ヒト免疫遺伝研究チーム

  1. Xiao Q, Mears J, Nathan A, Ishigaki K, Baglaenko Y, Lim N, Cooney LA, Harris KM, Anderson MS, Fox DA, Smilek DE, Krueger JG, Raychaudhuri S. Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin. Nat Commun. 2023 Oct 7;14(1):6268. doi: 10.1038/s41467-023-41984-2. PMID: 37805522.
  2. Sakaue S, Gurajala S, Curtis M, Luo Y, Choi W, Ishigaki K, Kang JB, Rumker L, Deutsch AJ, Schönherr S, Forer L, LeFaive J, Fuchsberger C, Han B, Lenz TL, de Bakker PIW, Okada Y, Smith AV, Raychaudhuri S. Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease. Nat Protoc. 2023 Sep;18(9):2625-2641. doi: 10.1038/s41596-023-00853-4. Epub 2023 Jul 26. PMID: 37495751.
  3. 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 Nov;82(11):1455-1463. doi: 10.1136/ard-2023-224421. Epub 2023 Jul 19. PMID: 37468219.
  4. Kojima S, Koyama S, Ka M, Saito Y, Parrish EH, Endo M, Takata S, Mizukoshi M, Hikino K, Takeda A, Gelinas AF, Heaton SM, 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. Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk. Nat Genet. 2023 Jun;55(6):939-951. doi: 10.1038/s41588-023-01390-2. Epub 2023 May 11. PMID: 37169872.
  5. Hatano H, Ishigaki K (corresponding author). Functional Genetics to Understand the Etiology of Autoimmunity. Genes (Basel). 2023 Feb 24;14(3):572. doi: 10.3390/genes14030572. PMID: 36980846.
  6. 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 Jun;82(6):809-819. doi: 10.1136/ard-2022-223645. Epub 2023 Mar 14. PMID: 36918189.
  7. Akiyama M, Sakaue S, Takahashi A, Ishigaki K, Hirata M, Matsuda K, Momozawa Y, Okada Y, Ninomiya T; Biobank Japan project; Terao C, Murakami Y, Kubo M, Kamatani Y. Genome-wide association study reveals BET1L associated with survival time in the 137,693 Japanese individuals. Commun Biol. 2023 Feb 3;6(1):143. doi: 10.1038/s42003-023-04491-0. PMID: 36737517.
  8. Akiyama M, Miyake M, Momozawa Y, Arakawa S, Maruyama-Inoue M, Endo M, Iwasaki Y, Ishigaki K, Matoba N, Okada Y, Yasuda M, Oshima Y, Yoshida S, Nakao SY, Morino K, Mori Y, Kido A, Kato A, Yasukawa T, Obata R, Nagai Y, Takahashi K, Fujisawa K, Miki A, Nakamura M, Honda S, Ushida H, Yasuma T, Nishiguchi KM, Mori R, Tanaka K, Wakatsuki Y, Yamashiro K, Kadonosono K, Terao C, Ishibashi T, Tsujikawa A, Sonoda KH, Kubo M, Kamatani Y. Genome-Wide Association Study of Age-Related Macular Degeneration Reveals 2 New Loci Implying Shared Genetic Components with Central Serous Chorioretinopathy. Ophthalmology. 2023 Apr;130(4):361-372. doi: 10.1016/j.ophtha.2022.10.034. Epub 2022 Nov 22. PMID: 36423732.
  9. Koido M, Hon CC, Koyama S, Kawaji H, Murakawa Y, Ishigaki K, Ito K, Sese J, Parrish NF, Kamatani Y, Carninci P, Terao C. Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning. Nat Biomed Eng. 2023 Jun;7(6):830-844. doi: 10.1038/s41551-022-00961-8. Epub 2022 Nov 21. PMID: 36411359.
  10. Ishigaki K, Sakaue S, Terao C, Luo Y, Sonehara K, Yamaguchi K, Amariuta T, Too CL, Laufer VA, Scott IC, Viatte S, Takahashi M, Ohmura K, Murasawa A, Hashimoto M, Ito H, Hammoudeh M, Emadi SA, Masri BK, Halabi H, Badsha H, Uthman IW, Wu X, Lin L, Li T, Plant D, Barton A, Orozco G, Verstappen SMM, Bowes J, MacGregor AJ, Honda S, Koido M, Tomizuka K, Kamatani Y, Tanaka H, Tanaka E, Suzuki A, Maeda Y, Yamamoto K, Miyawaki S, Xie G, Zhang J, Amos CI, Keystone E, Wolbink G, van der Horst-Bruinsma I, Cui J, Liao KP, Carroll RJ, Lee HS, Bang SY, Siminovitch KA, de Vries N, Alfredsson L, Rantapää-Dahlqvist S, Karlson EW, Bae SC, Kimberly RP, Edberg JC, Mariette X, Huizinga T, Dieudé P, Schneider M, Kerick M, Denny JC; BioBank Japan Project; Matsuda K, Matsuo K, Mimori T, Matsuda F, Fujio K, Tanaka Y, Kumanogoh A, Traylor M, Lewis CM, Eyre S, Xu H, Saxena R, Arayssi T, Kochi Y, Ikari K, Harigai M, Gregersen PK, Yamamoto K, Louis Bridges S Jr, Padyukov L, Martin J, Klareskog L, Okada Y, Raychaudhuri S. Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis. Nat Genet. 2022 Nov;54(11):1640-1651. doi: 10.1038/s41588-022-01213-w. Epub 2022 Nov 4. PMID: 36333501.
