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Establishment of individualized anti-cytokine therapy based on functional analysis of risk polymorphisms for autoimmune diseases

Research Project

Project/Area Number 23K24373
Project/Area Number (Other) 22H03114 (2022-2023)
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeMulti-year Fund (2024)
Single-year Grants (2022-2023)
Section一般
Review Section Basic Section 54020:Connective tissue disease and allergy-related
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Ishigaki Kazuyoshi  国立研究開発法人理化学研究所, 生命医科学研究センター, チームリーダー (00790338)

Project Period (FY) 2024-04-01 – 2025-03-31
Project Status Completed (Fiscal Year 2024)
Budget Amount *help
¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000)
Fiscal Year 2024: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2023: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2022: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Keywordsヒト免疫 / 自己免疫疾患 / リスク多型 / ゲノム編集 / 抗サイトカイン療法 / サイトカイン / ゲノム医療
Outline of Research at the Start

抗サイトカイン療法によって自己免疫疾患の臨床転帰は平均的には改善したが、治療反応性に大きな個人差がある。近年、ゲノムワイド関連解析によって自己免疫疾患の発症に関連する多型(リスク多型)が多数同定されたが、各リスク多型とサイトカインとの具体的な対応関係は確認できていない。本研究の目的は、①ゲノム編集技術を駆使してリスク多型機能を高効率に評価する新しい実験系を確立し、②各リスク多型とサイトカインとの対応を明らかにすることである。本研究によって、個々の患者の遺伝子型情報を基にした個別化抗サイトカイン療法という新しい枠組みの治療方法が確立し、個々の患者レベルでの臨床転帰が改善することが期待される。

Outline of Final Research Achievements

We have established a technology that enables the manipulation of autoimmune disease risk polymorphisms in vitro using genome editing technology targeting human immune cells. Additionally, we have developed a new experimental system, “UNIChro-seq,” which allows for the evaluation of polymorphisms with high sensitivity, accuracy, and efficiency. This enables the assessment of the effects on chromatin structure of a total of 55 autoimmune disease-related risk polymorphisms using human immune cells at multiple stimulation time points.This technological advancement has established a technical foundation for comprehensively analyzing the functions of risk polymorphisms under diverse cytokine stimulation conditions. Furthermore, the existence of biases in polymorphism function evaluation associated with genome editing was first revealed, and methods for elucidating these biases were proposed.

Academic Significance and Societal Importance of the Research Achievements

自己免疫疾患は原因不明の難病であるが、抗サイトカイン療法の登場により臨床転帰は改善した。しかし、治療反応性に大きな個人差があるため、個々の患者レベルでは十分な治療効果が得られていない。より多くの患者が抗サイトカイン療法による恩恵を受けるためには、個々の患者毎に最適化された治療戦略(個別化抗サイトカイン療法)を確立することが求められている。本課題で開発する技術の応用によって、各リスク多型とサイトカインとの対応関係を実験的に紐づけることが可能となり、個々の患者のリスク多型の遺伝子型情報を基にした個別化抗サイトカイン療法を考案できると期待される。

Report

(4 results)
  • 2024 Annual Research Report   Final Research Report ( PDF )
  • 2023 Annual Research Report
  • 2022 Annual Research Report
  • Research Products

    (33 results)

All 2025 2024 2023 2022

All Journal Article (21 results) (of which Int'l Joint Research: 15 results,  Peer Reviewed: 21 results,  Open Access: 12 results) Presentation (11 results) (of which Int'l Joint Research: 6 results,  Invited: 4 results) Patent(Industrial Property Rights) (1 results)

  • [Journal Article] Asian diversity in human immune cells2025

    • Author(s)
      Kock Kian Hong、Tan Le Min、Han Kyung Yeon、Ando Yoshinari、...、Ishigaki Kazuyoshi、Okada Yukinori、Yamamoto Kazuhiko、Carninci Piero、Chambers John C.、Hon Chung-Chau、Matangkasombut Ponpan、Charoensawan Varodom、Majumder Partha P.、Shin Jay W.、Park Woong-Yang、Prabhakar Shyam
    • Journal Title

      Cell

      Volume: 188 Issue: 8 Pages: 2288-2306.e24

    • DOI

      10.1016/j.cell.2025.02.017

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Peripheral blood immunophenotypic diversity in patients with rheumatoid arthritis and its impact on therapeutic responsiveness2025

