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Volumn 5, Issue FEB, 2014, Pages

Multilayer-omics analyses of human cancers: Exploration of biomarkers and drug targets based on the activities of the International Human Epigenome Consortium

Author keywords

DNA methylation; Epigenetics; Epigenome; International Human Epigenome Consortium (IHEC); Multilayer integrated disease omics analyses

Indexed keywords

BIOLOGICAL MARKER; DNA; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 3B; MESSENGER RNA; MICRORNA; PROTEOME; RNA POLYMERASE II; TRANSCRIPTOME;

EID: 84897704591     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00024     Document Type: Short Survey
Times cited : (18)

References (32)
  • 1
    • 84865339838 scopus 로고    scopus 로고
    • Single-CpG-resolution methylome analysis identifies clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas
    • doi: 10.1093/carcin/bgs177
    • Arai, E., Chiku, S., Mori, T., Gotoh, M., Nakagawa, T., Fujimoto, H., et al. (2012). Single-CpG-resolution methylome analysis identifies clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas. Carcinogenesis 33, 1487-1493. doi: 10.1093/carcin/bgs177.
    • (2012) Carcinogenesis , vol.33 , pp. 1487-1493
    • Arai, E.1    Chiku, S.2    Mori, T.3    Gotoh, M.4    Nakagawa, T.5    Fujimoto, H.6
  • 2
    • 77954133525 scopus 로고    scopus 로고
    • DNA methylation profiles in precancerous tissue and cancers: carcinogenetic risk estimation and prognostication based on DNA methylation status
    • doi: 10.2217/epi.10.16
    • Arai, E., and Kanai, Y. (2010). DNA methylation profiles in precancerous tissue and cancers: carcinogenetic risk estimation and prognostication based on DNA methylation status. Epigenomics 2, 467-481. doi: 10.2217/epi.10.16.
    • (2010) Epigenomics , vol.2 , pp. 467-481
    • Arai, E.1    Kanai, Y.2
  • 3
    • 33745213611 scopus 로고    scopus 로고
    • Regional DNA hypermethylation and DNA methyltransferase (DNMT) 1 protein overexpression in both renal tumors and corresponding nontumorous renal tissues
    • doi:10.1002/ijc.21807
    • Arai, E., Kanai, Y., Ushijima, S., Fujimoto, H., Mukai, K., and Hirohashi, S. (2006). Regional DNA hypermethylation and DNA methyltransferase (DNMT) 1 protein overexpression in both renal tumors and corresponding nontumorous renal tissues. Int. J. Cancer 119, 288-296. doi:10.1002/ijc.21807.
    • (2006) Int. J. Cancer , vol.119 , pp. 288-296
    • Arai, E.1    Kanai, Y.2    Ushijima, S.3    Fujimoto, H.4    Mukai, K.5    Hirohashi, S.6
  • 4
    • 60149106402 scopus 로고    scopus 로고
    • Genome-wide DNA methylation profiles in both precancerous conditions and clear cell renal cell carcinomas are correlated with malignant potential and patient outcome
    • doi: 10.1093/carcin/bgn268
    • Arai, E., Ushijima, S., Fujimoto, H., Hosoda, F., Shibata, T., Kondo, T., et al. (2009a). Genome-wide DNA methylation profiles in both precancerous conditions and clear cell renal cell carcinomas are correlated with malignant potential and patient outcome. Carcinogenesis 30, 214-221. doi: 10.1093/carcin/bgn268.
    • (2009) Carcinogenesis , vol.30 , pp. 214-221
    • Arai, E.1    Ushijima, S.2    Fujimoto, H.3    Hosoda, F.4    Shibata, T.5    Kondo, T.6
  • 5
    • 71849115857 scopus 로고    scopus 로고
    • Genome-wide DNA methylation profiles in liver tissue at the precancerous stage and in hepatocellular carcinoma
    • doi: 10.1002/ijc.24708
    • Arai, E., Ushijima, S., Gotoh, M., Ojima, H., Kosuge, T., Hosoda, F., et al. (2009b). Genome-wide DNA methylation profiles in liver tissue at the precancerous stage and in hepatocellular carcinoma. Int. J. Cancer 125, 2854-2862. doi: 10.1002/ijc.24708.
    • (2009) Int. J. Cancer , vol.125 , pp. 2854-2862
    • Arai, E.1    Ushijima, S.2    Gotoh, M.3    Ojima, H.4    Kosuge, T.5    Hosoda, F.6
  • 6
    • 84889649328 scopus 로고    scopus 로고
    • Perspectives of international human epigenome consortium
    • doi: 10.5808/GI.2013.11.1.7
    • Bae, J. B. (2013). Perspectives of international human epigenome consortium. Genomics Inform. 11, 7-14. doi: 10.5808/GI.2013.11.1.7.
