Landscape of genome-wide age-related DNA methylation in breast tissue

Abstract

Despite known age-related DNA methylation (aDNAm) changes in breast tumors, little is known about aDNAm in normal breast tissues. Breast tissues from a cross-sectional study of 121 cancer-free women, were assayed for genome-wide DNA methylation. mRNA expression was assayed by microarray technology. Analysis of covariance was used to identify aDNAm’s. Altered methylation was correlated with expression of the corresponding gene and with DNA methyltransferase protein DNMT3A, assayed by immunohistochemistry. Publically-available TCGA-BRCA data were used for replication. 1,214 aDNAm’s were identified; 97% with increased methylation, and all on autosomes. Sites with increased methylation were predominantly in CpG lslands and non-enhancers. aDNAm’s with decreased methylation were generally located in intergenic regions, non-CpG Islands, and enhancers. Of the aDNAm’s identified, 650 are known to be involved in cancer, including ESR1 and beta-estradiol responsive genes. Expression of DNMT3A was positively associated with age. Two aDNAm’s showed borderline significant associations with DNMT3A expression; KRR1 (OR 6.57, 95% CI: 2.51–17.23) and DHRS12 (OR 6.08, 95% CI: 2.33–15.86). A subset of aDNAm’s co-localized within vulnerable regions for somatic mutations in cancers including breast cancer. Expression of C19orf48 was inversely and significantly correlated with its methylation level. In the TCGA dataset, 84% and 64% of the previously identified aDNAm’s were correlated with age in both normal-adjacent and tumor breast tissues, with differential associations by histological subtype. Given the similarity of findings in the breast tissues of healthy women and breast tumors, aDNAm’s may be one pathway for increased breast cancer risk with age.

Age-related DNA methylation in paired normal and tumour breast tissue in Chinese breast cancer patients

“…In this study, we identified age-related methylation sites that were consistently reported in normal breast tissue across at least two previously published studies [4,6,7]. We confirm that previously reported age-related methylation in normal breast tissue is also present to a large degree in tumouradjacent normal tissue and among Asian women.…”

A comparison of epigenetic mitotic-like clocks for cancer risk prediction

“…We obtained Illumina 450k DNAm data from studies profiling normal tissue, not adjacent to cancer. Briefly, we obtained normal samples from the lung (n = 21) [36], breast (n = 171: 50 derived from [37] and 121 from [61]), oral/buccal (n = 790) [36], liver (n = 26) [62], stomach (n = 61) [24], colon (n = 8) [63], skin (n = 19) [64], esophagus (n = 52) [28], and whole blood (n = 487: 335 from Liu et al [65] and 152 from Teschendorff et al [36]). In all cases, we used the normalized data as described in our previous publications, or were normalized de novo using the same procedure as in these previous studies, i.e., using minfi [66] and BMIQ [67].…”

“…The main Illumina DNA methylation 450k datasets used here are freely available from public repositories, including GEO (www.ncbi.nlm.nih.gov/geo), ArrayExpress (www.ebi.ac.uk/arrayexpress), and EGA (www.ebi.ac.uk/ega/home) (see Methods for relevant references). Details: Hannum (656 whole blood, GEO: GSE40279) [47]; MESA (214 purified CD4+ T cells and 1202 Monocyte samples, GEO: GSE56046 and GSE56581) [69]; Tserel (98 CD8+ T cells, GEO: GSE59065) [70]; BLUEPRINT (139 matched CD4+ T cells, Monocytes and Neutrophils, EGA: EGAS00001001456) [72]; Liu (335 whole blood, GEO: GSE42861) [65]; Gastric tissue (191 normal and metaplasia, GEO: GSE103186) [24]; Colon tissue (47 normal and adenoma, ArrayExpress: E-MTAB-6450) [63]; Breast Erlangen (50 normal, GEO: GSE69914) [37]; Breast2 (121 normal, GEO: GSE101961) [61]; Liver (26 normal, GEO: GSE61258) [62]; Skin (19 epidermal non-sun exposed, GEO: GSE51954) [64]; Esophagus (52 normal, GEO: GSE104707) [28]; SCM2 (37 fetal tissue samples, GEO: GSE31848) [45]; Cord blood (15 samples, GEO: GSE72867) [46]. TCGA data was downloaded from https://gdc.cancer.gov.…”

Improved prediction of chronological age from DNA methylation limits it as a biomarker of ageing

“…A total of 319,607 probes (No Pruned Set) passed our quality control and 128,405 probes (Pruned Set) were retained after pruning based upon the pairwise correlation of probes (see next section). To test the performance of age predictors in non-blood tissues, we downloaded 13 cohorts from GEO database with accession ID GSE61431 (brain) 37 , GSE59685 (brain) 38 GSE80970 (brain), GSE101961 (breast) 39 , GSE108213 (breast), GSE48325 (liver) 40 , GSE61257 (adipose) 41 , GSE61258 (liver) 41 , GSE61259 (breast) 41 , GSE88883 (breast) 42 , GSE90060 (endometrium) 43 , GSE92767 (saliva) 44 , GSE99029 (saliva) 45…”