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Breast Cancer Research
Published in: Breast Cancer Research 1/2009

Open Access 01-06-2009 | Research article

Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer

Authors: Stella Tommasi, Deborah L Karm, Xiwei Wu, Yun Yen, Gerd P Pfeifer

Published in: Breast Cancer Research | Issue 1/2009

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Abstract

Introduction

Aberrant methylation of CpG islands is a hallmark of cancer and occurs at an early stage in breast tumorigenesis. However, its impact on tumor development is not fully determined, and its potential as a diagnostic biomarker remains to be validated. Methylation profiling of invasive breast carcinoma has been largely explored. Conversely, very little and sparse information is available on early-stage breast cancer. To gain insight into the epigenetic switches that may promote and/or contribute to the initial neoplastic events during breast carcinogenesis, we have analyzed the DNA methylation profile of ductal carcinoma in situ, a premalignant breast lesion with a great potential to progress toward invasive carcinoma.

Methods

We have utilized a comprehensive and sensitive array-based DNA mapping technique, the methylated-CpG island recovery assay, to profile the DNA methylation pattern in ductal carcinoma in situ. Differential methylation of CpG islands was compared genome-wide in tumor DNA versus normal DNA utilizing a statistical linear model in the LIMMA software package.

Results

Using this approach, we have identified 108 significant CpG islands that undergo aberrant DNA methylation in ductal carcinoma in situ and stage I breast tumors, with methylation frequencies greater than or comparable with those of more advanced invasive carcinoma (50% to 93%). A substantial fraction of these hypermethylated CpG islands (32% of the annotated CpG islands) is associated with several homeobox genes, such as the TLX1, HOXB13, and HNF1B genes. Fifty-three percent of the genes hypermethylated in early-stage breast cancer overlap with known Polycomb targets and include homeobox genes and other developmental transcription factors.

