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Home  > Genomic Pathology  > Publications

Publications

2017


  • Konishi H, Komura D, Katoh H, Atsumi S, Koda H, Yamamoto A, Seto Y, Fukayama M, Yamaguchi R, Imoto S, Ishikawa S.
    Capturing the Difference in Humoral Immunity between Normal and Tumor Environments from RNA Sequences of B-Cell Receptors Using Supervised Machine Learning.
    bioRXiv (preprint) 2017, 187120.


  • Komura D, Ishikawa S.
    Machine learning methods for histopathological image analysis.
    arXiv (preprint) 2017, arXiv:1709.00786.


  • Katoh H, Komura D, Konishi H, Suzuki R, Yamamoto A, Kakiuchi M, Sato R, Ushiku T, Yamamoto S, Tatsuno K, Oshima T, Nomura S, Seto Y, Fukayama M, Aburatani H, Ishikawa S.
    Immunogenetic Profiling for Gastric Cancers Identifies Sulfated Glycosaminoglycans as Major and Functional B Cell Antigens in Human Malignancies.
    (equal contribution)
    Cell Reports 2017 Aug;20(5):1073-1087. doi: 10.1016/j.celrep.2017.07.016


  • Ito Y, Maeda D, Yoshida M, Yoshida A, Kudo-Asabe Y, Nanjyo H, Izumi C, Yamamoto F, Inoue M, Shibata H, Katoh H, Ishikawa S, Nakamura H, Totoki Y, Shibata T, Yachida S, Goto A.
    Cardiac intimal sarcoma with PDGFRβ mutation and co-amplification of PDGFRα and MDM2: an autopsy case analyzed by whole-exome sequencing.
    Virchows Arch. 2017 May 4. doi: 10.1007/s00428-017-2135-x. [Epub ahead of print] PubMed PMID: 28474091.

  • Kon S, Ishibashi K, Katoh H, Kitamoto S, Shirai T, Tanaka S, Kajita M, Ishikawa S, Yamauchi H, Yako Y, Kamasaki T, Matsumoto T, Watanabe H, Egami R, Sasaki A, Nishikawa A, Kameda I, Maruyama T, Narumi R, Morita T, Sasaki Y, Enoki R, Honma S, Imamura H, Oshima M, Soga T, Miyazaki JI, Duchen MR, Nam JM, Onodera Y, Yoshioka S, Kikuta J, Ishii M, Imajo M, Nishida E, Fujioka Y, Ohba Y, Sato T, Fujita Y.
    Cell competition with normal epithelial cells promotes apical extrusion of transformed cells through metabolic changes.
    Nat Cell Biol. 2017 May;19(5):530-541. doi: 10.1038/ncb3509. Epub 2017 Apr 17. PubMed PMID: 28414314.

  • Shikata Y, Yoshimaru T, Komatsu M, Katoh H, Sato R, Kanagaki S, Okazaki Y, Toyokuni S, Tashiro E, Ishikawa S, Katagiri T, Imoto M.
    Protein kinase A inhibition facilitates the antitumor activity of xanthohumol, a valosin-containing protein inhibitor.
    Cancer Sci. 2017 Apr;108(4):785-794. doi:10.1111/cas.13175. Epub 2017 Apr 20. PubMed PMID: 28122154; PubMed Central PMCID:PMC5406609.

2016



  • Katoh H, Ishikawa S.
    Genomic pathobiology of gastric carcinoma.
    Pathol Int. 2016 Dec 22. doi: 10.1111/pin.12493. [Epub ahead of print] PubMed PMID: 28004449.

  • Oikawa Y, Morita KI, Kayamori K, Tanimoto K, Sakamoto K, Katoh H, Ishikawa S, Inazawa J, Harada H.
    Receptor tyrosine kinase amplification is predictive of distant metastasis in patients with oral squamous cell carcinoma.
    Cancer Sci. 2016 Nov 27. doi: 10.1111/cas.13126. [Epub ahead of print] PubMed PMID: 27889930.

