Kinome-wide synthetic lethal screen identifies PANK4 as modulator of resistance in glioblastoma

Abstract

Abstract Temozolomide (TMZ) represents the cornerstone of therapy for glioblastoma (GBM). However, acquisition of resistance limits its therapeutic potential and therefore poses the need to identify new therapeutic combinations that could improve treatment outcomes. Despite the human kinome has proved to be an undisputable source of druggable targets, our knowledge remains confined to a limited fraction of it, with a multitude of under-investigated proteins yet to be characterised. Using a kinome-wide RNAi screen, we found that abrogation of pantothenate kinase 4 (PANK4) enhances the antiproliferative effects of TMZ in GBM in vitro. Further validation of our top-hit across various TMZ-resistant GBM cell models, patient-derived GBM cell lines and tissue samples, as well as in vivo studies, corroborated the potential translational significance of our findings. We showed that PANK4 expression is induced during TMZ treatment, and its expression is associated with a worse clinical outcome. Using a Tandem Mass Tag (TMT)-based quantitative proteomic approach, a comprehensive global protein dynamics analysis was undertaken to identify key response signatures upon PANK4 knockdown, in the presence or absence of TMZ. We revealed that silencing of PANK4 leads to a marked downregulation of a subset of proteins involved in cellular detoxification. More specifically, as cells undergo genotoxic stress during TMZ exposure, PANK4 depletion represents a synthetic vulnerability, focal point that can lead to critical cellular damage, accumulation of toxic metabolites, and subsequent cell death. Taken together, we unveil a previously unreported role for PANK4 in mediating therapeutic resistance to TMZ in GBM.