DNA methylation epigenotypes in breast cancer molecular subtypes

Breast Cancer Research

Volumn 12, Issue 5, 2010, Pages

  Bediaga, Naiara G ^a   Acha Sagredo, Amelia ^a   Guerra, Isabel ^b   Viguri, Amparo ^b   Albaina, Carmen ^b   Ruiz Diaz, Irune ^c   Rezola, Ricardo ^d   Alberdi, María Jesus ^d   Dopazo, Joaquín ^e   Montaner, David ^e   de Renobales, Mertxe ^a   Fernández, Agustín F ^f   Field, John K ^g   Fraga, Mario F ^h   Liloglou, Triantafillos ^g   de Pancorbo, Marian M ^a  

^a UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

^b HOSPITAL TXAGORRITXU   (Spain)

^c HOSPITAL DONOSTIA   (Spain)

^d Instituto Oncologico   (Spain)

^e CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

^f DEPARTAMENTO DE BIOQUÍMICA Y BIOLOGÍA MOLECULAR   (Spain)

^g UNIVERSITY OF LIVERPOOL   (United Kingdom)

^h CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; CD40 ANTIGEN; DNA; EPIDERMAL GROWTH FACTOR RECEPTOR 2; FIBROBLAST GROWTH FACTOR 2; GENOMIC DNA; KI 67 ANTIGEN; MICRORNA; MICRORNA 10A; MICRORNA 93; OSTEONECTIN; PROTEIN P53; RAS ASSOCIATION DOMAIN FAMILY PROTEIN 1A; TRANSCRIPTION FACTOR HOXA9; TRANSCRIPTION FACTOR SOX1; TRANSCRIPTION FACTOR SOX17; TRANSCRIPTION FACTOR TAL1; UNCLASSIFIED DRUG; ERBB2 PROTEIN, HUMAN;

ADULT; ARTICLE; BREAST CARCINOMA; CANCER CLASSIFICATION; CONTROLLED STUDY; CORRELATION ANALYSIS; CPG ISLAND; DIAGNOSTIC TEST ACCURACY STUDY; DIFFERENTIAL DIAGNOSIS; DNA METHYLATION; DNA MICROARRAY; EPIGENETICS; EPIGENOTYPE; FEMALE; FGF 2 GENE; GENE; GENE EXPRESSION; GENOTYPE; HISTOPATHOLOGY; HS3ST2 GENE; HUMAN; HUMAN TISSUE; LET 7A GENE; MAJOR CLINICAL STUDY; MOLECULAR TYPING; NPY GENE; NUCLEOTIDE SEQUENCE; PREDICTION; PROGNOSIS; PYROSEQUENCING; RASSF 1 GENE; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS; AGED; BREAST TUMOR; CANCER GRADING; CLASSIFICATION; GENE EXPRESSION PROFILING; GENETIC EPIGENESIS; GENETICS; METABOLISM; MIDDLE AGED; MUTATION; TUMOR SUPPRESSOR GENE;

AGED; BREAST NEOPLASMS; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENES, P53; GENOTYPE; HUMANS; KI-67 ANTIGEN; MIDDLE AGED; MUTATION; NEOPLASM GRADING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RECEPTOR, ERBB-2; TUMOR SUPPRESSOR PROTEIN P53;

EID: 78650877915     PISSN: 14655411     EISSN: 1465542X     Source Type: Journal    
DOI: 10.1186/bcr2721     Document Type: Article

References (44)

1. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lønning PE, Børresen-Dale AL, Brown PO, Botstein D. Molecular portraits of human breast tumours. Nature 2000, 406:747-752. 10.1038/35021093, 10963602.
2. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Eystein Lønning P, Børresen-Dale AL. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001, 98:10869-10874. 10.1073/pnas.191367098, 58566, 11553815.
3. Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PS. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 2009, 27:1160-1167. 10.1200/JCO.2008.18.1370, 2667820, 19204204.
4. Cheang MC, Chia SK, Voduc D, Gao D, Leung S, Snider J, Watson M, Davies S, Bernard PS, Parker JS, Perou CM, Ellis MJ, Nielsen TO. Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. J Natl Cancer Inst 2009, 101:736-750. 10.1093/jnci/djp082, 2684553, 19436038.
5. Mulero-Navarro S, Esteller M. Epigenetic biomarkers for human cancer: the time is now. Crit Rev Oncol Hematol 2008, 68:1-11. 10.1016/j.critrevonc.2008.03.001, 18430583.
6. Feinberg AP, Ohlsson R, Henikoff S. The epigenetic progenitor origin of human cancer. Nat Rev Genet 2006, 7:21-33. 10.1038/nrg1748, 16369569.
7. Fraga MF, Esteller M. Towards the human cancer epigenome: a first draft of histone modifications. Cell Cycle 2005, 4:1377-1381.
8. Yuan J, Luo RZ, Fujii S, Wang L, Hu W, Andreeff M, Pan Y, Kadota M, Oshimura M, Sahin AA, Issa JP, Bast RC, Yu Y. Aberrant methylation and silencing of ARHI, an imprinted tumor suppressor gene in which the function is lost in breast cancers. Cancer Res 2003, 63:4174-4180.
9. Fujii S, Luo RZ, Yuan J, Kadota M, Oshimura M, Dent SR, Kondo Y, Issa JP, Bast RC, Yu Y. Reactivation of the silenced and imprinted alleles of ARHI is associated with increased histone H3 acetylation and decreased histone H3 lysine 9 methylation. Hum Mol Genet 2003, 12:1791-1800. 10.1093/hmg/ddg204, 12874100.
10. Dammann R, Yang G, Pfeifer GP. Hypermethylation of the cpG island of Ras association domain family 1A (RASSF1A), a putative tumor suppressor gene from the 3p21.3 locus, occurs in a large percentage of human breast cancers. Cancer Res 2001, 61:3105-3109.
11. Krop IE, Sgroi D, Porter DA, Lunetta KL, LeVangie R, Seth P, Kaelin CM, Rhei E, Bosenberg M, Schnitt S, Marks JR, Pagon Z, Belina D, Razumovic J, Polyak K. HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells. Proc Natl Acad Sci USA 2001, 98:9796-9801. 10.1073/pnas.171138398, 55532, 11481438.
12. Fackler MJ, McVeigh M, Evron E, Garrett E, Mehrotra J, Polyak K, Sukumar S, Argani P. DNA methylation of RASSF1A, HIN-1, RAR-beta, cyclin D2 and twist in in situ and invasive lobular breast carcinoma. Int J Cancer 2003, 107:970-975. 10.1002/ijc.11508, 14601057.
13. Murata H, Khattar NH, Kang Y, Gu L, Li GM. Genetic and epigenetic modification of mismatch repair genes hMSH2 and hMLH1 in sporadic breast cancer with microsatellite instability. Oncogene 2002, 21:5696-5703. 10.1038/sj.onc.1205683, 12173039.
14. Ferguson AT, Evron E, Umbricht CB, Pandita TK, Chan TA, Hermeking H, Marks JR, Lambers AR, Futreal PA, Stampfer MR, Sukumar S. High frequency of hypermethylation at the 14-3-3 sigma locus leads to gene silencing in breast cancer. Proc Natl Acad Sci USA 2000, 97:6049-6054. 10.1073/pnas.100566997, 18556, 10811911.
15. Du Y, Carling T, Fang W, Piao Z, Sheu JC, Huang S. Hypermethylation in human cancers of the RIZ1 tumor suppressor gene, a member of a histone/protein methyltransferase superfamily. Cancer Res 2001, 61:8094-8099.
