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Department of Cancer Genome Research

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Chief (Principal Investigator) Hirofumi Nakaoka, Ph.D. Researchmap
e-mail: h-nakaoka
Research Scientist Rose Maria Mathew, Ph.D. e-mail: rose.m.mathew
Visiting Scientist Yuichi Ishikawa, M.D., Ph.D. The Cancer Institute, Japanese Foundation for Cancer Research Researchmap
Visiting Scientist Ituro Inoue, Ph.D. Researchmap
Visiting Scientist Shigeki Mitsunaga, Ph.D. Researchmap
Research Student Yusuke Kawamura National Defense Medical College
Research Student Kotaro Takahashi Niigata University School of Medicine

*Please add @po.kyoundo.jp after e-mail address

Overview

Projects

Publications

Last 5 years

  1. Takahashi K, Yachida N, Tamura R, Adachi S, Kondo S, Abé T, Umezu H, Nyuzuki H, Okuda S, Nakaoka H, Yoshihara K: Clonal origin and genomic diversity in Lynch syndrome-associated endometrial cancer with multiple synchronous tumors: Identification of the pathogenicity of MLH1 p.L582H. Genes Chromosomes Cancer 63: e23231, 2024.
  2. Nishimura L, Tanino A, Ajimoto M, Katsumura T, Ogawa M, Koganebuchi K, Waku D, Kumagai M, Sugimoto R, Nakaoka H, Oota H, Inoue I: Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. PLoS One 19: e0295924, 2024.
  3. Akashi H, Yachida N, Ueda H, Yamaguchi M, Yamawaki K, Tamura R, Suda K, Ishiguro T, Adachi S, Nagase Y, Ueda Y, Ueda M, Abiko K, Kagabu M, Baba T, Nakaoka H, Enomoto T, Murai J, Yoshihara K: SLFN11 is a BRCA Independent Biomarker for the Response to Platinum-Based Chemotherapy in High-Grade Serous Ovarian Cancer and Clear Cell Ovarian Carcinoma. Mol Cancer Ther 23: 106-116, 2024.
  4. Mitsunaga S, Fujito N, Nakaoka H, Imazeki R, Nagata E, Inoue I: Detection of APP gene recombinant in human blood plasma. Sci Rep 13: 21703, 2023.
  5. Tamura R, Nakaoka H, Yachida N, Ueda H, Ishiguro T, Motoyama T, Inoue I, Enomoto T, Yoshihara K: Spatial genomic diversity associated with APOBEC mutagenesis in squamous cell carcinoma arising from ovarian teratoma. Cancer Science 114: 2145-2157, 2023.
  6. Toyoda Y, Nakatochi M, Nakayama A, Kawamura Y, Nakaoka H, Wakai K, Matsuo K, Matsuo H; Japan Gout Genomics Consortium: SNP-based heritability estimates of gout and its subtypes determined by genome-wide association studies of clinically defined gout. Rheumatology (Oxford) 62: e144-e146, 2023.
  7. Banerjee P, Kubo F, Nakaoka H, Ajima R, Sato T, Hirata T, Iwasato T: Spontaneous activity in whisker-innervating region of neonatal mouse trigeminal ganglion. Sci. Rep. 12: 16311, 2022.
  8. Yoshioka A, Nakaoka H, Fukumoto T, Inoue I, Nishigori C, Kunisada M. The landscape of genetic alterations of UVB-induced skin tumors in DNA repair-deficient mice. Exp. Dermatol. 31: 1607-1617, 2022.
  9. Rose MM, Dhamodharan S, Revathidevi S, Chakkarappan SR, Mani JG, Shanmugam S, Nakaoka H, Inoue I, Murugan AK, Munirajan AK: High incidence of PI3K pathway gene mutations in South Indian cervical cancers. Cancer Genet. 264-265: 100-108, 2022.
  10. Iwaya K, Arai H, Takatou N, Morita Y, Ozeki R, Nakaoka H, Sakamoto M, Kouno T, Soma M: A sheet pocket to prevent cross-contamination of formalin-fixed paraffin-embedded block for application in next generation sequencing. PLoS One 17(5):e0266947, 2022.
