DNA methylation array analysis identifies breast cancer associated RPTOR, MGRN1 and RAPSN hypomethylation in peripheral blood DNA

Abstract

DNA methylation changes in peripheral blood DNA have been shown to be associated with solid tumors. We sought to identify methylation alterations in whole blood DNA that are associated with breast cancer (BC). Epigenome-wide DNA methylation profiling on blood DNA from BC cases and healthy controls was performed by applying Infinium HumanMethylation450K BeadChips. Promising CpG sites were selected and validated in three independent larger sample cohorts via MassARRAY EpiTyper assays. CpG sites located in three genes (cg06418238 in RPTOR, cg00736299 in MGRN1 and cg27466532 in RAPSN), which showed significant hypomethylation in BC patients compared to healthy controls in the discovery cohort (p < 1.00 × 10−6) were selected and successfully validated in three independent cohorts (validation I, n =211; validation II, n=378; validation III, n=520). The observed methylation differences are likely not cell-type specific, as the differences were only seen in whole blood, but not in specific sub cell-types of leucocytes. Moreover, we observed in quartile analysis that women in the lower methylation quartiles of these three loci had higher ORs than women in the higher quartiles. The combined AUC of three loci was 0.79 (95%CI 0.73-0.85) in validation cohort I, and was 0.60 (95%CI 0.54-0.66) and 0.62 (95%CI 0.57-0.67) in validation cohort II and III, respectively. Our study suggests that hypomethylation of CpG sites in RPTOR, MGRN1 and RAPSN in blood is associated with BC and might serve as blood-based marker supplements for BC if these could be verified in prospective studies.

Whole-Blood DNA Methylation Markers in Early Detection of Breast Cancer: A Systematic Literature Review

“…Of the included 33 studies, 25 studies applied a gene-specific approach and reported 70 methylation markers, and eight studies (20, 22, 23, 27-29, 35, 46) identified methylation markers using array-based technologies (Illumina 27K or 450K beadchip) and reported 285 differentially methylated CpG sites. Among these 285 CpG sites, nine CpG sites including C7orf50-cg03916490, GREB1-cg18584561, HYAL2-cg27091787, MGRN1-cg00736299, RPTOR-cg06418238, RAPSN-cg27466532, PNKD-cg01741999, TMC3-cg27639199, and S100P-cg22266967 were further confirmed in independent samples from the same studies (20,22,23,27). We summarized these nine CpG sites together with the 70 gene-specific markers in Table 1 and present the other 276 CpG sites in Supplementary Table S2.…”

“…The study characteristics are provided in Supplementary Table S1. Of the 33 identified studies, 16 were carried out in Europe [five studies from Germany (20,22,23,26,35) and five studies from the United Kingdom (16,18,28,36,37)], nine studies were from Asian countries (17,19,21,33,(38)(39)(40)(41)(42) and three studies were from the United States (29,43,44). The majority of included studies recruited breast cancer cases from clinical settings and one study (45) was restricted to cases with family history of breast cancer.…”

“…Array-based assays, such as the Infinium HumanMethylation 27K or 450K Beadchip were applied in eight studies (20, 22, 23, 27-29, 35, 46). The majority of the identified studies did not use a validation set to confirm their results, and only eight studies (18,20,22,23,(27)(28)(29)35) performed independent validations.…”

“…Previous investigations of DNA methylation changes in plasma and serum have revealed that DNA methylation of gene-specific loci could provide a promising alternative for non-invasive breast cancer screening (10)(11)(12)(13)(14)(15). Moreover, several investigations on whole blood also indicated the potential utility of peripheral blood cell or white blood cell (WBC) DNA methylation for prediction of breast cancer (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29). In this article, we systematically reviewed published DNA methylation studies in whole-blood-borne DNA from patients with breast cancer and healthy controls, to provide an overview on the performance of DNA methylation markers for breast cancer risk evaluation and/or early detection.…”

Longitudinal Study of Leukocyte DNA Methylation and Biomarkers for Cancer Risk in Older Adults

“…This specific CpG has been previously presented as a marker to differentiate between different medulloblastoma subtypes [67]. Another study has also indicated that the decrease in methylation in RPTOR measured in peripheral blood may be a biomarker for breast cancer, although this failed replication in a follow-up study [68, 69]. Similar to REC8 , there was more negative change in β-value from Year 1 to 6 in individuals closer to receiving a cancer diagnosis.…”