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Home > Organization > Divisions and Independent Research Units > Group for Development of Molecular diagnostics and Individualized Therapy > Division of Epigenomics > Research Papers

Research Papers

  1. Honda H, Ushijima T, Wakazono K, Oda H, Tanaka Y, Aizawa S-i, Ishikawa T, Yazaki Y and Hirai H.  Acquired loss of p53 induced blastic transformation in p210bcr/abl-expressing hematopoietic cells: a transgenic study for blast crisis of human CML.  Blood, 95: 1144-1150, 2000.  PMID: 10666183
  2. Ushijima T, Yamamoto M, Suzui M, Kuramoto T, Yoshida Y, Nomoto T, Tatematsu M, Sugimura T and Nagao M.  Chromosomal mapping of genes controlling development, histological grade, depth of invasion and size of rat stomach carcinomas.  Cancer Res, 60: 1092-1096, 2000.  PMID: 10706129
  3. Ashida A, Fukutomi T, Tsuda H, Akashi-Tanaka S and Ushijima T.  Atypical medullary carcinoma of the breast with cartilaginous metaplasia in a patient with a BRCA1 germline mutation.  Jpn J Clin Oncol, 30: 30-32, 2000.  PMID: 10770566
  4. Takahashi S, Ikeda Y, Kimoto N, Okochi E, Cui L, Nagao M, Ushijima T and Shirai T.  Mutation induction by mechanical irritation caused by uracil-induced urolithiasis in Big Blue rats.  Mutat Res, 447: 275-280, 2000.  PMID: 10751611
  5. Sugimura T and Ushijima T.  Genetic and epigenetic alterations in carcinogenesis.  Mutat Res, 462: 235-246, 2000.  PMID: 10767635
  6. Stuart GR, Thorleifson E, Okochi E, Boer JGd, Ushijima T, Nagao M and Glickman BW.  Interpretation of mutational spectra from different genes: analyses of PhIP-induced mutational specificity in the lacI and cII transgenes from colon of Big Blue rats.  Mutat Res, 452: 101-121, 2000.  PMID: 10894896
  7. Higo K, Ushijima T, Oyabu A, Ye C, Yagyu S, Takahashi H and Matsuyama M.  Generation of a polymorphic marker linked to thymoma susceptibility gene of rat 1 by genetically-directed representational difference analysis.  Exp Anim, 49: 189-195, 2000.  PMID: 11109541
  8. Takai D, Yagi Y, Habib N, Sugimura T and Ushijima T.  Hypomethylation of LINE1 retrotransposon in human hepatocellular carcinomas, but not in surrounding liver cirrhosis.  Jpn J Clin Oncol, 30: 306-309, 2000.  PMID: 11007163
  9. Yamashita S, Yoshida Y, Kurahashi A, Sugimura T and Ushijima T.  Construction of a high-throughput rat genetic mapping system with 466 arbitrarily primed-representational difference analysis markers.  Mamm Genome, 11: 982-988, 2000.  PMID: 11063254
  10. Niwa T, Yamashita S, Nakamura A, Shiojiri N and Ushijima T.  Isolation of a genetic marker linked to the Bh gene by genetically directed representational difference analysis of closed colony Japanese quails.  Zoolog Sci, 18: 37-41, 2001.  PMID: Pubmedに無し
  11. Kuramoto T, Kitada K, Inui T, Sasaki Y, Ito K, Hase T, Kawagachi S, Ogawa Y, Nakao K, Barsh GS, Nagao M, Ushijima T and Serikawa T.  Attractin/Mahogany/Zitter plays a critical role in myelination of the central nervous system.  Proc Natl Acad Sci USA, 98: 559-564, 2001.  PMID: 11209055
  12. Watanabe N, Okochi E, Hirayama Y, Shimada Y, Yanagihara K, Yoshida MC, Takahashi S, Mochizuki M, Sugimura T, Nagao M and Ushijima T.  Single nucleotide instability without microsatellite instability in rat mammary carcinomas.  Cancer Res, 61: 2632-2640, 2001.  PMID: 11289141
  13. Kuramoto T, Nomoto T, Sugimura T and Ushijima T.  Cloning of the rat agouti gene and identification of the rat nonagouti mutation.  Mamm Genome, 12: 469-471, 2001.  PMID: 11353396
  14. Kuramoto T, Nomoto T, Sugimura T and Ushijima T.  Linkage mapping of the rat Interleukin 1 Receptor Antagonist gene on chromosome 3.  Exp Anim, 12: 355-357, 2001.  PMID: 11515103
  15. Spinola M, Nomoto T, Manenti G, Falvella FS, Brega Massone PP, Conti B, Cataldo I, Valagussa P, Incarbone M, Miyamoto K, Ushijima T and Dragani TA.  Linkage disequilibrium pattern in the L-myc gene in Italian and Japanese non-small-cell lung-cancer patients.  Int J Cancer, 95: 329-331, 2001.  PMID: 11494234
  16. Nagao M, Ochiai M, Okochi E, Ushijima T and Sugimura T.  lacI transgenic animal study: relationships among DNA-adduct levels, mutant frequencies and cancer incidences.  Mutat Res, 477: 119-124, 2001.  PMID: 11376693
  17. Takai D, Wakazono K, Ohishi N, Morita H, Sugimura T and Ushijima T.  Silencing of HTR1B and reduced expression of EDN1 in human lung cancers, revealed by methylation-sensitive representational difference analysis.  Oncogene, 20: 7505-7513, 2001.  PMID: 11709722
  18. Watanabe N, Okochi E, Mochizuki M, Sugimura T and Ushijima T.  The presence of single nucleotide instability in human breast cancer cell lines.  Cancer Res, 61: 7739-7742, 2001.  PMID: 11691786
  19. Kuramoto T, Morimura K, Yamashita S, Okochi E, Watanabe N, Ohta T, Ohki M, Fukushima S, Sugimura T and Ushijima T.  Etiology-specific gene expression profiles in rat mammary carcinomas.  Cancer Res, 62: 3592-3597, 2002.  PMID: 12097258
  20. Kuramoto T, Nomoto T, Fujiwara A, Mizutani M, Sugimura T and Ushijima T.  Insertional mutation of the Attractin gene in the black tremor hamster.  Mamm Genome, 13: 36-40, 2002.  PMID: 11773967
  21. Takahashi S, Suzuki S, Inaguma S, Ikeda Y, Cho YM, Nishiyama N, Fujita T, Inoue T, Hioki T, Sugimura Y, Ushijima T and Shirai T.  Down-regulation of human X-box binding protein 1 (hXBP-1) expression correlates with tumor progression in human prostate cancers.  Prostate, 50: 154-161, 2002.  PMID: 11813207
  22. Takahashi S, Suzuki S, Inaguma S, Cho YM, Ikeda Y, Hayashi N, Inoue T, Sugimura Y, Nishiyama N, Fujita T, Ushijima T and Shirai T.  Down-regulation of Lsm1 is involved in human prostate cancer progression.  Br J Cancer, 86: 940-946, 2002.  PMID: 11953827
  23. Miyamoto K, Fukutomi T, Asada K, Wakazono K, Tsuda H, Asahara T, Sugimura T and Ushijima T.  Promoter hypermethylation and post-transcriptional mechanisms for reduced BRCA1 immunoreactivity in sporadic human breast cancers.  Jpn J Clin Oncol, 32: 79-84, 2002.  PMID: 11956301
  24. Nagao M, Ushijima T, Watanabe N, Okochi E, Ochiai M, Nakagama H and Sugimura T.  Studies on mammary carcinogenesis induced by a heterocyclic amine, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine, in mice and rats.  Environ Mol Mutagen, 39: 158-164, 2002.  PMID: 11921184
  25. Li QL, Ito K, Sakakura C, Fukamachi H, Chi XZ, Lee KY, Lee CW, Han SB, Kim HM, Kim WJ, Inoue K, Nomura S, Yamamoto H, Yamashita N, Yano T, Ikeda T, Itohara S, Inazawwa J, Abe T, Hagiwara A, Yamagishi H, Ooe A, Kaneda A, Sugimura T, Ushijima T, Bae SC and Ito Y.  Causal relationship between the loss of RUNX3 expression and gastric cancer.  Cell, 109: 113-124, 2002.  PMID: 11955451
