{"id":"hum0214","secondaryIds":[],"version":3,"url":"https://humandbs.dbcls.jp/research/hum0214/v3","datePublished":"2021-04-28","versions":[{"version":1,"datePublished":"2020-10-09"},{"version":2,"datePublished":"2021-03-05"},{"version":3,"datePublished":"2021-04-28"},{"version":4,"datePublished":"2022-01-21"},{"version":5,"datePublished":"2022-03-09"},{"version":6,"datePublished":"2022-08-25"},{"version":7,"datePublished":"2023-03-28"},{"version":8,"datePublished":"2023-07-06"},{"version":9,"datePublished":"2024-02-08"},{"version":10,"datePublished":"2026-06-09"}],"title":{"ja":"ヒト免疫系の機能ゲノム学による統合的理解とこれを用いた免疫疾患の発症予防のためのインターベンション戦略の構築","en":"Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases"},"summary":{"aims":{"ja":"免疫細胞における遺伝子発現制御と免疫疾患に対する寄与を解明する","en":"To elucidate the regulation of gene expression in each immune cell subset and its contribution to autoimmune diseases."},"methods":{"ja":"JGAS000220：全身性強皮症21症例、antineutrophil cytoplasmic antibody（ANCA）関連血管炎26症例、対照健常者28名の末梢血免疫細胞画分を分取し各画分から抽出したtotal RNAを用いたRNA-seqを実施した。\nE-GEAD-397 / E-GEAD-398 / E-GEAD-420：全身性エリテマトーデス、筋炎、全身性強皮症、混合性結合組織病、シェーグレン症候群、関節リウマチ、ベーチェット病、成人スチル病、ANCA関連血管炎、高安動脈炎、対照健常者の全血及び末梢血免疫細胞28画分を分取し、全血より全ゲノムシーケンス、各画分サンプルを用いてRNA-seqを実施した。サンプルのフィルタリングと遺伝子発現量の標準化の上で、各免疫細胞画分でeQTL解析を実施した。","en":"JGAS000220: Various immune cell subsets from 21 systemic sclerosis patients, 26 ANCA associated vasculitis, and 28 healthy controls were collected (Naive_B, SM_B, USM_B, DN_B, Plasmablast, Th1, Th2, Th17, Tfh, Naive_CD4, Mem_CD4, Fr._II_eTreg, Naive_CD8, Mem_CD8, mDC, pDC, CD16p_Mono, CD16n_Mono, NK, Neu) and total RNAs were extracted from each subset. RNA-seq was performed for each sample.\nE-GEAD-397 / E-GEAD-398 / E-GEAD-420: Whole blood and 28 immune cell subsets from study population were collected (Naive_CD4, Mem_CD4, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, EM_CD8, CM_CD8, TEMRA_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, LDG, Neu). Whole genome sequencing was performed with whole blood samples. RNA-seq was performed with each immune cell subset samples. After filtering and normalization of the gene expression data, eQTL analysis was performed in each immune cell type."},"targets":{"ja":"全身性強皮症、全身性エリテマトーデス、筋炎、混合性結合組織病、シェーグレン症候群、関節リウマチ、ベーチェット病、成人スチル病、ANCA関連血管炎、高安動脈炎、対照健常者","en":"Systemic Sclerosis, Systemic Lupus Erythematosus, Myositis, Mixed Connective Tissue Disease, Sjögren's Syndrome, Rheumatoid Arthritis, Behçet's Disease, Adult Onset Still's Disease, ANCA-associated Vasculitis, Takayasu's Arteritis, healthy individuals"},"url":{"ja":[{"url":"https://ryumachi.umin.jp/","text":"https://ryumachi.umin.jp/"}],"en":[{"url":"https://www.h.u-tokyo.ac.jp/english/centers-services/clinical-divisions/allergy-and-rheumatology/index.html","text":"https://www.h.u-tokyo.ac.jp/english/centers-services/clinical-divisions/allergy-and-rheumatology/index.html"}]}},"listingSummary":{},"releaseNote":{"ja":"全身性エリテマトーデス、筋炎、全身性強皮症、混合性結合組織病、シェーグレン症候群、関節リウマチ、ベーチェット病、成人スチル病、ANCA関連血管炎、高安動脈炎、対照健常者の全血及び末梢血免疫細胞28画分を分取し、全血より全ゲノムシーケンス、各画分サンプルを用いてRNA-seqを実施した。サンプルのフィルタリングと遺伝子発現量の標準化の上で、各免疫細胞画分でeQTL解析を実施した（合計416名）。臨床情報および各遺伝子にマップされたリード数、eQTLサマリーデータを提供する（txt）。","en":"Whole blood and 28 immune cell subsets from Systemic Lupus Erythematosus, Myositis, Systemic Sclerosis, Mixed Connective Tissue Disease, Sjögren's Syndrome, Rheumatoid Arthritis, Behçet's Disease, Adult Onset Still's Disease, ANCA-associated Vasculitis, Takayasu's Arteritis patients and healthy controls were collected. Whole genome sequencing was performed with whole blood samples. RNA-seq was performed with each immune cell subset samples. After filtering and normalization of the gene expression data, eQTL analysis was performed in each immune cell type (416 individuals in total). Clinical data, read count data and eQTL summary data are provided as txt files."