Epigenetic insights: unveiling the impact of hypomethylated CACNA2D3 and FLNA genes in breast cancer progression

Breast Cancer (BC) remains a significant cause of cancer-related mortality in women, impacted by complex genetic and epigenetic alterations in its progression. Among these processes is DNA hypomethylation, which promotes cancer growth. This study aimed to detect the expression level and methylation status of CACNA2D3 and FLNA genes in breast cancer patients and then assess the relationship between the mRNA expression and clinicopathological characteristics, as well as the survival rate of these genes. Two advanced techniques, whole genome bisulfite sequencing (WGBS) and differentially expressed WGBS (DEGs), were used to assess the expression and methylation levels. To analyze the pathways that were altered in breast cancer, the WebGestalt over-representation analysis tool (ORA) was used to perform gene ontology (GO) for the highly expressed hypomethylated genes in BC samples. Moreover, the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohort, The Cancer Genome Atlas (TCGA), and Kaplan-Meier Plotter datasets were used to examine the predictive significance of the CACNA2D3 and FLNA genes. Then, 5-aza-2′-deoxycytidine (5-AZA) treatment was applied to examine the relationship between DNA methylation and gene expression in MCF7 and MCF10A cells. The results of these advanced techniques indicated that CACNA2D3 and FLNA exhibited a significant difference in gene expression and methylation levels between breast cancer patients and controls. The data analysis from several public domains of BC datasets showed that the MAPK pathway was the most significant pathway in BC (p-value 0.035) with four overlapping aberrant hypomethylated genes (ANGPT1, CACNA2D3, FLNA, and IKBKG). Moreover, the CACNA2D3 gene was associated with tumor size, histological grade, estrogen receptor (ER), and progesterone receptor (PR) status. Furthermore, CACNA2D3 gene expression was increased after 5-AZA treatment in two cell lines, while FLNA gene showed fluctuations in its expression, suggesting that additional factors regulate FLNA expression, which could be related to tumor size, histology, ER, and PR. In conclusion, DNA methylation could be a regulatory factor for CACNA2D3 and its high expression was linked to clinicopathological characteristics of breast cancer patients, especially with a good prognosis.