  26. Yamashita S, Wakazono K, Sugimura T and Ushijima T.  Profiling and selection of genes differentially expressed in the pylorus of rat strains with different proliferative responses and stomach cancer susceptibility.  Carcinogenesis, 23: 923-928, 2002.  PMID: 12082013
  27. Yamashita S, Furumoto K, Nobukiyo A, Kamohara M, Ushijima T and Furukawa T.  Mapping of a gene responsible for cataract formation and its modifier in the UPL rat.  Invest Ophthalmol Vis Sci, 43: 3153-3159, 2002.  PMID: 12356818
  28. Okochi E, Ichimura S, Sugimura T and Ushijima T.  The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.  Jpn J Cancer Res, 93: 501-506, 2002.  PMID: 12036445
  29. Okochi E, Watanabe N, Sugimura T and Ushijima T.  Single nucleotide instability: a wide involvement in human and rat mammary carcinogenesis?  Mutat Res, 101: 506-507, 2002.  PMID: 12351149
  30. Okochi E, Miyamoto K, Wakazono K, Shima H, Sugimura T and Ushijima T.  Reduced Brca1 protein expression in 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine-induced rat mammary carcinomas.  Mol Carcinog, 34: 211-218, 2002.  PMID: 12203372
  31. Kaneda A, Kaminishi M, Nakanishi Y, Sugimura T and Ushijima T.  Reduced expression of the insulin-induced protein 1 and p41 Arp2/3 complex genes in human gastric cancers.  Int J Cancer, 100: 57-62, 2002.  PMID: 12115587
  32. Kaneda A, Kaminishi M, Yanagihara K, Sugimura T and Ushijima T.  Identification of silencing of nine genes in human gastric cancers.  Cancer Res, 62: 6645-6650, 2002.  PMID: 12438262
  33. Kuwamura M, Maeda M, Kuramoto T, Kitada K, Kanehara T, Moriyama M, Nakane Y, Yamate J, Ushijima T, Kotani T and Serikawa T.  The myelin vacuolation (mv) rat with a null mutation in the attractin gene.  Laboratory Investigation, 82: 1279-1286, 2002.  PMID: 12379762
  34. Abe M, Okochi E, Kuramoto T, Kaneda A, Takato T, Sugimura T and Ushijima T.  Cloning of the 5’ upstream region of the rat p16 gene and its role in silencing.  Jpn J Cancer Res, 93: 1100-1106, 2002.  PMID: 12417039
  35. Yamashita S, Nomoto T, Ohta T, Ohki M, Sugimura T, and Ushijima T.  Differential expression of genes related to levels of mucosal cell proliferation among multiple rat strains by using oligonucleotide microarrays.  Mamm Genome, 14: 845-852, 2003.  PMID: 14724737
  36. Ushijima T, Watanabe N, Okochi E, Kaneda A, Sugimura T, and Miyamoto K.  Fidelity of the methylation pattern and its variation in the genome.  Genome Res, 13: 868-874, 2003.  PMID: 12727906
  37. Tsukamoto T, Yamamoto M, Ogasawara N, Ushijima T, Nomoto T, Fujita H, Matsushima T, Nozaki K, Cao X, and Tatematsu M.  beta-Catenin mutations and nuclear accumulation during progression of rat stomach adenocarcinomas.  Cancer Sci, 94: 1046-1051, 2003.  PMID: 14662019
  38. Takahashi S, Suzuki S, Inaguma S, Ikeda Y, Cho YM, Hayashi N, Inoue T, Sugimura Y, Nishiyama N, Fujita T, Chao J, Ushijima T, and Shirai T.  Down-regulated expression of prostasin in high-grade or hormone-refractory human prostate cancers.  Prostate, 54: 187-193, 2003.  PMID: 12518323
  39. Miyamoto K, Asada K, Fukutomi T, Okochi E, Yagi Y, Hasegawa T, Asahara T, Sugimura T, and Ushijima T.  Methylation-associated silencing of heparan sulfate D-glucosaminyl 3-O-sulfotransferase-2 (3-OST-2) in human breast, colon, lung and pancreatic cancers.  Oncogene, 22: 274-280, 2003.  PMID: 12527896
  40. Kaneda A, Takai D, Kaminishi M, Okochi E, and Ushijima T.  Methylation-sensitive representational difference analysis and its application to cancer research.  Ann N Y Acad Sci, 983: 131-141, 2003.  PMID: 12724218
  41. Huang H, Ushijima T, Nagao M, Sugimura T, and Ohgaki H.  beta-Catenin mutations in liver tumors induced by 2-amino-3,4-dimethylimidazo[4,5-f]quinoline in CDF1 mice.  Cancer Lett, 198: 29-35, 2003.  PMID: 12893427
  42. Asada K, Miyamoto K, Fukutomi T, Tsuda H, Yagi Y, Wakazono K, Oishi S, Fukui H, Sugimura T, and Ushijima T.  Reduced expression of GNA11 and silencing of MCT1 in human breast cancers.  Oncology, 64: 380-388, 2003.  PMID: 12759536
  43. Abe M, Yamashita S, Kuramoto T, Hirayama Y, Tsukamoto T, Ohta T, Tatematsu M, Ohki M, Takato T, Sugimura T, and Ushijima T.  Global expression analysis of N-methyl-N'-nitro-N-nitrosoguanidine-induced rat stomach carcinomas using oligonucleotide microarrays.  Carcinogenesis, 24: 861-867, 2003.  PMID: 12771029
  44. Furuta J, Umebayashi Y, Miyamoto K, Kikuchi K, Otsuka F, Sugimura T and Ushijima T.  Promoter methylation profiling of 30 genes in human malignant melanoma.  Cancer Sci, 95: 962-968, 2004.  PMID: 15596045
  45. Hagihara A, Miyamoto K, Furuta J, Hiraoka N, Wakazono K, Seki S, Fukushima S, Tsao MS, Sugimura T and Ushijima T.  Identification of 27 5' CpG islands aberrantly methylated and 13 genes silenced in human pancreatic cancers.  Oncogene, 23: 8705-8710, 2004.  PMID: 15467763
  46. Hoshi M, Morimura K, Wanibuchi H, Wei M, Okochi E, Ushijima T, Takaoka K and Fukushima S.  No-observed effect levels for carcinogenicity and for in vivo mutagenicity of a genotoxic carcinogen.  Toxicol Sci, 81: 273-279, 2004.  PMID: 15282409
  47. Kaneda A, Kaminishi M, Sugimura T and Ushijima T.  Decreased expression of the seven ARP2/3 complex genes in human gastric cancers.  Cancer Lett, 212: 203-210, 2004.  PMID: 15279900
  48. Kaneda A, Tsukamoto T, Takamura-Enya T, Watanabe N, Kaminishi M, Sugimura T, Tatematsu M and Ushijima T.  Frequent hypomethylation in multiple promoter CpG islands is associated with global hypomethylation, but not with frequent promoter hypermethylation.  Cancer Sci, 95: 58-64, 2004.  PMID: 14720328
  49. Kaneda A, Wakazono K, Tsukamoto T, Watanabe N, Yagi Y, Tatematsu M, Kaminishi M, Sugimura T and Ushijima T.  Lysyl oxidase is a tumor suppressor gene inactivated by methylation and loss of heterozygosity in human gastric cancers.  Cancer Res, 64: 6410-6415, 2004.  PMID: 15374948
  50. Mizoshita T, Inada K, Tsukamoto T, Nozaki K, Joh T, Itoh M, Yamamura Y, Ushijima T, Nakamura S and Tatematsu M.  Expression of the intestine-specific transcription factors, Cdx1 and Cdx2, correlates shift to an intestinal phenotype in gastric cancer cells.  J Cancer Res Clin Oncol, 130: 29-36, 2004.  PMID: 14615935
  51. Okochi-Takada E, Ichimura S, Kaneda A, Sugimura T and Ushijima T.  Establishment of a detection system for demethylating agents using an endogenous promoter CpG island.  Mutat Res, 568: 187-194, 2004.  PMID: 15542106
