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

Oncotarget. 2016 Sep 27;7(39):64191-64202. doi: 10.18632/oncotarget.11640.


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 x 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.

Keywords: DNA methylation; MGRN1; RAPSN; RPTOR; breast cancer.

Publication types

  • Comparative Study
  • Validation Study

MeSH terms

  • Adult
  • Aged
  • Area Under Curve
  • Biomarkers, Tumor / blood
  • Biomarkers, Tumor / genetics*
  • Breast Neoplasms / blood
  • Breast Neoplasms / genetics*
  • Breast Neoplasms / pathology
  • Circulating Tumor DNA / blood
  • Circulating Tumor DNA / genetics*
  • CpG Islands
  • DNA Methylation*
  • Epigenesis, Genetic*
  • Female
  • Gene Expression Profiling / methods*
  • Genetic Predisposition to Disease
  • Humans
  • Logistic Models
  • Middle Aged
  • Muscle Proteins / blood
  • Muscle Proteins / genetics*
  • Odds Ratio
  • Oligonucleotide Array Sequence Analysis*
  • Predictive Value of Tests
  • ROC Curve
  • Regulatory-Associated Protein of mTOR / blood
  • Regulatory-Associated Protein of mTOR / genetics*
  • Reproducibility of Results
  • Retrospective Studies
  • Risk Factors
  • Ubiquitin-Protein Ligases / blood
  • Ubiquitin-Protein Ligases / genetics*


  • Biomarkers, Tumor
  • Circulating Tumor DNA
  • Muscle Proteins
  • RPTOR protein, human
  • Regulatory-Associated Protein of mTOR
  • peripheral membrane protein 43K
  • MGRN1 protein, human
  • Ubiquitin-Protein Ligases