  • Komura D, Isagawa T, Kishi K, Suzuki R, Sato R, Tanaka M, Katoh H, Yamamoto S, Tatsuno K, Fukayama M, Aburatani H, Ishikawa S.
    CASTIN: a system for comprehensive analysis of cancer-stromal interactome.
    BMC Genomics. 2016 Nov 9;17(1):899. PubMed PMID: 27829362; PubMed Central PMCID: PMC5103609.


  • Ito T, Matsubara D, Tanaka I, Makiya K, Tanei ZI, Kumagai Y, Shiu SJ, Nakaoka HJ, Ishikawa S, Isagawa T, Morikawa T, Shinozaki-Ushiku A, Goto Y, Nakano T, Tsuchiya T, Tsubochi H, Komura D, Aburatani H, Dobashi Y, Nakajima J, Endo S, Fukayama M, Sekido Y, Niki T, Murakami Y.
    Loss of YAP1 Defines Neuroendocrine Differentiation of Lung Tumors.
    Cancer Sci. 2016 Oct;107(10):1527-1538. doi:10.1111/cas.13013. PubMed PMID: 27418196.


  • Matsusaka K, Ushiku T, Urabe M, Fukuyo M, Abe H, Ishikawa S, Seto Y, Aburatani H, Hamakubo T, Kaneda A, Fukayama M.
    Coupling CDH17 and CLDN18 markers forcomprehensive membrane-targeted detection of human gastric cancer.
    Oncotarget. 2016 Sep 27;7(39):64168-64181. doi: 10.18632/oncotarget.11638. PubMed PMID: 27580354.


  • Ichimura T, Abe H, Morikawa T, Yamashita H, Ishikawa S, Ushiku T, Seto Y, Fukayama M.
    Low density of CD204-positive M2 type tumor-associated macrophages in Epstein-Barr virus-associated gastric cancer: a clinicopathological study with digital image analysis.
    Hum Pathol. 2016 Oct;56:74-80. doi:10.1016/j.humpath.2016.06.002. PubMed PMID: 27342912.


  • Matsusaka K, Ishikawa S, Nakayama A, Ushiku T, Nishimoto A, Urabe M, Kaneko N, Kunita A, Kaneda A, Aburatani H, Fujishiro M, Seto Y, Fukayama M.
    Tumor Content Chart-Assisted HER2/CEP17 Digital PCR Analysis of Gastric Cancer Biopsy Specimens.
    PLoS One. 2016 Apr 27;11(4):e0154430. doi:10.1371/journal.pone.0154430. eCollection 2016. PMID: 27119558.


  • Ishikawa S.
    Opposite RHOA functions within the ATLL category.
    Blood. 2016 Feb 4;127(5):524-5. doi: 10.1182/blood-2015-12-683458. PMID:26847067

2015



  • Maeda D, Akiyama Y, Morikawa T, Kunita A, Ota Y, Katoh H, Niimi A, Nomiya A, Ishikawa S, Goto A, Igawa Y, Fukayama M, Homma Y.
    Hunner-Type (Classic) Interstitial Cystitis: A Distinct Inflammatory Disorder Characterized by Pancystitis, with Frequent Expansion of Clonal B-Cells and Epithelial Denudation.
    PLoS One 2015 Nov 20;10(11):e0143316. doi: 10.1371/journal.pone.0143316. PMID: 26587589


  • Ushiku T, Ishikawa S, Kakiuchi M, Tanaka A, Katoh H, Aburatani H, Lauwers GY, Fukayama M.
    RHOA mutation in diffuse-type gastric cancer: a comparative clinicopathology analysis of 87 cases.
    Gastric Cancer. 2016 Apr;19(2):403-11. doi: 10.1007/s10120-015-0493-0. Epub 2015 Apr 1. PubMed PMID: 25823974; PubMed Central PMCID: PMC4824805.