  52. Takada T, Yagi Y, Maekita T, Imura M, Nakagawa S, Tsao SW, Miyamoto K, Yoshino O, Yasugi T, Taketani Y and Ushijima T.  Methylation-associated silencing of the Wnt antagonist SFRP1 gene in human ovarian cancers.  Cancer Sci, 95: 741-744, 2004.  PMID: 15471560
  53. Tsukamoto T, Inada K, Tanaka H, Mizoshita T, Mihara M, Ushijima T, Yamamura Y, Nakamura S and Tatematsu M.  Down-regulation of a gastric transcription factor, Sox2, and ectopic expression of intestinal homeobox genes, Cdx1 and Cdx2: inverse correlation during progression from gastric/intestinal-mixed to complete intestinal metaplasia.  J Cancer Res Clin Oncol, 130: 135-145, 2004.  PMID: 14655050
  54. Ushijima T and Sasako M.  Focus on gastric cancer.  Cancer Cell, 5: 121-125, 2004.  PMID: 14998488
  55. Yamashita S, Nomoto T, Abe M, Tatematsu M, Sugimura T and Ushijima T.  Persistence of gene expression changes in stomach mucosae induced by short-term N-methyl-N'-nitro-N-nitrosoguanidine treatment and their presence in stomach cancers.  Mutat Res, 549: 185-193, 2004.  PMID: 15120970
  56. Abe M, Ohira M, Kaneda A, Yagi Y, Yamamoto S, Kitano Y, Takato T, Nakagawara A and Ushijima T.  CpG island methylator phenotype is a strong determinant of poor prognosis in neuroblastomas.  Cancer Res, 65: 828-834, 2005.  PMID: 15705880
  57. Chi XZ, Yang JO, Lee KY, Ito K, Sakakura C, Li QL, Kim HR, Cha EJ, Lee YH, Kaneda A, Ushijima T, Kim WJ, Ito Y and Bae SC.  RUNX3 suppresses gastric epithelial cell growth by inducing p21(WAF1/Cip1) expression in cooperation with transforming growth factor {beta}-activated SMAD.  Mol Cell Biol, 25: 8097-8107, 2005.  PMID: 16135801
  58. Furuta J, Kaneda A, Umebayashi Y, Otsuka F, Sugimura T and Ushijima T.  Silencing of the thrombomodulin gene in human malignant melanoma.  Melanoma Res, 15: 15-20, 2005.  PMID: 15714116
  59. Goldberg GS, Kunimoto T, Alexander DB, Suenaga K, Ishidate F, Miyamoto K, Ushijima T, Teng CT, Yokota J, Ohta T and Tsuda H.  Full length and delta lactoferrin display differential cell localization dynamics, but do not act as tumor markers or significantly affect the expression of other genes.  Med Chem, 1: 57-64, 2005.  PMID: 16789886
  60. Kuramoto T, Morimura K, Nomoto T, Namiki C, Hamada S, Fukushima S, Sugimura T, Serikawa T and Ushijima T.  Sparse and wavy hair: a new model for hypoplasia of hair follicle and mammary glands on rat chromosome 17.  J Hered, 96: 339-345, 2005.  PMID: 15829729
  61. Miyamoto K, Fukutomi T, Akashi-Tanaka S, Hasegawa T, Asahara T, Sugimura T and Ushijima T.  Identification of 20 genes aberrantly methylated in human breast cancers.  Int J Cancer, 116: 407-414, 2005.  PMID: 15818620
  62. Miyamoto K and Ushijima T.  Diagnostic and therapeutic applications of epigenetics.  Jpn J Clin Oncol, 35: 293-301, 2005.  PMID: 15930038
  63. Niwa T, Yamashita S, Tsukamoto T, Kuramoto T, Nomoto T, Wakazono K, Fujita H, Matsushima T, Tatematsu M, Sugimura T and Ushijima T.  Whole-genome analyses of loss of heterozygosity and methylation analysis of four tumor-suppressor genes in N-methyl-N'-nitro-N-nitrosoguanidine-induced rat stomach carcinomas.  Cancer Sci, 96: 409-413, 2005.  PMID: 16053512
  64. Tsukamoto T, Mizoshita T, Mihara M, Tanaka H, Takenaka Y, Yamamura Y, Nakamura S, Ushijima T and Tatematsu M.  Sox2 expression in human stomach adenocarcinomas with gastric and gastric-and-intestinal-mixed phenotypes.  Histopathology, 46: 649-658, 2005.  PMID: 15910596
  65. Ushijima T.  Detection and interpretation of altered methylation patterns in cancer cells.  Nat Rev Cancer, 5: 223-231, 2005.  PMID: 15719030
  66. Ushijima T and Okochi-Takada E.  Aberrant methylations in cancer cells: Where do they come from?  Cancer Sci, 96: 206-211, 2005.  PMID: 15819717
  67. Ushijima T, Watanabe N, Shimizu K, Miyamoto K, Sugimura T and Kaneda A.  Decreased fidelity in replicating CpG methylation patterns in cancer cells.  Cancer Res, 65: 11-17, 2005.  PMID: 15665274
  68. Yamashita S, Suzuki S, Nomoto T, Kondo Y, Wakazono K, Tsujino Y, Sugimura T, Shirai T, Homma Y and Ushijima T.  Linkage and microarray analyses of susceptibility genes in ACI/Seg rats: a model for prostate cancers in the aged.  Cancer Res, 65: 2610-2616, 2005.  PMID: 15805257
  69. Yamashita S, Wakazono K, Nomoto T, Tsujino Y, Kuramoto T and Ushijima T.  Expression quantitative trait Loci analysis of 13 genes in the rat prostate.  Genetics, 171: 1231-1238, 2005.  PMID: 16079240
  70. Yamashita S, Tsujino Y, Moriguchi K, Tatematsu M and Ushijima T.  Chemical genomic screening for methylation-silenced genes in gastric cancer cell lines using 5-aza-2'-deoxycytidine treatment and oligonucleotide microarray.  Cancer Sci, 97: 64-71, 2006.  PMID: 16367923
  71. Watanabe N, Okochi-Takada E, Yagi Y, Furuta JI and Ushijima T.  Decreased fidelity in replicating DNA methylation patterns in cancer cells leads to dense methylation of a CpG island.  Curr Top Microbiol Immunol, 310: 199-210, 2006.  PMID: 16909912
  72. Ushijima T, Nakajima T and Maekita T.  DNA methylation as a marker for the past and future.  J Gastroenterol, 41: 401-407, 2006.  PMID: 16799880
  73. Okochi-Takada E, Nakazawa K, Wakabayashi M, Mori A, Ichimura S, Yasugi T and Ushijima T.  Silencing of the UCHL1 gene in human colorectal and ovarian cancers.  Int J Cancer, 119: 1338-1344, 2006.  PMID: 16642472
  74. Murayama A, Sakura K, Nakama M, Yasuzawa-Tanaka K, Fujita E, Tateishi Y, Wang Y, Ushijima T, Baba T, Shibuya K, Shibuya A, Kawabe Y and Yanagisawa J.  A specific CpG site demethylation in the human interleukin 2 gene promoter is an epigenetic memory.  EMBO J, 25: 1081-1092, 2006.  PMID: 16498406
  75. Maekita T, Nakazawa K, Mihara M, Nakajima T, Yanaoka K, Iguchi M, Arii K, Kaneda A, Tsukamoto T, Tatematsu M, Tamura G, Saito D, Sugimura T, Ichinose M and Ushijima T.  High levels of aberrant DNA methylation in Helicobacter pylori-infected gastric mucosae and its possible association with gastric cancer risk.  Clin Cancer Res, 12: 989-995, 2006.  PMID: 16467114
  76. Lieb JD, Beck S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T and Greally JM.  Applying whole-genome studies of epigenetic regulation to study human disease.  Cytogenet Genome Res, 114: 1-15, 2006.  PMID: 16717444
  77. Imura M, Yamashita S, Cai LY, Furuta JI, Wakabayashi M, Yasugi T and Ushijima T.  Methylation and expression analysis of 15 genes and three normally-methylated genes in 13 ovarian cancer cell lines.  Cancer Lett, 241: 213-220, 2006.  PMID: 16303245
  78. Hatada I, Fukasawa M, Kimura M, Morita S, Yamada K, Yoshikawa T, Yamanaka S, Endo C, Sakurada A, Sato M, Kondo T, Horii A, Ushijima T and Sasaki H.  Genome-wide profiling of promoter methylation in human.  Oncogene, 25: 3059-3064, 2006.  PMID: 16407832
