p53 exerts anticancer effects by regulating enhancer formation and activity

The abnormality of p53 tumor suppressor is crucial in lung cancer development, and p53 may regulate target gene promoters to combat cancer. Recent studies have shown extensive p53 binding to enhancer elements. However, whether p53 exert a tumor suppressor role by shaping the enhancer landscape remains poorly understood. In the current study, we employed several functional genomics approaches to assess the enhancer activity at p53 binding sites throughout the genome based on our established p53 knockout human bronchial epithelial cells (BEAS-2B). A total of 943 active regular enhancers and 370 super-enhancers (SEs) disappeared upon the deletion of p53, indicating that p53 modulates the activity of hundreds of enhancer elements. We found that one p53-dependent SE, located on chromosome 9 and designated as KLF4-SE, regulated the expression of the KLF4 gene. Furthermore, deletion of p53 significantly decreased the KLF4-SE enhancer activity and the KLF4 expression, but increased colony formation ability in the NNK-induced nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone cell transformation model. Subsequently, in p53 knockout cells, the overexpression of KLF4 partially reversed the increased clonogenic capacity caused by p53 deficiency. Consistently, KLF4 expression also decreased in lung cancer tissues and cell lines. Overexpression of Krüppel-like factor 4 (KLF4) significantly suppressed lung cancer cell proliferation and migration. Collectively, our results suggest that the regulation of enhancer formation and activity by p53 is an integral component of the p53 tumor suppressor function. Therefore, our findings offer novel insights into the regulation mechanism of p53 in lung oncogenesis and introduces a new strategy for screening therapeutic targets.