乳癌為台灣女性最好發的癌症, DNA胞嘧啶第五個位置的甲基化修飾(5mC),是重要的表觀遺傳的修飾,它參與了組織的分化,在癌症中也頻繁地被改變。近期的證據顯示,在哺乳類動物的中,拾-拾壹轉位蛋白 (TET) 以及異檸檬酸脫氫酶(IDH) 參與DNA的5mC轉變成羥甲基胞嘧啶(5hmC)的過程。本研究的目的為確認5mC以及5hmC的表現量是否與侵襲性乳腺癌的腫瘤發生，臨床病理特徵以及存活率有關聯性。我們同時也研究表觀遺傳修飾者(如TET1，TET2，IDH1和IDH2)在侵襲性乳腺癌中，對5mC、5hmC、腫瘤形成能力以及疾病預後的影響。本研究利用組織免疫化學染色法，以微組織矩陣晶片來檢測20個乳房纖維化囊腫病人的正常乳腺組織，309個腫瘤鄰近正常乳腺組織以及309個侵襲性乳腺癌組織中5mC、5hmC、TET1、TET2、DH1和IDH2的表現量。資料顯示5mC以及5hmC的表現量，在侵襲性乳腺癌組織的表現量比腫瘤鄰近正常乳腺組織以及乳房纖維化囊腫病人的正常乳腺組織來的低。在侵襲性乳腺癌組織，我們也發現5mC相比於5hmC表現量,下降的幅度較為平緩，此外， 5mC低表現量與腫瘤分化差具關聯性，而5hmC低表現量與侵襲性乳腺癌患者的疾病特定存活期以及無病生存期較短具關聯性，我們也發現5mC以及5hmC低表現量，分別在管腔B型以及Her-2過度表現型中與侵襲性乳腺癌患者的疾病特定存活期較短具關聯性。而與腫瘤鄰近正常乳腺組織以及乳房纖維化囊腫病人相比較，也發現TET1-n，TET2-n，IDH1和IDH2在侵襲性乳腺癌表現量有下調的現象。利用多變項線性迴歸分析模式預測5hmC顯示，細胞核內的TET1可作為一個獨立的預測因子。此外，IDH1 低表現量與臨床病理晚期及淋巴轉移有關聯性，而TET2-n 低表現量與患者的淋巴轉移及腫瘤分化差有關聯性。整體而言，下調5mC、5hmC、TET1-n、TET2-n、IDH1 以及IDH2的表現量在侵襲性乳腺癌患者中會促使腫瘤形成。而5mC、5hmC、TET1-n、TET2-n、IDH1 以及IDH2在侵襲性乳腺癌組織中，表現量高的病人，其預後較好，特別是5hmC是存活的獨立預測因子。

Breast cancer is the most common cancer in Taiwanese women. DNA methylation at the 5-position of cytosine (5mC) represents an important epigenetic modification involved in tissue differentiation and is frequently altered in cancer. Recent evidence suggests that 5mC can be converted to 5-hydroxymethylcytosine (5hmC) in mammalian DNA by The ten-eleven-translocation (TET) and isocitrate dehydrogenase (IDH) enzymes. The purpose of this study was to identify whether the expression of 5mC and 5hmC were correlated with the tumorigenesis, clinicopathological features, and survival of invasive ductal carcinoma (IDC) patients. The impact of epigenetic modifiers, such as TET1, TET2, IDH1, and IDH2 on 5mC, 5hmC, tumorigenesis, and prognosis in IDC were also investigated. The expression levels of 5mC, 5hmC, TET1, TET2, IDH1, and IDH2 were evaluated by immunohistochemistry in 20 breast fibrosis tissues, 309 tumor adjacent normal (TAN), and 309 IDC, using tissue microarray slides. Our data showed a significant reduction of 5mC and 5hmC levels in IDC tissues as compared to TAN tissues and breast fibrosis tissues. In IDC tissues, only moderate reduction of 5mC was observed as compared to 5hmC obvious losses. In addition, lower level of 5mC was correlated with poor differentiation of tumor. The low levels of 5hmC was significantly associated with shorter disease-specific survival (p = 0.016) and disease-free survival (p = 0.008) in IDC patients. We also found that the low levels of 5mC expression was significantly associated with poor DSS for those with luminal B, and the decreased 5hmC expression was significantly associated with poor DSS for those with Her 2 overexpression. All TET1-n, TET2-n, IDH1, and IDH2 were significantly down-regulated in IDC. The multivariate linear regression model showed that TET1-n was an independent predictor for 5hmC. Furthermore, a low expression level of IDH1 was correlated with the advance stage of disease and lymph node metastasis. A low level of TET2-n was correlated with the advanced pN stage and poor differentiation of tumor. In conclusion, the decreased expression of 5mC, 5hmC, TET1-n, TET2-n, IDH1, and IDH2 were involved in the tumorigenesis of IDC. The higher levels of their expression might be the favorable prognosis markers for IDC, particularly for 5hmC in survival.

