Identification and validation of key long non-coding RNAs using co-expression network analysis in Crohn’s disease

Abstract

Crohn's disease (CD) is a chronic inflammatory disease of the digestive tract. The underlying molecular mechanism of CD remains unclear. The aim of this study was to investigate the differentially expressed long non-coding RNA (lncRNA) in CD and its possible mechanism, and to verify the expression of lncRNA. Microarray GSE67106 and GSE83448 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed lncRNAs (DELs) and messenger RNAs (mRNAs, DEGs), when normalized through the betaqn package in the R, were determined via the limma package. Gene Ontology (GO) and Kyoto Encyclopedia of genes and genomes (KEGG) pathways were studied using the database for the annotation, visualization and integrated discovery (DAVID) version 6.7, along with Gene Set Enrichment Analysis (GSEA) version 3.0. The co-expression of lncRNAs-mRNAs were determined using weighted gene co expression network analysis (WGCNA). The micro RNAs (miRNAs) related to the DELs and DEGs were forecast. A competing endogenous RNA (ceRNA) network was established. There were 42 DEGs and 551 DEGs identified in total among the samples of the CD and normal control, respectively. These DEGs were enriched in such pathways as retinol metabolism, renin angiotensin system, and maturation-related signaling pathways. A lncRNA-mRNA co-expression network was constructed by WGCNA, with CDKN2B-AS (ANRIL), CTC-210G5.1.1, RP11-467L20.10.1, RP11-325F22.5.1, and RP11-59E19.1.1 as hub DELs. Together with miRNAs, a ceRNA network was constructed and functional analysis showed that the cell brush border and plasma membrane, synthesis and transport of lipoprotein, and angiotensin maturation, metabolism, and regulation of blood pressure were involved in the progression of CD. We successfully validated 1 lncRNA ANRIL, in our clinical specimens, ANRIL, which can feature prominently in CD. However, the exact mechanism of lncRNA ANRIL in CD prediction and diagnosis requires further exploration. This study showed that lncRNA ANRIL has a certain predictive effect on CD occurrence and development and could be a new potential treatment target.