Transcriptomic footprinting following restoration of p53 sequence and function utilising Adenine Base Editing

The tumor suppressor TP53 is the most frequently mutated gene in human cancer. Here, we utilised a Adenine Base Editing system to efficiently repair the p53-R273H hotspot mutation in four cancer cell lines of different origins followed by transcriptomic analysis at three different timepoints to unveil the molecular network of p53 tumor suppression. Moreover, we were able to repair the p53-R175H hotspot in two cell lines of different origins. Our data demonstrates that recovery of wildtype TP53 leads to restoration of p53 function and suggests a preserved network of p53's tumor-suppressive activities following mutation repair that is irrespective of cell type, mutation profile, and epigenetic cell state. Furthermore, we attempted correcting a nonsense mutation in the tumor suppressor gene SMAD4 in one cell line leading to a progressive depletion of cancer cells, albeit with a milder phenotype compared to the one following TP53 repair. Taken together, our data provide a molecular framework following driver mutations repair, besides providing insights into key players orchestrating transcription leading to cell apoptosis. Our findings demonstrate the utility of this Base Editing system to systematically interrogate the functional consequences of cancer driver mutations and the downstream effects on gene expression.