Conclusions

We have identified a series of new potential methylation biomarkers that may help elucidate the underlying mechanisms of breast tumorigenesis. More specifically, our results are suggestive of a critical role of homeobox gene methylation in the insurgence and/or progression of breast cancer.
Appendix
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Literature
1.
Althuis MD, Dozier JM, Anderson WF, Devesa SS, Brinton LA: Global trends in breast cancer incidence and mortality 1973–1997. Int J Epidemiol. 2005, 34: 405-412. 10.1093/ije/dyh414.CrossRefPubMed
2.
Ting AH, McGarvey KM, Baylin SB: The cancer epigenome – components and functional correlates. Genes Dev. 2006, 20: 3215-3231. 10.1101/gad.1464906.CrossRefPubMed
3.
Baylin SB, Esteller M, Rountree MR, Bachman KE, Schuebel K, Herman JG: Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum Mol Genet. 2001, 10: 687-692. 10.1093/hmg/10.7.687.CrossRefPubMed
4.
Herman JG, Baylin SB: Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med. 2003, 349: 2042-2054. 10.1056/NEJMra023075.CrossRefPubMed
5.
Esteller M: Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum Mol Genet. 2007, 16 (Spec No 1): R50-R59. 10.1093/hmg/ddm018.CrossRefPubMed
6.
Yang X, Yan L, Davidson NE: DNA methylation in breast cancer. Endocr Relat Cancer. 2001, 8: 115-127. 10.1677/erc.0.0080115.CrossRefPubMed
7.
Widschwendter M, Jones PA: DNA methylation and breast carcinogenesis. Oncogene. 2002, 21: 5462-5482. 10.1038/sj.onc.1205606.CrossRefPubMed
8.
Szyf M, Pakneshan P, Rabbani SA: DNA methylation and breast cancer. Biochem Pharmacol. 2004, 68: 1187-1197. 10.1016/j.bcp.2004.04.030.CrossRefPubMed
9.
Li S, Rong M, Iacopetta B: DNA hypermethylation in breast cancer and its association with clinicopathological features. Cancer Lett. 2006, 237: 272-280. 10.1016/j.canlet.2005.06.011.CrossRefPubMed
10.
Agrawal A, Murphy RF, Agrawal DK: DNA methylation in breast and colorectal cancers. Mod Pathol. 2007, 20: 711-721. 10.1038/modpathol.3800822.CrossRefPubMed
11.
Krassenstein R, Sauter E, Dulaimi E, Battagli C, Ehya H, Klein-Szanto A, Cairns P: Detection of breast cancer in nipple aspirate fluid by CpG island hypermethylation. Clin Cancer Res. 2004, 10 (1 Pt 1): 28-32. 10.1158/1078-0432.CCR-0410-3.CrossRefPubMed
12.
Lehmann U, Langer F, Feist H, Glockner S, Hasemeier B, Kreipe H: Quantitative assessment of promoter hypermethylation during breast cancer development. Am J Pathol. 2002, 160: 605-612.CrossRefPubMedPubMedCentral
13.
Yan PS, Venkataramu C, Ibrahim A, Liu JC, Shen RZ, Diaz NM, Centeno B, Weber F, Leu YW, Shapiro CL, Eng C, Yeatman TJ, Huang TH: Mapping geographic zones of cancer risk with epigenetic biomarkers in normal breast tissue. Clin Cancer Res. 2006, 12: 6626-6636. 10.1158/1078-0432.CCR-06-0467.CrossRefPubMed
14.
Cheng AS, Culhane AC, Chan MW, Venkataramu CR, Ehrich M, Nasir A, Rodriguez BA, Liu J, Yan PS, Quackenbush J, Nephew KP, Yeatman TJ, Huang TH: Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome. Cancer Res. 2008, 68: 1786-1796. 10.1158/0008-5472.CAN-07-5547.CrossRefPubMedPubMedCentral
15.
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.CrossRefPubMed
16.
Lewis CM, Cler LR, Bu DW, Zochbauer-Muller S, Milchgrub S, Naftalis EZ, Leitch AM, Minna JD, Euhus DM: Promoter hypermethylation in benign breast epithelium in relation to predicted breast cancer risk. Clin Cancer Res. 2005, 11: 166-172.PubMed
17.
Shinozaki M, Hoon DS, Giuliano AE, Hansen NM, Wang HJ, Turner R, Taback B: Distinct hypermethylation profile of primary breast cancer is associated with sentinel lymph node metastasis. Clin Cancer Res. 2005, 11: 2156-2162. 10.1158/1078-0432.CCR-04-1810.CrossRefPubMed
18.
Fackler MJ, Malone K, Zhang Z, Schilling E, Garrett-Mayer E, Swift-Scanlan T, Lange J, Nayar R, Davidson NE, Khan SA, Sukumar S: Quantitative multiplex methylation-specific PCR analysis doubles detection of tumor cells in breast ductal fluid. Clin Cancer Res. 2006, 12 (11 Pt 1): 3306-3310. 10.1158/1078-0432.CCR-05-2733.CrossRefPubMed
19.
Lee JS, Fackler MJ, Teo WW, Lee JH, Choi C, Park MH, Yoon JH, Zhang Z, Argani P, Sukumar S: Quantitative promoter hypermethylation profiles of ductal carcinoma in situ in north american and korean women: potential applications for diagnosis. Cancer Biol Ther. 2008, 7: 1398-1406. 10.1158/1535-7163.MCT-08-0192.CrossRefPubMed