    • Author(s)
      Kubo Satoshi、Miyazaki Yusuke、Nishino Takahiro、Fujita Yuya、Kono Michihiro、Kawashima Tsugumi、Ishigaki Kazuyoshi、Kusaka Katsuhide、Tanaka Hiroaki、Ueno Masanobu、Satoh-Kanda Yurie、Inoue Yoshino、Todoroki Yasuyuki、Miyagawa Ippei、Hanami Kentaro、Nakayamada Shingo、Tanaka Yoshiya
    • Journal Title

      Annals of the Rheumatic Diseases

      Volume: 84 Issue: 2 Pages: 210-220

    • DOI

      10.1136/ard-2024-226228

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Single-cell RNA sequencing of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases2024

    • Author(s)
      Tian Chi、Zhang Yuntian、Tong Yihan、Kock Kian Hong、Sim Donald Yuhui、Liu Fei、Dong Jiaqi、Jing Zhixuan、Wang Wenjing、Gao Junbin、....、Ishigaki Kazuyoshi、Okamura Tomohisa、Fujio Keishi、Okada Yukinori、Park Woong-Yang、Shin Jay W.、Roca Xavier、Prabhakar Shyam、Liu Boxiang
    • Journal Title

      Nature Genetics

      Volume: 56 Issue: 12 Pages: 2739-2752

    • DOI

      10.1038/s41588-024-02019-8

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Naturally arising memory-phenotype CD4+ T lymphocytes contain an undifferentiated population that can generate TH1, TH17, and Treg cells2024

    • Author(s)
      Kawajiri A, Li J, Koinuma K, Yang Z, Yoon HJ, Yi J, Nagashima H, Ishii M, Gao F, Sato K, Tayama S, Harigae H, Iwakura Y, Ishii N, Sher A, Ishigaki K, Zhu J, Kim KS, Kawabe T.
    • Journal Title

      Sci Adv

      Volume: 10 Issue: 49

    • DOI

      10.1126/sciadv.adq6618

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases2024

    • Author(s)
      Oguchi Akiko、Suzuki Akari、Komatsu Shuichiro、...、Ishigaki Kazuyoshi、Ishikawa Yuki、Komatsu Shuichiro、Kono Michihiro、Murakawa Yasuhiro、Nakano Masahiro、Oguchi Akiko、Son Raku、Suzuki Akari、Takeuchi Kazuhiro、Tanaka Nao、Terao Chikashi、Tomizuka Kohei、Yamamoto Kazuhiko、Yoshino Soichiro、ITEC Consortium‡
    • Journal Title

      Science

      Volume: 385 Issue: 6704

    • DOI

      10.1126/science.add8394

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms2024

    • Author(s)
      Inamo Jun、Suzuki Akari、Ueda Mahoko Takahashi、Yamaguchi Kensuke、Nishida Hiroshi、Suzuki Katsuya、Kaneko Yuko、Takeuchi Tsutomu、Hatano Hiroaki、Ishigaki Kazuyoshi、Ishihama Yasushi、Yamamoto Kazuhiko、Kochi Yuta
    • Journal Title

      Nature Communications

      Volume: 15 Issue: 1 Pages: 1-19

    • DOI

      10.1038/s41467-024-48615-4

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A genome-wide association study identified PTPN2 as a population-specific susceptibility gene locus for primary biliary cholangitis.2024

    • Author(s)
      Hitomi Y, Ueno K, Aiba Y, et al.
    • Journal Title

      Hepatology

      Volume: in press Issue: 4 Pages: 776-790

    • DOI

      10.1097/hep.0000000000000894

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The genetic basis of autoimmunity seen through the lens of T cell functional traits2024

    • Author(s)
      Lagattuta Kaitlyn A.、Park Hannah L.、Rumker Laurie、Ishigaki Kazuyoshi、Nathan Aparna、Raychaudhuri Soumya
    • Journal Title

      Nature Communications

      Volume: 15 Issue: 1

    • DOI

      10.1038/s41467-024-45170-w

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Age-associated CD4+ T cells with B cell-promoting functions are regulated by ZEB2 in autoimmunity.2024

    • Author(s)
      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.
    • Journal Title

      Sci Immunol.

