title: DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status.
abstract: It is now understood that epigenetic alterations occur frequently in sporadic breast carcinogenesis, but little is known about the epigenetic alterations associated with familial breast tumors. We performed genome-wide DNA-methylation profiling on familial breast cancers (n = 33) to identify patterns of methylation specific to the different mutation groups (BRCA1, BRCA2, and BRCAx) or intrinsic subtypes of breast cancer (basal, luminal A, luminal B, HER2-amplified, and normal-like). We used methylated DNA immunoprecipitation (MeDIP) on Affymetrix promoter chips to interrogate methylation profiles across 25,500 distinct transcripts. Using a support vector machine classification algorithm, we demonstrated that genome-wide methylation profiles predicted tumor mutation status with estimated error rates of 19% (BRCA1), 31% (BRCA2), and 36% (BRCAx) but did not accurately predict the intrinsic subtypes defined by gene expression. Furthermore, using unsupervised hierarchical clustering, we identified a distinct subgroup of BRCAx tumors defined by methylation profiles. We validated these findings in the 33 tumors in the test set, as well as in an independent validation set of 47 formalin-fixed, paraffin-embedded familial breast tumors, by pyrosequencing and Epityper. Finally, gene-expression profiling and SNP CGH array previously performed on the same samples allowed full integration of methylation, gene-expression, and copy-number data sets, revealing frequent hypermethylation of genes that also displayed loss of heterozygosity, as well as of genes that show copy-number gains, providing a potential mechanism for expression dosage compensation. Together, these data show that methylation profiles for familial breast cancers are defined by the mutation status and are distinct from the intrinsic subtypes.
authors.affiliation: CRUK Viral Oncology Group, UCL Cancer Institute, London WC1E 6BT, UK. j.flanagan@imperial.ac.uk
authors.forename: James M
authors.initials: JM
authors.lastname: Flanagan
authors.forename: Sibylle
authors.initials: S
authors.lastname: Cocciardi
authors.forename: Nic
authors.initials: N
authors.lastname: Waddell
authors.forename: Cameron N
authors.initials: CN
authors.lastname: Johnstone
authors.forename: Anna
authors.initials: A
authors.lastname: Marsh
authors.forename: Stephen
authors.initials: S
authors.lastname: Henderson
authors.forename: Peter
authors.initials: P
authors.lastname: Simpson
authors.forename: Leonard
authors.initials: L
authors.lastname: da Silva
authors.forename: Kumkum
authors.initials: K
authors.lastname: Khanna
authors.forename: Sunil
authors.initials: S
authors.lastname: Lakhani
authors.forename: Chris
authors.initials: C
authors.lastname: Boshoff
authors.forename: Georgia
authors.initials: G
authors.lastname: Chenevix-Trench
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism*; D018899:CpG Islands; D019175:DNA Methylation / Q000235:genetics*; D004273:DNA, Neoplasm / Q000235:genetics* / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling; D019398:Genes, BRCA1; D024522:Genes, BRCA2; D006801:Humans; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic
chemical_list: D004273:DNA, Neoplasm