  79. Furuta J, Nobeyama Y, Umebayashi Y, Otsuka F, Kikuchi K and Ushijima T.  Silencing of peroxiredoxin 2 and aberrant methylation of 33 CpG islands in putative promoter regions in human malignant melanomas.  Cancer Res, 66: 6080-6086, 2006.  PMID: 16778180
  80. Nakajima T, Maekita T, Oda I, Gotoda T, Yamamoto S, Umemura S, Ichinose M, Sugimura T, Ushijima T and Saito D.  Higher methylation levels in gastric mucosae significantly correlate with higher risk of gastric cancers.  Cancer Epidemiol Biomarkers Prev, 15: 2317-2321, 2006.  PMID: 17119066
  81. Mihara M, Yoshida Y, Tsukamoto T, Inada K, Nakanishi Y, Yagi Y, Imai K, Sugimura T, Tatematsu M and Ushijima T.  Methylation of multiple genes in gastric glands with intestinal metaplasia: a disorder with polyclonal origins.  Am J Pathol, 169: 1643-1651, 2006.  PMID: 17071588
  82. Ushijima T.  Epigenetic field for cancerization.  J Biochem Mol Biol, 40: 142-150, 2007.  PMID: 17394762
  83. Takasu S, Tsukamoto T, Ushijima T, Yamashita S, Ogasawara N, Ban H, Yanai T, Masegi T and Tatematsu M.  Cyclin D1 overexpression in N-methyl-N'-nitro-N-nitrosoguanidine-induced rat gastric adenocarcinomas.  Exp Toxicol Pathol, 59: 171-175, 2007.  PMID: 17855062
  84. Nobeyama Y, Okochi-Takada E, Furuta J, Miyagi Y, Kikuchi K, Yamamoto A, Nakanishi Y, Nakagawa H and Ushijima T.  Silencing of tissue factor pathway inhibitor-2 gene in malignant melanomas.  Int J Cancer, 121: 301-307, 2007.  PMID: 17372906
  85. Moriguchi K, Yamashita S, Tsujino Y, Tatematsu M and Ushijima T.  Larger numbers of silenced genes in cancer cell lines with increased de novo methylation of scattered CpG sites.  Cancer Lett, 249: 178-187, 2007.  PMID: 16971039
  86. Hsu CH, Stedeford T, Okochi-Takada E, Ushijima T, Noguchi H, Muro-Cacho C, Holder JW and Banasik M.  Framework analysis for the carcinogenic mode of action of nitrobenzene.  J Environ Sci Health C Environ Carcinog Ecotoxicol Rev, 25: 155-184, 2007.  PMID: 17558784
  87. Enomoto S, Maekita T, Tsukamoto T, Nakajima T, Nakazawa K, Tatematsu M, Ichinose M and Ushijima T.  Lack of association between CpG island methylator phenotype in human gastric cancers and methylation in their background non-cancerous gastric mucosae.  Cancer Sci, 98: 1853-1861, 2007.  PMID: 17900260
  88. Cai LY, Abe M, Izumi S, Imura M, Yasugi T and Ushijima T.  Identification of PRTFDC1 silencing and aberrant promoter methylation of GPR150, ITGA8 and HOXD11 in ovarian cancers.  Life Sci, 80: 1458-1465, 2007.  PMID: 17303177
  89. Abe M, Westermann F, Nakagawara A, Takato T, Schwab M and Ushijima T.  Marked and independent prognostic significance of the CpG island methylator phenotype in neuroblastomas.  Cancer Lett, 247: 253-258, 2007.  PMID: 16759796
  90. Nakajima T, Enomoto S and Ushijima T.  DNA methylation: a marker for carcinogen exposure and cancer risk.  Environ Health Prev Med, 13: 8-15, 2008.  PMID: 19568874
  91. Zhao Y, Miyashita K, Ando T, Kakeji Y, Yamanaka T, Taguchi K, Ushijima T, Oda S and Maehara Y.  Exclusive KRAS mutation in microsatellite-unstable human colorectal carcinomas with sequence alterations in the DNA mismatch repair gene, MLH1.  Gene, 423: 188-193, 2008.  PMID: 18692554
  92. Yamashita S, Takahashi S, McDonell N, Watanabe N, Niwa T, Hosoya K, Tsujino Y, Shirai T and Ushijima T.  Methylation silencing of transforming growth factor-beta receptor type II in rat prostate cancers.  Cancer Res, 68: 2112-2121, 2008.  PMID: 18381416
  93. Jones PA, Baylin SB, Bernsten BE, Feinberg AP, Greally JM, Jenuwein T, Jirtle R, Ushijima T, Pierotta V, Allis CD, Elgin SC, Rine J and Wu C.  Moving AHEAD with an international human epigenome project.  Nature, 454: 711-715, 2008.  PMID: 18685699
  94. Imaoka T, Yamashita S, Nishimura M, Kakinuma S, Ushijima T and Shimada Y.  Gene expression profiling distinguishes between spontaneous and radiation-induced rat mammary carcinomas.  J Radiat Res (Tokyo), 49: 349-360, 2008.  PMID: 18421211
  95. Abe, M, Watanabe, N, McDonell, N, Takato, T, Ohira, M, Nakagawara, A and Ushijima, T.  Identification of genes targeted by CpG island methylator phenotype in neuroblastomas, and their possible integrative involvement in poor prognosis.  Oncology, 74: 50-60, 2008.  PMID: 18544995
  96. Yamashita S, Hosoya K, Gyobu K, Takeshima H and Ushijima T.  Development of a novel output value for quantitative assessment in methylated DNA immunoprecipitation-CpG island microarray analysis.  DNA Res, 16: 275-286, 2009.  PMID: 19767598
  97. Ushijima T and Yamashita S.  Methylation-sensitive representational difference analysis (MS-RDA).  Methods Mol Biol, 507: 117-130, 2009.  PMID: 18987811
  98. Terada K, Okochi-Takada E, Akashi-Tanaka S, Miyamoto K, Taniyama K, Tsuda H, Asada K, Kaminishi M and Ushijima T.  Association between frequent CpG island methylation and HER2 amplification in human breast cancers.  Carcinogenesis, 30: 466-471, 2009.  PMID: 19168584
  99. Takeshima H, Yamashita S, Shimazu T, Niwa T and Ushijima T.  The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands.  Genome Res, 19: 1974-1982, 2009.  PMID: 19652013
  100. Oka D, Yamashita S, Tomioka T, Nakanishi Y, Kato H, Kaminishi M and Ushijima T.  The presence of aberrant DNA methylation in noncancerous esophageal mucosae in association with smoking history: a target for risk diagnosis and prevention of esophageal cancers.  Cancer, 115: 3412-3426, 2009.  PMID: 19472401
  101. Ogasawara N, Tsukamoto T, Mizoshita T, Inada KI, Ban H, Kondo S, Takasu S, Ushijima T, Ito K, Ito Y, Ichinose M, Ogawa T, Joh T and Tatematsu M.  RUNX3 expression correlates with chief cell differentiation in human gastric cancers.  Histol Histopathol, 24: 31-40, 2009.  PMID: 19012242
  102. Nakajima T, Yamashita S, Maekita T, Niwa T, Nakazawa K and Ushijima T.  The presence of a methylation fingerprint of Helicobacter pylori infection in human gastric mucosae.  Int J Cancer, 124: 905-910, 2009.  PMID: 19035455
  103. Hosoya K, Yamashita S, Ando T, Nakajima T, Itoh F and Ushijima T.  Adenomatous polyposis coli 1A is likely to be methylated as a passenger in human gastric carcinogenesis.  Cancer Lett, 285: 182-189, 2009.  PMID: 19527921
  104. Cho YM, Imai T, Hasumura M, Watanabe N, Ushijima T, Hirose M and Nishikawa A.  Increased H-ras mutation frequency in mammary tumors of rats initiated with N-methyl-N-nitrosourea (MNU) and treated with acrylamide.  J Toxicol Sci, 34: 407-412, 2009.  PMID: 19652463