20.
Melnikov AA, Scholtens DM, Wiley EL, Khan SA, Levenson VV: Array-based multiplex analysis of DNA methylation in breast cancer tissues. J Mol Diagn. 2008, 10: 93-101. 10.2353/jmoldx.2008.070077.CrossRefPubMedPubMedCentral
21.
Yan PS, Chen CM, Shi H, Rahmatpanah F, Wei SH, Caldwell CW, Huang TH: Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer Res. 2001, 61: 8375-8380.PubMed
22.
Chen CM, Chen HL, Hsiau TH, Hsiau AH, Shi H, Brock GJ, Wei SH, Caldwell CW, Yan PS, Huang TH: Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes. Am J Pathol. 2003, 163: 37-45.CrossRefPubMedPubMedCentral
23.
Miyamoto K, Fukutomi T, Akashi-Tanaka S, Hasegawa T, Asahara T, Sugimura T, Ushijima T: Identification of 20 genes aberrantly methylated in human breast cancers. Int J Cancer. 2005, 116: 407-414. 10.1002/ijc.21054.CrossRefPubMed
24.
Piotrowski A, Benetkiewicz M, Menzel U, de Ståhl TD, Mantripragada K, Grigelionis G, Buckley PG, Jankowski M, Hoffman J, Bała D, Srutek E, Laskowski R, Zegarski W, Dumanski JP: Microarray-based survey of CpG islands identifies concurrent hyper- and hypomethylation patterns in tissues derived from patients with breast cancer. Genes Chromosomes Cancer. 2006, 45: 656-667. 10.1002/gcc.20331.CrossRefPubMed
25.
Ordway JM, Budiman MA, Korshunova Y, Maloney RK, Bedell JA, Citek RW, Bacher B, Peterson S, Rohlfing T, Hall J, Brown R, Lakey N, Doerge RW, Martienssen RA, Leon J, McPherson JD, Jeddeloh JA: Identification of novel high-frequency DNA methylation changes in breast cancer. PLoS ONE. 2007, 2: e1314-10.1371/journal.pone.0001314.CrossRefPubMedPubMedCentral
26.
Hu M, Yao J, Carroll DK, Weremowicz S, Chen H, Carrasco D, Richardson A, Violette S, Nikolskaya T, Nikolsky Y, Bauerlein EL, Hahn WC, Gelman RS, Allred C, Bissell MJ, Schnitt S, Polyak K: Regulation of in situ to invasive breast carcinoma transition. Cancer Cell. 2008, 13: 394-406. 10.1016/j.ccr.2008.03.007.CrossRefPubMedPubMedCentral
27.
Rauch T, Pfeifer GP: Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest. 2005, 85: 1172-1180. 10.1038/labinvest.3700311.CrossRefPubMed
28.
Rauch T, Li H, Wu X, Pfeifer GP: MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res. 2006, 66: 7939-7947. 10.1158/0008-5472.CAN-06-1888.CrossRefPubMed
29.
Coletta RD, Jedlicka P, Gutierrez-Hartmann A, Ford HL: Transcriptional control of the cell cycle in mammary gland development and tumorigenesis. J Mammary Gland Biol Neoplasia. 2004, 9: 39-53. 10.1023/B:JOMG.0000023587.40966.f6.CrossRefPubMed
30.
31.
Chen H, Sukumar S: Role of homeobox genes in normal mammary gland development and breast tumorigenesis. J Mammary Gland Biol Neoplasia. 2003, 8: 159-175. 10.1023/A:1025996707117.CrossRefPubMed
32.
Greene FL, Page DL, Balch CM, Fleming ID, Morrow M: AJCC Cancer Staging Manual. 2002, Springer-Verlag New York, LLC, 6CrossRef
33.
Rauch TA, Zhong X, Wu X, Wang M, Kernstine KH, Wang Z, Riggs AD, Pfeifer GP: High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proc Natl Acad Sci USA. 2008, 105: 252-257. 10.1073/pnas.0710735105.CrossRefPubMed
34.
35.
Rauch T, Wang Z, Zhang X, Zhong X, Wu X, Lau SK, Kernstine KH, Riggs AD, Pfeifer GP: Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci USA. 2007, 104: 5527-5532. 10.1073/pnas.0701059104.CrossRefPubMedPubMedCentral
36.
Abate-Shen C: Deregulated homeobox gene expression in cancer: cause or consequence?. Nat Rev Cancer. 2002, 2: 777-785. 10.1038/nrc907.CrossRefPubMed
37.
Bloushtain-Qimron N, Yao J, Snyder EL, Shipitsin M, Campbell LL, Mani SA, Hu M, Chen H, Ustyansky V, Antosiewicz JE, Argani P, Halushka MK, Thomson JA, Pharoah P, Porgador A, Sukumar S, Parsons R, Richardson AL, Stampfer MR, Gelman RS, Nikolskaya T, Nikolsky Y, Polyak K: Cell type-specific DNA methylation patterns in the human breast. Proc Natl Acad Sci USA. 2008, 105: 14076-14081. 10.1073/pnas.0805206105.CrossRefPubMedPubMedCentral
38.
Euhus DM, Bu D, Milchgrub S, Xie XJ, Bian A, Leitch AM, Lewis CM: DNA methylation in benign breast epithelium in relation to age and breast cancer risk. Cancer Epidemiol Biomarkers Prev. 2008, 17: 1051-1059. 10.1158/1055-9965.EPI-07-2582.CrossRefPubMed
39.
Rodriguez BA, Cheng AS, Yan PS, Potter D, Agosto-Perez FJ, Shapiro CL, Huang TH: Epigenetic repression of the estrogen-regulated Homeobox B13 gene in breast cancer. Carcinogenesis. 2008, 29: 1459-1465. 10.1093/carcin/bgn115.CrossRefPubMedPubMedCentral