  • Saito S, Morishima K, Ui T, Hoshino H, Matsubara D, Ishikawa S, Aburatani H, Fukayama M, Hosoya Y, Sata N, Lefor AK, Yasuda Y, Niki T.
    The role of HGF/MET and FGF/FGFR in fibroblast-derived growth stimulation and lapatinib-resistance of esophageal squamous cell carcinoma.
    BMC Cancer. 2015 Feb 25;15:82. doi: 10.1186/s12885-015-1065-8. PMID: 25884729

2014



  • Katsuda T, Kurata H, Tamai R, Banas A, Ishii T, Ishikawa S, Ochiya T.
    The in vivo evaluation of the therapeutic potential of human adipose tissue-derived mesenchymal stem cells for acute liver disease.
    Methods Mol Biol. 2014;1213:57-67. doi: 10.1007/978-1-4939-1453-1_6. PMID: 25173374


  • Totoki Y, Tatsuno K, Covington KR, Ueda H, Creighton CJ, Kato M, Tsuji S, Donehower LA, Slagle BL, Nakamura H, Yamamoto S, Shinbrot E, Hama N, Lehmkuhl M, Hosoda F, Arai Y, Walker K, Dahdouli M, Gotoh K, Nagae G, Gingras MC, Muzny DM, Ojima H, Shimada K, Midorikawa Y, Goss JA, Cotton R, Hayashi A, Shibahara J, Ishikawa S, Guiteau J, Tanaka M, Urushidate T, Ohashi S, Okada N, Doddapaneni H, Wang M, Zhu Y, Dinh H, Okusaka T, Kokudo N, Kosuge T, Takayama T, Fukayama M, Gibbs RA, Wheeler DA, Aburatani H, Shibata T.
    Trans-ancestry mutational landscape of hepatocellular carcinoma genomes.
    Nat Genet. 2014 Dec;46(12):1267-73. doi: 10.1038/ng.3126. Epub 2014 Nov 2. PubMed PMID: 25362482.


  • Kobayashi S, Hara A, Isagawa T, Manabe I, Takeda K, MaruYama T.
    The Nuclear IκB Family Protein IκBNS Influences the Susceptibility to Experimental Autoimmune Encephalomyelitis in a Murine Model.
    PLoS One. 2014 Oct 27;9(10):e110838. doi: 10.1371/journal.pone.0110838. eCollection 2014. PMID: 25347393


  • Hanihara-Tatsuzawa F, Miura H, Kobayashi S, Isagawa T, Okuma A, Manabe I, MaruYama T.
    Control of Toll-like Receptor-Mediated T Cell-Independent Type 1 Antibody Responses by the Inducible Nuclear Protein IκB-ζ
    J Biol Chem. 2014 Nov 7;289(45):30925-36. doi: 10.1074/jbc.M114.553230. Epub 2014 Aug 14. PubMed PMID: 25124037; PubMed Central PMCID: PMC4223300.


  • Ibrahim R, Matsubara D, Osman W, Morikawa T, Goto A, Morita S, Ishikawa S, Aburatani H, Takai D, Nakajima J, Fukayama M, Niki T, Murakami Y.
    Expression of PRMT5 in lung adenocarcinoma and its significance in epithelial-mesenchymal transition.
    Hum Pathol. 2014 Jul;45(7):1397-405. doi:10.1016/j.humpath.2014.02.013. Epub 2014 Feb 28. PubMed PMID: 24775604.


  • Kakiuchi M, Nishizawa T, Ueda H, Gotoh K, Tanaka A, Hayashi A, Yamamoto S, Tatsuno K, Katoh H, Watanabe Y, Ichimura T, Ushiku T, Funahashi S, Tateishi K, Wada I, Shimizu N, Nomura S, Koike K, Seto Y, Fukayama M, Aburatani H, Ishikawa S.
    Recurrent gain-of-function mutations of RHOA in diffuse-type gastric carcinoma.
    Nat Genet. 2014 Jun;46(6):583-7. doi: 10.1038/ng.2984. Epub 2014 May 11. PubMed PMID: 24816255.