  11. Sakaue S, Hosomichi K, Hirata J, Nakaoka H, Yamazaki K, Yawata M, Yawata N, Naito T, Umeno J, Kawaguchi T, Matsui T, Motoya S, Suzuki Y, Inoko H, Tajima A, Morisaki T, Matsuda K, Kamatani Y, Yamamoto K, Inoue I, Okada Y: Decoding the diversity of killer immunoglobulin-like receptors by deep sequencing and a high-resolution imputation method. Cell Genomics 2(3): 100101, 2022.
  12. Toyoda Y, Nakayama A, Nakatochi M, Kawamura Y, Nakaoka H, Yamamoto K, Shimizu S, Ooyama H, Ooyama K, Shimizu T, Nagase M, Hidaka Y, Ichida K, Inoue I, Shinomiya N, Matsuo H; Japan Gout Genomics Consortium (Japan Gout): Genome-wide meta-analysis between renal overload type and renal underexcretion type of clinically defined gout in Japanese populations. Mol. Genet. Metab. (published online) 2022. doi: 10.1016/j.ymgme.2022.01.100.
  13. Takahashi M, Hosomichi K, Nakaoka H, Sakata H, Uesato N, Murakami K, Kano M, Toyozumi T, Matsumoto Y, Isozaki T, Sekino N, Otsuka R, Inoue I, Matsubara H: Biased expression of mutant alleles in cancer-related genes in esophageal squamous cell carcinoma. Esophagus 19(2): 294-302, 2022.
  14. Revathidevi S, Nakaoka H†, Suda K, Fujito N, Munirajan AK, Yoshihara K, Enomoto T, Inoue I†: APOBEC mediated mutagenesis drives genomic heterogeneity in endometriosis. J. Hum. Genet. (6): 323-329, 2022. †Corresponding author.
  15. Yamaguchi M*, Nakaoka H*, †, Suda K*, Yoshihara K*, †, Ishiguro T, Yachida N, Saito K, Ueda H, Sugino K, Mori Y, Yamawaki K, Tamura R, Revathidevi S, Motoyama T, Tainaka K, Verhaak RGW, Inoue I†, Enomoto T†: Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium. Nat. Commun. 13(1): 943, 2022. *Co-first author. †Corresponding author.
  16. Jinam TA, Hosomichi K, Nakaoka H, Phipps ME, Saitou N, Inoue I: Allelic and haplotypic HLA diversity in indigenous Malaysian populations explored using Next Generation Sequencing. Hum. Immunol. 83(1): 17-26, 2022.
  17. Tamura R, Yoshihara K, Matsuo K, Yachida N, Miyoshi A, Takahashi K, Sugino K, Yamaguchi M, Mori Y, Suda K, Ishiguro T, Okuda S, Motoyama T, Nakaoka H, Kikuchi A, Ueda Y, Inoue I, Enomoto T: Proposing a molecular classification associated with hypercoagulation in ovarian clear cell carcinoma. Gynecol. Oncol. 163(2): 327-333, 2021.
  18. Toyoda Y, Kawamura Y, Nakayama A, Nakaoka H, Higashino T, Shimizu S, Ooyama H, Morimoto K, Uchida N, Shigesawa R, Takeuchi K, Inoue I, Ichida K, Suzuki H, Shinomiya N, Takada T, Matsuo H: Substantial anti-gout effect conferred by common and rare dysfunctional variants of URAT1/SLC22A12. Rheumatology 60: 5224-5232, 2021.
  19. Sugimoto R, Nishimura L, Nguyen PT, Ito J, Parrish NF, Mori H, Kurokawa K, Nakaoka H, Inoue I: Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more. PLoS Comput. Biol. 17: e1009428, 2021.
  20. Aamer W, Hassan HY, Nakaoka H, Hosomichi K, Jaeger M, Tahir H, Abdelraheem MH, Netea MG, and Inoue I: Analysis of HLA gene polymorphisms in East Africans reveals evidence of gene flow in two Semitic populations from Sudan. Eur. J. Hum. Genet. 29: 1259-1271, 2021.
  21. Yachida N, Yoshihara K, Suda K, Nakaoka H, Ueda H, Sugino K, Yamaguchi M, Mori Y, Yamawaki K, Tamura R, Ishiguro T, Kase H, Motoyama T, and Enomoto T: Biological significance of KRAS mutant allele expression in ovarian endometriosis. Cancer Sci. 112(5): 2020-2032, 2021.
