{"id":"hum0468","version":1,"url":"https://humandbs.dbcls.jp/research/hum0468/v1","datePublished":"2025-08-01","versions":[{"version":1,"datePublished":"2025-08-01"}],"title":{"ja":"免疫・炎症病態の解析","en":"Analysis of immune and inflammatory pathology"},"summary":{"aims":{"ja":"自己免疫疾患や炎症性疾患の罹患組織における炎症病態は臓器構成細胞と免疫細胞の相互作用により生じる。一方で、罹患臓器局所に存在する細胞の詳細な性質は十分には理解されていない。近年の解析技術の進歩により、ヒト検体に含まれる細胞の詳細な解析が可能になってきた。これらの解析により、例えば免疫細胞において末梢血液に存在するものと組織に存在するもので遺伝子の発現が異なり、罹患組織の細胞を解析する重要性が明らかになっている。本研究では自己免疫疾患や炎症性疾患の罹患組織における構成細胞や免疫細胞を詳細に解析することで、ヒトでの自己免疫・炎症病態を解明することを目的とする。さらに、DNA解析の同意を得られている対象者の遺伝子背景と組織や末梢血における遺伝子発現の関連を解析することで、GWASなどで疾患に関連が指摘されているものの機能が不明であった遺伝子変異の病態における役割を解明する。","en":"The detailed characteristics of the cells present in the local tissues of affected organs are not well understood. Recent advances in analytical techniques have made it possible to analyze cells in human specimens in detail. These analyses have shown, for example, that the gene expression of immune cells in peripheral blood differs from that in tissues, and the importance of analyzing cells in diseased tissues has become clear. This study aims to elucidate the pathophysiology of autoimmune and inflammatory diseases in humans by analyzing the constituent cells and immune cells in affected tissues of autoimmune and inflammatory diseases in detail."},"methods":{"ja":"single cell RNA-seq、bulk RNA-seq、scASAP-seq CITE-seq、VDJ-seq、空間トランスクリプトーム（Xenium）","en":"single-cell RNA-seq, bulk RNA-seq, scASAP-seq, CITE-seq, VDJ-seq, Spacial RNA expression analysis (Xenium)"},"targets":{"ja":"【scRNA-seq】 関節リウマチ11＋10症例由来の血液検体（10＋9検体）、関節液検体（4＋4検体）、滑膜検体（11＋10検体）、および、対照健常者3名由来の血液検体（3検体）、関節リウマチ1症例の関節液T細胞と対照健常者1名の血液単球を共培養した検体（1検体）\n【bulk RNA-seq】 関節リウマチ1症例由来の関節液検体（1検体）、対照健常者1名由来の血液検体（1検体）\n【scASAP-seq】 関節リウマチ1症例由来の滑膜検体（1検体）\n【CITE-seq】 関節リウマチ10症例由来の血液検体（9検体）、関節液検体（4検体）、滑膜検体（10検体）、関節リウマチ1症例の関節液T細胞と対照健常者1名の血液単球を共培養した検体（1検体）\n【VDJ-seq】 関節リウマチ10症例由来の血液検体（9検体）、関節液検体（4検体）、滑膜検体（10検体）\n【Xenium】 関節リウマチ3症例由来の滑膜検体（3検体）","en":"[scRNA-seq] Blood (10 + 9), joint fluid (4 + 4), and synovial membrane (11 + 10) samples from 11 + 10 rheumatoid arthritis patients, Blood samples from 3 healthy controls, Co-culture of joint fluid (1) from another rheumatoid arthritis patient and blood sample from control subject (1)\n[bulk RNA-seq] Joint fluid (1) samples from 1 rheumatoid arthritis patient, Blood samples from 1 healthy controls\n[scASAP-seq] Synovial membrane (1) samples from 1 rheumatoid arthritis patient\n[CITE-seq] Blood (9), joint fluid (4), and synovial membrane (10) samples from 10 rheumatoid arthritis patients, Co-culture of joint fluid (1) from another rheumatoid arthritis patient and blood sample from control subject (1)\n[VDJ-seq] Blood (9), joint fluid (4), and synovial membrane (10) samples from 10 rheumatoid arthritis patients\n[Xenium] Synovial membrane (3) samples from 3 rheumatoid arthritis patients"},"url":{"ja":null,"en":null}},"listingSummary":{"methods":{"ja":"発現\nクロマチン構造","en":"Expression profiling; Chromatin structure"},"targets":{"ja":"関節リウマチ：23症例\n対照健常者：4名\n（日本人）","en":"23 rheumatoid arthritis\n4 healty controls\n(Japanese)"},"typeOfData":{"ja":"NGS\n（scRNA-seq、bulk RNA-seq、scASAP-seq、CITE-seq、VDJ-seq）\nXenium In Situ Gene Expression","en":"NGS (scRNA-seq, bulk RNA-seq, scASAP-seq, CITE-seq, VDJ-seq); Xenium In Situ Gene Expression"}},"releaseNote":{"ja":"・関節リウマチ12症例の組織、ならびに、対照健常者3名の血液から分離したCD4陽性T細胞、もしくは滑膜検体について全細胞を網羅するようソートした検体より抽出したRNAを用いたscRNA-seqならびにbulk RNA-seq解析データをfastqおよびh5ファイル形式にて提供する。