Key Potential Long Non-Coding RNAs Related to Plaque Instability in Patients with Carotid Artery Stenosis Analyzed by RNA Sequencing

Abstract

Aim: We aimed to characterize the profiles of long non-coding RNA (lncRNA) and mRNA associated with plaque instability in carotid artery stenosis (CAS). Methods: Three stable and three unstable plaque tissues were collected for RNA sequencing to filtrate differential expressed lncRNAs (DE-lncRNAs) and mRNAs (DE-mRNAs). Identified genes were then used for functional analyses, and six DE-lncRNAs as well as six inflammation-related DE-mRNAs were verified using RT-qPCR (reverse transcription quantitative polymerase chain reaction). Results: Using sequencing, we identified 920 DE-mRNAs (639 upregulated and 281 downregulated mRNAs) and 178 DE-lncRNAs (128 upregulated and 50 downregulated lncRNAs) in unstable plaques. According to functional analysis, these identified genes were obviously enriched in “signal transduction”, “phagocytosis”, “PI3K-Akt (phosphatidylinositol 3 kinase (PI3K)/protein kinaseB) signaling pathway”, “sphingolipid transporter activity”, “TNF (tumor necrosis factor) signaling pathway”, “ICAM-3 (intercellular adhesion molecule-3) receptor activity”, “Jak-STAT (Janus kinase-signal transducer and activator of transcription) signaling pathway”, “interleukin-6 receptor binding”, “Th17 (T helper cell 17) cell differentiation”, “HIF-1 (hypoxia-inducible factor-1) signaling pathway”, “Th1 (helper T lymphocyte 1) and Th2 (helper T lymphocyte 2) cell differentiation”, “NF-κB (nuclear factor kappa-B) signaling pathway”, and “sphingolipid signaling pathway”. Compared to stable plaque tissues, lncRNAs FAM30A, MIAT, and LUCAT1 were significantly upregulated in unstable plaque tissues (p < 0.05), whereas XIST (X inactive-specific transcript) and DLX6-AS1 were markedly downregulated (p < 0.05), based on RT-qPCR results. These findings corroborated expression patterns of lncRNA sequencing data. Compared with stable plaque tissues, expression of CCL19 (chemokine (C-C motif) ligand 19), IL6 (interleukin 6), CCL21 (chemokine (C-C motif) ligand 21), and IL18R1 (interleukin 18 receptor 1) was significantly upregulated, whereas SFRP5 (secreted frizzled related protein 5) was downregulated in unstable plaque tissues. Conclusions: DE-lncRNAs FAM30A, MIAT, LUCAT, XIST, and DLX6-AS1 may be potential targets for plaque instability, and the PI3K-Akt, Jak-STAT, NF-κB, TNF, and HIF-1 signaling pathways may have connection with plaque instability in patients with CAS.