Transcriptome-wide analysis reveals the coregulation of RNA-binding proteins and alternative splicing genes in the development of atherosclerosis

Abstract

RNA-binding proteins (RBPs) are involved in the regulation of RNA splicing, stability, and localization. How RBPs control the development of atherosclerosis, is not fully understood. To explore the relevant RNA-binding proteins (RBPs) and alternative splicing events (ASEs) in atherosclerosis. We made a comprehensive work to integrate analyses of differentially expressed genes, including differential RBPs, and variable splicing characteristics related to different stages of atherosclerosis in dataset GSE104140. A total of 3712 differentially expressed genes (DEGs) were identified, including 2921 upregulated genes and 791 downregulated genes. Further analysis screened out 54 RBP genes, and 434 AS genes overlapped DEGs. We selected high expression ten RBP genes (SAMHD1, DDX60 L, TLR7, RBM47, MYEF2, RNASE6, PARP12, APOBEC3G, SMAD9, and RNASE1) for co-expression analysis. Meanwhile, we found seven regulated alternative splicing genes (RASGs) (ABI1, FXR1, CHID1, PLEC, PRKACB, BNIP2, PPP3CB) that could be regulated by RBPs. The co-expression network was used to further elucidate the regulatory and interaction relationship between RBPs and AS genes. Apoptotic process and innate immune response, revealed by the functional enrichment analysis of RASGs regulated by RBPs were closely related to atherosclerosis. In addition, 26 of the 344 alternative splicing genes regulated by the above 10 RBPs were transcription factors (TFs), We selected high expression nine TFs (TFDP1, RBBP7, STAT2, CREB5, ERG, ELF1, HMGN3, BCLAF1, and ZEB2) for co-expression analysis. The target genes of these TFs were mainly enriched in inflammatory and immune response pathways that were associated with atherosclerosis. indicating that AS abnormalities of these TFs may have a function in atherosclerosis. Furthermore, the expression of differentially expressed RBPs and the alternative splicing events of AS genes was validated by qRT-PCR in umbilical vein endothelial cells (HUVEC). The results showed that RBM47 were remarkedly difference in HUVEC treated with ox-LDL and the splicing ratio of AS in BCLAF1which is regulated by RBM47 significantly changed. In conclusion, the differentially expressed RBPs identified in our analysis may play important roles in the development of atherosclerosis by regulating the AS of these TF genes.

Differential Expression of Subsets of Genes Related to HDL Metabolism and Atherogenesis in the Peripheral Blood in Coronary Artery Disease

“…The latter may be associated with the increase in platelet activation with the increase in HDL-C at CAD. The loss of the PRKAC β2 splice variant, the latter being measured in our study, can increase the inflammatory susceptibility of macrophages [ 66 ] and Cβ2 transcripts were reduced in human fibroatheroma, which may cause plaque progression [ 67 ]. Thus, HDL’s proatherogenic property follows from the negative contribution of PRKACB to HDL-C variability.…”

Functions of RNA-Binding Proteins in Cardiovascular Disease

“…It is a cornerstone of cardiovascular mortality and morbidity [3]. The atherogenesis occurs in four steps: maladaptive morphological changes to endothelial cells, fatty streak formation and concomitant inflammation, proliferation of the atherosclerotic fibrous plaque and cap, and plaque destabilization [50,51]. Each step is an active cellular process regulated, at least in part, at the transcriptomic level that mediates changes in immune cells, endothelial cells, and SMC phenotypes [52].…”

“…RBPs play a crucial role in the differential expression of transcription factors, specifically within their alternative splicing [51]. BCLAF1 is necessary for SMC survival and transdifferentiation to the macrophage-like/foam cell phenotype in advanced atherosclerotic plaques and is involved in the inflammatory immune response [54].…”

“…BCLAF1 is necessary for SMC survival and transdifferentiation to the macrophage-like/foam cell phenotype in advanced atherosclerotic plaques and is involved in the inflammatory immune response [54]. Mimicking cholesterol (ox-LDL) overload in the endothelium during atherosclerosis in vitro, an RBP RBM47-mediated, significant increase in the alternative splicing of BCLAF1 was shown, resulting in increased inflammation [51].…”