      Volume: 9 Issue: 93 Pages: 1-16

    • DOI

      10.1126/sciimmunol.adk1643

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identification of a regulatory pathway governing TRAF1 via an arthritis-associated non-coding variant2024

    • Author(s)
      Wang Qiang、Martnez-Bonet Marta、Kim Taehyeung、Sparks Jeffrey A.、Ishigaki Kazuyoshi. et. al.
    • Journal Title

      Cell Genomics

      Volume: 4 Issue: 2 Pages: 100502-100502

    • DOI

      10.1016/j.xgen.2024.100502

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk2023

    • Author(s)
      6.Kojima S, Koyama S, Ka M, Saito Y, Parrish EH, Endo M, Takata S, Mizukoshi M, Hikino K, Takeda A, Gelinas AF, HeatonSM, Koide R, Kamada AJ, Noguchi M, Hamada M; Biobank Japan Project Consortium; Kamatani Y, Murakawa Y, Ishigaki K,Nakamura Y, Ito K, Terao C, Momozawa Y, Parrish NF
    • Journal Title

      Nature Genetics

      Volume: 55 Issue: 6 Pages: 939-951

    • DOI

      10.1038/s41588-023-01390-2

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Functional Genetics to Understand the Etiology of Autoimmunity2023

    • Author(s)
      Hatano Hiroaki、Ishigaki Kazuyoshi
    • Journal Title

      Genes

      Volume: 14 Issue: 3 Pages: 572-572

    • DOI

      10.3390/genes14030572

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Immunomics analysis of rheumatoid arthritis identified precursor dendritic cells as a key cell subset of treatment resistance.2023

    • Author(s)
      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
    • Journal Title

      Ann Rheum Dis

      Volume: Epub ahead of print Issue: 6 Pages: 1-11

    • DOI

      10.1136/ard-2022-223645

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genome-wide association study reveals BET1L associated with survival time in the 137,693 Japanese individuals2023

    • Author(s)
      Akiyama Masato、Sakaue Saori、Takahashi Atsushi、Ishigaki Kazuyoshi、Hirata Makoto、Matsuda Koichi、Momozawa Yukihide、Okada Yukinori、Ninomiya Toshiharu、Koido Masaru、Morisaki Takayuki、Nagai Akiko、Sagiya Yoji、Terao Chikashi、Murakami Yoshinori、Kubo Michiaki、Kamatani Yoichiro、The Biobank Japan project
    • Journal Title

      Communications Biology

      Volume: 6 Issue: 1 Pages: 143-143

    • DOI

      10.1038/s42003-023-04491-0

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning2022

    • Author(s)
      Koido Masaru、Hon Chung-Chau、Koyama Satoshi、Kawaji Hideya、Murakawa Yasuhiro、Ishigaki Kazuyoshi、Ito Kaoru、Sese Jun、Parrish Nicholas F.、Kamatani Yoichiro、Carninci Piero、Terao Chikashi
    • Journal Title

      Nature Biomedical Engineering

      Volume: Online Issue: 6 Pages: 830-844

    • DOI

      10.1038/s41551-022-00961-8

    • Related Report
      2023 Annual Research Report 2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis2022

    • Author(s)
      Ishigaki K, Sakaue S, Terao C, Luo Y, Sonehara KvYamaguchi K, Amariuta T, Too CL, Laufer VA, Scott IC, Viatte S, Takahashi M, Ohmura K, Murasawa A, Hashimoto M, Ito H, ..., Okada Y et al.
    • Journal Title

      Nature Genetics

      Volume: 54 Issue: 11 Pages: 1640-1651

    • DOI

      10.1038/s41588-022-01213-w

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Control of naive and effector CD4 T cell receptor repertoires by rheumatoid-arthritis-risk HLA alleles2022

    • Author(s)
      Nagafuchi Yasuo、Ota Mineto、Hatano Hiroaki、Inoue Mariko、Kobayashi Satomi、Okubo Mai、Sugimori Yusuke、Nakano Masahiro、Yamada Saeko、Yoshida Ryochi、Tsuchida Yumi、Iwasaki Yukiko、Shoda Hirofumi、Okada Yukinori、Yamamoto Kazuhiko、Ishigaki Kazuyoshi、Okamura Tomohisa、Fujio Keishi
    • Journal Title

      Journal of Autoimmunity

      Volume: 133 Pages: 102907-102907

    • DOI

      10.1016/j.jaut.2022.102907

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci2022

    • Author(s)
      Yamaguchi Kensuke、Ishigaki Kazuyoshi、Suzuki Akari、Tsuchida Yumi、Tsuchiya Haruka、Sumitomo Shuji、Nagafuchi Yasuo、Miya Fuyuki、Tsunoda Tatsuhiko、Shoda Hirofumi、Fujio Keishi、Yamamoto Kazuhiko、Kochi Yuta
    • Journal Title

      Nature Communications

      Volume: 13 Issue: 1 Pages: 4659-4659

    • DOI

      10.1038/s41467-022-32358-1

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Distinct transcriptome architectures underlying lupus establishment and exacerbation2022

    • Author(s)
      Nakano Masahiro et al.
    • Journal Title

      Cell

      Volume: 185 Issue: 18 Pages: 3375-3389.e21

    • DOI

      10.1016/j.cell.2022.07.021

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Single-cell eQTL models reveal dynamic T cell state dependence of disease loci2022

