Integrated analysis of high-resolution DNA methylation profiles, gene expression, germline genotypes and clinical end points in breast cancer patients

International Journal of Cancer

Volumn 134, Issue 11, 2014, Pages 2615-2625

  Fleischer, Thomas ^a,b   Edvardsen, Hege ^a   Solvang, Hiroko K ^a   Daviaud, Christian ^c   Naume, Bjørn ^a   Børresen Dale, Anne Lise ^a,b   Kristensen, Vessela N ^a,b,d   Tost, Jörg ^c  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

^c CENTRE NATIONAL DE GÉNOTYPAGE   (France)

^d AKERSHUS UNIVERSITY HOSPITAL   (Norway)

Author keywords

breast cancer; clinical parameters; gene expression; methylation; SNP; survival

Indexed keywords

INTERLEUKIN 8;

ACVR1 GENE; ARTICLE; BCAP31 GENE; BREAST CANCER; CANCER PATIENT; CANCER SURVIVAL; CONTROLLED STUDY; CORRELATIONAL STUDY; DNA METHYLATION; FEMALE; GENE; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; GENOTYPE; GERM LINE; HUMAN; HUMAN TISSUE; IL8 GENE; MAJOR CLINICAL STUDY; MST1R GENE; OGG1 GENE; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROMOTER REGION; PYROSEQUENCING; ST6GAL1 GENE; TFF1 GENE;

BREAST CANCER; CLINICAL PARAMETERS; GENE EXPRESSION; METHYLATION; SNP; SURVIVAL;

BREAST; BREAST NEOPLASMS; CASE-CONTROL STUDIES; COHORT STUDIES; DNA METHYLATION; FEMALE; FOLLOW-UP STUDIES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOTYPE; GERM CELLS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; PROMOTER REGIONS, GENETIC; SURVIVAL RATE; TUMOR MARKERS, BIOLOGICAL; VALIDATION STUDIES AS TOPIC;

EID: 84896405425     PISSN: 00207136     EISSN: 10970215     Source Type: Journal    
DOI: 10.1002/ijc.28606     Document Type: Article

References (42)