  105. Ando T, Yoshida T, Enomoto S, Asada K, Tatematsu M, Ichinose M, Sugiyama T and Ushijima T.  DNA methylation of microRNA genes in gastric mucosae of gastric cancer patients: its possible involvement in the formation of epigenetic field defect.  Int J Cancer, 124: 2367-2374, 2009.  PMID: 19165869
  106. Akagi I, Miyashita M, Makino H, Nomura T, Hagiwara N, Takahashi K, Cho K, Mishima T, Ishibashi O, Ushijima T, Takizawa T and Tajiri T.  Overexpression of PIK3CA is associated with lymph node metastasis in esophageal squamous cell carcinoma.  Int J Oncol, 34: 767-775, 2009.  PMID: 19212681
  107. Ushijima T and Asada K.  Aberrant DNA methylation in contrast with mutations.  Cancer Sci, 101: 300-305, 2010.  PMID: 19958364
  108. Tomita H, Hirata A, Yamada Y, Hata K, Oyama T, Mori H, Yamashita S, Ushijima T and Hara A.  Suppressive effect of global DNA hypomethylation on gastric carcinogenesis.  Carcinogenesis, 31: 1627-1633, 2010.  PMID: 20622006
  109. Takeshima H and Ushijima T.  Methylation destiny: Moira takes account of histones and RNA polymerase II.  Epigenetics, 5: 89-95, 2010.  PMID: 20160507
  110. Niwa T and Ushijima T.  Induction of epigenetic alterations by chronic inflammation and its significance on carcinogenesis.  Adv Genet, 71: 41-56, 2010.  PMID: 20933125
  111. Niwa T, Tsukamoto T, Toyoda T, Mori A, Tanaka H, Maekita T, Ichinose M, Tatematsu M and Ushijima T.  Inflammatory processes triggered by Helicobacter pylori infection cause aberrant DNA methylation in gastric epithelial cells.  Cancer Res, 70: 1430-1440, 2010.  PMID: 20124475
  112. Nakajima T, Enomoto S, Yamashita S, Ando T, Nakanishi Y, Nakazawa K, Oda I, Gotoda T and Ushijima T.  Persistence of a component of DNA methylation in gastric mucosae after Helicobacter pylori eradication.  J Gastroenterol, 45: 37-44, 2010.  PMID: 19821005
  113. Kuzumaki N, Ikegami D, Tamura R, Sasaki T, Niikura K, Narita M, Miyashita K, Imai S, Takeshima H, Ando T, Igarashi K, Kanno J, Ushijima T and Suzuki T.  Hippocampal epigenetic modification at the doublecortin gene is involved in the impairment of neurogenesis with aging.  Synapse, 64: 611-616, 2010.  PMID: 20340168
  114. Kuzumaki N, Ikegami D, Imai S, Narita M, Tamura R, Yajima M, Suzuki A, Miyashita K, Niikura K, Takeshima H, Ando T, Ushijima T and Suzuki T.  Enhanced IL-1beta production in response to the activation of hippocampal glial cells impairs neurogenesis in aged mice.  Synapse, 64: 721-728, 2010.  PMID: 20336624
  115. Ishii G, Hashimoto H, Asada K, Ito T, Hoshino A, Fujii S, Kojima M, Kuwata T, Harigaya K, Nagai K, Ushijima T and Ochiai A.  Fibroblasts associated with cancer cells keep enhanced migration activity after separation from cancer cells: a novel character of tumor educated fibroblasts.  Int J Oncol, 37: 317-325, 2010.  PMID: 20596659
  116. Ikegami D, Narita M, Imai S, Miyashita K, Tamura R, Takagi S, Yokomizo A, Takeshima H, Ando T, Igarashi K, Kanno J, Kuzumaki N, Ushijima T and Suzuki T.  Epigenetic modulation at the CCR2 gene correlates with the maintenance of behavioral sensitization to methamphetamine.  Addict Biol, 15: 358-361, 2010.  PMID: 20624155
  117. Herceg Z and Ushijima T.  Introduction: epigenetics and cancer.  Adv Genet, 70: 1-23, 2010.  PMID: 20920743
  118. Herceg Z and Ushijima T.  Epigenetics is a fascinating field of modern biology. Preface.  Adv Genet, 71: xi-xii, 2010.  PMID: 20933123
  119. Yoshida T, Yamashita S, Takamura-Enya T, Niwa T, Ando T, Enomoto S, Maekita T, Nakazawa K, Tatematsu M, Ichinose M and Ushijima T.  Alu and Satα hypomethylation in Helicobacter pylori-infected gastric mucosae.  Int J Cancer, 128: 33-39, 2011.  PMID: 20602342
  120. Kuzumaki N, Ikegami D, Tamura R, Hareyama N, Imai S, Narita M, Torigoe K, Niikura K, Takeshima H, Ando T, Igarashi K, Kanno J, Ushijima T, Suzuki T and Narita M.  Hippocampal epigenetic modification at the brain-derived neurotrophic factor gene induced by an enriched environment.  Hippocampus, 21: 127-132, 2011.  PMID: 20232397
  121. Hur K, Niwa T, Toyoda T, Tsukamoto T, Tatematsu M, Yang HK and Ushijima T.  Insufficient role of cell proliferation in aberrant DNA methylation induction and involvement of specific types of inflammation.  Carcinogenesis, 32: 35-41, 2011.  PMID: 20980348
  122. Gyobu K, Yamashita S, Matsuda Y, Igaki H, Niwa T, Oka D, Kushima R, Osugi H, Lee S, Suehiro S and Ushijima T.  Identification and validation of DNA methylation markers to predict lymph node metastasis of esophageal squamous cell carcinomas.  Ann Surg Oncol, 18: 1185-1194, 2011.  PMID: 21042947
  123. Hattori N, Okochi-Takada E, Kikuyama M, Wakabayashi M, Yamashita S and Ushijima T.  Methylation silencing of angiopoietin-like 4 in rat and human mammary carcinomas.  Cancer Sci, 102: 1337-1343, 2011.  PMID: 21489049
  124. Takeshima H, Yamashita S, Shimazu T and Ushijima T.  Effects of genome architecture and epigenetic factors on susceptibility of promoter CpG islands to aberrant DNA methylation induction.  Genomics, 98: 182-188, 2011.  PMID: 21683780
  125. Colombo F, Falvella FS, Galvan A, Frullanti E, Kunitoh H, Ushijima T and Dragani TA.  A 5’-region polymorphism modulates promoter activity of the tumor suppressor gene MFSD2A.  Mol Cancer, 10: 81, 2011.  PMID: 21736709
  126. Cai LY, Izumi S, Abe M, Imura M, Yasugi T, Wakazono K, Ohnuki Y, Kondo A and Ushijima T.  Does Aberrant DNA Methylation Occur in Human Uterine Leiomyomas? An Attempt of Genome-Wide Screening by MS-RDA.  Tokai J Exp Clin Med, 36: 84-90, 2011.  PMID: 21932190
  127. Lee YC, Wang HP, Wang CP, Ko JY, Lee JM, Chiu HM, Lin JT, Yamashita S, Oka D, Watanabe N, Matsuda Y, Ushijima T and Wu MS.  Revisit of Field Cancerization in Squamous Cell Carcinoma of Upper Aerodigestive Tract: Better Risk Assessment with Epigenetic Markers.  Cancer Prev Res, 4: 1982-1992, 2011.  PMID: 21952583
  128. Katsurano M, Niwa T, Yasui Y, Shigematsu Y, Yamashita S, Takeshima H, Lee MS, Kim YJ, Tanaka T and Ushijima T.  Early-stage formation of an epigenetic field defect in a mouse colitis model, and non-essential roles of T- and B-cells in DNA methylation induction.  Oncogene, 31: 342-351, 2012.  PMID: 21685942
  129. Watanabe M, Kato J, Inoue I, Yoshimura N, Yoshida T, Mukoubayashi C, Deguchi H, Enomoto S, Ueda K, Maekita T, Iguchi M, Tamai H, Utsunomiya H, Yamamichi N, Fujishiro M, Iwane M, Tekeshita T, Mohara O, Ushijima T and Ichinose M.  Development of gastric cancer in nonatrophic stomach with highly active inflammation identified by serum levels of pepsinogen and Helicobacter pylori antibody together with endoscopic rugal hyperplastic gastritis.  Int J Cancer, 131: 2632-2642, 2012.  PMID: 22383377
