Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program

Abstract

Although TP53 is the most commonly mutated gene in human cancers, the p53-dependent transcriptional programs mediating tumor suppression remain incompletely understood.Here, to uncover critical components downstream of p53 in tumor suppression, we perform unbiased RNAi and CRISPR/Cas9-based genetic screens in vivo. These screens converge upon the p53-inducible gene Zmat3, encoding an RNA-binding-protein, and we demonstrate that ZMAT3 is an important tumor suppressor downstream of p53 in mouse Kras G12D -driven lung and liver cancers and human carcinomas. Integrative analysis of the ZMAT3 RNA-binding landscape and transcriptomic profiling reveals that ZMAT3 directly modulates exon inclusion in transcripts encoding proteins of diverse functions, including the p53 inhibitors MDM4 and MDM2, splicing regulators, and components of varied cellular processes. Interestingly, these exons are enriched in NMD signals, and, accordingly, ZMAT3 broadly affects target transcript stability. Collectively, these studies reveal ZMAT3 as a novel RNA-splicing and homeostasis regulator and key component of p53-mediated tumor suppression.We thank Laurakay Bruhn, Steven Altschuler, Ben Borgo, Peter Sheffield and Carsten Carstens of Agilent Inc. for oligonucleotide synthesis and helpful discussions. We thank Lin He for the Eμ-Myc lymphoma cells, Andreas Strasser and Ana Janic for the Zmat3 null MEFs, and Julien Sage and Aaron Gitler for critical reading of the manuscript.

p53 and Tumor Suppression: It Takes a Network

“…Combined CLIP-seq and RNA-seq analyses revealed that Zmat3 regulates an alternative splicing program by binding RNAs upstream of 3′ splice sites of specific introns and regulating exon skipping, leading to changes in the transcriptome. These findings, along with a recent study that found that ZMAT3 inhibits clonogenicity of colon cancer cells by controlling the splicing of CD44, suggest a link between p53-mediated tumor suppression and splicing [7,8]. Zmat3 deficiency did not promote tumor growth to the extent of p53 loss, suggesting that Zmat3 is one of multiple tumor suppression effectors downstream of p53.…”

“…Zmat3 deficiency did not promote tumor growth to the extent of p53 loss, suggesting that Zmat3 is one of multiple tumor suppression effectors downstream of p53. The significance of ZMAT3 to cancer suppression in humans is supported by recent metaanalyses of CRISPR/Cas9 and shRNA screens in human cell lines, which revealed that ZMAT3 depletion significantly promotes proliferation in cells with functional p53 but not with p53deficiency [7,9]. ZMAT3 and p21 were the two p53 target gene effectors to reach the threshold of significant enrichment in wild-type versus p53-deficient cells set in this 'Cancer Dependency Map' (DepMap) meta-analysis, suggesting a centrality of these two target genes to the p53 tumor suppression network [9].…”

“…The finding that p53 25,26 activates only a small subset of p53 target genes yet remains an active tumor suppressor presented an opportunity to interrogate genes downstream of p53 involved in tumor suppression in a focused manner [4]. Gene expression analysis identified 87 genes activated in both oncogene-expressing p53 +/+ and p53 25,26/25,26 murine embryonic fibroblasts (MEFs) [7]. In an unbiased approach to probe tumor suppressor activity in vivo, oncogene-expressing MEFs expressing shRNA or sgRNA libraries targeting these 87 genes were each transplanted subcutaneously into mice to seed tumors.…”

“…LUAD and hepatocellular carcinoma (HCC) GEMMs [7]. Combined CLIP-seq and RNA-seq analyses revealed that Zmat3 regulates an alternative splicing program by binding RNAs upstream of 3′ splice sites of specific introns and regulating exon skipping, leading to changes in the transcriptome.…”

Exploration and Verification of a Six-RNA Binding Proteins-based Prognosis Evaluating Model for Hepatocellular Carcinoma

“…RBP CPEB3 [12] inhibits the proliferation of colorectal cancer through the JAL/STAT pathway. Zmat3 [13] is a crucial factor in maintaining the stability of transcript which participates in the tumor suppressing process mediated by p53 in many types of cancers. RBPs NONO, QKI, and RBMX [14] may deteriorate the outcome of breast cancer patients by interacting with long non-coding RNA ST8SIA6-AS1.…”