Co-expression Network Analysis Of LncRNA Associated With Overexpression Of DNMT1 In Esophageal Epithelial Cells

Objective: Screening and preliminary identification of DNMT1 high expression related LncRNA,which is involved in various inter-related signaling pathways,has revealed a theoretical basis for various types of disease mechanisms.Methods: Highly expression DNMT1 esophageal epithelial cell line as the experimental group(3 cases),normal esophageal epithelial cell line HEEC as the control group(3 cases).LncRNA and mRNA differential expression profiles were identified on Agilent Human LncRNA V5 Microarray,genes with a two-sided P value of <0.05 and Fold Change>2.0 were regarded as statistically significant genes;the 10 LncRNAs with high levels of variation were identified by qRT-PCR;the Gene Ontology(GO)functional annotation analysis and KEGG pathway analysis were used to dissect out differentially expressed mRNAs.Six signal pathways were selected based on the KEGG results of the LncRNA-mRNA co-expression network analysis.Results: 1.There were 6987 significant differentially expressed LncRNA,3654 of which were upregulated,and 3333 were downregulated.A total of 7421 differentially expressed mRNA were identified,2254 of them were upregulated,and 5167 were downregulated.2.The validation results of 10 selected LncRNAs by qRT-PCR was consistent with the microarray.3.GO analysis showed that,in the upregulated mRNAs,there were 1825,1817,and 1937 mRNAs associated with biological processes,cell components,and molecular functions,respectively,and the corresponding highest levels of enrichment were blood coagulation,extracellular space,and two protein dimer activity;among the mRNAs that were down regulated,there were 3517,3283,and 3655 mRNAs related to biological processes,cell components,and molecular functions,respectively.The functions that corresponded to the highest levels of enrichment were viral processes,cytoplasm,and protein binding.KEGG Pathway analysis showed that high expression of DNMT1 in esophageal epithelial cells,9 pathways regulated by mRNA upregulation,natural killer cell mediated cytotoxicity,glycosaminoglycan biosynthesis of chondroitin/dermatan sulfate and anabolic steroids and many other biological pathways were obviously enriched;46 pathways were regulated by downregulated mRNA,ribosome,pancreatic cancer,ErbB signal pathway,Epithelial cell signaling in Helicobacter pylori,Sphingolipid signaling pathway,P53 signaling pathway in multiple biological pathways showed obvious enrichment.4.Co-expression network analysis showed that the 8 mRNAs and 16 LncRNAs were linked to P53 signaling pathway;22 LncRNAs interacted with 11 mRNAs in the Erb B signaling pathway;19 LncRNAs interacted with 8 mRNAs in epithelial cell signal transduction of Helicobacter pylori infection.19 LncRNAs interacted with 5 mRNAs in sphingolipid signaling pathway;21 LncRNAs interacted with 12 mRNAs in the PI3K-Akt signaling pathway;22 LncRNAs interacted with 9 mRNAs in natural killer cells mediated cytotoxicity.Conclusions: The differential expression of LncRNA and mRNA is found in overexpression of DNMT1 in esophageal epithelial cells and normal esophageal epithelial cells by microarray analysis.KEGG analysis find that differentially expressed mRNAs are enriched in multiple pathways such as ribosomes,pancreatic cancer,ErbB signaling pathway,natural killer cell mediated cytotoxicity,and steroid biosynthesis.LncRNA-mRNA co-expression analysis determine that LncRNA is involved in the P53 signaling pathway,ErbB signaling pathway,Helicobacter pylori infection of epithelial cell signal transduction,sphingolipid signaling pathway,PI3K-Akt signaling pathway and NK cell mediated cytotoxicity.