  130. Kong D, Piao YS, Yamashita S, Oshima H, Oguma K, Fushida S, Fujimura T, Minamoto T, Seno H, Yamada Y, Satou K, Ushijima T, Ishikawa TO and Oshima M.  Inflammation-induced repression of tumor suppressor miR-7 in gastric tumor cells.  Oncogene, 31: 3949-3960, 2012.  PMID: 22139078
  131. Chiba T, Marusawa H and Ushijima T.  Inflammation-associated cancer development in digestive organs: mechanisms and roles for genetic and epigenetic modulation.  Gastroenterol, 143: 550-563, 2012.  PMID: 22796521
  132. Frau M, Tomasi ML, Simile MM, Demartis MI, Salis F, Latte G, Calvisi DF, Seddaiu MA, Daino L, Feo CF, Brozzetti S, Solinas G, Yamashita S, Ushijima T, Feo F and Pascale RM.  Role of transcriptional and posttranscriptional regulation of methionine adenosyltransferases in liver cancer progression.  Hepatology, 56: 165-175, 2012.  PMID: 22318685
  133. Kikuyama M, Takeshima H, Kinoshita T, Okochi-Takada E, Wakabayashi M, Akashi-Tanaka S, Ogawa T, Seto Y and Ushijima T.  Development of a novel approach, the epigenome-based outlier approach, to identify tumor-suppressor genes silenced by aberrant DNA methylation.  Cancer Lett, 322: 204-212, 2012.  PMID: 22433712
  134. Matsuda Y, Yamashita S, Lee YC, Niwa T, Yoshida T, Gyobu K, Igaki H, Kushima R, Lee S, Wu MS, Osugi H, Suehiro S and Ushijima T.  Hypomethylation of Alu repetitive elements in esophageal mucosa, and its potential contribution to the epigenetic field for cancerization.  Cancer Causes Control, 23: 865-873, 2012.  PMID: 22527164
  135. Nanjo S, Asada K, Yamashita S, Nakajima T, Nakazawa K, Maekita T, Ichinose M, Sugiyama T and Ushijima T.  Identification of gastric cancer risk markers that are informative in individuals with past H. pylori infection.  Gastric Cancer, 15: 382-388, 2012.  PMID: 22237657
  136. Shigematsu Y, Niwa T, Yamashita S, Taniguchi H, Kushima R, Katai H, Ito S, Tsukamoto T, Ichinose M and Ushijima T.  Identification of a DNA methylation marker that detects the presence of lymph node metastases of gastric cancers.  Oncol Lett, 4: 268-274, 2012.  PMID: 22844368
  137. Ushijima T and Hattori N.  Molecular pathways: involvement of Helicobacter pylori-triggered inflammation in the formation of an epigenetic field defect, and its usefulness as cancer risk and exposure markers.  Clin Cancer Res, 18: 923-929, 2012.  PMID: 22205689
  138. Takeshima H, Ikegami D, Wakabayashi M, Niwa T, Kim YJ and Ushijima T.  Induction of aberrant trimethylation of histone H3 lysine 27 by inflammation in mouse colonic epithelial cells.  Carcinogenesis, 33: 2384-2390, 2012.  PMID: 22976929
  139. Niwa T, Toyoda T, Tsukamoto T, Mori A, Tatematsu M and Ushijima T.  Prevention of Helicobacter pylori–induced gastric cancers in gerbils by a DNA demethylating agent.  Cancer Prev Res, 6: 263-270, 2013.  PMID: 23559452
  140. Hirata A, Utika J, Yamashita S, Aoki H, Watanabe A, Yamamoto T, Okano H, Bardeesy N, Kunisada T, Ushijima T, Hara A, Jaenisch R, Hochedlinger K and Yamada Y.  Dose-dependent roles for canonical Wnt signaling in de novo crypt formation and cell cycle properties of the colonic epithelium.  Development, 140: 66-75, 2013.  PMID: 23222438
  141. Kim JG, Takeshima H, Niwa T, Rehnberg E, Shigematsu Y, Yoda Y, Yamashita S, Kushima R, Maekita T, Ichinose M, Katai H, Park WS, Hong YS, Park CH and Ushijima T.  Comprehensive DNA methylation and extensive mutation analyses reveal an association between the CpG island methylator phenotype and oncogenic mutations in gastric cancers.  Cancer Lett, 330: 33-40, 2013.  PMID: 23196062
  142. Imai S, Ikegami D, Yamashita A, Shimizu T, Narita M, Niikura K, Furuya M, Kobayashi Y, Miyashita K, Okutsu D, Kato A, Nakamura A, Araki A, Omi K, Nakamura M, Okano HJ, Okano H, Ando T, Takeshima H, Ushijima T, Kuzumaki N, Suzuki T and Narita M.  Epigenetic transcriptional activation of monocyte chemotactic protein 3 contributes to long-lasting neuropathic pain.  Brain, 136: 828-843, 2013.  PMID: 23364351
  143. Asada K, Ando T, Niwa T, Nanjo S, Watanabe N, Okochi-Takada E, Yoshida T, Miyamoto K, Enomoto S, Ichinose M, Tsukamoto T, Ito S, Tatematsu M, Sugiyama T and Ushijima T.  FHL1 on chromosome X is a single-hit gastrointestinal tumor-suppressor gene and contributes to the formation of an epigenetic field defect.  Oncogene, 32: 2140-2149, 2013.  PMID: 22689052
  144. Asada K, Watanabe N, Nakamura Y, Ohira M, Westermann F, Schwab M, Nakagawara A and Ushijima T.  Stronger prognostic power of the CpG island methylator phenotype than methylation of individual genes in neuroblastomas.  Jpn J Clin Oncol, 43: 641-645, 2013.  PMID: 23619990
  145. Yoshida T, Kato J, Maekita T, Yamashita S, Enomoto S, Ando T, Niwa T, Deguchi H, Ueda K, Inoue I, Iguchi M, Tamai H, Ushijima T and Ichinose M.  Altered mucosal DNA methylation in parallel with highly active Helicobacter pylori-related gastritis.  Gastric Cancer, 16: 488-497, 2013.  PMID: 23292007
  146. Ito Y, Yamada Y, Asada K, Ushijima T, Iwasa S, Kato K, Hamaguchi T and Shimada Y.  EGFR L2 domain mutation is not correlated with resistance to cetuximab in metastatic colorectal cancer patients.  J Cancer Res Clin Oncol, 139: 1391-1396, 2013.  PMID: 23722667
  147. Hattori N, Niwa T, Kimura K, Helin K and Ushijima T.  Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells.  Nucleic Acids Res, 41: 7231-7239, 2013.  PMID: 23761442
  148. Asada K, Abe M and Ushijima T.  Clinical application of the CpG island methylator phenotype to prognostic diagnosis in neuroblastomas.  J Hum Genet, 58: 428-433, 2013.  PMID: 23739128
  149. Zhu Y, Li Y, Haraguchi S, Yu M, Ohira M, Ozaki T, Nakagawa A, Ushijima T, Isogai E, Koseki H, Nakamura Y, Kong C, Mehlen P, Arakawa H and Nakagawara A.  Dependence receptor UNC5D mediates nerve growth factor depletion-induced neuroblastoma regression.  J Clin Invest, 123: 2935-2947, 2013.  PMID: 23778138
  150. Shigematsu Y, Niwa T, Rehnberg E, Toyoda T, Yoshida S, Mori A, Wakabayashi M, Iwakura Y, Ichinose M, Kim YJ and Ushijima T.  Interleukin-1b induced by Helicobacter pylori infection enhances mouse gastric carcinogenesis.  Cancer Lett, 340: 141-147, 2013.  PMID: 23920123
  151. Suzuki T, Yamashita S, Ushijima T, Takumi S, Sano T, Michikawa T and Nohara K.  Genome-wide analysis of DNA methylation changes induced by gestational arsenic exposure in liver tumors.  Cancer Sci, 104: 1575-1585, 2013.  PMID: 24118411
  152. Takahashi T, Matsuda Y, Yamashita S, Hattori N, Kushima R, Lee YC, Igaki H, Tachimori Y, Nagino M and Ushijima T.  Estimation of the fraction of cancer cells in a tumor DNA sample using DNA methylation.  PLoS One, 8: e82302, 2013.  PMID: 24312652
