japan
| | - A Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Centre Hospital, Shizuoka, Japan
| | - K Komori
- Department of Surgery, Aichi Cancer Centre Hospital, Aichi, Japan
| | - M Ohue
- Department of Gastroenterological Surgery, Suita Municipal Hospital, Osaka International Cancer Institute, Japan
| | - Y Akazai
- Department of Surgery, Okayama Saiseikai General Hospital, Okayama, Japan
| | - M Shiozawa
- Department of Surgery, Kanagawa Cancer Centre, Kanagawa, Japan
| | - T Yamaguchi
- Department of Surgery, Kyoto Medical Centre, Kyoto, Japan
| | - H Bando
- Department of Surgery, Ishikawa Prefectural Central Hospital, Ishikawa, Japan
| | - A Tsuchida
- Department of Surgery, Tokyo Medical University Hospital, Tokyo, Japan
| | - S Okamura
- Department of Surgery, Suita Municipal Hospital, Osaka, Japan
| | - Y Akagi
- Department of Surgery, Kurume University, Fukuoka, Japan
| | - N Takiguchi
- Department of Gastrointestinal Surgery, Chiba Cancer Centre, Chiba, Japan
| | - Y Saida
- Department of Surgery, Toho University Ohashi Medical Centre, Tokyo, Japan
| | - T Akasu
- Hospital of the Imperial Household, Tokyo, Japan
| | - Y Moriya
- Department of Surgery, Miki Hospital, Iwate, Japan
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