EPCO-12. SINGLE CELL PROFILING OF LONG NON-CODING RNAS IN GLIOMA

Abstract

Abstract Non-coding RNAs have critical functions across biological processes that regulate glioma initiation and progression, and deregulated expression of long non-coding RNAs (lncRNAs) have been implicated in the onset and progression of malignancies. The majority of these transcripts exhibit tissue- and cancer-specific expression but little has been investigated at the single-cell level. We performed single cell RNA Sequencing (10x Genomics) for 9 IDH-wild-type glioblastomas from 7 patients. In total 66,825 cells dissociated from tumor tissues and not sorted were included in this analysis which encompassed 41,989 mean sequencing reads and 2,619 median coding genes per cell. Single cell analysis of lncRNAs in captured 190 median lncRNAs per cell and demonstrated a distinct lncRNA expression profile for glioma cells compared to the non-tumor cells with SOX2-OT significantly upregulated (2X) in glioma cells. Consistent with this finding, SOX2-OT is known to be overexpressed in a variety of cancers and has been previously implicated in glioma proliferation and migration. We then examined patterns of lncRNA expression in GBM expression subtypes. Subtype correlation indicated overexpression of RMST (classical subtype), PCED1B-AS1 (mesenchymal) and LINC00689 (proneural) lncRNAs in these expression subtypes. Consistent with these findings, upregulation of each of these 3 lncRNAs have previously been implicated on pro-tumorigenic effects, including in glioma. Examination of an independent published single cell GBM dataset also validated PCED1B-AS1 in the mesenchymal subtype. Comparison with bulk tumor GBM profiles (IDHwt TCGA GBM dataset) also showed correlations with the expression of RMST, PCED1B-AS1 and LINC00689 lncRNAs in the classical, mesenchymal and proneural subtypes respectively. Overall, these results indicate lncRNA expression can be determined in 10x-generated glioma single cell data and may reveal additional insights about cellular state and glioma biology.