  153. Yoshida T, Kato J, Inoue I, Yoshimura N, Deguchi H, Mukoubayashi C, Oka M, Watanabe M, Enomoto S, Niwa T, Maekita T, Iguchi M, Tamai H, Utsunomiya H, Yamamichi N, Fujishiro M, Iwane M, Takeshita T, Ushijima T and Ichinose M.  Cancer development based on chronic active gastritis and resulting gastric atrophy as assessed by serum levels of pepsinogen and Helicobacter pylori antibody titer.  Int J Cancer, 134: 1445-1457, 2014.  PMID: 24009139
  154. Imaoka T, Nishimura M, Doi K, Tani S, Ishikawa K, Yamashita S, Ushijima T, Imai T and Shimada Y.  Molecular characterization of cancer reveals interactions between ionizing radiation and chemicals on rat mammary carcinogenesis.  Int J Cancer, 134: 1529-1538, 2014.  PMID: 24105445
  155. Okochi-Takada E, Hattori N, Tsukamoto T, Miyamoto K, Ando T, Ito S, Yamamura Y, Wakabayashi M, Nobeyama Y and Ushijima T.  ANGPTL4 is a secreted tumor-suppressor that inhibits angiogenesis.  Oncogene, 33: 2273-2278, 2014.  PMID: 23686315
  156. Brücher BL, Lyman G, van Hillegersberg R, Pollock RE, Lordick F, Yang HK, Ushijima T, Yeoh KG, Skricka T, Polkowski W, Wallner G, Verwaal V, Garofalo A, D'Ugo D, Roviello F, Steinau HU, Wallace TJ, Daumer M, Maihle N, Reid TJ III, Ducreux M, Kitagawa Y, Knuth A, Zilberstein B, Steele SR and Jamall IS.  Imagine a world without cancer.  BMC Cancer, 14: 186, 2014.  PMID: 24629025
  157. Yamada M, Fukagawa T, Nakajima T, Asada K, Sekine S, Yamashita S, Okochi-Takada E, Taniguchi H, Kushima R, Oda I, Saito Y, Ushijima T and Katai H.  Hereditary diffuse gastric cancer in a Japanese family with a large deletion involving CDH1.  Gastric Cancer, 17: 750-756, 2014.  PMID: 24037103
  158. Liu Z, Zhang J, Gao Y, Pei L, Zhou J, Gu L, Zhang L, Zhu B, Hattori N, Ji J, Yuasa Y, Kim W, Ushijima T, Shi H and Deng D.  Large-scale characterization of DNA methylation changes in human gastric carcinomas with and without metastasis.  Clin Cancer Res, 20: 4598-4612, 2014.  PMID: 25009298
  159. Ueda Y, Ando T, Nanjo S, Ushijima T and Sugiyama T.  DNA methylation of microRNA-124a is a potential risk marker of colitis-associated cancer in patients with ulcerative colitis.  Dig Dis Sci, 59: 2444-2451, 2014.  PMID: 24825593
  160. Ushijima T.  Cancer epigenetics: Now harvesting fruit and seeding for common diseases.  Biochem Biophys Res Commun, 455: 1-2, 2014.  PMID: 25434294
  161. Hattori N and Ushijima T.  Compendium of aberrant DNA methylation and histone modifications in cancer.  Biochem Biophys Res Commun, 455: 3-9, 2014.  PMID: 25194808
  162. Yoda Y, Takeshima H, Niwa T, Kim JG, Ando T, Kushima R, Sugiyama T, Katai H, Noshiro H and Ushijima T.  Integrated analysis of cancer-related pathways affected by genetic and epigenetic alterations in gastric cancer.  Gastric Cancer, 18: 65-76, 2015.  PMID: 24510342
  163. Asada K, Nakajima T, Shimazu T, Yamamichi N, Maekita T, Yokoi C, Oda I, Ando T, Yoshida T, Nanjo S, Fujishiro M, Gotoda T, Ichinose M and Ushijima T.  Demonstration of the usefulness of epigenetic cancer risk prediction by a multicenter prospective cohort study.  Gut, 64: 388-396, 2015.  PMID: 25379950
  164. Takahashi T, Yamashita S, Matsuda Y, Kishino T, Nakajima T, Kushima R, Kato K, Igaki H, Tachimori Y, Osugi H, Nagino M and Ushijima T.  ZNF695 methylation predicts a response of esophageal squamous cell carcinoma to definitive chemoradiotherapy.  J Cancer Res Clin Oncol, 141: 453-463, 2015.  PMID: 25273507
  165. Takeshima H, Niwa T, Takahashi T, Wakabayashi M, Yamashita S, Ando T, Inagawa Y, Taniguchi H, Katai H, Sugiyama T, Kiyono T and Ushijima T.  Frequent involvement of chromatin remodeler alterations in gastric field cancerization.  Cancer Lett, 357: 328-338, 2015.  PMID: 25462860
  166. Takeshima H, Wakabayashi M, Hattori N, Yamashita S and Ushijima T.  Identification of co-existence of DNA methylation and H3K27me3 specifically in cancer cells as a promising target for epigenetic therapy.  Carcinogenesis, 36: 192-201, 2015.  PMID: 25477340
  167. Descalzi G, Ikegami D, Ushijima T, Nestler EJ, Zachariou V and Narita M.  Epigenetic mechanisms of chronic pain.  Trends Neurosci, 38: 237-246, 2015.  PMID: 25765319
  168. Yamaguchi T, Mukai H, Yamashita S, Fujii S and Ushijima T.  Comprehensive DNA methylation and extensive mutation analyses of HER2-positive breast cancer.  Oncology, 88: 377-384, 2015.  PMID: 25591616
  169. Shimazu T, Asada K, Charvat H, Kusano C, Otake Y, Kakugawa Y, Watanabe H, Gotoda T, Ushijima T and Tsugane S.  Association of gastric cancer risk factors with DNA methylation healthy Japanese: a cross-sectional study.  Carcinogenesis, 36: 1291-1298, 2015.  PMID: 26354778
  170. Wei FZ, Cao Z, Wang X, Wang H, Cai MY, Li T, Hattori N, Wang D, Du Y, Song B, Cao LL, Shen C, Wang L, Wang H, Yang Y, Xie D, Wang F, Ushijima T, Zhao Y and Zhu WG.  Epigenetic regulation of autophagy by the methyltransferase EZH2 through an MTORdependent pathway.  Autophagy, 11: 2309-2322, 2015.  PMID: 26735435
  171. Matsuda Y, Ishiwata T, Yoshimura H, Yamashita S, Ushijima T and Arai T.  Systemic administration of small interfering RNA targeting human nestin inhibits pancreatic cancer cell proliferation and metastasis.  Pancreas, 45: 93-100, 2016.  PMID: 26335012
  172. Kuboki Y, Yamashita S, Niwa T, Ushijima T, Nagatsuma A, Kuwata T, Yoshino T, Doi T, Ochiai A and Ohtsu A.  Comprehensive analyses using next-generation sequencing and immunohistochemistry enable precise treatment in advanced gastric cancer.  Ann Oncol, 27: 127-133, 2016.  PMID: 26489445
  173. Hattori N and Ushijima T.  Epigenetic impact of infection on carcinogenesis: mechanisms and applications.  Genome Med, 8: 10, 2016.  PMID: 26823082
  174. Nakazato H, Takeshima H, Kishino T, Kubo E, Hattori N, Nakajima T, Yamashita S, Igaki H, Tachimori Y, Kuniyoshi Y and Ushijima T.  Early-stage induction of SWI/SNF mutations during esophageal squamous cell carcinogenesis.  PLoS One, 11: e0147372, 2016.  PMID: 26812616
  175. Zong L, Hattori N, Yoda Y, Yamashita S, Takeshima H, Takahashi T, Maeda M, Katai H, Nanjo S, Ando T, Seto Y, and Ushijima T.  Establishment of a DNA methylation marker to evaluate cancer cell fraction in gastric cancer.  Gastric Cancer, 19: 361-369, 2016.  PMID: 25678126
  176. Sasaki Y, Hamaguchi T, Yamada Y, Takahashi N, Shoji H, Honma Y, Iwasa S, Okita N, Takashima A, Kato K, Nagai Y, Taniguchi H, Boku N, Ushijima T and Shimada Y.  Value of KRAS, BRAF, and PIK3CA Mutations and Survival Benefit from Systemic Chemotherapy in Colorectal Peritoneal Carcinomatosis.  Asian Pac J Cancer Prev, 17: 539-543, 2016.  PMID: 26925640