1. Jones PA, Baylin SB,. The epigenomics of cancer. Cell 2007; 128: 683-92.
2. Hanahan D, Weinberg RA,. Hallmarks of cancer: the next generation. Cell 2011; 144: 646-74.
3. Champion HR, Wallace IW, Prescott RJ,. Histology in breast cancer prognosis. Br J Cancer 1972; 26: 129-38.
4. Engelsman E, Persijn JP, Korsten CB, et al. Oestrogen receptor in human breast cancer tissue and response to endocrine therapy. Br Med J 1973; 2: 750-2.
5. Borresen AL, Andersen TI, Garber J, et al. Screening for germ line TP53 mutations in breast cancer patients. Cancer Res 1992; 52: 3234-6.
6. Sorlie T, Perou CM, Tibshirani R, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001; 98: 10869-74.
7. Russnes HG, Vollan HK, Lingjaerde OC, et al. Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Sci Transl Med 2010; 2: 38ra47.
8. Holm K, Hegardt C, Staaf J, et al. Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Res 2010; 12: R36.
9. Rønneberg JA, Fleischer T, Solvang HK, et al. Methylation profiling with a panel of cancer related genes: association with estrogen receptor, TP53 mutation status and expression subtypes in sporadic breast cancer. Mol Oncol 2011; 5: 61-76.
10. Caldeira RD, Bettiol H, Barbieri MA, et al. Prevalence and risk factors for work related asthma in young adults. Occup Environ Med 2006; 63: 694-9.
11. Tao MH, Shields PG, Nie J, et al. DNA hypermethylation and clinicopathological features in breast cancer: the Western New York Exposures and Breast Cancer (WEB) Study. Breast Cancer Res Treat 2009; 114: 559-68.
12. Li S, Rong M, Iacopetta B,. DNA hypermethylation in breast cancer and its association with clinicopathological features. Cancer Lett 2006; 237: 272-80.
13. Birgisdottir V, Stefansson OA, Bodvarsdottir SK, et al. Epigenetic silencing and deletion of the BRCA1 gene in sporadic breast cancer. Breast Cancer Res 2006; 8: R38.
14. Widschwendter M, Siegmund KD, Muller HM, et al. Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen. Cancer Res 2004; 64: 3807-13.
15. Fiegl H, Millinger S, Goebel G, et al. 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.
16. Dejeux E, Rønneberg JA, Solvang H, et al. DNA methylation profiling in doxorubicin treated primary locally advanced breast tumours identifies novel genes associated with survival and treatment response. Mol Cancer 2010; 9: 68.
17. Sun Z, Asmann YW, Kalari KR, et al. Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One 2011; 6: e17490.
18. Van der Auwera I, Yu W, Suo L, et al. Array-based DNA methylation profiling for breast cancer subtype discrimination. PLoS One 2010; 5: e12616.
19. Hon GC, Hawkins, RD, Caballero, OL, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 2012; 22: 246-58.
20. Laurent L, Wong E, Li G, et al. Dynamic changes in the human methylome during differentiation. Genome Res 2010; 20: 320-31.
21. Rønneberg JA, Tost J, Solvang HK, et al. GSTP1 promoter haplotypes affect DNA methylation levels and promoter activity in breast carcinomas. Cancer Res 2008; 68: 5562-71.
22. Naume B, Zhao X, Synnestvedt M, et al. Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer. Mol Oncol 2007; 1: 160-71.
23. Perou CM, Sorlie T, Eisen MB, et al. Molecular portraits of human breast tumours. Nature 2000; 406: 747-52.
24. Enerly E, Steinfeld I, Kleivi K, et al. miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors. PLoS One 2011; 6: e16915.
25. Nordgard SH, Johansen FE, Alnaes GI, et al. Genome-wide analysis identifies 16q deletion associated with survival, molecular subtypes, mRNA expression, and germline haplotypes in breast cancer patients. Genes Chromosomes Cancer 2008; 47: 680-96.
26. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 2012; 490: 61-70.
27. Tost J, Gut IG,. DNA methylation analysis by pyrosequencing. Nat Protoc 2007; 2: 2265-75.
28. Van LP, Nordgard, SH, Lingjaerde, OC, et al. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci USA 2010; 107: 16910-5.
29. R Development Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing, 2012.
30. Benjamini Y, Hochberg Y,. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 1995; 57: 289-300.
31. Akaike H,. A new look at the statistical model identification. IEEE Trans Autom Control 1974; 16: 716-23.
32. Ogino S, Hazra A, Tranah GJ, et al. MGMT germline polymorphism is associated with somatic MGMT promoter methylation and gene silencing in colorectal cancer. Carcinogenesis 2007; 28: 1985-90.
33. Mrkonjic M, Roslin NM, Greenwood CM, et al. Specific variants in the MLH1 gene region may drive DNA methylation, loss of protein expression, and MSI-H colorectal cancer. PLoS One 2010; 5: e13314.
34. Chanock SJ, Burdett L, Yeager M, et al. Somatic sequence alterations in twenty-one genes selected by expression profile analysis of breast carcinomas. Breast Cancer Res 2007; 9: R5.
35. Vestergaard EM, Nexo E, Torring N, et al. Promoter hypomethylation and upregulation of trefoil factors in prostate cancer. Int J Cancer 2010; 127: 1857-65.
36. Dietrich D, Lesche R, Tetzner R, et al. Analysis of DNA methylation of multiple genes in microdissected cells from formalin-fixed and paraffin-embedded tissues. J Histochem Cytochem 2009; 57: 477-89.
37. Ribieras S, Lefebvre O, Tomasetto C, et al. Mouse Trefoil factor genes: genomic organization, sequences and methylation analyses. Gene 2001; 266: 67-75.
38. Carvalho R, Kayademir T, Soares P, et al. Loss of heterozygosity and promoter methylation, but not mutation, may underlie loss of TFF1 in gastric carcinoma. Lab Invest 2002; 82: 1319-26.
39. Singh RK, Varney ML,. IL-8 expression in malignant melanoma: implications in growth and metastasis. Histol Histopathol 2000; 15: 843-9.
40. Kim SW, Hayashi M, Lo JF, et al. Tid1 negatively regulates the migratory potential of cancer cells by inhibiting the production of interleukin-8. Cancer Res 2005; 65: 8784-91.
41. Iwasawa R, Mahul-Mellier AL, Datler C, et al. Fis1 and Bap31 bridge the mitochondria-ER interface to establish a platform for apoptosis induction. EMBO J 2011; 30: 556-68.
42. Singh KP, Treas J, Tyagi T, et al. DNA demethylation by 5-aza-2-deoxycytidine treatment abrogates 17 beta-estradiol-induced cell growth and restores expression of DNA repair genes in human breast cancer cells. Cancer Lett 2012; 316: 62-9.