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先端医療開発センター

Home > Organization > Division of Translational Informatics(Kashiwa) > Publications

Publications

Kazuya Tsuchihara

  1. Yamazaki K, Taniguchi H, Yoshino T, Akagi K, Ishida H, Ebi H, Nakatani K, Muro K, Yatabe Y, Yamaguchi K, Tsuchihara K. Japanese Society of Medical Oncology Clinical Guidelines: Molecular Testing for Colorectal Cancer Treatment, Third Edition. Cancer Sci. 2018 Jun;109(6):2074-2079.
  2. Fujioka R, Mochizuki N, Ikeda M, Sato A, Nomura S, Owada S, Yomoda S, Tsuchihara K, Kishino S, Esumi H. Change in plasma lactate concentration during arctigenin administration in a phase I clinical trial in patients with gemcitabine-refractory pancreatic cancer. PLoS One. 2018 Jun 1;13(6):e0198219.
  3. Kageyama SI, Nihei K, Karasawa K, Sawada T, Koizumi F, Yamaguchi S, Kato S, Hojo H, Motegi A, Tsuchihara K, Akimoto T. Radiotherapy increases plasma levels of tumoral cell-free DNA in non-small cell lung cancer patients. Oncotarget. 2018 Apr 10;9(27):19368-19378.
  4. Sereewattanawoot S, Suzuki A, Seki M, Sakamoto Y, Kohno T, Sugano S, Tsuchihara K, Suzuki Y. Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines. Sci Rep. 2018 Mar 21;8(1):4926.
  5. Makinoshima H, Umemura S, Suzuki A, Nakanishi H, Maruyama A, Udagawa H, Mimaki S, Matsumoto S, Niho S, Ishii G, Tsuboi M, Ochiai A, Esumi H, Sasaki T, Goto K, Tsuchihara K. Metabolic Determinants of Sensitivity to Phosphatidylinositol 3-Kinase Pathway Inhibitor in Small-Cell Lung Carcinoma. Cancer Res. 2018 May 1;78(9):2179-2190.
  6. Kashima Y, Suzuki A, Liu Y, Hosokawa M, Matsunaga H, Shirai M, Arikawa K, Sugano S, Kohno T, Takeyama H, Tsuchihara K, Suzuki Y. Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response. Sci Rep. 2018 Feb 22;8(1):3482.
  7. Suzuki A, Kawano S, Mitsuyama T, Suyama M, Kanai Y, Shirahige K, Sasaki H, Tokunaga K, Tsuchihara K, Sugano S, Nakai K, Suzuki Y. DBTSS/DBKERO for integrated analysis of transcriptional regulation. Nucleic Acids Res. 2018 Jan 4;46(D1):D229-D238.
  8. Suzuki A, Suzuki M, Mizushima-Sugano J, Frith MC, Makalowski W, Kohno T, Sugano S, Tsuchihara K, Suzuki Y. Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer. DNA Res. 2017 Dec 1;24(6):585-596.
  9. Shinozaki E, Yoshino T, Yamazaki K, Muro K, Yamaguchi K, Nishina T, Yuki S, Shitara K, Bando H, Mimaki S, Nakai C, Matsushima K, Suzuki Y, Akagi K, Yamanaka T, Nomura S, Fujii S, Esumi H, Sugiyama M, Nishida N, Mizokami M, Koh Y, Abe Y, Ohtsu A, Tsuchihara K. Clinical significance of BRAF non-V600E mutations on the therapeutic effects of anti-EGFR monoclonal antibody treatment in patients with pretreated metastatic colorectal cancer: the Biomarker Research for anti-EGFR monoclonal Antibodies by Comprehensive Cancer genomics (BREAC) study. Br J Cancer. 2017 Nov 7;117(10):1450-1458. doi: 10.1038/bjc.2017.308. Epub 2017 Oct 3.
  10. Nukaga S, Yasuda H, Tsuchihara K, Hamamoto J, Masuzawa K, Kawada I, Naoki K, Matsumoto S, Mimaki S, Ikemura S, Goto K, Betsuyaku T, Soejima K. Amplification of EGFR Wild-Type Alleles in Non-Small Cell Lung Cancer Cells Confers Acquired Resistance to Mutation-Selective EGFR Tyrosine Kinase Inhibitors. Cancer Res. 2017 Apr 15;77(8):2078-2089.
  11. Miyoshi T, Umemura S, Matsumura Y, Mimaki S, Tada S, Makinoshima H, Ishii G, Udagawa H, Matsumoto S, Yoh K, Niho S, Ohmatsu H, Aokage K, Hishida T, Yoshida J, Nagai K, Goto K, Tsuboi M, Tsuchihara K. Genomic Profiling of Large-Cell Neuroendocrine Carcinoma of the Lung. Clin Cancer Res. 2017 Feb 1;23(3):757-765.
  12. Mimaki S, Totsuka Y, Suzuki Y, Nakai C, Goto M, Kojima M, Arakawa H, Takemura S, Tanaka S, Marubashi S, Kinoshita M, Matsuda T, Shibata T, Nakagama H, Ochiai A, Kubo S, Nakamori S, Esumi H, Tsuchihara K. Hypermutation and unique mutational signatures of occupational cholangiocarcinoma in printing workers exposed to haloalkanes. Carcinogenesis. 2016 Aug;37(8):817-826.
  13. Makinoshima H, Takita M, Saruwatari K, Umemura S, Obata Y, Ishii G, Matsumoto S, Sugiyama E, Ochiai A, Abe R, Goto K, Esumi H, Tsuchihara K. Signaling through the Phosphatidylinositol 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Axis Is Responsible for Aerobic Glycolysis mediated by Glucose Transporter in Epidermal Growth Factor Receptor (EGFR)-mutated Lung Adenocarcinoma. J Biol Chem. 2015 Jul 10;290(28):17495-504.
  14. Suzuki A, Matsushima K, Makinoshima H, Sugano S, Kohno T, Tsuchihara K, Suzuki Y. Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment. Genome Biol. 2015 Apr 3;16:66.
  15. Suzuki A, Makinoshima H, Wakaguri H, Esumi H, Sugano S, Kohno T, Tsuchihara K, Suzuki Y. Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines. Nucleic Acids Res. 2014 Dec 16;42(22):13557-72.
  16. Umemura S, Mimaki S, Makinoshima H, Tada S, Ishii G, Ohmatsu H, Niho S, Yoh K, Matsumoto S, Takahashi A, Morise M, Nakamura Y, Ochiai A, Nagai K, Iwakawa R, Kohno T, Yokota J, Ohe Y, Esumi H, Tsuchihara K, Goto K. Therapeutic priority of the PI3K/AKT/mTOR pathway in small cell lung cancers as revealed by a comprehensive genomic analysis. J Thorac Oncol. 2014 Sep;9(9):1324-31.
  17. Nasuno T, Mimaki S, Okamoto M, Esumi H, Tsuchihara K. Effect of a poly(ADP-ribose) polymerase-1 inhibitor against esophageal squamous cell carcinoma cell lines. Cancer Sci. 2014 Feb;105(2):202-10.
  18. Suzuki A, Mimaki S, Yamane Y, Kawase A, Matsushima K, Suzuki M, Goto K, Sugano S, Esumi H, Suzuki Y, Tsuchihara K. Identification and characterization of cancer mutations in Japanese lung adenocarcinoma without sequencing of normal tissue counterparts. PLoS One. 2013 Sep 12;8(9):e73484.
  19. Suzuki M, Makinoshima H, Matsumoto S, Suzuki A, Mimaki S, Matsushima K, Yoh K, Goto K, Suzuki Y, Ishii G, Ochiai A, Tsuta K, Shibata T, Kohno T, Esumi H, Tsuchihara K. Identification of a lung adenocarcinoma cell line with CCDC6-RET fusion gene and the effect of RET inhibitors in vitro and in vivo. Cancer Sci. 2013 Jul;104(7):896-903.