  11. 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 Dec;133:102907. doi: 10.1016/j.jaut.2022.102907. Epub 2022 Sep 18. PMID: 36126366.
  12. Yamaguchi K, Ishigaki K, Suzuki A, Tsuchida Y, Tsuchiya H, Sumitomo S, Nagafuchi Y, Miya F, Tsunoda T, Shoda H, Fujio K, Yamamoto K, Kochi Y. Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci. Nat Commun. 2022 Aug 24;13(1):4659. doi: 10.1038/s41467-022-32358-1. PMID: 36002455.
  13. 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 (co-corresponding author), Fujio K. Distinct transcriptome architectures underlying lupus establishment and exacerbation. Cell. 2022 Sep 1;185(18):3375-3389.e21. doi: 10.1016/j.cell.2022.07.021. Epub 2022 Aug 22. PMID: 35998627.
  14. Nathan A, Asgari S, Ishigaki K, Valencia C, Amariuta T, Luo Y, Beynor JI, Baglaenko Y, Suliman S, Price AL, Lecca L, Murray MB, Moody DB, Raychaudhuri S. Single-cell eQTL models reveal dynamic T cell state dependence of disease loci. Nature. 2022 Jun;606(7912):120-128. doi: 10.1038/s41586-022-04713-1. Epub 2022 May 11. PMID: 35545678.
  15. Ishigaki K, Lagattuta KA, Luo Y, James EA, Buckner JH, Raychaudhuri S. HLA autoimmune risk alleles restrict the hypervariable region of T cell receptors. Nat Genet. 2022 Apr;54(4):393-402. doi: 10.1038/s41588-022-01032-z. Epub 2022 Mar 24. PMID: 35332318; PMCID: PMC9010379.
  16. Lagattuta KA, Kang JB, Nathan A, Pauken KE, Jonsson AH, Rao DA, Sharpe AH, Ishigaki K (co-corresponding author), Raychaudhuri S. Repertoire analyses reveal T cell antigen receptor sequence features that influence T cell fate. Nat Immunol. 2022 Mar;23(3):446-457. doi: 10.1038/s41590-022-01129-x. Epub 2022 Feb 17. PMID: 35177831; PMCID: PMC8904286.
  17. Ishigaki K. Beyond GWAS: from simple associations to functional insights. Semin Immunopathol. 2022 Jan;44(1):3-14. doi: 10.1007/s00281-021-00894-5. Epub 2021 Oct 4. PMID: 34605948.
  18. Nathan A, Beynor JI, Baglaenko Y, Suliman S, Ishigaki K, Asgari S, Huang CC, Luo Y, Zhang Z, Lopez K, Lindestam Arlehamn CS, Ernst JD, Jimenez J, Calderón RI, Lecca L, Van Rhijn I, Moody DB, Murray MB, Raychaudhuri S. Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease. Nat Immunol. 2021 Jun;22(6):781-793. doi: 10.1038/s41590-021-00933-1. Epub 2021 May 24. PMID: 34031617; PMCID: PMC8162307.
  19. 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 May 27;184(11):3006-3021.e17. doi: 10.1016/j.cell.2021.03.056. Epub 2021 May 1. PMID: 33930287.
  20. Amariuta T, Ishigaki K (co-first author), Sugishita H, Ohta T, Koido M, Dey KK, Matsuda K, Murakami Y, Price AL, Kawakami E, Terao C, Raychaudhuri S. Improving the trans- ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements. Nat Genet. 2020 Dec;52(12):1346-1354. doi: 10.1038/s41588-020-00740-8. Epub 2020 Nov 30. PMID: 33257898; PMCID: PMC8049522.
  21. 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 Nov 2:annrheumdis-2020-218189. doi: 10.1136/annrheumdis-2020-218189. Epub ahead of print. Erratum in: Ann Rheum Dis. 2022 Jan;81(1):e17. PMID: 33139312.