    • Author(s)
      Nathan Aparna、Asgari Samira、Ishigaki Kazuyoshi、Valencia Cristian、Amariuta Tiffany、Luo Yang、Beynor Jessica I.、Baglaenko Yuriy、Suliman Sara、Price Alkes L.、Lecca Leonid、Murray Megan B.、Moody D. Branch、Raychaudhuri Soumya
    • Journal Title

      Nature

      Volume: 606 Issue: 7912 Pages: 120-128

    • DOI

      10.1038/s41586-022-04713-1

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] HLA autoimmune risk alleles restrict the hypervariable region of T cell receptors2022

    • Author(s)
      Ishigaki Kazuyoshi、Lagattuta Kaitlyn A.、Luo Yang、James Eddie A.、Buckner Jane H.、Raychaudhuri Soumya
    • Journal Title

      Nature Genetics

      Volume: 54 Issue: 4 Pages: 393-402

    • DOI

      10.1038/s41588-022-01032-z

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Polygenic risk of rheumatoid arthritis regulates the abundance of circulating regulatory T cells.2024

    • Author(s)
      浅原健一郎, 石垣和慶
    • Organizer
      American Society of Human Genetics Annual Meeting 2024.
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research
  • [Presentation] New quantitative and qualitative analytical framework of scRNAseq data reveals the pathophysiology of systemic lupus erythematosus.2024

    • Author(s)
      中野正博, 石垣和慶
    • Organizer
      The 53rd Annual Meeting of the Japanese Society for Immunology.
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Unravelling the gene regulatory networks driving the polygenetic risk of human complex diseases2024

    • Author(s)
      髙橋悠, 石垣和慶
    • Organizer
      The 53rd Annual Meeting of the Japanese Society for Immunology.
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research
  • [Presentation] New directions of T cell receptor research~ beyond classical views ~.2024

    • Author(s)
      石垣和慶
    • Organizer
      The 53rd Annual Meeting of the Japanese Society for Immunology.
    • Related Report
      2024 Annual Research Report
    • Invited
  • [Presentation] T細胞受容体による免疫制御2024

    • Author(s)
      石垣和慶
    • Organizer
      第45回日本炎症・再生医学会
    • Related Report
      2024 Annual Research Report
    • Invited
  • [Presentation] Immunogenetics to understand the etiology of autoimmunity.2024

    • Author(s)
      石垣和慶
    • Organizer
      第68回日本リウマチ学会総会・学術集会
    • Related Report
      2024 Annual Research Report
    • Invited
  • [Presentation] Autoimmunity pathology elucidated by functional genetics studies2023

    • Author(s)
      石垣和慶
    • Organizer
      日本人類遺伝学会第68回大会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Autoimmunity risk variants exert dynamic allelic effects on the chromosome accessibility of stimulated CD4+ T cells.2023

    • Author(s)
      Kono M., Hatano H., Suzuki A., Nakano M., Oguchi A., Murakawa Y., Terao C., Yamamoto K., Ishigaki K
    • Organizer
      American Society of Human Genetics Annual Meeting 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Chromatin interaction inferences based on the paired transcriptome and chromatin accessibility datasets identify candidate risk genes of autoimmunity.2023

    • Author(s)
      Hatano H., Suzuki A., Nakano M., Oguchi A., Murakawa Y., Terao C., Yamamoto K., Ishigaki K
    • Organizer
      American Society of Human Genetics Annual Meeting 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] An efficient functional assay platform of autoimmunity risk alleles using CRISPR genome editing.2023

    • Author(s)
      Kono M., Arakawa T., Nakano M., Hatano H., Ishigaki K.
    • Organizer
      Annual Meeting of the Federation of Clinical Immunology Societies 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Actively transcribed regulatory regions explain the genetic risk of rheumatoid arthritis2022

    • Author(s)
      Hiroaki Hatano, Akari Suzuki, Matteo Guerrini, Michihiro Kono, Masahiro Nakano, Akiko Oguchi, Chikashi Terao,Yasuhiro Murakawa, Kazuhiko Yamamoto, Kazuyoshi Ishigaki
    • Organizer
      第51回日本免疫学会学術集会
    • Related Report
      2022 Annual Research Report
  • [Patent(Industrial Property Rights)] 改良されたATAC-seq法及びキット2023

    • Inventor(s)
      石垣 和慶
    • Industrial Property Rights Holder
      石垣 和慶
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2023-084002
    • Filing Date
      2023
    • Related Report
      2023 Annual Research Report

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Published: 2022-04-19   Modified: 2026-01-16  

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