Computational Study Of Transcript Variation In Cardiomyocytes After SARS-CoV-2 Infection

BackgroundSARS-CoV-2 belongs to the β-genre virus that can penetrate into myocardial muscle to the heart during the period of short virus hemia or infected with macrophafphomas.Causes symptoms such as myocardial injury,thereby increasing risk of death.However,the pathogenesis of SARS-CoV-2 infection leading to death in some patients due to myocardial injury is still unclear.RNA processing mechanisms,including RNA editing,selective polyadenylation(APA)and alternative splicing(AS),are crucial for the regulation of most human genes in many types of infectious diseases.After SARS-CoV-2 infection,the transcriptome of myocardial cells may undergo Reprogramming,resulting in abnormal transcript variation,thus adjusting the changes in response to viral infection.To further reveal and confirm this hypothetical mechanism,this study selected hiPSC-CM and human myocardial tissue data for comparative analysis,and explored the mechanism of pathological development of myocardial cells after SARS-CoV-2 infection from the perspective of transcriptional variations generated by RNA editing,APA and AS,respectively.Objective1.To describe the changes in host cell RNA editing after SARS-CoV-2 infection of cardiomyocytes and to understand the effects of SARS-CoV-2 infection on cardiomyocytes by RNA editing RNA processing mechanism.2.To understand the role of alternative splicing events in the response of cardiomyocytes to SARS-CoV-2 infection through the analysis of alternative splicing events after SARS-CoV-2 infection of cardiomyocytes.3.To analyze the significant differential alternative polyadenylation events after SARS-CoV-2 infection of cardiomyocytes and to explore its potential role.Methods1.Data collection: three sets of transcriptome sequencing data sets(GSE150392,GSE164784 and GSE156754)containing human induced pluripotent stem cell differentiated cardiomyocyte(hiPSC-CM)infected with SARS-CoV-2 and two set of transcriptome sequencing data(GSE169241 and GSE151880)containing human myocardial tissue of patients with COVID-19 and non-COVID-19 were selected and downloaded from NCBI database.2.Data pre-processing: quality control of the data using fastp on the downloaded raw sequencing data.3.Identification and annotation of RES: use SPRINT software to identify RNA editing site(RES),use REDIportal database and ANNOVAR software to annotate the obtained RES,and identify and analyze the differential editing sites.4.Use the software rMATS to identify and analyze alternative splicing events events.5.Identification and analysis of alternative polyadenylation using the software DaPars.Results1.SARS-CoV-2 infection alters the A-to-I RNA editing events in myocardial cells,and high-quality editing sites affect connections between myocardial cellsThis study found that the A-to-I RNA editing sites in three sets of hiPSC-CM modeling groups and two sets of human myocardial tissue groups mainly underwent base substitutions of AG and TC.The RNA editing sites were mainly located in the Alu elements of the non coding region of the genome,and these editing sites tended to be clustered and mainly distributed in introns,inter gene regions,and other regions.The A-to-I RNA editing sites located in the exon region mainly underwent non synonymous substitutions.The very conservative sequence pattern was found in the interval of one base before and after the editing site in the transcriptome data of the hiPSC-CM modeling group and human myocardial tissue,that is,the former base G of editing site A tends to be missing,and the latter base G has a higher probability of appearing.Moreover,the editing level of the infected group in the hiPSC-CM modeling group was significantly higher than that of the Mock group,while the editing level of the infected group in both sets of human myocardial tissue groups was significantly lower than that of the non infected group.However,their distribution of A-to-I editing sites at different editing levels tended to be consistent.The common high-quality editing sites of the five sets of data show that SARS-CoV-2 infection affects the cell adhesion molecule and tight junctions of cardiomyocytes,and F11 R,PVR,BVES are the genes of high-quality editing sites.2.SARS-CoV-2 infection affects the adhesion of myocardial cells and matrix between the selective shear of the transcriptionbook and the connection between myocardial cellsAmong the AS events in the above-mentioned five sets of transcriptome data,exon hopping was found to be the most common alternative splicing event.The AS event reflects the impact of SARS-CoV-2 infection on the connectivity of myocardial cells,but the performance of the myocardial cell modeling group is slightly different from that of the human myocardial tissue group: Genes that produce significantly different AS events commonly found in the infected myocardial cell modeling group are enriched in adjacent cell adhesion pathways,with CSNK2A1,ACTN1,LMO7,PARD3,SORS1,and CCM2 being the genes involved.Genes that produce significantly different AS events commonly found in the human myocardial group tend to be enriched in focal adhesion between myocardial cells and extracellular matrix,tight junction pathways between myocardial cells,etc.These genes are ACTN1,FN1,VEGFA,FLNB,ITGB1,TJP2 and DLG1.From these five sets of transcriptome data,only six common genes that produce significantly different alternative splicing events were found: ACTN1,RPS24,SLMAP,SNHG14,TPM1 O and SBPL9.Among them,ACTN1,SLMAP and TPM1 are genes that produce significantly different exon hopping events,ACTN1 also plays a role in cell junction.3.SARS-CoV-2 infection changed the APA event of myocardial cells,affected cell junction and caused the development of myocardial pathologyThe genes with significantly different APA events in the infected cardiomyocyte modeling group have different tendencies,while the genes with significantly different APA events in the two data sets of the human cardiomyocyte group tend to use longer3’UTR.The three sets of hiPSC-CM modeling groups showed that the common genes that produced significant differential APA sites,which mainly enriched antigen processing and presentation,tight junction and other pathways,and the genes involved were HSPA4,while in the group of two sets of human myocardial tissues,the significantly enriched pathways of the common genes that produced significant differential APA sites were related to focal adhesion and diabetic cardiomyopathy and the common genes involved were RAC1,COL1A1,COL1A2 and PPP1CC.ConclusionThe analysis of RNA editing,selective splicing and selective polyadenylation events showed that SARS-CoV-2 infected cardiomyocytes changed gene expression regulation,transcriptome and proteome of cardiomyocytes,resulting in pathological processes of cardiomyocytes,affecting the adhesion between cardiomyocytes and matrix and the connection between cardiomyocytes,This also reflects the response mechanism of myocardial cells to viral infection and possible factors affecting the occurrence and development of cellular pathology.