},"dataProviders":[{"name":{"ja":"藤尾 圭志","en":"Keishi Fujio"},"organization":{"name":{"ja":"東京大学大学院 医学系研究科 アレルギー・リウマチ学","en":"Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo"}}}],"researchProjects":[{"name":{"ja":"免疫疾患の免疫細胞マルチオミクス解析","en":"Immune cell multi-omics analysis of immune-mediated diseases"},"url":{"ja":[{"url":"https://ryumachi.umin.jp/","text":"https://ryumachi.umin.jp/"}],"en":[{"url":"https://www.h.u-tokyo.ac.jp/english/centers-services/clinical-divisions/allergy-and-rheumatology/index.html","text":"https://www.h.u-tokyo.ac.jp/english/centers-services/clinical-divisions/allergy-and-rheumatology/index.html"}]}}],"grants":[{"title":{"ja":null,"en":null},"agency":{"ja":"中外製薬株式会社との共同研究費","en":"Collaborative research fund with Chugai Pharmaceutical Co., Ltd."},"grantIds":null}],"relatedPublications":[{"title":"Integrated bulk and single-cell RNA-sequencing identified disease-relevant monocytes and a gene network module underlying systemic sclerosis","doi":"https://doi.org/10.1016/j.jaut.2020.102547","datasets":["JGAD000309","E-GEAD-344"]},{"title":"Identifying the most influential gene expression profile in distinguishing ANCA-associated vasculitis from healthy controls","doi":"https://doi.org/10.1016/j.jaut.2021.102617","datasets":["JGAD000310"]},{"title":"Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases","doi":"https://doi.org/10.1016/j.cell.2021.03.056","datasets":["E-GEAD-397","E-GEAD-398","E-GEAD-420"]}],"datasets":["JGAD000309","JGAD000310","E-GEAD-397","E-GEAD-398","E-GEAD-420"],"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":["JGAD000309","JGAD000310","JGAD000371","JGAD000372","JGAD000373","JGAD000406","JGAD000602","JGAD000603","JGAD000727","JGAD000755","JGAD000756","JGAD000778"]},{"principalInvestigator":{"en":"Ana Rita Grosso"},"affiliation":{"en":"Computational Multi-Omics Lab, Department of Life Sciences, Universidade Nova de Lisboa - NOVA School of Science and Technology"},"country":{"ja":"ポルトガル","en":"Portugal"},"researchTitle":{"en":"Assessing transcriptional dyregulation of repetitive elements and monoallelic-expressed genes in lupus"},"periodStart":"2023-04-25","periodEnd":"2026-04-10","datasets":["JGAD000603"]},{"principalInvestigator":{"en":"jiucun wang"},"affiliation":{"en":"jiu-cunwang lab , jiu-cun wang , department of anthropology and human genetics, department of anthropology and human genetics of fudan university"},"country":{"ja":"中国","en":"China"},"researchTitle":{"en":"The role and mechanism study of glycosyltransferase-B3GNT2 in regulating macrophages of Ankylosing Spondylitis"},"periodStart":"2023-03-08","periodEnd":"2024-03-01","datasets":["JGAD000309","JGAD000603"]},{"principalInvestigator":{"en":"Jacob Jaffe"},"affiliation":{"en":"Data Science, Odyssey Therapeutics"},"country":{"ja":"アメリカ合衆国 (マサチューセッツ州)","en":"Massachusetts, United States"},"researchTitle":{"en":"Investigation of immune cell transition states in autoimmune disease"},"periodStart":"2023-04-06","periodEnd":"2023-11-02","datasets":["JGAD000309","JGAD000371","JGAD000372","JGAD000603"]},{"principalInvestigator":{"ja":"武田 吉人","en":"yoshito takeda"},"affiliation":{"ja":"大学院医学系研究科　呼吸器免疫内科学, 大阪大学","en":"Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"呼吸器系・免疫疾患における細胞外小胞に着目した病態解明および診断法の開発","en":"Pathophysiology and diagnostic development with a focus on extracellular vesicles in respiratory and immunological diseases"},"periodStart":"2023-04-12","periodEnd":"2025-01-17","datasets":["JGAD000310","JGAD000371","JGAD000372","JGAD000373"]},{"principalInvestigator":{"en":"Yong-Fei WANG"},"affiliation":{"en":"Warshel Institue