Contents
論文審定書…………………………………………………......…………………………i
誌謝………………………………………………………………………..…………...…ii
Abbreviations…………………………………………………………....………………iii
Abstract in Chinese ………………………………………………………………….iv-v
Abstract in English ………………………………………………….………………vi-vii
Contents …………………………………………………………….…...…………..viii-x
1. Introduction ………………………………………………………..…....……….……1
1.1 Breast cancer………………………………………………..…….....….………1
1.2 Epigenetics modification…………………………………………..…....………2
1.3 DNA methylation in Breast Cancer………………………..……..…..…..……4
1.4 The sixth base 5-hydroxymethylcytosine……………………..…..….….……6
1.5 5-hydroxymethylcytosine in Cancer……………………………….………..…7
1.6 Ten-Eleven- Translocation (TET) family………………...………………....…9
1.7 Isocitrate dehydrogenase (IDH) .………….………………………...…….…11
2. Specific Aims ………………………………………………………..……...........…13
3. Subjects and Methods ……………………………………………………..........…15
4. Results …………………………………………………………………………….....21
4.1 Breast cancer molecular subtypes and clinicopathological parameter.......21
4.2 A significant reduction of 5mC and 5hmC levels in invasive ductal
carcinoma………………………………………………………….................…22
4.3 Expression levels of the levels of 5mC and 5hmC in normal ductal epithelial
tissue, tumor-adjacent normal ductal epithelial tissue, tumor and, recurrence
tissue………………………………………………………….………......……23
4.4 Association of the expression level of 5mC and 5hmC with the demographic
and clinicopathological parameters, as well as survival.…………….….....24
4.5 Only moderate reduction of 5mC was observed as compared with 5hmC
obvious losses in IDC…………………..…………………………….…......…28
4.6 Downregulation of epigenetic modifier expression in IDC tissues……...…28
4.7 The four epigenetic modifiers might lead to 5hmC loss in IDC…….…..….29
4.8 Expression levels of the levels of epigenetic modifier in normal ductal
epithelial tissue, tumor-adjacent normal ductal epithelial tissue, tumor and,
recurrence tissue…………………………………………………...…......……31
4.9 Association between the expression level of epigenetic modifiers and
demographic, clinicopathological parameters and survival…….……....….33
5. Discussion…………………………………………………..…………........……37
5.1 5mC levels were increased by dot blotting assay but decreased by IHC assays
in IDC…………………………………………………..………....…………......37
5.2 5mC and 5hmC were decreased in IDC………………………..……………38
5.3 Association of 5mC and 5hmC levels with clinicopathological characteristics
of IDC patients…………………………………..……………………......……38
5.4 Epigenetic regulation and survival in several distinct molecular subtypes of
breast cancer……………………………………….…………………...…..…41
5.5 Decreased 5hmC is closely associated with the reduction of TET1 (n)
expression in IDC…………………………………...…………………...……43
5.6 Association of TET2 level with clinicopathological characteristics of IDC
patients………………………………………………...…………….……...…45
5.7 Association of IDH1 and IDH2 levels with clinicopathological characteristics
of IDC patients…………………………………….………………...…...……46
6. Conclusion………………………………………………………………………..…47
7. References …………………………………………….……………………...……48
8. Tables ……………………………………….………………………….......………57
9. Figures …………………………………………….………………………..………86