  22. Terao C, Suzuki A, Momozawa Y, Akiyama M, Ishigaki K, Yamamoto K, Matsuda K, Murakami Y, McCarroll SA, Kubo M, Loh PR, Kamatani Y. Chromosomal alterations among age-related haematopoietic clones in Japan. Nature. 2020 Aug;584(7819):130-135. doi: 10.1038/s41586-020-2426-2. Epub 2020 Jun 24. PMID: 32581364; PMCID: PMC7489641.
  23. Chen M, Sidore C, Akiyama M, Ishigaki K, Kamatani Y, Schlessinger D, Cucca F, Okada Y, Chiang CWK. Evidence of Polygenic Adaptation in Sardinia at Height- Associated Loci Ascertained from the Biobank Japan. Am J Hum Genet. 2020 Jul 2;107(1):60-71. doi: 10.1016/j.ajhg.2020.05.014. Epub 2020 Jun 12. PMID: 32533944; PMCID: PMC7332648.
  24. Ishigaki K, Akiyama M, Kanai M, Takahashi A, Kawakami E, Sugishita H, Sakaue S, Matoba N, Low SK, Okada Y, Terao C, Amariuta T, Gazal S, Kochi Y, Horikoshi M, Suzuki K, Ito K, Koyama S, Ozaki K, Niida S, Sakata Y, Sakata Y, Kohno T, Shiraishi K, Momozawa Y, Hirata M, Matsuda K, Ikeda M, Iwata N, Ikegawa S, Kou I, Tanaka T, Nakagawa H, Suzuki A, Hirota T, Tamari M, Chayama K, Miki D, Mori M, Nagayama S, Daigo Y, Miki Y, Katagiri T, Ogawa O, Obara W, Ito H, Yoshida T, Imoto I, Takahashi T, Tanikawa C, Suzuki T, Sinozaki N, Minami S, Yamaguchi H, Asai S, Takahashi Y, Yamaji K, Takahashi K, Fujioka T, Takata R, Yanai H, Masumoto A, Koretsune Y, Kutsumi H, Higashiyama M, Murayama S, Minegishi N, Suzuki K, Tanno K, Shimizu A, Yamaji T, Iwasaki M, Sawada N, Uemura H, Tanaka K, Naito M, Sasaki M, Wakai K, Tsugane S, Yamamoto M, Yamamoto K, Murakami Y, Nakamura Y, Raychaudhuri S, Inazawa J, Yamauchi T, Kadowaki T, Kubo M, Kamatani Y. Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases. Nat Genet. 2020 Jul;52(7):669-679. doi: 10.1038/s41588-020-0640-3. Epub 2020 Jun 8. PMID: 32514122; PMCID: PMC7968075.
  25. Akiyama M, Ishigaki K, Sakaue S, Momozawa Y, Horikoshi M, Hirata M, Matsuda K, Ikegawa S, Takahashi A, Kanai M, Suzuki S, Matsui D, Naito M, Yamaji T, Iwasaki M, Sawada N, Tanno K, Sasaki M, Hozawa A, Minegishi N, Wakai K, Tsugane S, Shimizu A, Yamamoto M, Okada Y, Murakami Y, Kubo M, Kamatani Y. Author Correction: Characterizing rare and low-frequency height-associated variants in the Japanese population. Nat Commun. 2020 Mar 9;11(1):1350. doi: 10.1038/s41467-020-15202-2. Erratum for: Nat Commun. 2019 Sep 27;10(1):4393. PMID: 32152314; PMCID: PMC7062748.
  26. Matoba N, Akiyama M, Ishigaki K, Kanai M, Takahashi A, Momozawa Y, Ikegawa S, Ikeda M, Iwata N, Hirata M, Matsuda K, Murakami Y, Kubo M, Kamatani Y, Okada Y. GWAS of 165,084 Japanese individuals identified nine loci associated with dietary habits. Nat Hum Behav. 2020 Mar;4(3):308-316. doi: 10.1038/s41562-019-0805-1. Epub 2020 Jan 20. PMID: 31959922.
  27. Terao C, Momozawa Y, Ishigaki K, Kawakami E, Akiyama M, Loh PR, Genovese G, Sugishita H, Ohta T, Hirata M, Perry JRB, Matsuda K, Murakami Y, Kubo M, Kamatani Y. GWAS of mosaic loss of chromosome Y highlights genetic effects on blood cell differentiation. Nat Commun. 2019 Oct 17;10(1):4719. doi: 10.1038/s41467-019-12705-5. PMID: 31624269; PMCID: PMC6797717.
  28. Matoba N, Akiyama M, Ishigaki K, Kanai M, Takahashi A, Momozawa Y, Ikegawa S, Ikeda M, Iwata N, Hirata M, Matsuda K, Kubo M, Okada Y, Kamatani Y. GWAS of smoking behaviour in 165,436 Japanese people reveals seven new loci and shared genetic architecture. Nat Hum Behav. 2019 May;3(5):471-477. doi: 10.1038/s41562-019-0557-y. Epub 2019 Mar 25. PMID: 31089300.
