PRMT5 promotes growth of pediatric high grade glioma [bulk RNA-seq]
Background. Pediatric high-grade gliomas (PHGG) are aggressive, undifferentiated CNS tumors with poor outcomes, for which no standard-of-care drug therapy currently exists. Through a knockdown screen for epigenetic regulators, we identified PRMT5 as essential for PHGG cell growth. We hypothesized that, similar to its effect in normal cells, PRMT5 promotes self-renewal of stem-like PHGG tumor initiating cells (TICs) essential for tumor growth. Methods. We conducted in vitro analyses, including limiting dilution studies of self-renewal, to determine the phenotypic effects of PRMT5 KD. We performed ChIP-Seq to identify  PRMT5-mediated epigenetic changes and gene set enrichment analysis to identify pathways that PRMT5 regulates. Using an orthotopic xenograft model of PHGG, we tracked survival and histological characteristics resulting from PRMT5 KD or administration of a PRMT5 inhibitor ± radiation therapy (RT). Results. In vitro, PRMT5 KD slowed cell cycle progression, tumor growth and self-renewal.  PRMT5 KD reduced H3K4me3 occupancy at genes associated with self-renewal, tumor formation and growth. In vivo, PRMT5 KD increased survival and reduced tumor aggressiveness; however, pharmacological inhibition of PRMT5 with or without RT did not improve survival. Conclusion. PRMT5 KD epigenetically reduced TIC self-renewal, leading to increased survival in preclinical models. Pharmacological inhibition of PRMT5 enzymatic activity may have failed in vivo due to insufficient reduction of PRMT5 activity by chemical inhibition, or this failure may suggest that non-enzymatic activities of PRMT5 are more relevant. Overall design: Bulk RNA-Seq data comparing gene expression in pediatric high grade glioma (DMG or cortical PHGG) cells with PRMT5 knockdown (KD) by lentiviral transduction with cells containing empty vector control shRNA.  There are 5 cell lines:  BT245, SU-DIPG-IV, HSJD-DIPG-7, SU-DIPG-XIII* and HSJD-GBM-001. For each cell line, there is one control (empty vector) shRNA and three PRMT5 KD shRNAs used, for a total of four samples per cell line. The shRNA vectors are:  Control - SHC002; PRMT5 targeting shRNAs:  TRCN0000379612, TRCN0000303446, and TRCN0000381130.