1. Cancer Registry annual Report, Department of Health 2014.
2. (2011). Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615.
3. Alves, G., Tatro, A., and Fanning, T. (1996). Differential methylation of human LINE-1 retrotransposons in malignant cells. Gene 176, 39-44.
4. Bacher, U., Haferlach, C., Schnittger, S., Kohlmann, A., Kern, W., and Haferlach, T. (2010). Mutations of the TET2 and CBL genes: novel molecular markers in myeloid malignancies. Ann Hematol 89, 643-652.
5. Baylin, S.B., Esteller, M., Rountree, M.R., Bachman, K.E., Schuebel, K., and Herman, J.G. (2001). Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum Mol Genet 10, 687-692.
6. Bediaga, N.G., Acha-Sagredo, A., Guerra, I., Viguri, A., Albaina, C., Ruiz Diaz, I., Rezola, R., Alberdi, M.J., Dopazo, J., Montaner, D., et al. (2010). DNA methylation epigenotypes in breast cancer molecular subtypes. Breast cancer research : BCR 12, R77.
7. Calza, S., Hall, P., Auer, G., Bjohle, J., Klaar, S., Kronenwett, U., Liu, E.T., Miller, L., Ploner, A., Smeds, J., et al. (2006). Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patients. Breast cancer research : BCR 8, R34.
8. Chappuis, P.O., Kapusta, L., Begin, L.R., Wong, N., Brunet, J.S., Narod, S.A., Slingerland, J., and Foulkes, W.D. (2000). Germline BRCA1/2 mutations and p27(Kip1) protein levels independently predict outcome after breast cancer. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 18, 4045-4052.
9. Chen, M.L., Shen, F., Huang, W., Qi, J.H., Wang, Y., Feng, Y.Q., Liu, S.M., and Yuan, B.F. (2013). Quantification of 5-methylcytosine and 5-hydroxymethylcytosine in genomic DNA from hepatocellular carcinoma tissues by capillary hydrophilic-interaction liquid chromatography/quadrupole TOF mass spectrometry. Clinical chemistry 59, 824-832.
10. Chen, R.Z., Pettersson, U., Beard, C., Jackson-Grusby, L., and Jaenisch, R. (1998). DNA hypomethylation leads to elevated mutation rates. Nature 395, 89-93.
11. Chen, Z.X., and Riggs, A.D. (2011). DNA methylation and demethylation in mammals. J Biol Chem 286, 18347-18353.
12. Chowdhury, R., Yeoh, K.K., Tian, Y.M., Hillringhaus, L., Bagg, E.A., Rose, N.R., Leung, I.K., Li, X.S., Woon, E.C., Yang, M., et al. (2011). The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep 12, 463-469.
13. Chuang, L.S., Ian, H.I., Koh, T.W., Ng, H.H., Xu, G., and Li, B.F. (1997). Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1. Science 277, 1996-2000.
14. Dahl, C., Gronbaek, K., and Guldberg, P. (2011). Advances in DNA methylation: 5-hydroxymethylcytosine revisited. Clinica chimica acta; international journal of clinical chemistry 412, 831-836.
15. Dang, L., White, D.W., Gross, S., Bennett, B.D., Bittinger, M.A., Driggers, E.M., Fantin, V.R., Jang, H.G., Jin, S., Keenan, M.C., et al. (2009). Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462, 739-744.