16. Di Vinci A, Perdelli L, Banelli B, Salvi S, Casciano I, Gelvi I, Allemanni G, Margallo E, Gatteschi B, Romani M. p16(INK4a) promoter methylation and protein expression in breast fibroadenoma and carcinoma. Int J Cancer 2005, 114:414-421. 10.1002/ijc.20771, 15578730.
17. Hu XC, Loo WT, Chow LW. E-cadherin promoter methylation can regulate its expression in invasive ductal breast cancer tissue in Chinese woman. Life Sci 2002, 71:1397-1404. 10.1016/S0024-3205(02)01843-X, 12127160.
18. Khan S, Kumagai T, Vora J, Bose N, Sehgal I, Koeffler PH, Bose S. PTEN promoter is methylated in a proportion of invasive breast cancers. Int J Cancer 2004, 112:407-410. 10.1002/ijc.20447, 15382065.
19. Wei M, Grushko TA, Dignam J, Hagos F, Nanda R, Sveen L, Xu J, Fackenthal J, Tretiakova M, Das S, Olopade OI. BRCA1 promoter methylation in sporadic breast cancer is associated with reduced BRCA1 copy number and chromosome 17 aneusomy. Cancer Res 2005, 65:10692-10699. 10.1158/0008-5472.CAN-05-1277, 16322213.
20. Orlando FA, Brown KD. Unraveling breast cancer heterogeneity through transcriptomic and epigenomic analysis. Ann Surg Oncol 2009, 16:2270-2279. 10.1245/s10434-009-0500-y, 19452229.
21. Feng W, Shen L, Wen S, Rosen DG, Jelinek J, Hu X, Huan S, Huang M, Liu J, Sahin AA, Hunt KK, Bast RC, Shen Y, Issa JP, Yu Y. Correlation between CpG methylation profiles and hormone receptor status in breast cancers. Breast Cancer Res 2007, 9:R57. 10.1186/bcr1762, 2206733, 17764565.
22. Fiegl H, Millinger S, Goebel G, Muller-Holzner E, Marth C, Laird PW, Widschwendter M. Breast cancer DNA methylation profiles in cancer cells and tumor stroma: association with HER-2/neu status in primary breast cancer. Cancer Res 2006, 66:29-33. 10.1158/0008-5472.CAN-05-2508, 16397211.
23. Bertolo C, Guerrero D, Vicente F, Cordoba A, Esteller M, Ropero S, Guillen-Grima F, Martinez-Peñuela JM, Lera JM. Differences and molecular immunohistochemical parameters in the subtypes of infiltrating ductal breast cancer. Am J Clin Pathol 2008, 130:414-424. 10.1309/J3QV9763DYPV338D, 18701415.
24. Bibikova M, Lin Z, Zhou L, Chudin E, Garcia EW, Wu B, Doucet D, Thomas NJ, Wang Y, Vollmer E, Goldmann T, Seifart C, Jiang W, Barker DL, Chee MS, Floros J, Fan JB. High-throughput DNA methylation profiling using universal bead arrays. Genome Res 2006, 16:383-393. 10.1101/gr.4410706, 1415217, 16449502.
25. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I. Controlling the false discovery rate in behavior genetics research. Behav Brain Res 2001, 125:279-284. 10.1016/S0166-4328(01)00297-2, 11682119.
26. Gene Expression Omnibus, GEO. , http://www.ncbi.nlm.nih.gov/geo/
27. Daskalos A, Nikolaidis G, Xinarianos G, Savvari P, Cassidy A, Zakopoulou R, Kotsinas A, Gorgoulis V, Field JK, Liloglou T. Hypomethylation of retrotransposable elements correlates with genomic instability in non-small cell lung cancer. Int J Cancer 2009, 124:81-87. 10.1002/ijc.23849, 18823011.
28. Blenkiron C, Goldstein LD, Thorne NP, Spiteri I, Chin SF, Dunning MJ, Barbosa-Morais NL, Teschendorff AE, Green AR, Ellis IO, Tavaré S, Caldas C, Miska EA. MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol 2007, 8:R214. 10.1186/gb-2007-8-10-r214, 2246288, 17922911.
29. Geli J, Kiss N, Karimi M, Lee JJ, Backdahl M, Ekstrom TJ, Larsson C. Global and regional CpG methylation in pheochromocytomas and abdominal paragangliomas: association to malignant behavior. Clin Cancer Res 2008, 14:2551-2559. 10.1158/1078-0432.CCR-07-1867, 18451216.
