Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network

Abstract

TP53, the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible geneZmat3as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seqUltrasomatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorialin vivoCRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We establishedZmat3as a core component of p53-mediated tumor suppression and identifiedCdkn1aas the most potent cooperating p53-induced gene in tumor suppression. We discovered thatZMAT3/CDKN1Aserve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combinedZmat3-Cdkn1ainactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings placeZMAT3andCDKN1Aas hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.