Riu Yamashita

  1. Matsumoto A*, Pasut A*, Matsumoto M*, Yamashita R*, Fung J, Monteleone E, Saghatelian A, Nakayama KI, Clohessy JG, Pandolfi PP., mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide., Nature., 2017 Jan 12;541(7636):228-232. doi: 10.1038/nature21034. Epub 2016 Dec 26.
  2. Yamagishi J, Sato Y, Shinozaki N, Ye B, Tsuboi A, Nagasaki M, Yamashita R., Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes., PLoS One. 2016 Apr 22;11(4):e0154389. doi: 10.1371/journal.pone.0154389. eCollection 2016.
  3. Sato Y*, Yamagishi J*, Yamashita R*, Shinozaki N, Ye B, Yamada T, Yamamoto M, Nagasaki M, Tsuboi A. Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals. PLoS One. 2015 Jun 29;10(6):e0131607. doi: 10.1371/journal.pone.0131607. eCollection 2015.
  4. Yamashita R., Sugano S., Suzuki Y. and Nakai K. DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. Nucleic Acids Res, 40(1), D150-4, Jan 2012.
  5. Yamashita R.*, Sathira N.P.*, Kanai A., Tanimoto K., Arauchi T., Tanaka Y., Hashimoto S., Sugano S., Nakai K. and Suzuki Y. Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res, 21(5), 775-89, May 2011.
  6. Yamashita R., Suzuki Y., Takeuchi N., Wakaguri H., Ueda T., Sugano S. and Nakai K. Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics. Nucleic Acids Res, 36(11), 3707-15, Jun 2008.
  7. Yamashita R., Suzuki Y., Sugano S. and Nakai K. Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene, 350(2), 129-36, May 9 2005.
  8. Kato K., Yamashita R., Matoba R., Monden M., Noguchi S., Takagi T. and Nakai K. Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Res, 33(Database issue), D533-6, Jan 1 2005.
  9. Ota T., et al., Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet, 36(1), 40-5, Jan 2004.
  10. Yamashita R., Suzuki Y., Nakai K. and Sugano S. Small open reading frames in 5' untranslated regions of mRnas. C R Biol, 326(10-11), 987-91, Oct-Nov 2003.

