MDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors

Abstract

Malignant rhabdoid tumors (MRT) are highly aggressive pediatric cancers that respond poorly to current therapies. In this study, we screened several MRT cell lines with large-scale RNAi, CRISPR-Cas9, and small-molecule libraries to identify potential drug targets specific for these cancers. We discovered MDM2 and MDM4, the canonical negative regulators of p53, as significant vulnerabilities. Using two compounds currently in clinical development, idasanutlin (MDM2-specific) and ATSP-7041 (MDM2/4-dual), we show that MRT cells were more sensitive than other p53 wild-type cancer cell lines to inhibition of MDM2 alone as well as dual inhibition of MDM2/4. These compounds caused significant upregulation of the p53 pathway in MRT cells, and sensitivity was ablated by CRISPR-Cas9-mediated inactivation of TP53. We show that loss of SMARCB1, a subunit of the SWI/SNF (BAF) complex mutated in nearly all MRTs, sensitized cells to MDM2 and MDM2/4 inhibition by enhancing p53-mediated apoptosis. Both MDM2 and MDM2/4 inhibition slowed MRT xenograft growth in vivo, with a 5-day idasanutlin pulse causing marked regression of all xenografts, including durable complete responses in 50% of mice. Together, these studies identify a genetic connection between mutations in the SWI/SNF chromatin-remodeling complex and the tumor suppressor gene TP53 and provide preclinical evidence to support the targeting of MDM2 and MDM4 in this often-fatal pediatric cancer.Significance: This study identifies two targets, MDM2 and MDM4, as vulnerabilities in a deadly pediatric cancer and provides preclinical evidence that compounds inhibiting these proteins have therapeutic potential. Analysis and interpretation of data (e.g., statistical analysis, biostatistics, computational analysis):

Genome-wide CRISPR and small-molecule screens uncover targetable dependencies in ATRT

“…In contrast, synthetic lethal interactions, in which a non-self-association is correlated with a specific genetic dependency, account for some of the observed essentialities. All ATRT cell lines were highly sensitive to alterations in the p53 signaling pathway (Figure 2), in line with observations that rhabdoid tumors are particularly sensitive to MDM2/4 inhibition (Howard et al, 2019). Furthermore, the CDK4/6 signaling axis in ATRTs reflects distinct mechanisms of gene essentiality, contributing to mutual exclusive dependencies on either CDK4 or CDK6.…”

“…All TP53 wild-type ATRT cell lines were sensitive to loss of negative regulators of p53 signaling MDM2 and MDM4 (Figure 2A), representing a vertical pathway synthetic lethal dependency. Of note, loss of TP53 enhanced proliferation of all ATRT cell lines as the top enriched gene across our screens, further supporting previous results describing the p53 axis as a therapeutic vulnerability in rhabdoid tumors (Howard et al, 2019). As an example for an expression driven paralog lethality, we identified low expression of CDK6 to predict CDK4 dependency in ATRT cells ( Figure 2B), a feature also seen in other tumor types regardless of tissue origin (McDonald et al, 2017).…”

The role of the SWI/SNF chromatin remodeling complex in pancreatic ductal adenocarcinoma

“…ARID1A‐deficient cancer is also vulnerable to PI3K inhibitor 44 and tyrosine kinase inhibitor dasatinib 45 . MDM2 and MDM4, which inhibit p53 function, are targets for p53‐intact SMARCB1‐deficient cancer 46 . Protein synthesis and the endoplasmic reticulum (ER)‐stress pathway as downstream factors of Myc could also be synthetic lethal targets for SMARCB1 ‐deficient cancer 47 .…”

Development and Regulatory Challenges for Peptide Therapeutics

“…Stapled α−helical peptides have also arisen as a promising new class of macrocyclic peptides 24,26,34 -36 and have recently advanced into the clinic (ie, ALRN-6924). 37 ATSP-7041 31,38 -40 (a progenitor of ALRN-6924) is a benchmark stapled α−helical peptide to explore cellular permeability that seems to fit into a third mechanism which has been dubbed lipophilic partitioning that is different from the passive transport properties of CsA and the cationic partitioning (and endosomal pathway) of cyclic CPPs. These 3 general mechanisms of cellular uptake are recognized to effectively enable peptide entry into the cell to subsequently engage and modulate the functional properties of a therapeutic target (Figure 4).…”