Abstract TP104: Exploring the Noncoding Transcriptome for Novel Therapeutic Targets Against Cerebral Ischemia

The mammalian genome pervasively transcribes a variety of functional noncoding transcripts, including the recently discovered long noncoding RNAs (lncRNAs). LncRNAs play major roles in regulating gene expression in mammals, but their expression and functions in the post-stroke brain remain largely unknown. Using a mouse model of transient focal ischemia, we applied RNA-sequencing to evaluate for the first time the unbiased, genome-wide expression of lncRNAs as a function of reperfusion time in the cerebral cortex. A 1h middle cerebral artery occlusion was conducted in adult male mice and ipsilateral cortices were harvested at 6h, 12h or 24h of reperfusion. RNA was isolated and used for Illumina sequencing. The reads were assembled and mapped to mouse reference genome GRCm38/mm10 and differential expression between the groups was evaluated using TopHat-Cufflinks. We observed that the baseline expression of lncRNAs in the healthy cortex was low, but hundreds of lncRNAs were highly altered after stroke. We identified 1311 isoforms at 6h (1146 upregulated; 165 downregulated), 1287 isoforms at 12h (954 upregulated; 333 downregulated), and 1090 isoforms at 24h (907 upregulated; 183 downregulated) of reperfusion that were significantly altered (absolute fold-change ≥ 2; q-value <0.05) versus sham controls. Of these, 1261 (98%), 1221 (95%) and 1039 (95%) isoforms at 6, 12 and 24h of reperfusion, respectively, were novel lncRNAs. Importantly, hundreds of transcripts that were not detectable in the healthy cortex were robustly expressed in response to stroke, thus representing ischemia-specific lncRNAs. A total of 975 isoforms (74%) at 6h, 815 isoforms (63%) at 12h, and 800 isoforms (73%) at 24h were detected exclusively in the post-stroke cortex. Barring 3 isoforms at 6h, 1 isoform at 12h and 2 isoforms at 24h, all were novel transcripts. Overall, this study reveals a plethora of previously undiscovered, disease-related lncRNAs in the adult post-stroke cortex and identifies distinct reperfusion time-point-dependent expression characteristics. Further investigation of these lncRNAs will elucidate their functional roles in the progression of the post-stroke pathophysiology and may identify new opportunities for therapeutic intervention.