Small-Molecule and CRISPR Screening Converge to Reveal Receptor Tyrosine Kinase Dependencies in Pediatric Rhabdoid Tumors

Elaine Oberlick ,Elizabeth A Stewart,Jaime H Cheah,Matthew G Rees,Alykhan F Shamji,C Suk-Yee Hon,Jake M Bieber,Geoffrey M Nelson,Paul A Clemons,Xiaofeng Wang,Robin M Meyers,Aviad Tsherniak,Todd R Golub,Neekesh V Dharia,Phil Montgomery,Michael A Dyer,Kimberly Stegmaier,David E Root,John M Krill-Burger,Charles W.M Roberts,Sandi Radko,Peter J Park,Mahmoud Ghandi,Stuart L Schreiber,Barbara A Weir,William C Hahn,Brinton Seashore‐Ludlow ,Francisca Vázquez

doi:10.1016/j.celrep.2019.07.021

Abstract

Cancer is often seen as a disease of mutations and chromosomal abnormalities. However, some cancers, including pediatric rhabdoid tumors (RTs), lack recurrent alterations targetable by current drugs and need alternative, informed therapeutic options. To nominate potential targets, we performed a high-throughput small-molecule screen complemented by a genome-scale CRISPR-Cas9 gene-knockout screen in a large number of RT and control cell lines. These approaches converged to reveal several receptor tyrosine kinases (RTKs) as therapeutic targets, with RTK inhibition effective in suppressing RT cell growth invitro and against a xenograft model invivo. RT cell lines highly express and activate (phosphorylate) different RTKs, creating dependency without mutation or amplification. Downstream of RTK signaling, we identified PTPN11, encoding the pro-growth signaling protein SHP2, as a shared dependency across all RT cell lines. This study demonstrates that large-scale perturbational screening can uncover vulnerabilities in cancers with "quiet" genomes.

Highlights

Large-scale perturbational screening of cancer cell lines aims to provide mechanistic insight into cancer biology and identify therapeutic vulnerabilities, which may prove especially useful for cancers that lack obvious targetable genetic alterations
We find that receptor tyrosine kinases (RTKs) activation, driven in part by increased expression caused by loss of SMARCB1, rather than genomic alterations, is a hallmark of rhabdoid tumors (RTs) model systems and that high levels of RTK expression are observed in primary RT patient samples
RTK Inhibitors Selectively Target RT Cell Lines Previously, we reported a small-molecule sensitivity dataset (Cancer Therapeutics Response Portal) describing the effects of a library of 481 small molecules, an informer set enriched for U.S Food and Drug Administration (FDA)-approved oncology drugs and clinical candidates, on the viability of 840 individual cancer cell lines (CCLs) representing 25 cancer lineages, which included 4 RT CCLs (Seashore-Ludlow et al, 2015; Rees et al, 2016)

Summary

Introduction

Large-scale perturbational screening of cancer cell lines aims to provide mechanistic insight into cancer biology and identify therapeutic vulnerabilities, which may prove especially useful for cancers that lack obvious targetable genetic alterations. We investigate the potential of large-scale perturbational screening to identify vulnerabilities in highly aggressive and lethal pediatric rhabdoid tumors (RTs). This genomically simple cancer is driven by a single recurrent genetic event: biallelic loss of the tumor suppressor SMARCB1, or much less commonly SMARCA4, core subunits of the SWI/SNF (BAF) chromatin-remodeling complex. The average mutation burden in RTs is more than 20-fold lower than the average across cancer types; recent genomic characterization of large numbers of primary patient RTs has revealed that 80% of RTs have SMARCB1 loss as the sole recurrent. The range of RT tissue origins and sub-classes complicates treatment recommendations, as dependency relationships are often unclear

Results

Discussion

Conclusion