Identification of Hub mRNAs and lncRNAs in Atrial Fibrillation Using Weighted Co-expression Network Analysis With RNA-Seq Data

Abstract

Atrial fibrillation (AF)/paroxysmal AF (PAF) is the main cause of cardiogenic embolism. In recent years, the progression from paroxysmal AF to persistent AF has attracted more and more attention. However, the molecular mechanism of the progression of AF is unclear. In this study, we performed RNA sequencing for normal samples, paroxysmal AF and persistent AF samples to identify differentially expressed gene (DEG) and explore the roles of these DEGs in AF. Totally, 272 differently expressed mRNAs (DEmRNAs) and 286 differentially expressed lncRNAs (DElncRNAs) were identified in paroxysmal AF compared to normal samples; 324 DEmRNAs and 258 DElncRNAs were found in persistent atrial fibrillation compared with normal samples; and 520 DEmRNAs and 414 DElncRNAs were identified in persistent AF compared to paroxysmal AF samples. Interestingly, among the DEGs, approximately 50% were coding genes and around 50% were non-coding RNAs, suggesting that lncRNAs may also have a crucial role in the progression of AF. Bioinformatics analysis demonstrated that these DEGs were significantly related to regulating multiple AF associated pathways, such as the regulation of vascular endothelial growth factor production and binding to the CXCR chemokine receptor. Furthermore, weighted gene co-expression network analysis (WGCNA) was conducted to identify key modules and hub RNAs and lncRNAs to determine their potential associations with AF. Five hub modules were identified in the progression of AF, including blue, brown, gray, turquoise and yellow modules. Interestingly, blue module and turquoise module were significantly negatively and positively correlated to the progression of AF respectively, indicating that they may have a more important role in the AF. Moreover, the hub protein-protein interaction (PPI) networks and lncRNA–mRNA regulatory network were constructed. Bioinformatics analysis on the hub PPI network in turquoise was involved in regulating immune response related signaling, such as leukocyte chemotaxis, macrophage activation, and positive regulation of α-β T cell activation. Our findings could clarify the underlying molecular changes associated fibrillation, and provide a useful resource for identifying AF marker.

Reviewing Atrial Fibrillation Pathophysiology from a Network Medicine Perspective: The Relevance of Structural Remodeling, Inflammation, and the Immune System

“…Six differentially expressed autophagy-related genes (BECN1, GAPDH, ATG7, MAPK3, BCL2L1, and MYC) and three immune cell subpopulations (T cells CD4 memory resting, T cells follicular helper, and neutrophils) were identified as the most significant potential regulators [ 34 ]. Yang et al (2021) and Qu et al (2021) also used WGCNA to identify hub mRNAs and non-coding RNAs in AF [ 35 , 36 ]. Comparing samples from subjects with and without AF, differentially expressed genes (DEGs) regulate multiple pathways, such as the modulation of vascular endothelial growth factor production and binding to the CXCR chemokine receptor.…”

“…Five hub modules were significantly negatively and positively correlated to the progression of AF. Besides the hub lncRNA–mRNA regulatory network, the hub protein–protein interaction (PPI) network was constructed and analyzed, showing the relevance of immune response signaling, such as leukocyte chemotaxis, macrophage activation, and positive regulation of α-β T cell activation in AF [ 35 ]. Qu et al (2021) identified two significant modules and two hub miRNAs (hsa-miR-146b-5p and hsa-miR-378a-5p) highly correlated with the AF phenotype and differentially expressed miRNAs and genes were predominantly enriched in inflammation-related functional items.…”

Analysis of lncRNAs and mRNA Expression in the ZBTB1 Knockout Monoclonal EL4 Cell Line and Combined Analysis With miRNAs and circRNAs

“…Long noncoding RNAs (lncRNAs) are a heterogeneous class of noncoding RNAs that play an important role in gene regulation and are associated with a variety of genetic diseases and cancers ( Dangelmaier and Lal, 2020 ; Ramakrishnaiah et al., 2020 ). LncRNAs play important functions in many fields, mainly divided into epigenetic regulation, transcriptional regulation and posttranscriptional regulation, can transcriptionally regulate mRNA expression in cis or in trans, and can also bind to microRNAs as ceRNAs to regulate mRNA expression ( Yang et al., 2021 ). Over the past decade, there has been growing evidence that the genomes of many species are commonly transcribed, resulting in numerous LNcRNAs.…”