    • (2013) Genomics Inform. , vol.11 , pp. 7-14
    • Bae, J.B.1
  • 7
    • 84865757142 scopus 로고    scopus 로고
    • Landscape of transcription in human cells
    • doi: 10.1038/nature11233
    • Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., et al. (2012). Landscape of transcription in human cells. Nature 489, 101-108. doi: 10.1038/nature11233.
    • (2012) Nature , vol.489 , pp. 101-108
    • Djebali, S.1    Davis, C.A.2    Merkel, A.3    Dobin, A.4    Lassmann, T.5    Mortazavi, A.6
  • 8
    • 1542319832 scopus 로고    scopus 로고
    • Increased DNA methyltransferase 1 (DNMT1) protein expression correlates significantly with poorer tumor differentiation and frequent DNA hypermethylation of multiple CpG islands in gastric cancers
    • doi: 10.1016/S0002-9440(10)63156-2
    • Etoh, T., Kanai, Y., Ushijima, S., Nakagawa, T., Nakanishi, Y., Sasako, M., et al. (2004). Increased DNA methyltransferase 1 (DNMT1) protein expression correlates significantly with poorer tumor differentiation and frequent DNA hypermethylation of multiple CpG islands in gastric cancers. Am. J. Pathol. 164, 689-699. doi: 10.1016/S0002-9440(10)63156-2.
    • (2004) Am. J. Pathol. , vol.164 , pp. 689-699
    • Etoh, T.1    Kanai, Y.2    Ushijima, S.3    Nakagawa, T.4    Nakanishi, Y.5    Sasako, M.6
  • 9
    • 35649020283 scopus 로고    scopus 로고
    • MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B
    • doi:10.1073/pnas.0707628104
    • Fabbri, M., Garzon, R., Cimmino, A., Liu, Z., Zanesi, N., Callegari, E., et al. (2007). MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc. Natl. Acad. Sci. U.S.A. 104, 15805-15810. doi:10.1073/pnas.0707628104.
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 15805-15810
    • Fabbri, M.1    Garzon, R.2    Cimmino, A.3    Liu, Z.4    Zanesi, N.5    Callegari, E.6
  • 10
    • 84881170401 scopus 로고    scopus 로고
    • Non-coding RNAs: multi-tasking molecules in the cell
    • doi: 10.3390/ijms140816010
    • Gomes, A. Q., Nolasco, S., and Soares, H. (2013). Non-coding RNAs: multi-tasking molecules in the cell. Int. J. Mol. Sci. 14, 16010-16039. doi: 10.3390/ijms140816010.
    • (2013) Int. J. Mol. Sci. , vol.14 , pp. 16010-16039
    • Gomes, A.Q.1    Nolasco, S.2    Soares, H.3
  • 11
    • 79952216770 scopus 로고    scopus 로고
    • Diagnosis and prognostication of ductal adenocarcinomas of the pancreas based on genome-wide DNA methylation profiling by bacterial artificial chromosome array-based methylated CpG island amplification
    • doi: 10.1155/2011/780836
    • Gotoh, M., Arai, E., Wakai-Ushijima, S., Hiraoka, N., Kosuge, T., Hosoda, F., et al. (2011). Diagnosis and prognostication of ductal adenocarcinomas of the pancreas based on genome-wide DNA methylation profiling by bacterial artificial chromosome array-based methylated CpG island amplification. J. Biomed. Biotechnol. 2011, 780836. doi: 10.1155/2011/780836.
    • (2011) J. Biomed. Biotechnol. , vol.2011 , pp. 780836
    • Gotoh, M.1    Arai, E.2    Wakai-Ushijima, S.3    Hiraoka, N.4    Kosuge, T.5    Hosoda, F.6
  • 12
    • 3042767202 scopus 로고    scopus 로고
    • MicroRNAs: small RNAs with a big role in gene regulation
    • doi: 10.1038/nrg1379
    • He, L., and Hannon, G. J. (2004). MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5, 522-531. doi: 10.1038/nrg1379.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 522-531
    • He, L.1    Hannon, G.J.2
  • 13
    • 77954234485 scopus 로고    scopus 로고
    • Down-regulated microRNA-152 induces aberrant DNA methylation in hepatitis B virus-related hepatocellular carcinoma by targeting DNA methyltransferase 1
    • doi: 10.1002/hep.23660
    • Huang, J., Wang, Y., Guo, Y., and Sun, S. (2010). Down-regulated microRNA-152 induces aberrant DNA methylation in hepatitis B virus-related hepatocellular carcinoma by targeting DNA methyltransferase 1. Hepatology 52, 60-70. doi: 10.1002/hep.23660.
