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Background In recent years, hypermethylation of gene promoters has emerged as one of the fundamental mechanisms for the inactivation of tumor suppressor genes and has a potential role in the early detection of breast cancer. The present study is a case-control study aimed to quantify the methylation levels in the promoters of secretoglobin 3A1 ( SCGB3A1 ), and ataxia-telangiectasia mutated ( ATM ) genes and evaluate their relation to clinicopathological features of the tumor in a cohort of Egyptian female patients with breast cancer. Methods Genomic deoxyribonucleic acid (DNA) was extracted from 100 tissue samples, 50 breast cancer tissues and 50 adjacent non-cancerous breast tissues, then, it was subjected to bisulfite conversion. The converted DNA was amplified by real-time PCR; then, pyrosequencing was performed to quantify DNA methylation levels in four CpG sites in  ATM  and  SCGB3A1  gene promoters. The methylation data were presented as the percentage of average methylation of all the observed CpG sites and were calculated for each sample and each gene. Results The percentage of DNA methylation of the  SCGB3A1  promoter was significantly higher in the tumor group than in the normal group ( P = 0.001). However, a non-statistical significance difference was found in the DNA methylation percentage of the  ATM  promoter in the tumor group compared to the normal group ( P  = 0.315). The  SCGB3A1  promoter methylation frequency was significantly associated with estrogen receptors (ER) and progesterone receptors (PR) positive tumors, lymph node metastasis, and lymphovascular invasion. However, no association was found between  ATM  methylation status and the different clinicopathological features of the tumor. Conclusions The findings of this work showed that the  SCGB3A1  promoter methylation was significantly higher in the tumor group and was significantly associated with different clinicopathologic features in breast cancer. It may be considered as a suitable biomarker for diagnosis and prognosis. However, the promoter methylation levels of the  ATM  gene in breast cancer cases were unable to distinguish between breast cancer tissues and adjacent normal tissues, and there is no evidence that epigenetic silencing by  ATM  methylation has a role in breast cancer pathogenesis.

SCGB3A1 gene DNA methylation status is associated with breast cancer in Egyptian female patients