DNA Methylation of Imprinted Genes KCNQ1, KCNQ1OT1, and PHLDA2 in Peripheral Blood Is Associated with the Risk of Breast Cancer

SIMPLE SUMMARY: DNA methylation alterations of imprinted genes lead to loss of imprinting, and studies have explored the mechanism of the loss of imprinting in breast cancer development. However, the association between the methylation of imprinted genes in peripheral blood and the risk of breast cancer is largely unknown. Our study is the first to identify the CpG sites of imprinted genes associated with the risk of breast cancer by utilizing HumanMethylation450 data from public datasets. We discovered and validated that peripheral blood DNA methylation of KCNQ1, KCNQ1OT1, and PHLDA2 at chromosome 11p15.4-15.5 is associated with breast cancer susceptibility. Individuals with KCNQ1OT1-region hypermethylation (>0.474) had a lower risk of breast cancer. Additionally, the methylation level of KCNQ1OT1 was also unaffected by leukocyte heterogeneity. In summary, the KCNQ1OT1 region could be a potential biomarker for breast cancer risk assessment. ABSTRACT: Methylation alterations of imprinted genes lead to loss of imprinting (LOI). Although studies have explored the mechanism of LOI in breast cancer (BC) development, the association between imprinted gene methylation in peripheral blood and BC risk is largely unknown. We utilized HumanMethylation450 data from TCGA and GEO (n = 1461) to identify the CpG sites of imprinted genes associated with BC risk. Furthermore, we conducted an independent case-control study (n = 1048) to validate DNA methylation of these CpG sites in peripheral blood and BC susceptibility. cg26709929, cg08446215, cg25306939, and cg16057921, which are located at KCNQ1, KCNQ1OT1, and PHLDA2, were discovered to be associated with BC risk. Subsequently, the association between cg26709929, cg26057921, and cg25306939 methylation and BC risk was validated in our inhouse dataset. All 22 CpG sites in the KCNQ1OT1 region were associated with BC risk. Individuals with a hypermethylated KCNQ1OT1 region (>0.474) had a lower BC risk (OR: 0.553, 95% CI: 0.397−0.769). Additionally, the methylation of the KCNQ1OT1 region was not significantly different among B cells, monocytes, and T cells, which was also observed at CpG sites in PHLDA2. In summary, the methylation of KCNQ1, KCNQ1OT1, and PHLDA2 was associated with BC risk, and KCNQ1OT1 methylation could be a potential biomarker for BC risk assessment.