Synthetic lethality between VPS4A and VPS4B triggers an inflammatory response in colorectal cancer

Somatic copy number alterations play a critical role in oncogenesis. Loss of chromosomal regions containing tumor suppressors can lead to collateral deletion of passenger genes. This can be exploited therapeutically if synthetic lethal partners of such passenger genes are known and represent druggable targets. Here, we report that VPS4B gene, encoding an ATPase involved in ESCRT-dependent membrane remodeling, is such a passenger gene frequently deleted in many cancer types, notably in colorectal cancer (CRC). We confirmed downregulation of VPS4B mRNA and protein levels from CRC patient samples. We identified VPS4A paralog as a synthetic lethal interactor for VPS4B in vitro and in mouse xenografts. Depleting both proteins profoundly altered the cellular transcriptome and induced cell death accompanied by the release of immunomodulatory molecules that mediate inflammatory and anti-tumor responses. Our results identify a pair of novel druggable targets for personalized oncology and provide a rationale to develop VPS4 inhibitors for precision therapy of VPS4B-deficient cancers. The aim of the study was to analyze transcriptional changes upon single depletion of VPS4A or VPS4B and double depletion of VPS4A and VPS4B (VPS4A+B) in human colorectal HCT116 cell line. For RNA-seq analysis 4 biological replicates were prepared, each encompassing following samples: 1/ non-transfected HCT116 (NT), 2/ HCT116 transfected with non -targeting siRNA (siCTRL#1), 3/ HCT116 transfected with non -targeting siRNA (siCTRL#2), 4/ HCT116 transfected with siRNA targeting VPS4A, sequence #1 (siVPS4A#1), 5/ HCT116 transfected with siRNA targeting VPS4A, sequence #2 (siVPS4A#2), 6/ HCT116 transfected with siRNA targeting VPS4B, sequence #1 (siVPS4B#1), 7/ HCT116 transfected with siRNA targeting VPS4B, sequence #2 (siVPS4B#2), 8/ HCT116 transfected with combination of siRNAs targeting VPS4A and VPS4B (siVPS4A#2 and VPS4B#1, referred thereafter as siVPS4A+B#1), 9/ HCT116 transfected with combination of siRNAs targeting VPS4A and VPS4B (siVPS4A#1 and VPS4B#2, referred thereafter as siVPS4A+B#2). Non-transfected and siCTRL#1-transfected cells served as reference samples.