  177. Nakamura T, Tateishi K, Niwa T, Matsushita Y, Tamura K, Kinoshita M, Tanaka K, Fukushima S, Takami H, Arita H, Kubo A, Shuto T, Ohno M, Miyakita Y, Kocialkowski S, Sasayama T, Hashimoto N, Maehara T, Shibui S, Ushijima T, Kawahara N, Narita Y and Ichimura K.  Recurrent mutations of CD79B and MYD88 are the hallmark of primary central nervous system lymphomas.  Neuropathol Appl Neurobiol, 42: 279-290, 2016.  PMID: 26111727
  178. Ichimura K, Fukushima S, Totoki Y, Matsushita Y, Otsuka A, Tomiyama A, Niwa T, Takami H, Nakamura T, Suzuki T, Fukuoka K, Yanagisawa T, Mishima K, Nakazato Y, Hosoda F, Narita Y, Shibui S, Yoshida A, Mukasa A, Saito N, Kumabe T, Kanamori M, Tominaga T, Kobayashi K, Shimizu S, Nagane M, Iuchi T, Mizoguchi M, Yoshimoto K, Tamura K, Maehara T, Sugiyama K, Nakada M, Sakai K, Kanemura Y, Nonaka M, Asai A, Yokogami K, Takeshima H, Kawahara N, Takayama T, Yao M, Kato M, Nakamura H, Hama N, Sakai R, Ushijima T, Matsutani M, Shibata T, Nishikawa R and The Intracranial Germ Cell Tumor Genome Analysis Consortium.  Recurrent neomorphic mutations of MTOR in central nervous system and testicular germ cell tumors may be targeted for therapy.  Acta Neuropathol, 131: 889-901, 2016.  PMID: 26956871
  179. Sekine S, Yamashita S, Tanabe T, Hashimoto T, Yoshida H, Taniguchi H, Kojima M, Shinmura K, Saito Y, Hiraoka N, Ushijima T and Ochiai A.  Frequent PTPRK-RSPO3 fusions and RNF43 mutations in colorectal traditional serrated adenoma.  J Pathol, 239: 133-138, 2016.  PMID: 26924569
  180. Abe M, Yamashita S, Mori Y, Abe T, Saijo H, Hoshi K, Ushijima T and Takato T.  High-risk oral leukoplakia is associated with aberrant promoter methylation of multiple genes.  BMC Cancer, 16: 350, 2016.  PMID: 27255271
  181. Mori G, Nakajima T, Asada K, Shimazu T, Yamamichi N, Maekita T, Yokoi C, Fujishiro M, Gotoda T, Ichinose M, Ushijima T and Oda I.  Incidence of and risk factors for metachronous gastric cancer after endoscopic resection and successful Helicobacter pylori eradication: results of a large-scale, multicenter cohort study in Japan.  Gastric Cancer, 19: 911-918, 2016.  PMID: 26420267
  182. Ushijima T and Yoshino T.  The moment that KRAS mutation started to evolve into precision medicine in metastatic colorectal cancer.  Cancer Res, 76: 6443-6444, 2016.  PMID: 28148677
  183. Kishino T, Niwa T, Yamahsita S, Takahashi T, Nakazato H, Nakajima T, Igaki H, Tachimori Y, Suzuki Y and Ushijima T.  Integrated analysis of DNA methylation and mutations in esophageal squamous cell carcinoma.  Mol Carcinogenesis, 55: 2077-2088, 2016.  PMID: 26756304
  184. Yoshida S, Yamashita S, Niwa T, Mori A, Ito S, Ichinose M and Ushijima T.  Epigenetic inactivation of FAT4 contributes to gastric field cancerization.  Gastric Cancer, 20: 136-145, 2017.  PMID: 26792292
  185. Nakamura T, Yamashita S, Fukumura K, Nakabayashi J, Tanaka K, Tamura K, Tateishi K, Kinoshita M, Fukushima S, Takami H, Fukuoka K, Yamazaki K, Matsushita Y, Ohno M, Miyakita Y, Shibui S, Kubo A, Shuto T, Kocialkowski S, Yamanaka S, Mukasa A, Sasayama T, Mishima K, Maehara T, Kawahara N, Nagane M, Narita Y, Mano H, Ushijima T and Ichimura K.  Genome-wide DNA methylation profiling identifies primary central nervous system lymphoma as a distinct entity different from systemic diffuse large B-cell lymphoma.  Acta Neuropathol, 133: 321-324, 2017.  PMID: 28058506
  186. Fukushima S, Yamashita S, Kobayashi H, Takami H, Fukuoka K, Nakamura T, Yamasaki K, Matsushita Y, Nakamura H, Totoki Y, Kato M, Suzuki T, Mishima K, Yanagisawa T, Mukasa A, Saito N, Kanamori M, Kumabe T, Tominaga T, Nagane M, Iuchi T, Yoshimoto K, Mizoguchi M, Tamura K, Sakai K, Sugiyama K, Nakada M, Yokogami K, Takeshima H, Kanemura Y, Matsuda M, Matsumura A, Kurozumi K, Ueki K, Nonaka M, Asai A, Kawahara N, Hirose Y, Takayama T, Nakazato Y, Narita Y, Shibata T, Matsutani M, Ushijima T, Nishikawa R, Ichimura K on behalf of The Intracranial Germ Cell Tumor Genome Analysis Consortium (The iGCTConsortium).  Genome-wide methylation profiles in primary intracranial germ cell tumors indicate a primordial germ cell origin for germinomas.  Acta Neuropathol, 133: 445-462, 2017.  PMID: 28078450
  187. Maeda M, Moro H and Ushijima T.  Mechanisms for the induction of gastric cancer by Helicobacter pylori infection: aberrant DNA methylation pathway.  Gastric Cancer, 20 (Suppl 1): 8-15, 2017.  PMID: 27718135
  188. Narita M, Shimura E, Nagasawa A, Aiuchi T, Suda Y, Hamada Y, Ikegami D, Iwasawa C, Arakawa K, Igarashi K, Kuzumaki N, Yoshioka Y, Ochiya T, Takeshima H, Ushijima T and Narita M.  Chronic treatment of non-small-cell lung cancer cells with gefitinib leads to an epigenetic loss of epithelial properties associated with reductions in microRNA-155 and -200c.  PLoS One, 12: e0172115, 2017.  PMID: 28225782
  189. Takeshima H, Niwa T, Toyoda T, Wakabayashi M, Yamashita S and Ushijima T.  Degree of methylation burden is determined by the exposure period to carcinogenic factors.  Cancer Sci, 108: 316-321, 2017.  PMID: 27992956
  190. Muhammad JS, Nanjo S, Ando T, Yamashita S, Maekita T, Ushijima T, Tabuchi Y and Sugiyama T.  Autophagy impairment by Helicobacter pylori-induced methylation silencing of MAP1LC3Av1 promotes gastric carcinogenesis.  Int J Cancer, 140: 2272-2283, 2017.  PMID: 28214334
  191. Fujii S, Yamashita S, Yamaguchi T, Takahashi M, Hozumi Y, Ushijima T and Mukai H.  Pathological complete response of HER2-positive breast cancer to trastuzumab and chemotherapy can be predicted by HSD17B4 methylation.  Oncotarget, 8: 19039-19048, 2017.  PMID: 28186977
  192. Maeda M, Nakajima T, Oda I, Shimazu T, Yamamichi N, Maekita T, Asada K, Yokoi C, Ando T, Yoshida T, Nanjo S, Fujishiro M, Gotoda T, Ichinose M and Ushijima T.  High impact of methylation accumulation on metachronous gastric cancer: 5-year follow up of a multicentre prospective cohort study.  Gut, online.  PMID: 28003322
  193. Okochi-Takada E, Hattori N, Ito A, Niwa T, Wakabayashi M, Kimura K, Yoshida M and Ushijima T.  Establishment of a high-throughput detection system for DNA demethylating agents.  Epigenetics, online.  PMID: 27935410
  194. Padmanabhan N, Ushijima T and Tan P.  How to stomach an epigenetic insult: the gastric cancer epigenome.  Nat Rev Gastroenterol Hepatol, online.  PMID:28513632
  195. Nakamura Y, Hattori N, Iida N, Yamashita S, Mori A, Kimura K, Yoshino T and Ushijima T.  Targeting of super-enhancers and mutant BRAF can suppress growth of BRAF-mutant colon cancer cells via repression of MAPK signaling pathway.  Cancer Lett, online.  PMID: 28576751