  22. Yamaguchi M, Yoshihara K, Suda K, Nakaoka H, Yachida N, Ueda H, Sugino K, Mori Y, Yamawaki K, Tamura R, Ishiguro T, Motoyama T, Watanabe Y, Okuda S, Tainaka K, and Enomoto T: Three-dimensional understanding of the morphological complexity of the human uterine endometrium. iScience. 24(4): 102258, 2021.
  23. Matsumoto Y, Nagayama H, Nakaoka H, Toyoda A, Goto T, and Koide T: Combined change of behavioral traits for domestication and gene-networks in mice selectively bred for active tameness. Genes Brain Behav. 20(3): e12721, 2021.
  24. Nishimura L, Sugimoto R, Inoue J, Nakaoka H, Kanzawa-Kiriyama H, Shinoda KI, and Inoue I: Identification of ancient viruses from metagenomic data of the Jomon people. J. Hum. Genet. 66(3): 287-296, 2021.
  25. Nakakura S, Hosomichi K, Uchino S, Murakami A, Oka A, Inoue I, and Nakaoka H: HLA-B*39:01:01 is a novel risk factor for antithyroid drug-induced agranulocytosis in Japanese population. Pharmacogenomics J. 21(1): 94-101, 2021.
  26. Revathidevi S, Murugan AK, Nakaoka H, Inoue I, and Munirajan AK: APOBEC: A molecular driver in cervical cancer pathogenesis. Cancer Lett. 496: 104-116, 2021.
  27. Yesbolatova A, Saito Y, Kitamoto N, Makino-Itou H, Ajima R, Nakano R, Nakaoka H, Fukui K, Gamo K, Tominari Y, Takeuchi H, Saga Y, Hayashi K, and Kanemaki MT: The auxin-inducible degron 2 technology gives superior degradation control in yeast, mammalian cells, and mice. Nat. Commun. 11(1): 5701, 2020.
  28. Ito J, Kimura I, Soper A, Coudray A, Koyanagi Y, Nakaoka H, Inoue I, Turelli P, Trono D, and Sato K: Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression. Sci. Adv. 6(43): eabc3020, 2020.
  29. Yachida N, Yoshihara K, Suda K, Nakaoka H, Ueda H, Sugino K, Yamaguchi M, Mori Y, Yamawaki K, Tamura R, Ishiguro T, Isobe M, Motoyama T, Inoue I, and Enomoto T: ARID1A protein expression is retained in ovarian endometriosis with ARID1A loss-of-function mutations: Implication for the two-hit hypothesis. Sci. Rep. 10(1): 14260, 2020.
  30. Kantake M, Ikeda N, Nakaoka H, Ohkawa N, Tanaka T, Miyabayashi K, Shoji H, and Shimizu T: IGF1 gene is epigenetically activated in preterm infants with intrauterine growth restriction. Clin. Epigenetics. 12(1): 108, 2020.
  31. Suda K, Cruz Diaz LA, Yoshihara K, Nakaoka H, Yachida N, Motoyama T, Inoue I, and Enomoto T: Clonal lineage from normal endometrium to ovarian clear cell carcinoma through ovarian endometriosis. Cancer Sci. 111(8): 3000–3009, 2020.
  32. Hata C, Nakaoka H, Xiang Y, Wang D, Yang A, Liu D, Liu F, Zou Q, Wei L, Zheng K, Inoue I, and You H: Germline mutations of multiple breast cancer-related genes are differentially associated with triple-negative breast cancers and prognostic factors. J. Hum. Genet. 65(7):577-587, 2020.
  33. Nakayama A*, Nakatochi M*, Kawamura Y*, Yamamoto K*, Nakaoka H*, Shimizu S, Higashino T, Koyama T, Hishida A, Kuriki K, Watanabe M, Shimizu T, Ooyama K, Ooyama H, Nagase M, Hidaka Y, Matsui D, Tamura T, Nishiyama T, Shimanoe C, Katsuura-Kamano S, Takashima N, Shirai Y, Kawaguchi M, Takao M, Sugiyama R, Takada Y, Nakamura T, Nakashima H, Tsunoda M, Danjoh I, Hozawa A, Hosomichi K, Toyoda Y, Kubota Y, Takada T, Suzuki H, Stiburkova B, Major TJ, Merriman TR, Kuriyama N, Mikami H, Takezaki T, Matsuo K, Suzuki S, Hosoya T, Kamatani Y, Kubo M, Ichida K, Wakai K, Inoue I, Okada Y, Shinomiya N, and Matsuo H on behalf of Japan Gout Genomics Consortium (Japan Gout). Subtype-specific gout susceptibility loci and enrichment of selection pressure on ABCG2 and ALDH2 identified by subtype genome-wide meta-analyses of clinically-defined gout patients. Ann Rheum Dis. 79(5):657-665, 2020. *Co-first author.