\n・関節リウマチ11症例の組織から分離したCD4陽性T細胞を対象としたscRNA-seq、Bulk RNA-seq、scASAP-seq、CITE-seq, VDJ-seq解析データをfastq、h5、tsv、csvファイル形式にて提供する。\n・関節リウマチ3症例の滑膜検体に対して実施したXenium高性能in situ遺伝子発現マッピングデータをcsv、h5、html、json、mtx、tiff、parquet、tsv、xenium、zarrファイルにて提供する。","en":"-RNAs extracted from the blood, joint fluid and synovial membrane samples from 12 rheumatoid arthritis patients and blood samples from 3 control individuals were used for single-cell RNA sequencing and bulk RNA sequencing analyses. Fastq andh5 files are provided.\n-RNAs extracted from the blood, joint fluid and synovial membrane samples from 11 rheumatoid arthritis patients and blood samples from control individual were used for single-cell RNA-seq, bulk RNA-seq, single-cell ASAP-seq, CITE-seq and VDJ-seq analyses. Fastq, h5, tsv and csv files are provided.\n-Synovial membrane samples of 3 rheumatoid arthritis patients were used for Xenium In Situ Gene Expression Assay. Csv, h5, html, json, mtx, tiff, parquet, tsv, xenium, and zarr files are provided."},"dataProviders":[{"name":{"ja":"吉富 啓之","en":"Hiroyuki Yoshitomi"},"organization":{"name":{"ja":"京都大学大学院医学研究科 免疫細胞生物学","en":"Department of Immunology, Graduate School of Medicine, Kyoto University"}}}],"researchProjects":[],"grants":[],"relatedPublications":[{"title":"Human CD4+ T cells regulate peripheral immune responses in rheumatoid arthritis via insulin-like growth factor like family member 2","doi":"https://doi.org/10.1126/sciimmunol.adr3838","datasets":["JGAD000860"]},{"title":"Stem-like and effector peripheral helper T cells comprise distinct subsets in rheumatoid arthritis","doi":"https://doi.org/10.1126/sciimmunol.adt3955","datasets":["JGAD000916"]}],"datasets":["JGAD000860","JGAD000916"],"controlledAccessUsers":[{"principalInvestigator":{"ja":"浜田 道昭","en":"Michiaki Hamada"},"affiliation":{"ja":"浜田研究室, 理工学術院, 早稲田大学","en":"Hamada Laboratory, Faculty of Science and Engineering, Waseda University"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"RNA標的創薬データベースの構築","en":"Construction of RNA-targeted Drug Discovery Database"},"periodStart":"2023-01-05","periodEnd":"2027-10-31","datasets":["JGAD000860","JGAD000916"]},{"principalInvestigator":{"ja":"松本 功","en":"Isao Matsumoto"},"affiliation":{"ja":"膠原病リウマチアレルギー内科学, 筑波大学医学医療系","en":"Department of Rheumatology, Institute of Medicine, University of Tsukuba"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"関節リウマチおよび関節炎モデルマウスにおけるCD4+T細胞の老化にともなう機能変化解析","en":"Investigation of aging-related functional alterations in CD4⁺ T cells in rheumatoid arthritis and experimental arthritis models"},"periodStart":"2025-12-05","periodEnd":"2029-03-31","datasets":["JGAD000860","JGAD000916"]},{"principalInvestigator":{"en":"Chiara Romagnani"},"affiliation":{"en":"Romagnani Lab, Institute of Medical Immunology, Charite - Universitaetsmedizin Berlin, Charite, Universitaetsmedizin Berlin"},"country":{"ja":"ドイツ","en":"Germany"},"researchTitle":{"en":"Retrospective analysis of transcriptional signatures of innate lymphocytes in childhood and adult rheumatic diseases"},"periodStart":"2026-07-29","periodEnd":"2027-12-31","datasets":["JGAD000860","JGAD000916"]},{"principalInvestigator":{"ja":"石垣 宏仁","en":"Hirohito Ishigaki"},"affiliation":{"ja":"病理学講座, 滋賀医科大学","en":"Dept. of Pathology, Shiga University of Medical Science"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"関節リウマチにおけるCD4/CD8 double positive T cellsの果たす役割の解析","en":"Analysis of the role and function of CD4/CD8 double positive T cells in Rheumatoid arthritis"},"periodStart":"2026-06-09","periodEnd":"2028-03-31","datasets":["JGAD000860","JGAD000916"]}]}