Mining Key Response Genes To Two Mastitis Pathogens In Dairy Cow Based On WGCNA

Mastitis is a common disease of dairy cattle,which has caused serious economic losses to the dairy industry.Due to the pathogenesis of Mastitis is complex,prevention and treatment is difficult,which is very important to analyze its regulation mechanism for finding the way to prevent and cure mastitis.Weighted Gene Co-expression Network Analysis(WGCNA)can find out covariant gene sets that highly related to the target trait and identify the key genes of the trait by constructing gene co-expression network.Therefore,the WGCNA method was used to explore the differences of the key response genes of primary bovine mammary epithelial cells(pbMEC)to Staphylococcus aureus(S.aureus)and Escherichia coli(E.coli),as well as the key response genes of pbMEC and breast tissue to E.coli infection.The similarities and differences are designed to provide theoretical references for mastitis resistance breeding and diagnosis and prevention.In this study,five transcriptome datasets,GSE25413,GSE24560,GSE15025,GSE24217 and GSE94056,were selected from GEO database.From the datasets,39 samples of pbMEC infected with S.aureus for 1 h,6 h and 24 h,and 40 samples of pbMEC infected with E.coli for 1 h,6 h and 24 h were selected,28 samples of cow mammary tissue infected with E.coli for 1 h,6 h and 24 h.For the selected data,the co-expression network was constructed,divided into modules,and the correlation analysis with the infection time was carried out,and the key modules were obtained.The top 30 of the connectivity in the module were selected as hub genes,and the Protein-Protein Interaction(PPI)network of the key modules was analyzed.Then,the core genes in PPI network were calculated by Cytoscape,and the intersection of the core genes with the hub genes was obtained.Finally,the 24 h target gene was analyzed by cluster analysis,and all the key modules were enriched by GO and KEGG.The main results are as follows:1.When S.aureus infected pbMEC for 24 h,two key modules were obtained,include202 genes.The target genes were mainly interferon-related genes(MX1/2,GBP 4,IFITM1,IFI44 L,IFI44 and IFI60)and ubiquitin-related genes(UBE2L6,UBA7,USP18,FBXO32,ISG15 and DTX3L).2.When pbMEC was infected with E.coli for 24 h,two key modules were obtained,include 495 genes.The function of the target gene was scattered,including proteasome related genes(PSME1,PSMB8,PSMB9),acute phase proteins(SAA3,CFB,HP),superoxide dismutase 2(SOD2),pyridoxal kinase(PDXK),pyridoxal kinase and other genes.3.When E.coli infects dairy cow mammary gland tissue 24 h,two key modules were got,include 1864 genes,6 target genes were obtained: ITGB2,UBA6,RNFT1,ACADM,SNX4 and TBC1D24.4.The KEGG enrichment of pbMEC infected by S.aureus and E.coli for 24 h showed a large number of the same pathways,these include “NF-kappa B signaling pathway”,“Toll-like receptor signaling pathway” and “TNF signaling pathway” etc.While "Viral protein interaction with cytokine and cytokine receptor" is unique to S.aureus infection,"IL-17 signaling pathway" and "Proteasome" are unique to E.coli infection.5.The KEGG enrichment results of the modules with the strongest correlation between E.coli infection with pbMEC and bovine mammary tissue for 24 h also had many repeated pathways,including "IL-17 signaling pathway","proteasome","NOD-like receptor signaling pathway",etc.While "PPAR signaling pathway","Glycerolipid metabolism" and "Fat digestion and absorption" are unique to infected cells,"T cell receptor signaling pathway","B cell receptor signaling pathway" and "Endocytosis" are unique to infected tissues.In summary,pbMEC respond to E.coli with more genes than S.aureus and respond to different types of genes.The key response genes of pbMEC and bovine mammary tissue infected with E.coli at 24 h are different.