  29. Amariuta T, Luo Y, Gazal S, Davenport EE, van de Geijn B, Ishigaki K, Westra HJ, Teslovich N, Okada Y, Yamamoto K; RACI Consortium, GARNET Consortium, Price AL, Raychaudhuri S. IMPACT: Genomic Annotation of Cell-State-Specific Regulatory Elements Inferred from the Epigenome of Bound Transcription Factors. Am J Hum Genet. 2019 May 2;104(5):879-895. doi: 10.1016/j.ajhg.2019.03.012. Epub 2019 Apr 18. PMID: 31006511; PMCID: PMC6506796.
  30. Suzuki K, Akiyama M, Ishigaki K, Kanai M, Hosoe J, Shojima N, Hozawa A, Kadota A, Kuriki K, Naito M, Tanno K, Ishigaki Y, Hirata M, Matsuda K, Iwata N, Ikeda M, Sawada N, Yamaji T, Iwasaki M, Ikegawa S, Maeda S, Murakami Y, Wakai K, Tsugane S, Sasaki M, Yamamoto M, Okada Y, Kubo M, Kamatani Y, Horikoshi M, Yamauchi T, Kadowaki T. Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet. 2019 Mar;51(3):379-386. doi: 10.1038/s41588-018-0332-4. Epub 2019 Feb 4. PMID: 30718926.
  31. Hirata J, Hosomichi K, Sakaue S, Kanai M, Nakaoka H, Ishigaki K, Suzuki K, Akiyama M, Kishikawa T, Ogawa K, Masuda T, Yamamoto K, Hirata M, Matsuda K, Momozawa Y, Inoue I, Kubo M, Kamatani Y, Okada Y. Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population. Nat Genet. 2019 Mar;51(3):470-480. doi: 10.1038/s41588-018-0336-0. Epub 2019 Jan 28. PMID: 30692682.
  32. Akizuki S, Ishigaki K, Kochi Y, Law SM, Matsuo K, Ohmura K, Suzuki A, Nakayama M, Iizuka Y, Koseki H, Ohara O, Hirata J, Kamatani Y, Matsuda F, Sumida T, Yamamoto K, Okada Y, Mimori T, Terao C. PLD4 is a genetic determinant to systemic lupus erythematosus and involved in murine autoimmune phenotypes. Ann Rheum Dis. 2019 Apr;78(4):509-518. doi: 10.1136/annrheumdis-2018-214116. Epub 2019 Jan 24. PMID: 30679154.
  33. Sakurai K, Ishigaki K, Shoda H, Nagafuchi Y, Tsuchida Y, Sumitomo S, Kanda H, Suzuki A, Kochi Y, Yamamoto K, Fujio K. HLA-DRB1 Shared Epitope Alleles and Disease Activity Are Correlated with Reduced T Cell Receptor Repertoire Diversity in CD4+ T Cells in Rheumatoid Arthritis. J Rheumatol. 2018 Jul;45(7):905-914. doi: 10.3899/jrheum.170909. Epub 2018 Apr 15. PMID: 29657145.
  34. Ishigaki K, Kochi Y, Yamamoto K. Genetics of human autoimmunity: From genetic information to functional insights. Clin Immunol. 2018 Jan;186:9-13. doi: 10.1016/j.clim.2017.08.017. Epub 2017 Sep 1. PMID: 28867252.
  35. Ishigaki K, Kochi Y, Suzuki A, Tsuchida Y, Tsuchiya H, Sumitomo S, Yamaguchi K, Nagafuchi Y, Nakachi S, Kato R, Sakurai K, Shoda H, Ikari K, Taniguchi A, Yamanaka H, Miya F, Tsunoda T, Okada Y, Momozawa Y, Kamatani Y, Yamada R, Kubo M, Fujio K, Yamamoto K. Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis. Nat Genet. 2017 Jul;49(7):1120-1125. doi: 10.1038/ng.3885. Epub 2017 May 29. PMID: 28553958.
  36. Tsuchida Y, Sumitomo S, Ishigaki K, Suzuki A, Kochi Y, Tsuchiya H, Ota M, Komai T, Inoue M, Morita K, Okamura T, Yamamoto K, Fujio K. TGF-β3 Inhibits Antibody Production by Human B Cells. PLoS One. 2017 Jan 4;12(1):e0169646. doi: 10.1371/journal.pone.0169646. PMID: 28052118; PMCID: PMC5215424.
  37. Ishigaki K, Shoda H, Kochi Y, Yasui T, Kadono Y, Tanaka S, Fujio K, Yamamoto K. Quantitative and qualitative characterization of expanded CD4+ T cell clones in rheumatoid arthritis patients. Sci Rep. 2015 Aug 6;5:12937. doi: 10.1038/srep12937. PMID: 26245356; PMCID: PMC4542667.