Loss of the USP22 deubiquitylase confers resistance to chemotherapy in small cell lung cancer [RNA-seq]

Small cell lung cancer (SCLC) responds exceptionally well to cytotoxic chemotherapy. However, relapse with the emergence of chemoresistant disease is rapid and accompanied by poor treatment outcomes. To understand the genetic basis of chemoresistance in SCLC, we applied in vivo CRISPR deletion screening to patient-derived xenograft (PDX) models. Top screen hits included genes encoding components of the transcriptional co-activator SAGA (Spt-Ada-Gcn5 acetyltransferase) complex. We demonstrate that deletion of the SAGA deubiquitylase USP22 conferred cisplatin/etoposide resistance in two chemosensitive PDX models, and that restoring expression in a PDX model harboring homozygous truncating mutation of USP22 re-sensitized tumors to chemotherapy. USP22 loss increased gene body histone H2A-K119 monoubiquitylation in genes encoding key regulators of neuronal differentiation, and suppressed neural and neuroendocrine gene expression including targets of ASCL1. Chemoresistance following USP22 loss reflected attenuated DNA damage-driven phosphorylation events and apoptosis, in conjunction with increased expression of glycolysis and hypoxia-related genes. Glycolysis program upregulation may reflect a targetable vulnerability, as inhibition of GLUT1 re-sensitized USP22-null tumors to chemotherapy.