Loss of tumour suppressor p53 rewires enhancer landscape and governs oncogenic progression

Abstract Mutations in tumour suppressor p53 confer enhanced metastasis and chemoresistance in colorectal cancer (CRC). Though the genetic events regulating CRC with p53 loss/mutation have been documented, the epigenetic events accompanying the loss of p53 have not been well understood. Epigenome based classification of CRC tumours has identified the active enhancer mark as a distinct marker for progression, however the role of the distal regulatory regions upon p53 loss in CRC remains to be established. This work investigates the influence of p53 loss on enhancer regulation in colorectal cancer cells. Genome wide profiling of active enhancer mark, H3K27ac in p53wt and p53-/- CRC cells reveal an overall gain of this mark around the promoters and intronic regions. These active enhancers show strong association with oncogenes and hallmark MYC and E2F targets suggesting an enhancer mediated regulation of MYC/E2F pathway governed by E2Fs, MAZ and PATZ1. Interestingly, we also observed a gain in oncogenic super enhancers mediated by E2Fs/KLFs accompanying loss of p53. The promoters of histone methyl transferases EZH2 and SuV39H1 (E2F targets) show elevated levels of H3K27ac suggesting a novel epigenetic regulation of CRC around the promoters and distal regulatory regions. Our validation of these findings in p53 deficient colon cancer cohorts shows that the super enhancer associated genes align more to the CMS4 subtype and exhibit lower survivability. The observed cancer stemness and gain of oncogenic super enhancers with p53 loss presents a hitherto unexplored paradigm of enhancer mediated oncogenic progression which may be exploited for devising epigenetic therapy in p53-/- CRC patients. Significance Colorectal cancers (CRC) lose tumour-suppressor function and gain neomorphic functions with mutation/loss of p53. This work explores the epigenomic modulation of p53 null CRC cells by distal regulatory elements which has not been not clearly understood yet. We report a global increase in the active enhancer mark H3K27ac at active promoter and enhancer regions. We find that the gained enhancers/promoters are regulated by E2Fs/MAZ/PATZ1 which drive cancer stemness while the lost enhancers/promoters are regulated by tumour-suppressive IRFs. The activation of E2Fs correlates with elevated H3K27ac implying positive feedback driving E2F targets such as EZH2 and SuV39H1. The indirect activation of histone methyltransferases by p53 and the gain of oncogenic super-enhancers present a novel epigenetic regulatory paradigm which we also validated in p53 null CRC cohorts. These findings aid the design of epigenetic therapy for p53 deficient colorectal tumours.