Housekeeping Genes’ DNA Methylation Patterns in Breast and Endometrial Cancers

Abstract Little research has been conducted on housekeeping (HK) genes’ methylation patterns in breast cancer (BRCA) and uterine corpus endometrial carcinoma (UCEC). Using publicly available data, we conducted comprehensive analyses of HK genes’ methylation patterns at the cytosine guanine (CG) site level. Findings are summarized below. First, HK sites exhibited lower differential methylation (DM) rates than overall DM rates. UCEC demonstrated a higher DM rate than BRCA, and they shared a small percentage of DM sites and 18 common DM HK genes that are cancer-related. Second, DM sites’ locations were different between BRCA and UCEC, with notable disparities in CpG islands and shores. Third, UCEC had more highly co-methylated CG pairs than BRCA. Normal and tumor samples had different co-methylation distributions in both BRCA and UCEC. Fourth, some CG sites’ co-methylation patterns did change between normal and tumor, with some minor shifts regarding overall co-methylation differences between the Alive and Dead samples in both BRCA and UCEC. Fifth, only a small number of CG sites kept strong and stable co-methylation patterns in BRCA and UCEC, respectively, and these two cancers only shared a small percentage of these co-methylated CG sites. Despite the small common CG list, 11 HK genes and 27 non-HK genes were identified as common in BRCA and UCEC. 19 of these 38 genes were from the protocadherin gamma cluster (PCDHG@). Finally, 1 HK gene (CUX1) and 4 non-HK genes (TP73, FOXP1, BANP, and MIR199A1) may play dual roles as both oncogenes and tumor suppressor genes.