16. Dawlaty, M.M., Breiling, A., Le, T., Raddatz, G., Barrasa, M.I., Cheng, A.W., Gao, Q., Powell, B.E., Li, Z., Xu, M., et al. (2013). Combined deficiency of Tet1 and Tet2 causes epigenetic abnormalities but is compatible with postnatal development. Developmental cell 24, 310-323.
17. Delgado-Cruzata, L., Wu, H.C., Perrin, M., Liao, Y., Kappil, M.A., Ferris, J.S., Flom, J.D., Yazici, H., Santella, R.M., and Terry, M.B. (2012). Global DNA methylation levels in white blood cell DNA from sisters discordant for breast cancer from the New York site of the Breast Cancer Family Registry. Epigenetics : official journal of the DNA Methylation Society 7, 868-874.
18. Emdad, L., Sarkar, D., Su, Z.Z., and Fisher, P.B. (2005). Emerging roles of centrosomal amplification and genomic instability in cancer. Frontiers in bioscience : a journal and virtual library 10, 728-742.
19. Esteller, M. (2008). Epigenetics in cancer. N Engl J Med 358, 1148-1159.
20. Feinberg, A.P., and Vogelstein, B. (1983a). Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301, 89-92.
21. Feinberg, A.P., and Vogelstein, B. (1983b). Hypomethylation of ras oncogenes in primary human cancers. Biochemical and biophysical research communications 111, 47-54.
22. Fernandez, A.F., Assenov, Y., Martin-Subero, J.I., Balint, B., Siebert, R., Taniguchi, H., Yamamoto, H., Hidalgo, M., Tan, A.C., Galm, O., et al. (2012). A DNA methylation fingerprint of 1628 human samples. Genome Res 22, 407-419.
23. Figueroa, M.E., Abdel-Wahab, O., Lu, C., Ward, P.S., Patel, J., Shih, A., Li, Y., Bhagwat, N., Vasanthakumar, A., Fernandez, H.F., et al. (2010). Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18, 553-567.
24. Florl, A.R., Lower, R., Schmitz-Drager, B.J., and Schulz, W.A. (1999). DNA methylation and expression of LINE-1 and HERV-K provirus sequences in urothelial and renal cell carcinomas. Br J Cancer 80, 1312-1321.
25. Gama-Sosa, M.A., Slagel, V.A., Trewyn, R.W., Oxenhandler, R., Kuo, K.C., Gehrke, C.W., and Ehrlich, M. (1983). The 5-methylcytosine content of DNA from human tumors. Nucleic acids research 11, 6883-6894.
26. Gambichler, T., Sand, M., and Skrygan, M. (2013). Loss of 5-hydroxymethylcytosine and ten-eleven translocation 2 protein expression in malignant melanoma. Melanoma research 23, 218-220.
27. Gaudet, F., Hodgson, J.G., Eden, A., Jackson-Grusby, L., Dausman, J., Gray, J.W., Leonhardt, H., and Jaenisch, R. (2003). Induction of tumors in mice by genomic hypomethylation. Science 300, 489-492.
28. Globisch, D., Munzel, M., Muller, M., Michalakis, S., Wagner, M., Koch, S., Bruckl, T., Biel, M., and Carell, T. (2010). Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 5, e15367.
29. Gross, S., Cairns, R.A., Minden, M.D., Driggers, E.M., Bittinger, M.A., Jang, H.G., Sasaki, M., Jin, S., Schenkein, D.P., Su, S.M., et al. (2010). Cancer-associated metabolite 2-hydroxyglutarate accumulates in acute myelogenous leukemia with isocitrate dehydrogenase 1 and 2 mutations. J Exp Med 207, 339-344.
30. Guo, J.U., Su, Y., Zhong, C., Ming, G.L., and Song, H. (2011). Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145, 423-434.
