Genome-wide methylation patterns provide insight into differences in breast tumor biology between American women of African and European ancestry

Oncotarget

Volumn 5, Issue 1, 2014, Pages 237-248

  Ambrosone, Christine B ^a   Young, Allyson C ^a   Sucheston, Lara E ^a   Wang, Dan ^a   Yan, Li ^a   Liu, Song ^a   Tang, Li ^a   Hu, Qiang ^a   Freudenheim, Jo L ^b   Shields, Peter G ^c   Morrison, Carl D ^a   Demissie, Kitaw ^d   Higgins, Michael J ^a  

^a ROSWELL PARK CANCER INSTITUTE   (United States)

^b UNIVERSITY AT BUFFALO   (United States)

^c OHIO STATE UNIVERSITY   (United States)

^d RUTGERS SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

African American; Breast cancer; Disparities; DNA methylation; Estrogen receptor; Genome wide

Indexed keywords

ESTROGEN RECEPTOR; DNA;

ADULT; AFRICAN AMERICAN; AGED; ARTICLE; BREAST CANCER; CAUCASIAN; CLUSTER ANALYSIS; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; ESTROGEN RECEPTOR POSITIVE BREAST CANCER; FEMALE; GENETIC ASSOCIATION; HEALTH DISPARITY; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; RACE DIFFERENCE; BREAST TUMOR; ETHNOLOGY; GENETICS; GENOTYPE; METABOLISM; MIDDLE AGED; PATHOLOGY; RISK FACTOR;

AFRICAN AMERICANS; AGED; BREAST NEOPLASMS; CLUSTER ANALYSIS; DNA METHYLATION; DNA, NEOPLASM; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MIDDLE AGED; RECEPTORS, ESTROGEN; RISK FACTORS;

EID: 84893860385     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.1599     Document Type: Article

References (37)