  • Hamanaka W, Motoi N, Ishikawa S, Ushijima M, Inamura K, Hatano S, Uehara H, Okumura S, Nakagawa K, Nishio M, Horai T, Aburatani H, Matsuura M, Iwasaki A, Ishikawa Y.
    A subset of small cell lung cancer with low neuroendocrine expression and good prognosis: a comparison study of surgical and inoperable cases with biopsy.
    Hum Pathol. 2014 May;45(5):1045-56. doi: 10.1016/j.humpath.2014.01.001. Epub 2014 Jan 23. PMID: 24746210.


  • Tanaka M, Suzuki HI, Shibahara J, Kunita A, Isagawa T, Yoshimi A, Kurokawa M, Miyazono K, Aburatani H, Ishikawa S, Fukayama M.
    EVI1 oncogene promotes KRAS pathway through suppression of microRNA-96 in pancreatic carcinogenesis.
    Oncogene. 2014 May 8;33(19):2454-63. doi: 10.1038/onc.2013.204. Epub 2013 Jun 10. PubMed PMID: 23752186.


  • Hayashi A, Morikawa T, Kawai T, Kume H, Ishikawa S, Homma Y, Fukayama M.
    Clinicopathological and prognostic significance of EZH2 expression in upper urinary tract carcinoma.
    Virchows Arch. 2014 Apr;464(4):463-71. doi: 10.1007/s00428-014-1541-6. Epub 2014 Jan 21. PubMed PMID: 24446035


  • Kikuchi Y, Kunita A, Iwata C, Komura D, Nishiyama T, Shimazu K, Takeshita K, Shibahara J, Kii I, Morishita Y, Yashiro M, Hirakawa K, Miyazono K, Kudo A, Fukayama M, Kashima TG.
    The niche component periostin is produced by cancer-associated fibroblasts, supporting growth of gastric cancer through ERK activation.
    Am J Pathol. 2014 Mar;184(3):859-70. doi: 10.1016/j.ajpath.2013.11.012. Epub 2014 Jan 10. PubMed PMID: 24418260.


  • Hayashi A, Yamauchi N, Shibahara J, Kimura H, Morikawa T, Ishikawa S, Nagae G, Nishi A, Sakamoto Y, Kokudo N, Aburatani H, Fukayama M.
    Concurrent activation of acetylation and tri-methylation of H3K27 in a subset of hepatocellular carcinoma with aggressive behavior.
    PLoS One. 2014 Mar 10;9(3):e91330. doi:10.1371/journal.pone.0091330. eCollection 2014. PubMed PMID: 24614346


  • Ui T, Morishima K, Saito S, Sakuma Y, Fujii H, Hosoya Y, Ishikawa S, Aburatani H, Fukayama M, Niki T, Yasuda Y.
    The HSP90 inhibitor 17-N-allylamino-17-demethoxy geldanamycin (17-AAG) synergizes with cisplatin and induces apoptosis in cisplatin-resistant esophageal squamous cell carcinoma cell lines via the Akt/XIAP pathway.
    Oncol Rep. 2014 Feb;31(2):619-24. doi: 10.3892/or.2013.2899. PubMed PMID: 24317439


  • Ichimura T, Morikawa T, Kawai T, Nakagawa T, Matsushita H, Kakimi K, Kume H, Ishikawa S, Homma Y, Fukayama M.
    Prognostic Significance of CD204-Positive Macrophages in Upper Urinary Tract Cancer.
    Ann Surg Oncol. 2014 Jun;21(6):2105-12. doi: 10.1245/s10434-014-3503-2. Epub 2014 Feb 4. PubMed PMID: 24492923

2013


  • Goda S, Isagawa T, Chikaoka Y, Kawamura T, Aburatani H.
    Control of Histone H3 Lysine 9 (H3K9) Methylation State via Cooperative Two-step Demethylation by Jumonji Domain Containing 1A (JMJD1A) Homodimer.
    J Biol Chem. 2013 Dec 27;288(52):36948-56. doi: 10.1074/jbc.M113.492595. Epub 2013 Nov 8. PMID: 24214985


