Effects of VPS4 inhibition by VPS4A E228Q on gene expression in KMR19 and KMR46 mouse rhabdomyosarcoma cells

The AAA+ ATPase VPS4 drives the ESCRT machinery in diverse intracellular membrane remodeling events, including endocytic receptor sorting, membrane repair, and autophagosome closure. Tumor cells often lose one VPS4 paralog (VPS4A or VPS4B), making them dependent on the remaining enzyme and creating a potential therapeutic vulnerability. Here, we report that VPS4 inhibition triggered upregulation of cytokine and innate immune signaling, along with canonical NF-κB, stress response, and cell death pathways in KMR19 and KMR46 murine rhabdomyosarcoma cells (samples J and L [KMR19]; P and R [KMR46]). In a separate set of samples (A–F, KMR46), we show that the STING–IRF3 axis is responsible for cytokine upregulation following VPS4 inhibition.