1. Amend K, Hicks D, Ambrosone CB. Breast cancer in African-American women: Differences in tumor biology from European-American women. Cancer Research. 2006; 66: 8327-8330.
2. Tao MH, Marian C, Shields PG, Nie J, McCann SE, Millen A, Ambrosone CB, Hutson A, Edge SB, Krishnan SS, Xie B, Winston J, Vito D, Russell M, Nochajski TH, Trevisan, et al. Alcohol consumption in relation to aberrant DNA methylation in breast tumors. Alcohol. 2011; 45: 689-699.
3. Tao M., Marian C, Nie J, Ambrosone CB, Krishnan SS, Edge SB, Trevisan M, Shields PG, Freudenheim JL. Body mass and DNA promoter methylation in breast tumors in the Western New York Exposures and Breast Cancer Study. Am. J. Clin. Nutr. 2011; 94: 831-838.
4. Terry MB, Ferris JS, Pilsner R, Flom JD, Tehranifar P, Santella RM, Gamble MV, Susser E. Genomic DNA methylation among women in a multiethnic New York City birth cohort. Cancer Epidemiol. Biomarkers Prev. 2008; 17: 2306-2310.
5. Adkins RM, Krushkal J, Tylavsky FA, Thomas F. Racial differences in gene-specific DNA methylation levels are present at birth. Birth Defects Research Part A - Clinical and Molecular Teratology. 2011; 91: 728-736.
6. Dumitrescu RG, Marian C, Krishnan SS, Spear SL, Kallakury BVS, Perry DJ, Convit JR, Seillier-Moiseiwitsch F, Yang Y, Freudenheim JL, Sheilds PG. Familial and racial determinants of tumour suppressor genes promoter hypermethylation in breast tissues from healthy women. J. Cell. Mol. Med. 2010; 14: 1468-1475.
7. Kwabi-Addo B, Wang S, Chung W, Jelinek J, Patierno SR, Wang B, Andrawis R, Lee NH, Apprey V, Issa JP, IttmannM. Identification of differentially methylated genes in normal prostate tissues from African American and Caucasian men. Clinical Cancer Research. 2010; 16: 3539-3547.
8. Mehrotra J, Ganpat MM, Kanaan Y, Fackler MJ, McVeigh M, Lahti-Domenici J, Polyak K, Argani P, Naab T, Garrett E, Parmigiani G, Broome C, Sukumar S. Estrogen receptor/progesteronereceptor-negative breast cancers of young African-American women have a higher frequency of methylation of multiple genes than those of Caucasian women. Clin. Cancer Res. 2004; 10: 2052-2057.
9. Wang S, Dorsey TH, Terunuma A, Kittles RA, Ambs S, Kwabi-Addo B. Relationship between tumor DNA methylation status and patient characteristics in African-American and European-American women with breast cancer. PLoS ONE. 2012; 7: e37928.
10. Holm K, Hegardt C, Staaf J, Vallon-Christersson J, Jönsson G, Olsson H, Borg Å, Ringnér M. Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Research. 2010; 12: R36
11. Kamalakaran S, Varadan V, Giercksky Russnes HE, Levy D, Kendall J, Janevski A, Riggs M, Banerjee N, Synnestvedt M, Schlichting E, Karesen R, Shama Prasada K, Rotti H, Rao R, Rao L, et al. DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables. Molecular Oncology. 2011; 5: 77-92.
12. Fackler MJ, Umbricht CB, Williams D, Argani P, Cruz L, Merino VF, Teo WW, Zhang Z, Huang P, Visvananthan K, Marks J, Ethier S, Gray JW, Wolff AC, Cope LM, Sukumar S. Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence. Cancer Res. 2011; 71: 6195-6207.
13. Hochberg Y, Benjamini Y. More powerful procedures for multiple significance testing. Stat. Med.1990; 9: 811-818.
14. Teschendorff AE, West J, Beck S. Age-associated epigenetic drift: implications, and a case of epigenetic thrift? Hum. Mol. Genet. 2013; 22: R7-R15.
15. Boks MP, Derks EM, Weisenberger DJ, Strengman E, Janson E, Sommer IE, Kahn RS, Ophoff RA. The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PLoS One. 2009; 4: e6767.
16. Alisch RS, Barwick BG, Chopra P, Myrick LK, Satten GA, Conneely KN, Warren ST. Age-associated DNA methylation in pediatric populations. Genome Res. 2012; 22: 623-632.
17. Zhang B, Zhou Y, Lin N, Lowdon R., Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, Xing X, Zhou J, Sundaram V, Elliott G, Gu J, Shi T. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res. 2013; 23:1522-1540.
18. Widschwendter M, Jones PA. DNA methylation and breast carcinogenesis. Oncogene, 2002; 21:5462-5482.
19. 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 Lonning P, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad. Sci. U. S. A. 2001; 98: 10869-10874.
20. Christensen BC, Kelsey KT, Zheng S, Houseman EA, Marsit CJ, Wrensch MR, Wiemels JL, Nelson HH, Karagas MR, Kushi LH, Kwan ML, Wiencke JK. Breast cancer DNA methylation profiles are associated with tumor size and alcohol and folate intake. PLoS Genetics. 2010; 6: e1001043.
21. 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, Lonning PE, Borresen-Dale AL, et al. Molecular portraits of human breast tumours. Nature. 2000; 406: 747-752.
22. Curtis C, Shah SP, Chin S, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Graf S, Ha G, Haffari G, Bashashati A, Russell R, Mckinney S, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012; 486:346-352.
23. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Ronqione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP. The human colon cancer methylome shows similar hypo- and hypermethylation at the conserved tissue-specific CpG island shores. Nat. Genet.2009; 41: 178-186
24. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C., Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, et al. Conserved role of intragenic DNA methylation in regulating anternative promoters. Nature. 2010; 466:253-257
25. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000; 155: 945-959.
26. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, GundersonKL, Fan JB, Shen R. High density DNA methylation array with single CpG site resolution. Genomics.2011; 98: 288-295.
27. Sandoval J, Heyn HA, Moran S, Serra-Musach J, Pujana MA, Bibikova M, Esteller M. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics. 2011; 6:692-702.
28. Yan L, Ma C, Wang D, Hu Q, Qin M, Conroy JM, Sucheston LE, Ambrosone CB, Johnson CS, Wang J, Liu S. OSAT: A tool for sample-to-batch allocations in genomics experiments. BMC Genomics. 2012; 13: 689.
29. Maksimovic J, Gordon L, Oshlack A. SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol. 2012; 13: R44-2012-13-6-r44.
30. Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using Empirical Bayes Methods. Biostatistics. 2007; 8: 118-127.
31. Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. The SVA package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012; 28: 882-883.
32. Wang D, Yan L, Hu Q, Sucheston LE, Higgins MJ, Ambrosone CB, Johnson CS, Smiraglia DJ, Liu S. IMA: An R package for high-throughput analysis of illumina's 450K infinium methylation data. Bioinformatics. 2012; 28: 729-730.
33. Blair JD, Price EM. Illuminating potential technical artifacts of DNA-methylation array probes. Am. J. Hum. Genet. 2012; 91: 760-762.
34. Chen YA, Choufani S, Grafodatskaya D, Butcher DT, Ferreira JC, Weksberg R. Cross-reactive DNA microarray probes lead to false discovery of autosomal sex-associated DNA methylation. Am. J. Hum. Genet. 2012; 91: 762-764.
35. Zhang X, Mu W, Zhang W. On the analysis of the illumina 450k array data: Probes ambiguously mapped to the human genome. Front. Genet. 2012; 3: 73.
36. 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, Schultz TC, Robins A, Khanna A, et al. Human embryonic stem cells have a unique epigenetic signature. Genome Res. 2006; 16: 1075-1083.
37. 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.