    • (2010) Hepatology , vol.52 , pp. 60-70
    • Huang, J.1    Wang, Y.2    Guo, Y.3    Sun, S.4
  • 14
    • 58749113430 scopus 로고    scopus 로고
    • A three-dimensional view of the molecular machinery of RNA interference
    • doi: 10.1038/nature07755
    • Jinek, M., and Doudna, J. A. (2009). A three-dimensional view of the molecular machinery of RNA interference. Nature 457, 405-412. doi: 10.1038/nature07755.
    • (2009) Nature , vol.457 , pp. 405-412
    • Jinek, M.1    Doudna, J.A.2
  • 15
    • 49749094793 scopus 로고    scopus 로고
    • Alterations of DNA methylation and clinicopathological diversity of human cancers
    • doi: 10.1111/j.1440-1827.2008.02270.x
    • Kanai, Y. (2008). Alterations of DNA methylation and clinicopathological diversity of human cancers. Pathol. Int. 58, 544-558. doi: 10.1111/j.1440-1827.2008.02270.x.
    • (2008) Pathol. Int. , vol.58 , pp. 544-558
    • Kanai, Y.1
  • 16
    • 71849113808 scopus 로고    scopus 로고
    • Genome-wide DNA methylation profiles in precancerous conditions and cancers
    • doi: 10.1111/j.1349-7006.2009.01383.x
    • Kanai, Y. (2010). Genome-wide DNA methylation profiles in precancerous conditions and cancers. Cancer Sci. 101, 36-45. doi: 10.1111/j.1349-7006.2009.01383.x.
    • (2010) Cancer Sci. , vol.101 , pp. 36-45
    • Kanai, Y.1
  • 17
    • 36949016699 scopus 로고    scopus 로고
    • Alterations of DNA methylation associated with abnormalities of DNA methyltransferases in human cancers during transition from a precancerous to a malignant state
    • doi: 10.1093/carcin/bgm206
    • Kanai, Y., and Hirohashi, S. (2007). Alterations of DNA methylation associated with abnormalities of DNA methyltransferases in human cancers during transition from a precancerous to a malignant state. Carcinogenesis 28, 2434-2442. doi: 10.1093/carcin/bgm206.
    • (2007) Carcinogenesis , vol.28 , pp. 2434-2442
    • Kanai, Y.1    Hirohashi, S.2
  • 18
    • 0030476367 scopus 로고    scopus 로고
    • Aberrant DNA methylation on chromosome 16 is an early event in hepatocarcinogenesis
    • doi: 10.1111/j.1349-7006.1996.tb03135.x
    • Kanai, Y., Ushijima, S., Tsuda, H., Sakamoto, M., Sugimura, T., and Hirohashi, S. (1996). Aberrant DNA methylation on chromosome 16 is an early event in hepatocarcinogenesis. Jpn. J. Cancer Res. 87, 1210-1217. doi: 10.1111/j.1349-7006.1996.tb03135.x.
    • (1996) Jpn. J. Cancer Res. , vol.87 , pp. 1210-1217
    • Kanai, Y.1    Ushijima, S.2    Tsuda, H.3    Sakamoto, M.4    Sugimura, T.5    Hirohashi, S.6
  • 19
    • 55849135596 scopus 로고    scopus 로고
    • MicroRNA-directed transcriptional gene silencing in mammalian cells
    • doi: 10.1073/pnas.0808830105
    • Kim, D. H., Saetrom, P., Snøve, O. Jr., and Rossi, J. J. (2008). MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 105, 16230-16235. doi: 10.1073/pnas.0808830105.
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 16230-16235
    • Kim, D.H.1    Saetrom, P.2    Snøve Jr., O.3    Rossi, J.J.4
  • 20
    • 42749087226 scopus 로고    scopus 로고
    • Highly integrated single-base resolution maps of the epigenome in Arabidopsis
    • doi: 10.1016/j.cell.2008.03.029
    • Lister, R., O'Malley, R. C., Tonti-Filippini, J., Gregory, B. D., Berry, C. C., Millar, A. H., et al. (2008). Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536. doi: 10.1016/j.cell.2008.03.029.
