SNHG family lncRNAs promote Ewing sarcoma cell fitness through intronic snoRNA-guided rRNA modifications

Over 90% of Ewing sarcomas (EWS) are driven by the EWS-FLI1 fusion oncoprotein. EWS-FLI1 acts as a pioneer transcription factor, altering the expression of hundreds of genes including many long non-coding RNAs (lncRNAs). The role of these lncRNAs in the oncogenesis of EWS is mostly unknown. We developed a CRISPR interference (CRISPRi) strategy to knock down expression of lncRNA loci expressed in EWS and evaluate their effect on proliferation in vitro and tumor growth in vivo. While most lncRNA knockdown had minimal effect on cell proliferation, selective inhibition of SNHG1, SNHG12, and SNHG30 significantly reduced both proliferation of Ewing cells in vitro and the growth of Ewing tumors in vivo. These results were validated by individual knockdown followed by RNA-seq to assess their functional impact. We observed a decrease in post-transcriptional modifications (2'-O-methylation and pseudouridylation) at specific rRNA positions known to be guided by snoRNAs encoded in SNHG1 and SNHG12. Collectively, we demonstrate that expression of SNHG1, SNHG12, and SNHG30 in EWS cells contributes to the maintenance of cancer cell fitness via their role in intron-processed snoRNA genes. Thus, post-transcriptional regulation of rRNA may be a previously underappreciated consequence of EWS-FLI1 expression.