40.
Illingworth R, Kerr A, Desousa D, Jørgensen H, Ellis P, Stalker J, Jackson D, Clee C, Plumb R, Rogers J, Humphray S, Cox T, Langford C, Bird A: A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 2008, 6: e22-10.1371/journal.pbio.0060022.CrossRefPubMedPubMedCentral
41.
42.
Raman V, Martensen SA, Reisman D, Evron E, Odenwald WF, Jaffee E, Marks J, Sukumar S: Compromised HOXA5 function can limit p53 expression in human breast tumours. Nature. 2000, 405: 974-978. 10.1038/35016125.CrossRefPubMed
43.
Novak P, Jensen T, Oshiro MM, Wozniak RJ, Nouzova M, Watts GS, Klimecki WT, Kim C, Futscher BW: Epigenetic inactivation of the HOXA gene cluster in breast cancer. Cancer Res. 2006, 66: 10664-10670. 10.1158/0008-5472.CAN-06-2761.CrossRefPubMed
44.
45.
Ringrose L: Polycomb comes of age: genome-wide profiling of target sites. Curr Opin Cell Biol. 2007, 19: 290-297. 10.1016/j.ceb.2007.04.010.CrossRefPubMed
46.
Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, Chevalier B, Johnstone SE, Cole MF, Isono K, Koseki H, Fuchikami T, Abe K, Murray HL, Zucker JP, Yuan B, Bell GW, Herbolsheimer E, Hannett NM, Sun K, Odom DT, Otte AP, Volkert TL, Bartel DP, Melton DA, Gifford DK, Jaenisch R, Young RA: Control of developmental regulators by Polycomb in human embryonic stem cells. Cell. 2006, 125: 301-313. 10.1016/j.cell.2006.02.043.CrossRefPubMedPubMedCentral
47.
Kirmizis A, Bartley SM, Farnham PJ: Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy. Mol Cancer Ther. 2003, 2: 113-121.PubMed
48.
Bracken AP, Pasini D, Capra M, Prosperini E, Colli E, Helin K: EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J. 2003, 22: 5323-5335. 10.1093/emboj/cdg542.CrossRefPubMedPubMedCentral
49.
Raaphorst FM: Deregulated expression of Polycomb-group oncogenes in human malignant lymphomas and epithelial tumors. Hum Mol Genet. 2005, 14 (Spec No 1): R93-R100. 10.1093/hmg/ddi111.CrossRefPubMed
50.
Ding L, Kleer CG: Enhancer of Zeste 2 as a marker of preneoplastic progression in the breast. Cancer Res. 2006, 66: 9352-9355. 10.1158/0008-5472.CAN-06-2384.CrossRefPubMed
51.
Viré E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C, Morey L, Van Eynde A, Bernard D, Vanderwinden JM, Bollen M, Esteller M, Di Croce L, de Launoit Y, Fuks F: The Polycomb group protein EZH2 directly controls DNA methylation. Nature. 2006, 439: 871-874. 10.1038/nature04431.CrossRefPubMed
52.
Ohm JE, McGarvey KM, Yu X, Cheng L, Schuebel KE, Cope L, Mohammad HP, Chen W, Daniel VC, Yu W, Berman DM, Jenuwein T, Pruitt K, Sharkis SJ, Watkins DN, Herman JG, Baylin SB: A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat Genet. 2007, 39: 237-242. 10.1038/ng1972.CrossRefPubMedPubMedCentral
53.
Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, Eden E, Yakhini Z, Ben-Shushan E, Reubinoff BE, Bergman Y, Simon I, Cedar H: Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet. 2007, 39: 232-236. 10.1038/ng1950.CrossRefPubMed
54.
Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, Marth C, Weisenberger DJ, Campan M, Young J, Jacobs I, Laird PW: Epigenetic stem cell signature in cancer. Nat Genet. 2007, 39: 157-158. 10.1038/ng1941.CrossRefPubMed
55.
Hahn MA, Hahn T, Lee DH, Esworthy RS, Kim BW, Riggs AD, Chu FF, Pfeifer GP: Methylation of polycomb target genes in intestinal cancer is mediated by inflammation. Cancer Res. 2008, 68: 10280-10289. 10.1158/0008-5472.CAN-08-1957.CrossRefPubMedPubMedCentral
56.
Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK, Bell GW, Otte AP, Vidal M, Gifford DK, Young RA, Jaenisch R: Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature. 2006, 441: 349-353. 10.1038/nature04733.CrossRefPubMed
57.
Bracken AP, Dietrich N, Pasini D, Hansen KH, Helin K: Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 2006, 20: 1123-1136. 10.1101/gad.381706.CrossRefPubMedPubMedCentral
Metadata
Title
Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer
Authors
Stella Tommasi
Deborah L Karm
Xiwei Wu
Yun Yen
Gerd P Pfeifer
Publication date
01-06-2009
Publisher
BioMed Central
Published in
Breast Cancer Research / Issue 1/2009
Electronic ISSN: 1465-542X
DOI
https://doi.org/10.1186/bcr2233

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