RNA-sequencing Study Of Peripheral Blood Mononuclear Cells And Liver Tissue In Primary Biliary Cholangitis

Background and aims:PBC(primary biliary cholangitis),formerly known as primary biliary cirrhosis,is a chronic progressive autoimmune liver disease,characterised by cholestasis.PBC may lead to liver failure and cirrhosis.Destruction of intrahepatic bile ducts is the main histopathological characteristic.The precise cause of PBC remains unknown;considered to be caused by complex interplay of genetic susceptibility and environmental factors.Many studies have been done to clarify the pathogenesis and mechanisms of PBC,with much progress.For example,candidate gene based approaches found some SNPs associated with PBC;genome-wide association studies were used to clarify the genetic mechanism in PBC;several studies reported complex relations between HLA alleles and PBC.However,the precise mechanism of PBC still remains unclarified.Antimitochondrial antibody(AMA)is generally known as the serum biomarker of PBC,and present in about 95% of PBC patients and less than 1% of healthy people.AMA is negative in a few PBC patients.Ursodeoxycholic acid(UDCA)remaining the main drug for the treatment of PBC,has changed substantially the typical course of PBC.However,about 40% of PBC patients don't show biochemical response to UDCA and need new therapies.The aim of this study was to assay the transcriptome of peripheral blood mononuclear cells(PBMC)and liver tissue in PBC patients,to identify differentially expressed transcripts of peripheral blood mononuclear cells(PBMC)and liver tissue between PBC patients and healthy people,to reveal pathways in pathogenesis of PBC,and to provide basis for research on new biomarkers and therapeutic targets,by performing RNA-sequencing(RNA-seq)study.Methods:We performed the RNA-seq study of PBMC in 5 PBC patients vs.8 healthy controls,and liver tissues in 6 PBC patients vs.2 controls(from other liver diseases).Total RNA from PBMC and liver tissue were extracted(extraction in one PBC liver tissue failed),and RNA sequencing was performed after quality control.Then,bio-informatics was used to procure the expression profile of genes,identify the differentially expressed genes related to PBC.Functional annotation was performed using Gene Ontology and KEGG.Co-expression network was applied to analyze the co-expression of differential expressed lncRNAs and mRNAs.Results:RNA-seq results about mRNA: We identified a total of 6 differentially expressed genes in PBMC in PBC vs.control individuals.Among these genes,2 were up-regulated and 4 were down-regulated.The pathway related to differentially expressed genes in PBMC included Homologous recombination,Proteasome,African trypanosomiasis(q<0.05).52 differentially expressed genes in liver tissues in PBC vs.control individuals were identified.Among these genes,43 were up-regulated,and 9 were down-regulated.Results showed that the GO of 52 differentially expressed genes mainly related to nuclear chromosome,telomeric region,nucleosome,DNA packaging complex,chromosome,telomeric region,protein-DNA complex,chromosomal region,histone binding,negative regulation of hematopoietic progenitor cell differentiation,DNA replication-dependent nucleosome assembly,DNA replication-dependent nucleosome organization,protein heterotetramerization,protein heterotetramerization,regulation of hematopoietic progenitor cell differentiation,protein complex assembly,protein complex biogenesis,nucleosome assembly,macromolecular complex assembly,chromatin assembly nucleosome organization,protein heterooligomerization,protein-DNA complex assembly,chromatin assembly or disassembly,DNA packaging,negative regulation of megakaryocyte differentiation,cellular macromolecular complex assembly,protein-DNA complex subunit organization,DNA replication-independent nucleosome assembly,DNA replication-independent nucleosome organization,protein complex subunit organization,regulation of megakaryocyte differentiation,protein oligomerization,DNA conformation change(q<0.05).The pathways related to 52 differentially expressed genes included Systemic lupus erythematosus,Alcoholism,Viral carcinogenesis,Notch signaling pathway,Cyanoamino acid metabolism,Taurine and hypotaurine metabolism,Lipoic acid metabolism(q<0.05).In the protein-protein interaction networks of DEGs in liver tissues,the top 5 highest nodes included HIST1H4 C,H2AFY,ZNF79,TCEA2,HIST3H3.Differentially expressed alternate splicing genes in PBMC in PBC vs.control individuals were also identified:(1)A3SS:9,(2)A5SS:6,(3)MXE:6,(4)RI:5,(6)SE:193.Differentially expressed alternate splicing genes in liver tissue in PBC vs.control individuals were identified:(1)A3SS:3,(2)A5SS:3,(3)MXE:0,(4)RI:5,(5)SE:18.RNA-seq results about lncRNA: We identified a total of 270 differentially expressed lncRNAs in PBMC in PBC vs.control individuals.Among these lncRNAs,68 were up-regulated and 202 were down-regulated.A total of 1013 differentially expressed lncRNAs were identified in liver tissue in PBC vs.control individuals.Among these lncRNAs,442 were up-regulated and 571 were down-regulated.Conclusions:In this study,we report findings from an RNA-seq analysis of PBMC and liver tissue in PBC patients and control individuals,and transcriptome expression profile of PBMC and liver tissue in PBC were studied.We identified many DEGs and differentially expressed lncRNAs in PBMC and liver tissue in PBC vs.control individuals.The pathways related to differentially expressed genes included Systemic lupus erythematosus and so on,and some of the pathways may be associated with pathogenesis of PBC.However,further verification experiments and mechanistic studies on PBC are necessary.