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Abstract
BackgroundLong non-coding RNAs (lncRNAs) are involved in numerous physiological functions. Yet, their mechanisms in coronary artery disease (CAD) are not well understood.MethodsThe expression profile of genes associated to CAD was reannotated into the lncRNA-mRNA biphasic profile. The target microRNA data were used to design a global CAD triple network. Thereafter, we conducted a functional enrichment analysis and clustering using the triple network from the level of topology analyses. The expression of four non-coding RNAs (ncRNAs) was measured by qRT-PCR and the risk of CAD was calculated by nomogram. The prognostic value of three ncRNAs was evaluated using receiver operating characteristic (ROC) curve.ResultsA CAD lncRNA-miRNA-mRNA network was constructed which included 15 mRNAs, 3 miRNAs, 19 edges and one lncRNA. Nomogram showed that four ncRNAs were the risk of CAD. After RT-PCR validation in four ncRNAs between CAD and non-CAD samples, only three ncRNAs had significant meaning for further analysis. ROC curve showed that TWF1 presented an area under curve (AUC) of 0.862, the AUC of hsa -miR-142-3p was 0.856 and hsa -miR126-5p was 0.822. After the pairwise comparison, we found that TWF1 had significant statistical significance (PTWF1–142 < 0.05 and PTWF1–126 < 0.01). The results of functional enrichment analysis of interacting gene and microRNA showed that the shared lncRNA TWF1 may be a new factor for CAD.ConclusionsThis investigation on the regulatory networks of lncRNA-miRNA-mRNA in CAD suggests that a novel lncRNA, lncRNA TWF1 is a risk factor for CAD, and expands our understanding into the mechanisms involved in the pathogenesis of CAD.
Highlights
Long non-coding RNAs are involved in numerous physiological functions
Data preprocessing and identified differentially expressed items As shown the volcano plot in Fig. 2, After quality control and get rid of lots wrong expression, we identified a total of 752 Differentially expressed mRNAs (DEGs) including 627 up-regulated and 125 down-regulated in coronary artery disease (CAD) samples compared with control samples with adjust-P value (Pa) < 0.05 and |log 2| ≥ 2; 226 Differentially expressed miRNAs (DEMis) including 194 up-regulated and 32 down-regulated with Pa < 0.05 and |log 2| ≥ 1.2; 127 Differentially expressed Long non-coding RNAs (lncRNAs) (DELs) including 49 up-regulated and 78 down-regulated with Pa < 0.05 and |log 2| ≥ 2 for further analysis
Functional annotation, Protein-protein interaction analysis (PPI) network construction and identified hub items To elucidate the role of DEGs, 752 genes were respectively subjected to KEGG pathway enrichment, disease ontology (DO) functional and gene ontology (GO) analyses by R clusterProfiler package (Fig. 3 a to c)
Summary
Long non-coding RNAs (lncRNAs) are involved in numerous physiological functions. Their mechanisms in coronary artery disease (CAD) are not well understood. Coronary artery disease (CAD) remains one of the most common causes of death worldwide, killing nearly 17 million people each year [1]. Identification of CAD at high risk and adverse cardiovascular outcomes, using circulating or imaging biomarkers, may help in treatment [7]. There is increasing evidence that most non-coding RNAs (ncRNAs) have important functions in the modulation of physiological and pathological processes [10, 11]. Unlike the highly conserved short ncRNA which inhibits post-transcription, lncRNAs are involved in diverse processes and are not highly conserved [15, 16]
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