Transcriptional reprogramming by TP53 oncogenic mutations in breast carcinogenesis

TP53 tumor suppressor gene is mutated in more than 30% of breast cancer cases. Of these, hotspot mutations (R273H, R248W, R175H, R249S) affect the p53 DNA binding domain and are thought to provide additional cancer-related capabilities. Most efforts to understand the direct regulatory functions of mutant p53 were performed in transformed cells with different genetic backgrounds. Therefore, the precise contribution of specific p53 mutations to the transcriptional program driving the malignant cellular phenotypes and breast cancer progression is still not determined. Using an isogenic cell line to study carcinogenesis may reveal transcriptional changes caused by the p53 hotspot mutations, which may contribute to cancerous phenotypes. We analyzed MCF10A, immortalized breast epithelial cells, deficient for p53, and expressing p53 mutants R273H, R248W, R175H or R249S. RNA-seq measurements showed that core p53 programs are impaired in all cell lines, but more so in mutant cells than in p53-null cells. These genes were related to different cancer-associated functions, but mutant cells showed “anti-cancer” phenotypes including lower proliferation compared to wild-type and p53 null cells. Moreover, ATAC-seq and p53 ChIP-seq analysis show that ~80% of WT p53 binding loci have low accessibility that remained stable across the p53 mutants and KO cell lines. Interestingly, R273H p53 bound chromatin 2-fold more sites than WT, while R249S p53 lost 80% of it, and R175H p53 lost it entirely. p53 binding loci were co-localized with differentially expressed genes in the same topologically associated domain, suggesting that these genes are targeted by p53.