Differential Expression and Bioinformatics Analysis of CircRNA in PDGF-BB-Induced Vascular Smooth Muscle Cells

Abstract

Atherosclerosis is mediated by various factors and plays an important pathological foundation for cardiovascular and cerebrovascular diseases. Abnormal vascular smooth muscle cells (VSMCs) proliferation and migration have an essential role in atherosclerotic lesion formation. Circular RNAs (circRNA) have been widely detected in different species and are closely related to various diseases. However, the expression profiles and molecular regulatory mechanisms of circRNAs in VSMCs are still unknown. We used high-throughput RNA-seq as well as bioinformatics tools to systematically analyze circRNA expression profiles in samples from different VSMC phenotypes. Polymerase chain reaction (PCR), Sanger sequencing, and qRT-PCR were performed for circRNA validation. A total of 22191 circRNAs corresponding to 6273 genes (host genes) in the platelet-derived growth factor (PDGF-BB) treated group, the blank control group or both groups, were detected, and 112 differentially expressed circRNAs were identified between the PDGF-BB treated and control groups, of which 59 were upregulated, and 53 were downregulated. We selected 9 circRNAs for evaluation of specific headto-tail splicing, and 10 differentially expressed circRNAs between the two groups for qRT-PCR validation. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses enrichment analyses revealed that the parental genes of the circRNAs mainly participated in cardiac myofibril assembly and positive regulation of DNA-templated transcription, indicating that they might be involved in cardiovascular diseases. Finally, we constructed a circRNA-miRNA network based on the dysregulated circRNAs and VSMC-related microRNAs. Our study is the first to show the differential expression of circRNAs in PDGF-BB-induced VSMCs and may provide new ideas and targets for the prevention and therapy of vascular diseases.

Sensitive, reliable, and robust circRNA detection from RNA-seq with CirComPara2

“…CircRNA studies are likely to grow in several branches of biology, both on model (Weigelt et al 2020) and non-model organisms and beyond the biomedical field (Wu et al 2021a; Chu et al 2021; Liang et al 2019), prompting the development of improved tools allowing more extensive circRNA investigation to unravel circRNA-related condition peculiarities, such as differential circRNA expression (Gaffo et al 2019; Wu et al 2021c; Tian et al 2020), imbalances of the CLP (Buratin et al 2020), and prevailing circular transcript isoform expression (Izuogu et al 2018). CirComPara2 is a resource tool meeting these needs, as already proved by the successful application of its embryonic implementations in several studies of human diseases and of other species, including plants (Gaffo et al 2019; Frydrych Capelari et al 2019; Buratin et al 2020; Dal Molin et al 2020).…”

Blocking circ_UBR4 suppressed proliferation, migration, and cell cycle progression of human vascular smooth muscle cells in atherosclerosis

“…Recently, differential expression and bioinformatics analysis of circRNA in AS tissues and cell models in VSMCs had been disclosed, both under platelet-derived growth factor (PDGF-BB) stress and ox-LDL pressure [ 11 , 29 , 30 ]. There were several circRNAs involved in the dysfunction of VSMCs and the pathogenesis of AS.…”

Emerging Roles of Circular RNAs in Vascular Smooth Muscle Cell Dysfunction

“…Platelet-derived growth factor type BB (PDGF-BB) is known to induce VSMC dedifferentiation, migration and proliferation ( Lu et al, 2018 ). Tian et al used RNA-sequencing to profile circRNA expression of VSMCs exposed to PDGF-BB ( Tian et al, 2020 ). VSMCs were treated without or with PDGF-BB (10 ng/ml).…”