Splicing is an alternate oncogenic pathway activation mechanism in glioma
Robert Siddaway, Scott Milos, Arun Kumaran Anguraj Vadivel, Tara Dobson, Jyothishmathi Swaminathan, Scott Ryall, Sanja Pajovic, Palak Patel, Javad Nazarian, Oren J. Becher, Michael Brudno, Arun Ramani, Vidya Gopalakrishnan, Cynthia Hawkins
Abstract
High-grade diffuse glioma (HGG) is the leading cause of brain tumour death. While the genetic drivers of HGG have been well described, targeting these has thus far had little impact on survival suggesting other mechanisms are at play. Here we interrogate the alternative splicing landscape of pediatric and adult HGG through multi-omic analyses, uncovering an increased splicing burden compared with normal brain. The rate of recurrent alternative splicing in cancer drivers exceeds their mutation rate, a pattern that is recapitulated in pan-cancer analyses, and is associated with worse prognosis in HGG. We investigate potential oncogenicity by interrogating cancer pathways affected by alternative splicing in HGG; spliced cancer drivers include members of the RAS/MAPK pathway. RAS suppressor neurofibromin 1 is differentially spliced to a less active isoform in >80% of HGG downstream from REST upregulation, activating the RAS/MAPK pathway and reducing glioblastoma patient survival. Overall, our results identify non-mutagenic mechanisms by which cancers activate oncogenic pathways which need to accounted for in personalized medicine approaches.