31. Haffner, M.C., Chaux, A., Meeker, A.K., Esopi, D.M., Gerber, J., Pellakuru, L.G., Toubaji, A., Argani, P., Iacobuzio-Donahue, C., Nelson, W.G., et al. (2011). Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers. Oncotarget 2, 627-637.
32. Hansen, K.D., Timp, W., Bravo, H.C., Sabunciyan, S., Langmead, B., McDonald, O.G., Wen, B., Wu, H., Liu, Y., Diep, D., et al. (2011). Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43, 768-775.
33. Hershey, A.D., Dixon, J., and Chase, M. (1953). Nucleic acid economy in bacteria infected with bacteriophage T2. I. Purine and pyrimidine composition. J Gen Physiol 36, 777-789.
34. Holm, K., Hegardt, C., Staaf, J., Vallon-Christersson, J., Jonsson, G., Olsson, H., Borg, A., and Ringner, M. (2010). Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast cancer research : BCR 12, R36.
35. Hon, G.C., Hawkins, R.D., Caballero, O.L., Lo, C., Lister, R., Pelizzola, M., Valsesia, A., Ye, Z., Kuan, S., Edsall, L.E., et al. (2012). Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 22, 246-258.
36. Hsu, C.H., Peng, K.L., Kang, M.L., Chen, Y.R., Yang, Y.C., Tsai, C.H., Chu, C.S., Jeng, Y.M., Chen, Y.T., Lin, F.M., et al. (2012). TET1 suppresses cancer invasion by activating the tissue inhibitors of metalloproteinases. Cell Rep 2, 568-579.
37. Ito, S., D'Alessio, A.C., Taranova, O.V., Hong, K., Sowers, L.C., and Zhang, Y. (2010). Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466, 1129-1133.
38. Iyer, L.M., Tahiliani, M., Rao, A., and Aravind, L. (2009). Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle 8, 1698-1710.
39. Jaenisch, R., and Bird, A. (2003). Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33 Suppl, 245-254.
40. Jin, S.G., Jiang, Y., Qiu, R., Rauch, T.A., Wang, Y., Schackert, G., Krex, D., Lu, Q., and Pfeifer, G.P. (2011a). 5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations. Cancer research 71, 7360-7365.
41. Jin, S.G., Kadam, S., and Pfeifer, G.P. (2010). Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic acids research 38, e125.
42. Jin, S.G., Wu, X., Li, A.X., and Pfeifer, G.P. (2011b). Genomic mapping of 5-hydroxymethylcytosine in the human brain. Nucleic acids research 39, 5015-5024.
43. Jones, P.A., and Laird, P.W. (1999). Cancer epigenetics comes of age. Nat Genet 21, 163-167.
44. Jones, P.A., and Liang, G. (2009). Rethinking how DNA methylation patterns are maintained. Nat Rev Genet 10, 805-811.
45. Knudson, A.G., Jr. (1971). Mutation and cancer: statistical study of retinoblastoma. Proceedings of the National Academy of Sciences of the United States of America 68, 820-823.
46. Kothari, R.M., and Shankar, V. (1976). 5-Methylcytosine content in the vertebrate deoxyribonucleic acids: species specificity. J Mol Evol 7, 325-329.
47. Kraus, T.F., Globisch, D., Wagner, M., Eigenbrod, S., Widmann, D., Munzel, M., Muller, M., Pfaffeneder, T., Hackner, B., Feiden, W., et al. (2012). Low values of 5-hydroxymethylcytosine (5hmC), the "sixth base," are associated with anaplasia in human brain tumors. Int J Cancer 131, 1577-1590.
48. Kriaucionis, S., and Heintz, N. (2009). The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929-930.
49. Kudo, Y., Tateishi, K., Yamamoto, K., Yamamoto, S., Asaoka, Y., Ijichi, H., Nagae, G., Yoshida, H., Aburatani, H., and Koike, K. (2012). Loss of 5-hydroxymethylcytosine is accompanied with malignant cellular transformation. Cancer science 103, 670-676.