    • (2008) Cell , vol.133 , pp. 523-536
    • Lister, R.1    O'Malley, R.C.2    Tonti-Filippini, J.3    Gregory, B.D.4    Berry, C.C.5    Millar, A.H.6
  • 21
    • 33847763576 scopus 로고    scopus 로고
    • Genetic unmasking of an epigenetically silenced microRNA in human cancer cells
    • doi: 10.1158/0008-5472.CAN-06-4218
    • Lujambio, A., Ropero, S., Ballestar, E., Fraga, M. F., Cerrato, C., Setién, F., et al. (2007). Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. Cancer Res. 67, 1424-1429. doi: 10.1158/0008-5472.CAN-06-4218.
    • (2007) Cancer Res. , vol.67 , pp. 1424-1429
    • Lujambio, A.1    Ropero, S.2    Ballestar, E.3    Fraga, M.F.4    Cerrato, C.5    Setién, F.6
  • 22
    • 84866919003 scopus 로고    scopus 로고
    • Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
    • doi: 10.1093/nar/gks454
    • Miura, F., Enomoto, Y., Dairiki, R., and Ito, T. (2012). Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res. 40, e136. doi: 10.1093/nar/gks454.
    • (2012) Nucleic Acids Res. , vol.40
    • Miura, F.1    Enomoto, Y.2    Dairiki, R.3    Ito, T.4
  • 23
    • 17144413410 scopus 로고    scopus 로고
    • DNA hypermethylation on multiple CpG islands associated with increased DNA methyltransferase DNMT1 protein expression during multistage urothelial carcinogenesis
    • doi: 10.1097/01.ju.0000154632.11824.4d
    • Nakagawa, T., Kanai, Y., Ushijima, S., Kitamura, T., Kakizoe, T., and Hirohashi, S. (2005). DNA hypermethylation on multiple CpG islands associated with increased DNA methyltransferase DNMT1 protein expression during multistage urothelial carcinogenesis. J. Urol. 173, 1767-1771. doi: 10.1097/01.ju.0000154632.11824.4d.
    • (2005) J. Urol. , vol.173 , pp. 1767-1771
    • Nakagawa, T.1    Kanai, Y.2    Ushijima, S.3    Kitamura, T.4    Kakizoe, T.5    Hirohashi, S.6
  • 24
    • 71849096572 scopus 로고    scopus 로고
    • Genome-wide DNA methylation profiles in urothelial carcinomas and urothelia at the precancerous stage
    • doi: 10.1111/j.1349-7006.2009.01330.x
    • Nishiyama, N., Arai, E., Chihara, Y., Fujimoto, H., Hosoda, F., Shibata, T., et al. (2010). Genome-wide DNA methylation profiles in urothelial carcinomas and urothelia at the precancerous stage. Cancer Sci. 101, 231-240. doi: 10.1111/j.1349-7006.2009.01330.x.
    • (2010) Cancer Sci. , vol.101 , pp. 231-240
    • Nishiyama, N.1    Arai, E.2    Chihara, Y.3    Fujimoto, H.4    Hosoda, F.5    Shibata, T.6
  • 25
    • 33745627069 scopus 로고    scopus 로고
    • DNA methylation of multiple tumor-related genes in association with overexpression of DNA methyltransferase 1 (DNMT1) during multistage carcinogenesis of the pancreas
    • doi: 10.1093/carcin/bgi361
    • Peng, D. F., Kanai, Y., Sawada, M., Ushijima, S., Hiraoka, N., Kitazawa, S., et al. (2006). DNA methylation of multiple tumor-related genes in association with overexpression of DNA methyltransferase 1 (DNMT1) during multistage carcinogenesis of the pancreas. Carcinogenesis 27, 1160-1168. doi: 10.1093/carcin/bgi361.
    • (2006) Carcinogenesis , vol.27 , pp. 1160-1168
    • Peng, D.F.1    Kanai, Y.2    Sawada, M.3    Ushijima, S.4    Hiraoka, N.5    Kitazawa, S.6
  • 26
    • 0037162542 scopus 로고    scopus 로고
    • Overexpression of a splice variant of DNA methyltransferase 3b, DNMT3b4, associated with DNA hypomethylation on pericentromeric satellite regions during human hepatocarcinogenesis
    • doi: 10.1073/pnas.152121799
    • Saito, Y., Kanai, Y., Sakamoto, M., Saito, H., Ishii, H., and Hirohashi, S. (2002). Overexpression of a splice variant of DNA methyltransferase 3b, DNMT3b4, associated with DNA hypomethylation on pericentromeric satellite regions during human hepatocarcinogenesis. Proc. Natl. Acad. Sci. U.S.A. 99, 10060-10065. doi: 10.1073/pnas.152121799.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 10060-10065
    • Saito, Y.1    Kanai, Y.2    Sakamoto, M.3    Saito, H.4    Ishii, H.5    Hirohashi, S.6
  • 27
    • 33744805399 scopus 로고    scopus 로고
    • Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells
    • doi: 10.1016/j.ccr.2006.04.020
    • Saito, Y., Liang, G., Egger, G., Friedman, J. M., Chuang, J. C., and Coetzee. G. A., et al. (2006). Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell 9, 435-443. doi: 10.1016/j.ccr.2006.04.020.