  • Fustin JM, Doi M, Yamaguchi Y, Hayashi H, Nishimura S, Yoshida M, Isagawa T, Suimye-Morioka M, Kakeya H, Manabe I, Okamura H.
    RNA-methylation-dependent RNA processing controls the speed of the circadian clock.
    Cell. 2013 Nov 7;155(4):793-806. doi: 10.1016/j.cell.2013.10.026. PubMed PMID: 24209618


  • Kon A, Shih LY, Minamino M, Sanada M, Shiraishi Y, Nagata Y, Yoshida K, Okuno Y, Bando M, Nakato R, Ishikawa S, Sato-Otsubo A, Nagae G, Nishimoto A, Haferlach C, Nowak D, Sato Y, Alpermann T, Nagasaki M, Shimamura T, Tanaka H, Chiba K, Yamamoto R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Nakamaki T, Ishiyama K, Nolte F, Hofmann WK, Miyawaki S, Chiba S, Mori H, Nakauchi H, Koeffler HP, Aburatani H, Haferlach T, Shirahige K, Miyano S, Ogawa S.
    Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms.
    Nat Genet. 2013 Oct;45(10):1232-7. doi: 10.1038/ng.2731. Epub 2013 Aug 18. PubMed PMID: 23955599


  • Saito T, Takeda N, Amiya E, Nakao T, Abe H, Semba H, Soma K, Koyama K, Hosoya Y, Imai Y, Isagawa T, Watanabe M, Manabe I, Komuro I, Nagai R, Maemura K.
    VEGF-A induces its negative regulator, soluble form of VEGFR-1, by modulating its alternative splicing.
    FEBS Lett. 2013 Jul 11;587(14):2179-85. doi: 10.1016/j.febslet.2013.05.038. Epub 2013 May 24. PubMed PMID: 23711375


  • Yamamoto S, Tateishi K, Kudo Y, Yamamoto K, Isagawa T, Nagae G, Nakatsuka T, Asaoka Y, Ijichi H, Hirata Y, Otsuka M, Ikenoue T, Aburatani H, Omata M, Koike K.
    Histone demethylase KDM4C regulates sphere formation by mediating the cross talk between Wnt and Notch pathways in colonic cancer cells.
    Carcinogenesis. 2013 Oct;34(10):2380-8. doi: 10.1093/carcin/bgt174. Epub 2013 May 22. PubMed PMID: 23698634


  • Nakaya T, Kikuchi Y, Kunita A, Ishikawa S, Matsusaka K, Hino R, Aburatani H, Fukayama M.
    Enrichment of stem-like cell population comprises transformation ability of Epstein-Barr virus latent membrane protein 2A for non-transformed cells.
    Virus Res. 2013 Jun;174(1-2):108-15. doi: 10.1016/j.virusres.2013.03.009. Epub 2013 Mar 22. PubMed PMID: 23524324


  • Sato T, Kaneda A, Tsuji S, Isagawa T, Yamamoto S, Fujita T, Yamanaka R, Tanaka Y, Nukiwa T, Marquez VE, Ishikawa Y, Ichinose M, Aburatani H.
    PRC2 overexpression and PRC2-target gene repression relating to poorer prognosis in small cell lung cancer.
    Sci Rep. 2013;3:1911. doi: 10.1038/srep01911. PubMed PMID: 23714854


  • Li W, Katoh H, Wang L, Yu X, Du Z, Yan X, Zheng P, Liu Y.
    FOXP3 regulates sensitivity of cancer cells to irradiation by transcriptional repression of BRCA1.
    Cancer Res. 2013 Apr 1;73(7):2170-80. doi: 10.1158/0008-5472.CAN-12-2481. Epub 2013 Jan 14. PubMed PMID: 23319807