  34. Tamura R, Yoshihara K, Nakaoka H, Yachida N, Yamaguchi M, Suda K, Ishiguro T, Nishino K, Ichikawa H, Honma K, Kikuchi A, Ueda Y, Takei Y, Fujiwara H, Motoyama T, Okuda S, Wakai T, Inoue I, and Enomoto T. XCL1 expression correlates with CD8 positive T cells infiltration and PD-L1 expression in squamous cell carcinoma arising from mature cystic teratoma of the ovary. Oncogene. 39(17):3541-3554, 2020.
  35. Higashino T*, Morimoto K*, Nakaoka H*, Toyoda Y*, Kawamura Y*, Shimizu S*, Nakamura T, Hosomichi K, Nakayama A, Ooyama K, Ooyama H, Shimizu T, Ueno M, Ito T, Tamura T, Naito M, Nakashima H, Kawaguchi M, Takao M, Kawai Y, Osada N, Ichida K, Yamamoto K, Suzuki H, Shinomiya N, Inoue I, Takada T, and Matsuo H. Dysfunctional missense variant of OAT10/SLC22A13 decreases gout risk and serum uric acid levels. Ann. Rheum. Dis. 79(1):164-166, 2020.*Co-first author.
  36. Zhang S, Kohira Y, Orita H, Ishimine M, Kobayashi T, Chua SMB, Nakaoka H, Inoue I, Hino O, Yokomizo T, Fukunaga T, and Lee-Okada HC. Sensitization of gastric cancer cells to irinotecan by p53 activation. BPB Rep. 2: 130-133, 2019.
  37. Sugino K, Tamura R, Nakaoka H, Yachida N, Yamaguchi M, Mori Y, Yamawaki K, Suda K, Ishiguro T, Adachi S, Isobe M, Yamaguchi M, Kashima K, Motoyama T, Inoue I, Yoshihara K, and Enomoto T. Germline and somatic mutations of homologous recombination-associated genes in Japanese ovarian cancer patients. Sci. Rep. 9(1):17808, 2019.
  38. Suda K, Nakaoka H, Yoshihara K, Ishiguro T, Adachi S, Kase H, Motoyama T, Inoue I, and Enomoto T. Different mutation profiles between epithelium and stroma in endometriosis and normal endometrium. Hum. Reprod. 34(10):1899-1905, 2019.
  39. Hata C, Nakaoka H, Xiang Y, Wang D, Yang A, Liu D, Liu F, Zou Q, Zheng K, Inoue I, and You H. Exploration of intermediate-sized indels by next-generation multigene panel testing in Han Chinese patients with breast cancer. Hum. Genome Var.. 6:51, 2019.
  40. Kawamura Y*, Nakaoka H*, Nakayama A*, Okada Y*, Yamamoto K*, Higashino T, Sakiyama M, Shimizu T, Ooyama H, Ooyama K, Nagase M, Hidaka Y, Shirahama Y, Hosomichi K, Nishida Y, Shimoshikiryo I, Hishida A, Katsuura-Kamano S, Shimizu S, Kawaguchi M, Uemura H, Ibusuki R, Hara M, Naito M, Takao M, Nakajima M, Iwasawa S, Nakashima H, Ohnaka K, Nakamura T, Stiburkova B, Merriman TR, Nakatochi M, Ichihara S, Yokota M, Takada T, Saitoh T, Kamatani Y, Takahashi A, Arisawa K, Takezaki T, Tanaka K, Wakai K, Kubo M, Hosoya T, Ichida K, Inoue I, Shinomiya N, and Matsuo H. Genome-wide association study revealed novel loci which aggravate asymptomatic hyperuricaemia into gout. Ann. Rheum. Dis. 78(10):1430-1437, 2019. *Co-first author.
  41. Suda K, Nakaoka H, Hata C, Yahata N, Isobe M, Kameyama H, Wakai T, Motoyama T, Inoue I, Yoshihara K, and Enomoto T. Concurrent isolated retroperitoneal HGSC and STIC defined by somatic mutation analysis: a case report. Diagn. Pathol. 14(1):17, 2019.
  42. 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, and Okada Y. Genetic and phenotypic landscape of the major histocompatibility complex region in the Japanese population. Nat. Genet.51(3):470-480, 2019.