    • (2006) Cancer Cell , vol.9 , pp. 435-443
    • Saito, Y.1    Liang, G.2    Egger, G.3    Friedman, J.M.4    Chuang, J.C.5    Coetzee, G.A.6
  • 28
    • 84890408443 scopus 로고    scopus 로고
    • Epigenetic alterations and microRNA misexpression in cancer and autoimmune diseases: a critical review
    • doi: 10.1007/s12016-013-8401-z [Epub ahead of print].
    • Saito, Y., Saito, H., Liang, G., and Friedman, J. M. (2013). Epigenetic alterations and microRNA misexpression in cancer and autoimmune diseases: a critical review. Clin. Rev. Allergy Immunol. doi: 10.1007/s12016-013-8401-z [Epub ahead of print].
    • (2013) Clin. Rev. Allergy Immunol.
    • Saito, Y.1    Saito, H.2    Liang, G.3    Friedman, J.M.4
  • 29
    • 68149126345 scopus 로고    scopus 로고
    • Chromatin remodeling at Alu repeats by epigenetic treatment activates silenced microRNA-512-5p with downregulation of Mcl-1 in human gastric cancer cells
    • doi: 10.1038/onc.2009.140
    • Saito, Y., Suzuki, H., Tsugawa, H., Nakagawa, I., Matsuzaki, J., Kanai, Y., et al. (2009). Chromatin remodeling at Alu repeats by epigenetic treatment activates silenced microRNA-512-5p with downregulation of Mcl-1 in human gastric cancer cells. Oncogene 28, 2738-2744. doi: 10.1038/onc.2009.140.
    • (2009) Oncogene , vol.28 , pp. 2738-2744
    • Saito, Y.1    Suzuki, H.2    Tsugawa, H.3    Nakagawa, I.4    Matsuzaki, J.5    Kanai, Y.6
  • 30
    • 84900016421 scopus 로고    scopus 로고
    • Epigenetic clustering of lung adenocarcinomas based on DNA methylation profiles in adjacent lung tissue: its correlation with smoking history and chronic obstructive pulmonary disease
    • doi: 10.1002/ijc.28684.
    • Sato, T., Arai, E., Kohno T., Takahashi, Y., Miyata, S., Tsuta, K., et al. (2014). Epigenetic clustering of lung adenocarcinomas based on DNA methylation profiles in adjacent lung tissue: its correlation with smoking history and chronic obstructive pulmonary disease. Int. J. Cancer doi: 10.1002/ijc.28684.
    • (2014) Int. J. Cancer
    • Sato, T.1    Arai, E.2    Kohno, T.3    Takahashi, Y.4    Miyata, S.5    Tsuta, K.6
  • 31
    • 84875434627 scopus 로고    scopus 로고
    • DNA methylation profiles at precancerous stages associated with recurrence of lung adenocarcinoma
    • doi: 10.1371/journal.pone.0059444
    • Sato, T., Arai, E., Kohno, T., Tsuta, K., Watanabe, S., Soejima, K., et al. (2013). DNA methylation profiles at precancerous stages associated with recurrence of lung adenocarcinoma. PLoS ONE 8:e59444. doi: 10.1371/journal.pone.0059444.
    • (2013) PLoS ONE , vol.8
    • Sato, T.1    Arai, E.2    Kohno, T.3    Tsuta, K.4    Watanabe, S.5    Soejima, K.6
  • 32
    • 0029114538 scopus 로고
    • Silencing of the E-cadherin invasion-suppressor gene by CpG methylation in human carcinomas
    • doi: 10.1073/pnas.92.16.7416
    • Yoshiura, K., Kanai, Y., Ochiai, A., Shimoyama, Y., Sugimura, T., and Hirohashi, S. (1995). Silencing of the E-cadherin invasion-suppressor gene by CpG methylation in human carcinomas. Proc. Natl. Acad. Sci. U.S.A. 92, 7416-7419. doi: 10.1073/pnas.92.16.7416.
    • (1995) Proc. Natl. Acad. Sci. U.S.A. , vol.92 , pp. 7416-7419
    • Yoshiura, K.1    Kanai, Y.2    Ochiai, A.3    Shimoyama, Y.4    Sugimura, T.5    Hirohashi, S.6


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