30. Konishi K, Shen L, Wang S, Meltzer SJ, Harpaz N, Issa JP. Rare CpG island methylator phenotype in ulcerative colitis-associated neoplasias. Gastroenterology 2007, 132:1254-1260. 10.1053/j.gastro.2007.01.035, 17408633.
31. Christensen BC, Marsit CJ, Houseman EA, Godleski JJ, Longacker JL, Zheng S, Yeh RF, Wrensch MR, Wiemels JL, Karagas MR, Bueno R, Sugarbaker DJ, Nelson HH, Wiencke JK, Kelsey KT. Differentiation of lung adenocarcinoma, pleural mesothelioma, and nonmalignant pulmonary tissues using DNA methylation profiles. Cancer Res 2009, 69:6315-6321. 10.1158/0008-5472.CAN-09-1073, 2755616, 19638575.
32. Hinshelwood RA, Clark SJ. Breast cancer epigenetics: normal human mammary epithelial cells as a model system. J Mol Med 2008, 86:1315-1328. 10.1007/s00109-008-0386-3, 18716754.
33. Lo PK, Sukumar S. Epigenomics and breast cancer. Pharmacogenomics 2008, 9:1879-1902. 10.2217/14622416.9.12.1879, 2633440, 19072646.
34. Pogribny IP, Beland FA. DNA hypomethylation in the origin and pathogenesis of human diseases. Cell Mol Life Sci 2009, 66:2249-2261. 10.1007/s00018-009-0015-5, 19326048.
35. Terada K, Okochi-Takada E, Akashi-Tanaka S, Miyamoto K, Taniyama K, Tsuda H, Asada K, Kaminishi M, Ushijima T. Association between frequent CpG island methylation and HER2 amplification in human breast cancers. Carcinogenesis 2009, 30:466-471. 10.1093/carcin/bgp021, 19168584.
36. Holm K, Hegardt C, Staaf J, Vallon-Christersson J, Jonsson G, Olsson H, Borg A, Ringnér M. Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Res 2010, 12:R36. 10.1186/bcr2590, 2917031, 20565864.
37. Lim E, Vaillant F, Wu D, Forrest NC, Pal B, Hart AH, Asselin-Labat ML, Gyorki DE, Ward T, Partanen A, Feleppa F, Huschtscha LI, Thorne HJ, kConFab, Fox SB, Yan M, French JD, Brown MA, Smyth GK, Visvader JE, Lindeman GJ. Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers. Nat Med 2009, 15:907-913. 10.1038/nm.2000, 19648928.
38. Carey LA, Dees EC, Sawyer L, Gatti L, Moore DT, Collichio F, Ollila DW, Sartor CI, Graham ML, Perou CM. The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes. Clin Cancer Res 2007, 13:2329-2334. 10.1158/1078-0432.CCR-06-1109, 17438091.
39. Bibikova M, Chudin E, Wu B, Zhou L, Garcia EW, Liu Y, Shin S, Plaia TW, Auerbach JM, Arking DE, Gonzalez R, Crook J, Davidson B, Schulz TC, Robins A, Khanna A, Sartipy P, Hyllner J, Vanguri P, Savant-Bhonsale S, Smith AK, Chakravarti A, Maitra A, Rao M, Barker DL, Loring JF, Fan JB. Human embryonic stem cells have a unique epigenetic signature. Genome Res 2006, 16:1075-1083. 10.1101/gr.5319906, 1557765, 16899657.
40. Bibikova M, Laurent LC, Ren B, Loring JF, Fan JB. Unraveling epigenetic regulation in embryonic stem cells. Cell Stem Cell 2008, 2:123-134. 10.1016/j.stem.2008.01.005, 18371433.
41. Bloushtain-Qimron N, Yao J, Shipitsin M, Maruyama R, Polyak K. Epigenetic patterns of embryonic and adult stem cells. Cell Cycle 2009, 8:809-817.
42. Altun G, Loring JF, Laurent LC. DNA methylation in embryonic stem cells. J Cell Biochem 2010, 109:1-6.
43. Calvanese V, Horrillo A, Hmadcha A, Suarez-Alvarez B, Fernandez AF, Lara E, Casado S, Menendez P, Bueno C, Garcia-Castro J, Rubio R, Lapunzina P, Alaminos M, Borghese L, Terstegge S, Harrison NJ, Moore HD, Brüstle O, Lopez-Larrea C, Andrews PW, Soria B, Esteller M, Fraga MF. Cancer genes hypermethylated in human embryonic stem cells. PLoS One 2008, 3:e3294. 10.1371/journal.pone.0003294, 2546447, 18820729.
44. Pathiraja TN, Stearns V, Oesterreich S. Epigenetic regulation in estrogen receptor positive breast cancer-role in treatment response. J Mammary Gland Biol Neoplasia 2010, 15:35-47.