50. Kulis, M., Queiros, A.C., Beekman, R., and Martin-Subero, J.I. (2013). Intragenic DNA methylation in transcriptional regulation, normal differentiation and cancer. Biochimica et biophysica acta 1829, 1161-1174.
51. Lengauer, C., Kinzler, K.W., and Vogelstein, B. (1997). DNA methylation and genetic instability in colorectal cancer cells. Proceedings of the National Academy of Sciences of the United States of America 94, 2545-2550.
52. Lengauer, C., Kinzler, K.W., and Vogelstein, B. (1998). Genetic instabilities in human cancers. Nature 396, 643-649.
53. Lian, C.G., Xu, Y., Ceol, C., Wu, F., Larson, A., Dresser, K., Xu, W., Tan, L., Hu, Y., Zhan, Q., et al. (2012). Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell 150, 1135-1146.
54. Liu, C., Liu, L., Chen, X., Shen, J., Shan, J., Xu, Y., Yang, Z., Wu, L., Xia, F., Bie, P., et al. (2013). Decrease of 5-hydroxymethylcytosine is associated with progression of hepatocellular carcinoma through downregulation of TET1. PloS one 8, e62828.
55. Liu, Y., Jiang, W., Liu, J., Zhao, S., Xiong, J., Mao, Y., and Wang, Y. (2012). IDH1 mutations inhibit multiple alpha-ketoglutarate-dependent dioxygenase activities in astroglioma. J Neurooncol 109, 253-260.
56. Loenarz, C., and Schofield, C.J. (2009). Oxygenase catalyzed 5-methylcytosine hydroxylation. Chem Biol 16, 580-583.
57. Lu, L.J., Randerath, E., and Randerath, K. (1983). DNA hypomethylation in Morris hepatomas. Cancer Lett 19, 231-239.
58. Madzo, J., Vasanthakumar, A., and Godley, L.A. (2013). Perturbations of 5-hydroxymethylcytosine patterning in hematologic malignancies. Semin Hematol 50, 61-69.
59. Mariani, C.J., Madzo, J., Moen, E.L., Yesilkanal, A., and Godley, L.A. (2013). Alterations of 5-hydroxymethylcytosine in human cancers. Cancers (Basel) 5, 786-814.
60. Mellen, M., Ayata, P., Dewell, S., Kriaucionis, S., and Heintz, N. (2012). MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 151, 1417-1430.
61. Muller, T., Gessi, M., Waha, A., Isselstein, L.J., Luxen, D., Freihoff, D., Freihoff, J., Becker, A., Simon, M., Hammes, J., et al. (2012). Nuclear exclusion of TET1 is associated with loss of 5-hydroxymethylcytosine in IDH1 wild-type gliomas. The American journal of pathology 181, 675-683.
62. Nagarajan, R.P., and Costello, J.F. (2009). Epigenetic mechanisms in glioblastoma multiforme. Semin Cancer Biol 19, 188-197.
63. Ogino, S., Nosho, K., Kirkner, G.J., Kawasaki, T., Chan, A.T., Schernhammer, E.S., Giovannucci, E.L., and Fuchs, C.S. (2008). A cohort study of tumoral LINE-1 hypomethylation and prognosis in colon cancer. J Natl Cancer Inst 100, 1734-1738.
64. Ooi, S.K., and Bestor, T.H. (2008). The colorful history of active DNA demethylation. Cell 133, 1145-1148.
65. Orr, B.A., Haffner, M.C., Nelson, W.G., Yegnasubramanian, S., and Eberhart, C.G. (2012). Decreased 5-hydroxymethylcytosine is associated with neural progenitor phenotype in normal brain and shorter survival in malignant glioma. PloS one 7, e41036.