for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen"},"country":{"ja":"中国","en":"China"},"researchTitle":{"en":"Investigating the Molecular Mechanisms of Systemic Lupus Erythematosus Using Functional Genomics Data"},"periodStart":"2023-06-21","periodEnd":"2025-05-28","datasets":["JGAD000371","JGAD000372","JGAD000373","JGAD000603"]},{"principalInvestigator":{"ja":"久保田 晋平","en":"Shimpei Kubota"},"affiliation":{"ja":"遺伝子病制御研究所, 北海道大学","en":"Molecular Psychoneuroimmunology, Hokkaido University"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"関節リウマチおよび全身性エリテマトーデスにおける遺伝子発現および炎症増幅回路活性化因子の解析","en":"Gene expression and IL-6 amplifying circuit activators in rheumatoid arthritis and systemic lupus erythematosus"},"periodStart":"2024-02-26","periodEnd":"2026-03-31","datasets":["JGAD000309","JGAD000310","JGAD000371","JGAD000372","JGAD000373","JGAD000406","JGAD000602","JGAD000603","JGAD000727"]},{"principalInvestigator":{"ja":"ヴィセ ティモシー","en":"Timothy Vyse"},"affiliation":{"ja":"キングス・カレッジ・ロンドン, 分子遺伝学と医学遺伝学","en":"molecular and medical genetics, King's College London"},"country":{"ja":"イギリス","en":"United Kingdom"},"researchTitle":{"ja":"全身性狼瘡のシーケンスに基づく遺伝子解析","en":"Sequencing Based Genetic Analysis of Systemic Lupus"},"periodStart":"2023-08-25","periodEnd":"2025-10-16","datasets":["JGAD000603"]},{"principalInvestigator":{"ja":"鈴木 宏尚","en":"Hironao Suzuki"},"affiliation":{"ja":"新薬創生センター　薬理部, 科研製薬株式会社","en":"Pharmacology Department, Drug Research Center, Kaken Pharmaceutical,co.,LTD."},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"SLE患者検体の遺伝子発現データを用いたバイオインフォマティクス解析 ","en":"Bioinformatics analysis of immune cells from SLE patients"},"periodStart":"2024-05-09","periodEnd":"2025-04-17","datasets":["JGAD000603"]},{"principalInvestigator":{"en":"Hui Li"},"affiliation":{"en":"Department of Pathology, University of Virginia"},"country":{"ja":"アメリカ合衆国","en":"United States"},"researchTitle":{"en":"Gene fusions and RNA Trans-splicing in normal and neoplastic human cells"},"periodStart":"2025-06-25","periodEnd":"2026-12-31","datasets":["JGAD000309","JGAD000310","JGAD000371","JGAD000372","JGAD000406","JGAD000603","JGAD000727","JGAD000755","JGAD000756"]},{"principalInvestigator":{"ja":"藩 龍馬","en":"Tatsuma Ban"},"affiliation":{"ja":"大学院医学研究科・免疫学教室, 横浜市立大学","en":"Department of Immunology, Graduate School of Medicine, Yokohama City University"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"免疫系転写因子群に着目した自己免疫疾患の病態解明と治療法開発","en":"Pathophysiology and therapeutic development of autoimmune diseases focusing on transcription factors of the immune system"},"periodStart":"2024-11-12","periodEnd":"2027-03-31","datasets":["JGAD000371","JGAD000372","JGAD000373","JGAD000603","JGAD000756"]},{"principalInvestigator":{"en":"Pranidhi Sood"},"affiliation":{"en":"Wield Therapeutics, Inc"},"country":{"ja":"アメリカ合衆国 (カリフォルニア州)","en":"California, United States"},"researchTitle":{"en":"Identifying Gene Expression Based Biomarkers in Patients with Autoimmune Diseases to Predict\r\nResponse to New Therapies Developed by Wield Therapeutics"},"periodStart":"2025-06-25","periodEnd":"2027-04-23","datasets":["JGAD000309","JGAD000310","JGAD000371","JGAD000372","JGAD000373","JGAD000406","JGAD000602","JGAD000603","JGAD000727","JGAD000755","JGAD000756","JGAD000778"]},{"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":["JGAD000602","JGAD000603"]},{"principalInvestigator":{"ja":"板倉 英祐","en":"Eisuke Itakura"},"affiliation":{"ja":"大学院・理学研究院, 千葉大学","en":"Graduate School of Science, Chiba University"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"ImmuNexUTによるSLE症状と遺伝子発現多様性解析","en":"Linking SLE Symptoms to Gene Expression Variation through ImmuNexUT"},"periodStart":"2025-10-27","periodEnd":"2026-04-02","datasets":["JGAD000603"]}]}