Identification and Characterization of Vulnerabilities in Malignant Rhabdoid Tumors

Abstract

Malignant rhabdoid tumors (MRT) are highly aggressive pediatric cancers that respond poorly to current therapies. We screened several MRT cell lines with large-scale RNAi, CRISPR-Cas9, and small-molecule libraries to identify potential vulnerabilities specific for these cancers. From the genetic screens, 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 showed 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 induced significant upregulation of the p53 pathway in MRT cells, and sensitivity was ablated by CRISPR-Cas9-mediated inactivation of TP53. We showed that loss of SMARCB1, a subunit of the SWI/SNF (BAF) complex mutated in nearly all MRT, 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 five-day idasanutlin pulse causing marked regression of all xenografts including durable complete responses in 50% of mice. This work identifies a genetic connection between mutations in the SWI/SNF chromatin-remodeling complex and the tumor suppressor gene p53. Beyond the p53 pathway, from the small-molecule screen, we also identified the protein translation inhibitor homoharringtonine (HHT) as one of the most potent compounds at selectively decreasing viability of MRT cell lines. In our validation studies, we confirmed that MRT cell lines are as sensitive to HHT as CML cell lines, which represent the current approved clinical indication for HHT. We analyzed potential biomarkers for HHT sensitivity and discovered low expression of the anti-apoptotic BCL2L1 as the strongest predictor, with MRT cell lines and primary tumor samples expressing particularly low levels of this gene. Overexpression of BCL2L1 induced resistance to HHT in MRT cells, while depletion of BCL2L1 drove HHT-mediated apoptosis in a BCL2L1 high-expressing cell line. HHT treatment potently inhibited MRT xenograft growth in vivo. Together, these studies provide preclinical evidence to support three different therapies for the treatment of MRT. Idasanutlin, ATSP-7041, and HHT all hold therapeutic potential for the treatment of this often-fatal pediatric cancer.