66. Parrella, P. (2010). Epigenetic Signatures in Breast Cancer: Clinical Perspective. Breast Care (Basel) 5, 66-73.
67. Pattamadilok, J., Huapai, N., Rattanatanyong, P., Vasurattana, A., Triratanachat, S., Tresukosol, D., and Mutirangura, A. (2008). LINE-1 hypomethylation level as a potential prognostic factor for epithelial ovarian cancer. Int J Gynecol Cancer 18, 711-717.
68. Penn, N.W., Suwalski, R., O'Riley, C., Bojanowski, K., and Yura, R. (1972). The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem J 126, 781-790.
69. Perou, C.M., Sorlie, T., Eisen, M.B., van de Rijn, M., Jeffrey, S.S., Rees, C.A., Pollack, J.R., Ross, D.T., Johnsen, H., Akslen, L.A., et al. (2000). Molecular portraits of human breast tumours. Nature 406, 747-752.
70. Reik, W. (2007). Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447, 425-432.
71. Riehmer, V., Gietzelt, J., Beyer, U., Hentschel, B., Westphal, M., Schackert, G., Sabel, M.C., Radlwimmer, B., Pietsch, T., Reifenberger, G., et al. (2014). Genomic profiling reveals distinctive molecular relapse patterns in IDH1/2 wild-type glioblastoma. Genes Chromosomes Cancer 53, 589-605.
72. Robson, M.E., Chappuis, P.O., Satagopan, J., Wong, N., Boyd, J., Goffin, J.R., Hudis, C., Roberge, D., Norton, L., Begin, L.R., et al. (2004). A combined analysis of outcome following breast cancer: differences in survival based on BRCA1/BRCA2 mutation status and administration of adjuvant treatment. Breast cancer research : BCR 6, R8-R17.
73. Roman-Gomez, J., Jimenez-Velasco, A., Agirre, X., Cervantes, F., Sanchez, J., Garate, L., Barrios, M., Castillejo, J.A., Navarro, G., Colomer, D., et al. (2005). Promoter hypomethylation of the LINE-1 retrotransposable elements activates sense/antisense transcription and marks the progression of chronic myeloid leukemia. Oncogene 24, 7213-7223.
74. Rupninder Sandhu, M., 1,3,4 Joel S. Parker, MS,2,4 Wendell D. Jones, PhD,5 Chad A. Livasy, MD,1,3,4 William B. Coleman, PhD1,3,4 (2010). Microarray-Based Gene Expression Profiling for Molecular Classification of Breast Cancer and Identification of New Targets for Therapy. CE Update.
75. Saito, K., Kawakami, K., Matsumoto, I., Oda, M., Watanabe, G., and Minamoto, T. (2010). Long interspersed nuclear element 1 hypomethylation is a marker of poor prognosis in stage IA non-small cell lung cancer. Clin Cancer Res 16, 2418-2426.
76. Shibata, T., Kokubu, A., Miyamoto, M., Sasajima, Y., and Yamazaki, N. (2011). Mutant IDH1 confers an in vivo growth in a melanoma cell line with BRAF mutation. Am J Pathol 178, 1395-1402.
77. Song, C.X., Szulwach, K.E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.H., Zhang, W., Jian, X., et al. (2011). Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol 29, 68-72.
78. Sorlie, T., Perou, C.M., Tibshirani, R., Aas, T., Geisler, S., Johnsen, H., Hastie, T., Eisen, M.B., van de Rijn, M., Jeffrey, S.S., et al. (2001). Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proceedings of the National Academy of Sciences of the United States of America 98, 10869-10874.
79. Sorlie, T., Tibshirani, R., Parker, J., Hastie, T., Marron, J.S., Nobel, A., Deng, S., Johnsen, H., Pesich, R., Geisler, S., et al. (2003). Repeated observation of breast tumor subtypes in independent gene expression data sets. Proceedings of the National Academy of Sciences of the United States of America 100, 8418-8423.