Before 2019 (selected)

  1. Suda K*, Nakaoka H*, Yoshihara K, Ishiguro T, Tamura R, Mori Y, Yamawaki K, Adachi S, Takahashi T, Kase H, Tanaka K, Yamamoto T, Motoyama T, Inoue I, and Enomoto T. Clonal expansion and diversification of cancer-associated mutations in endometriosis and normal endometrium. Cell Rep. 24(7):1777-1789, 2018. *Co-first author.
  2. Nakaoka H, Gurumurthy A, Hayano T, Ahmadloo A, Omer WH, Yoshihara K, Yamamoto A, Kurose K, Enomoto T, Akira S, Hosomichi K, and Inoue I. Allelic imbalance in regulation of ANRIL through chromatin interaction at 9p21 endometriosis risk locus. PLOS Genet. 12(4): e1005893, 2016.
  3. Matsuo H*, Yamamoto K*, Nakaoka H*, Nakayama A*, Sakiyama M*, Chiba T, Takahashi A, Nakamura T, Nakashima H, Takada Y, Danjoh I, Shimizu S, Abe J, Kawamura Y, Terashige S, Ogata H, Tatsukawa S, Guang Y, Okada R, Morita E, Naito M, Tokumasu A, Onoue H, Iwaya K, Ito T, Takada T, Inoue K, Kato Y, Nakamura Y, Sakurai Y, Suzuki H, Kanai Y, Hosoya T, Hamajima N, Inoue I, Kubo M, Ichida K, Ooyama H, Shimizu T, and Shinomiya N. Genome-wide association study of clinically defined gout identifies multiple risk loci and its association with clinical subtypes. Ann. Rheum. Dis. 75(4): 652-659, 2016. *Co-first author.
  4. Nakaoka H and Inoue I. Distribution of HLA haplotypes across Japanese Archipelago: similarity, difference and admixture. J. Hum. Genet. 60(11): 683-690, 2015.
  5. Nakaoka H, Tajima A, Yoneyama T, Hosomichi K, Kasuya H, Mizutani T, and Inoue I. Gene expression profiling reveals distinct molecular signatures associated with the rupture of intracranial aneurysm. Stroke. 45(8): 2239-2245, 2014.
  6. Nakaoka H, Takahashi T, Akiyama K, Cui T, Tajima A, Krischek B, Kasuya H, Hata A, and Inoue I: Differential effects of chromosome 9p21 variation on subphenotypes of intracranial aneurysm: site distribution. Stroke. 41(8): 1593-1598, 2010.
  7. Nakaoka H and Inoue I: Meta-analysis of genetic association studies: methodologies, between-study heterogeneity and winner’s curse. J. Hum. Genet. 54(11): 615-623, 2009.