Yukie Kashima

  1. Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
    Yukie Kashima, Ayako Suzuki, Ying Liu, Masahito Hosokawa, Hiroko Matsunaga, Masataka Shirai, Koji Arikawa, Sumio Sugano, Takashi Kohno, Haruko Takeyama, Katsuya Tsuchihara, and Yutaka Suzuki, Scientific Reports (2018)
  2. Three-step transcriptional priming that drives the commitment of multipotent progenitors toward B cells
    Tomohiro Miyai, Junichiro Takano, Takaho A. Endo, Eiryo Kawakami, Yasutoshi Agata, Yasutaka Motomura, Masato Kubo, Yukie Kashima, Yutaka Suzuki, Hiroshi Kawamoto, and Tomokatsu Ikawa, Genes & Dev (2018)
  3. The UL12 protein of herpes simplex virus 1 is regulated by tyrosine phosphorylation.
    Hikaru Fujii, Akihisa Kato, Michio Mugitani, Yukie Kashima, Masaaki Oyama, Hiroko Kozuka-Hata, Jun Arii, and Yasushi Kawaguchi, J Virol (2014)

Sachiyo Mimaki

  1. Shinozaki E, Yoshino T, Yamazaki K, Muro K, Yamaguchi K, Nishina T, Yuki S, Shitara K, Bando H, Mimaki S, Nakai C, Matsushima K, Suzuki Y, Akagi K, Yamanaka T, Nomura S, Fujii S, Esumi H, Sugiyama M, Nishida N, Mizokami M, Koh Y, Abe Y, Ohtsu A, Tsuchihara K. Clinical significance of BRAF non-V600E mutations on the therapeutic effects of anti-EGFR monoclonal antibody treatment in patients with pretreated metastatic colorectal cancer: the Biomarker Research for anti-EGFR monoclonal Antibodies by Comprehensive Cancer genomics (BREAC) study. Br J Cancer. 2017 Nov 7;117(10):1450-1458.
  2. Nukaga S, Yasuda H, Tsuchihara K, Hamamoto J, Masuzawa K, Kawada I, Naoki K, Matsumoto S, Mimaki S, Ikemura S, Goto K, Betsuyaku T, Soejima K. Amplification of EGFR Wild-Type Alleles in Non-Small Cell Lung Cancer Cells Confers Acquired Resistance to Mutation-Selective EGFR Tyrosine Kinase Inhibitors. Cancer Res. 2017 Apr 15;77(8):2078-2089.
  3. Takahashi T, Elzawahry A, Mimaki S, Furukawa E, Nakatsuka R, Nakamura H, Nishigaki T, Serada S, Naka T, Hirota S, Shibata T, Tsuchihara K, Nishida T, Kato M. Genomic and transcriptomic analysis of imatinib resistance in gastrointestinal stromal tumors. Genes Chromosomes Cancer. 2017 Apr;56(4):303-313.
  4. Miyoshi T, Umemura S, Matsumura Y, Mimaki S, Tada S, Makinoshima H, Ishii G, Udagawa H, Matsumoto S, Yoh K, Niho S, Ohmatsu H, Aokage K, Hishida T, Yoshida J, Nagai K, Goto K, Tsuboi M, Tsuchihara K. Genomic Profiling of Large-Cell Neuroendocrine Carcinoma of the Lung. Clin Cancer Res. 2017 Feb 1;23(3):757-765.
  5. Mimaki S, Totsuka Y, Suzuki Y, Nakai C, Goto M, Kojima M, Arakawa H, Takemura S, Tanaka S, Marubashi S, Kinoshita M, Matsuda T, Shibata T, Nakagama H, Ochiai A, Kubo S, Nakamori S, Esumi H, Tsuchihara K. Hypermutation and unique mutational signatures of occupational cholangiocarcinoma in printing workers exposed to haloalkanes. Carcinogenesis. 2016 Aug;37(8):817-26.
  6. Umemura S, Mimaki S, Makinoshima H, Tada S, Ishii G, Ohmatsu H, Niho S, Yoh K, Matsumoto S, Takahashi A, Morise M, Nakamura Y, Ochiai A, Nagai K, Iwakawa R, Kohno T, Yokota J, Ohe Y, Esumi H, Tsuchihara K, Goto K. Therapeutic priority of the PI3K/AKT/mTOR pathway in small cell lung cancers as revealed by a comprehensive genomic analysis. J Thorac Oncol. 2014 Sep;9(9):1324-31.
  7. Suzuki A, Mimaki S, Yamane Y, Kawase A, Matsushima K, Suzuki M, Goto K, Sugano S, Esumi H, Suzuki Y, Tsuchihara K. Identification and characterization of cancer mutations in Japanese lung adenocarcinoma without sequencing of normal tissue counterparts. PLoS One. 2013 Sep 12;8(9):e73484.
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