Loss of UBP1 drives oxaliplatin resistance through a targetable dependency on translation initiation

Abstract

Oxaliplatin is a common component of various chemotherapeutic regimens for the treatment of gastrointestinal cancers. However, the majority of patients exhibit resistance to oxaliplatin-based therapy. Here, we integrated knockout and transcription-activation CRISPR screens in patient-derived gastric cancer organoids (GC PDOs) to comprehensively profile major genetic and transcriptomic changes observed over the course of resistance acquisition. Our screens identified UBP1, a transcription factor frequently lost in GC, as a critical determinant of oxaliplatin resistance development. Leveraging a large GC organoid biobank from a co-clinical trial and primary tumor omics data, we reveal that downregulation of specifically MYC-driven ribosome biogenesis drives oxaliplatin resistance, highlighting the drugs role as a ribosome biogenesis stressor. Mechanistically, UBP1 loss reduced expression of its direct target, MAX, a MYC cofactor, leading to downregulation of ribosome biogenesis and protection against nucleolar stress. Crucially, we discover that such downregulation is inevitably followed by a compensatory reliance on translation initiation, making it a therapeutic vulnerability in oxaliplatin-resistant tumors. Consequently, the resistance could be overcome by a synergistic action of the translation initiation repressor 4EGI, and the effect was also maintained in PDO that acquired resistance in vivo under clinically relevant conditions. Our data uncover a common marker of oxaliplatin resistance and identify a novel therapeutic strategy to reverse resistance to one of the most frequently used anticancer drugs.