Functional screen for mediators of onco-mRNA translation specificity [polysome-seq]
Oncogenic protein dosage is tightly regulated to enable cancer cells to adapt and survive. Whether this is regulated at the level of translational control and the key factors in cis and trans remain unknown. The Myc oncogene is a central paradigm of an exquisitely regulated oncogene and a major driver of pancreatic ductal adenocarcinoma (PDAC). Using a genome-wide 5'UTR CRISPRi screen in PDAC cells, we identified activators of selective MYC translation and validated four RNA binding proteins (RBPs), including epitranscriptome modifiers. Among these RBPs, RBM42 was our top hit, which is highly expressed in PDAC and predicts poor survival. Combining polysome sequencing and CLIP-seq analyses, we find that RBM42 binds and selectively regulates the translation of MYC and a precise, yet vital suite of pro-oncogenic transcripts, including JUN and EGFR. Mechanistically, employing IP-mass spectrometry analysis, we find that RMB42 is a novel ribosome-associated protein (RAP). Using DMS-Seq and mutagenesis analysis, we show that RBM42 directly binds and remodels the MYC 5'UTR RNA structure, facilitating the formation of the translation pre-initiation complex. Importantly, RBM42 is necessary for human PDAC cell growth and fitness and PDAC tumorigenesis in xenograft mouse models in a Myc-dependent manner in vivo. In PDAC patient samples, RBM42 expression is correlated with Myc protein levels and transcriptional activity. This work transforms our understanding of the translational code in cancer and offers a new therapeutic opening to target the expression of oncogenes. Overall design: To investigate the function of RBM42 on translation in PDAC cells, we knocked down RBM42 in Panc-1 cells with shRNA. We then performed total RNA-sequencing on pooled polysome fractions (poly-seq) in triplicate shSCR (control) and shRBM42-1.