Novel Transcript Discovery Expands the Repertoire of Pathologically-Associated, Long Non-Coding RNAs in Vascular Smooth Muscle Cells

Abstract

Vascular smooth muscle cells (VSMCs) provide vital contractile force within blood vessel walls, yet can also propagate cardiovascular pathologies through proliferative and pro-inflammatory activities. Such phenotypes are driven, in part, by the diverse effects of long non-coding RNAs (lncRNAs) on gene expression. However, lncRNA characterisation in VSMCs in pathological states is hampered by incomplete lncRNA representation in reference annotation. We aimed to improve lncRNA representation in such contexts by assembling non-reference transcripts in RNA sequencing datasets describing VSMCs stimulated in vitro with cytokines, growth factors, or mechanical stress, as well as those isolated from atherosclerotic plaques. All transcripts were then subjected to a rigorous lncRNA prediction pipeline. We substantially improved coverage of lncRNAs responding to pro-mitogenic stimuli, with non-reference lncRNAs contributing 21–32% for each dataset. We also demonstrate non-reference lncRNAs were biased towards enriched expression within VSMCs, and transcription from enhancer sites, suggesting particular relevance to VSMC processes, and the regulation of neighbouring protein-coding genes. Both VSMC-enriched and enhancer-transcribed lncRNAs were large components of lncRNAs responding to pathological stimuli, yet without novel transcript discovery 33–46% of these lncRNAs would remain hidden. Our comprehensive VSMC lncRNA repertoire allows proper prioritisation of candidates for characterisation and exemplifies a strategy to broaden our knowledge of lncRNA across a range of disease states.

INKILN is a Novel Long Noncoding RNA Promoting Vascular Smooth Muscle Inflammation via Scaffolding MKL1 and USP10

“…70 In our current study, we showed that INKILN positively regulates IL8 gene expression, which is consistent with our recent survey wherein a connection between IL8 and INKILN was suggested. 71 This finding, together with the epigenetic activation of IL8 by the enhancer lncRNA UMLILO , implies a new lncRNA-mediated regulatory mechanism underlying IL8 gene activation, which will have important implications for effectively targeting IL8 gene expression for therapy. Elegant studies using an innovative Tg mouse model, which carries a 166-kilobase BAC encompassing the entire human IL8 gene locus, have reported a crucial role for IL8 in aggravating inflammation and gastrointestinal tumor formation.…”

INKILNis a novel long noncoding RNA promoting vascular smooth muscle inflammation via scaffolding MKL1 and USP10

“…77 In our current study, we showed that INKILN positively regulates IL8 gene expression, which is consistent with our recent survey wherein a connection between IL8 and INKILN was suggested. 78 This finding together with the epigenetic activation of IL8 by the enhancer lncRNA UMLILO, implies a new lncRNA-mediated regulatory mechanism underlying IL8 gene activation, which will have important implications for effectively targeting IL8 gene expression for therapy. Elegant studies from Dr. Wang’s lab, using an innovative transgenic mouse model, which carries a 166 kilobase BAC encompassing the entire human IL8 gene locus, have reported a crucial role for IL8 in aggravating inflammation and gastrointestinal tumor formation.…”

Long Non-Coding RNAs Might Regulate Phenotypic Switch of Vascular Smooth Muscle Cells Acting as ceRNA: Implications for In-Stent Restenosis

“…Bennett et al described a repertoire of newly discovered lncRNAs in VSMCs stimulated with PDGF-BB, IL-1α, and vascular stiffness. Remarkably, they found an over-representation of novel VSMC-enriched lncRNAs with pathological association [ 36 ]. Our discovery pipeline allowed us to describe 289 newly-assembled transcripts, representing 9.8% of dysregulated lncRNAs ( Dataset S1 ).…”