DNA methylome analysis of parental and p53-knockout MCF-7 and T47D breast cancer cells treated with sodium arsenite

The study aimed to test the hypothesis that mutations in p53, a gene commonly altered in human malignancies, may influence cellular responses to an environmental non-mutagenic agent through potential epigenetic mechanisms. Utilizing the CRISPR-Cas9 system, p53 knockouts were generated in MCF7 and T47D breast cancer cell lines. DNA methylation patterns in these cell lines were characterized using targeted pyrosequencing and methylome-wide Infinium MethylationEPIC BeadChip arrays following exposure to sodium arsenite, a well-established human carcinogen known to impact the epigenome. The results demonstrated that the knockout of p53 alone was associated with extensive alterations in DNA methylation, characterized by predominant CpG hypermethylation alongside global demethylation. MCF7 and T47D breast cancer cell lines harboring p53 knockout mutations were generated using CRISPR-Cas9 gene editing. DNA methylation profiling was conducted using the Illumina Infinium MethylationEPIC BeadChip arrays to investigate the effects of the p53 knockout mutations on the epigenome, and to determine if these mutations affect cellular susceptibility to sodium arsenite-induced epigenetic alterations. Reconstitution of p53 in MCF7 knockout cell lines was conducted to evaluate its effects on restoring epigenetic stability.