80. Stoppa-Lyonnet, D., Ansquer, Y., Dreyfus, H., Gautier, C., Gauthier-Villars, M., Bourstyn, E., Clough, K.B., Magdelenat, H., Pouillart, P., Vincent-Salomon, A., et al. (2000). Familial invasive breast cancers: worse outcome related to BRCA1 mutations. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 18, 4053-4059.
81. Sun, M., Song, C.X., Huang, H., Frankenberger, C.A., Sankarasharma, D., Gomes, S., Chen, P., Chen, J., Chada, K.K., He, C., et al. (2013). HMGA2/TET1/HOXA9 signaling pathway regulates breast cancer growth and metastasis. Proceedings of the National Academy of Sciences of the United States of America 110, 9920-9925.
82. Tahiliani, M., Koh, K.P., Shen, Y., Pastor, W.A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L.M., Liu, D.R., Aravind, L., et al. (2009). Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930-935.
83. Tan, L., and Shi, Y.G. (2012). Tet family proteins and 5-hydroxymethylcytosine in development and disease. Development 139, 1895-1902.
84. Tan, Y.O., Han, S., Lu, Y.S., Yip, C.H., Sunpaweravong, P., Jeong, J., Caguioa, P.B., Aggarwal, S., Yeoh, E.M., and Moon, H. (2010). The prevalence and assessment of ErbB2-positive breast cancer in Asia: a literature survey. Cancer 116, 5348-5357.
85. Valinluck, V., and Sowers, L.C. (2007). Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res 67, 946-950.
86. Valinluck, V., Tsai, H.H., Rogstad, D.K., Burdzy, A., Bird, A., and Sowers, L.C. (2004). Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res 32, 4100-4108.
87. Widschwendter, M., and Jones, P.A. (2002). DNA methylation and breast carcinogenesis. Oncogene 21, 5462-5482.
88. Wu, H., D'Alessio, A.C., Ito, S., Xia, K., Wang, Z., Cui, K., Zhao, K., Sun, Y.E., and Zhang, Y. (2011). Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473, 389-393.
89. Xiang, T.X., Yuan, Y., Li, L.L., Wang, Z.H., Dan, L.Y., Chen, Y., Ren, G.S., and Tao, Q. (2013). Aberrant promoter CpG methylation and its translational applications in breast cancer. Chinese journal of cancer 32, 12-20.
90. Xu, W., Yang, H., Liu, Y., Yang, Y., Wang, P., Kim, S.H., Ito, S., Yang, C., Xiao, M.T., Liu, L.X., et al. (2011a). Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of alpha-ketoglutarate-dependent dioxygenases. Cancer cell 19, 17-30.
91. Xu, Y., Wu, F., Tan, L., Kong, L., Xiong, L., Deng, J., Barbera, A.J., Zheng, L., Zhang, H., Huang, S., et al. (2011b). Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell 42, 451-464.
92. Yang, H., Liu, Y., Bai, F., Zhang, J.Y., Ma, S.H., Liu, J., Xu, Z.D., Zhu, H.G., Ling, Z.Q., Ye, D., et al. (2013a). Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation. Oncogene 32, 663-669.
93. Yang, Q., Wu, K., Ji, M., Jin, W., He, N., Shi, B., and Hou, P. (2013b). Decreased 5-hydroxymethylcytosine (5-hmC) is an independent poor prognostic factor in gastric cancer patients. J Biomed Nanotechnol 9, 1607-1616.
94. Yegnasubramanian, S., Haffner, M.C., Zhang, Y., Gurel, B., Cornish, T.C., Wu, Z., Irizarry, R.A., Morgan, J., Hicks, J., DeWeese, T.L., et al. (2008). DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity. Cancer Res 68, 8954-8967.
95. Zhang, H., Zhang, X., Clark, E., Mulcahey, M., Huang, S., and Shi, Y.G. (2010). TET1 is a DNA-binding protein that modulates DNA methylation and gene transcription via hydroxylation of 5-methylcytosine. Cell research 20, 1390-1393.