Exploring Potential Biomarkers Of IgA Nephropathy Based On Weighted Gene Co-expression Network (WGCNA)

Objective: Screening of key genes and miRNA-m RNA regulatory networks during the development of IgAN through weighted gene co-expression networks in bioinformatic methods,exporing the potential biomarkers and possible pathogenesis.Methods:We download and collate two pieces of microarray data onto Gene Expresioun Omnibus,which is a large public Gene database,the weighted coexpression analysis of the two pieces of microarray data was performed by using the WGCNA package of R language to find out the key gene modules related to IgAN disease in two datasets,and to compare the functions of genes in the key modules identified by GO functional analysis and KEGG pathway analysis,which can verify the accuracy of WGCNA results and to confirm the functionality of key modules.The cross-linked co-expressed genes were then introduced into the STRING database to construct protein-protein interaction networks(PPI),and Cytoscape was used to screen central genes(hub-gene).Then the data set a chip expression matrix was used to analyze the differential expression level of the selected key genes and non-parametric test to further screen.Finally,miRNA microarray in GEO database was used to screen miRNA differentially expressed by limma packet of R language,and the target gene was predicted by four databases,the miRNA-IgAN m RNA regulatory network was constructed by crossing with the co-expressed genes screened from WGCNA,and the miRNA in the process of development was screened.Results: After WGCAN analysis,13 gene modules and 7 gene modules were identified in two dataset separately,and the pink module and blue module in GSE35487 were similar to the black module and magenta module in GSE35488,Identified as the key gene module involved in the development of the disease,the two groups were crosslinked and found that there were 1561 and 305 co-expressed genes respectively.The four modules were enriched by GO and KEGG,both the pink and black genes are enriched in the functions of " renal system development、extracellular stimulus response、negative regulation of Protein Serine / threonine kinase activity " and " TNF signal pathway、apoptosis、interleukin-17 signal pathway ",both the blue and magenta genes are enriched in the " type I interferon signaling pathway、the regulation of innate immune response、the positive regulation of cell adhesion " and the " MAPK signaling pathway、epstein-barr virus infection、ECM-receptor interaction ".After co-expressing genes were introduced into the STRING database to construct a PPI network,10 central genes were screened,and the central genes of the positively related co-expressing gene modules were "APP、PTPRC、ACTB、PTEN、CASP3、CD44、MAPK8、STAT1、CCNB1、ESR1 ”,the central gene of the negatively related co-expressed gene module is“ IL6、JUN、FOS、EGR1、ATF3、CCL2、SIRT1、DUSP1、FOSB、CDKN1A ”,and the key genes screened in dataset A GSE35487 are used to analys the different expression levels and non-parametric tests,which found that "FOS、JUN、EGR1、IL6、ATF3、CCL2、APP、PTPRC、ACTB、STAT1、SIRT1、FOSB、DUSP1、CDKN1A、PTEN" genes were obviously different expressed in normal and IgA groups.The obvious difference can be further excavated as a potential biomarker of IgAN.A total of 79 differentially expressed miRNAs were screened by the miRNA chip.The predicted target genes and the key modules of the WGCNA method coexisted,and a total of 655 miRNA-m RNA relationship pairs were predicted.The network topology analysis of the network revealed that hsa-mir-93-5p、hsa-mir-17-5p、hsa-mir-106b-5p、hsa-mir-20a-5p、hsa-mir-20b-5p are at the core of the network and may occur in the development of IgAN plays a key role in the process.Conclusion:(1)The expression levels of FOS,JUN,EGR1,IL6,ATF3,CCL2,APP,PTPRC,STAT1,SIRT1,FOSB,DUSP1,CDKN1 A and PTEN genes in the central gene were statistically significant in the normal group and the IgA group,which may be a potential biomarker for IgAN.(2)The key genes module KEGG signaling pathways are mainly TNF signaling pathways,cell apoptosis,interleukin 17 signaling pathway and MAPK signal pathway,enrichment to GO function mainly in dna-binding transcription activator activity,specificity of RNA polymerase II,MAP kinase serine/threonine tyrosine phosphatase activity,protein tyrosine phosphatase activity,and the regulation of innate immune response,these pathways and functions may be IgAN key gene regulation of the key mechanisms of disease,deserves further research.(3)In the miRNA-m RNA network of IgAN,hsa-mir-93-5p,hsa-mir-17-5p,hsa-mir-106b-5p,hsa-mir-20a-5p and hsa-mir-20b-5p are at the core of the network,and these miRNAs may play a key role in the occurrence and development of IgAN.