Abstract 2777: One-carbon metabolism genetic variant and genome-wide DNA methylation in breast tissues from healthy women
Authors: Song Min-Ae , Brasky Theodore M. , Marian Catalin , Weng Daniel Y. , Taslim Cenny , Llanos Adana A. , Dumitrescu Ramona G. , Liu Zhenhua , Mason Joel B. , Kallakury Bhaskar V. , Freudenheim Jo L. , Shields Peter G. 
Published: July 2016

Abstract
Altered DNA methylation is an early event in carcinogenesis. Little is known about the mechanism of altered methylation in breast tissue; possible factors include diet such as alcohol and folate intake, and genetic variation for enzymes in one carbon metabolism. Examination of the association of these factors with methylation in breast tissues from healthy women provides insight into these changes. Blood and glandular breast tissues from 81 women with no history of cancer and who underwent reduction mammoplasty were assayed. The 96-plex Illumina BeadXpress® or TaqMan® SNP Genotyping assays assessed SNPs, genome-wide DNA methylation profiling was performed using the Illumina Infinium HumanMethylation450 BeadChip.The Affymetrix GeneChip Human Trascriptome Array 2.0 was used to compare gene expression level with methylation change in fresh frozen breast tissues. Biological networks of differentially-methylated (DM) genes were assigned using the Ingenuity Pathway Analysis (IPA). Fifty-seven CpG sites were DM in comparisons of genotype for eight SNPs in FTHFD, MTHFD1, MTHFR, MTR, MTRR, and TYMS (P&lt;5.0 × 10-5 for each). SNPs in FTHFD were associated with 56% of the DM CpGs. SNPs in FTHFD and MTR were associated with DM CpG sites in their own genes. Six methylation and gene expression pairs were modestly to weakly correlated (P&lt;0.05), five positively correlated (HCN4, FRMD4A, FTHFD, SLC39A7, and LOC63930) and one negatively correlated (ADAMTS14). Four DM CpGs identified by SNPs in MTRR, MTHFR, and FTHFD were significantly associated with alcohol consumption and/or breast folate. Forty-five DM genes were available in the IPA database. IPA revealed enrichment for genes (91%) involved in cancers. The top-scoring network was “Energy Production, Molecular Transportation, Nucleic Acid Metabolism” (score = 32). The top molecular and cellular functions were Amino Acid Metabolism (ALDH1L1, MTR, and PTPRN2), Cell-to-Cell Signaling (DLG3, GRN, HLA-DQB1, PTPRN2, and SLC6A3), Cellular Function and Maintenance (ADAMTS14, ADMTS2, CRIPT, DCL1, DLG3, GRN, KAG2, PTPRN2, and RXRB). High concordance of methylation levels for all DM loci analyzed was found between HM450 and pyrosequencing on 75 technically validated samples (Spearman correlation r = 0.98, P&lt;1.0×10-47). This is the first comprehensive study of the association between variation in one-carbon metabolism genes and genome-wide DNA methylation in histologically normal breast tissues. These SNPs, particularly FTHFD, as well as alcohol intake and folate exposure appear to affect DNA methylation in the breast of healthy women. The finding that SNPs in FTHFD and MTR are associated with their own methylation is also novel and highlights a role for these SNPs as methylation quantitative trait loci. Understanding of the role of one carbon metabolism in altered DNA methylation could provide insight into prevention of breast tumors.
Citation Format: Min-Ae Song, Theodore M. Brasky, Catalin Marian, Daniel Y. Weng, Cenny Taslim, Adana A. Llanos, Ramona G. Dumitrescu, Zhenhua Liu, Joel B. Mason, Bhaskar V. Kallakury, Jo L. Freudenheim, Peter G. Shields. One-carbon metabolism genetic variant and genome-wide DNA methylation in breast tissues from healthy women. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2777.