Competing endogenous RNA network analysis explores the key lncRNAs, miRNAs, and mRNAs in type 1 diabetes

Abstract

Abstract Background Type 1 diabetes (T1D, named insulin-dependent diabetes) has a relatively rapid onset and significantly decreases life expectancy. This study is conducted to reveal the long non-coding RNA (lncRNA)-microRNA (miRNA)-mRNA regulatory axises implicated in T1D. Methods The gene expression profile under GSE55100 (GPL570 and GPL8786 datasets; including 12 T1D samples and 10 normal samples for each dataset) was extracted from Gene Expression Omnibus database. Using limma package, the differentially expressed mRNAs (DE-mRNAs), miRNAs (DE-miRNAs), and lncRNAs (DE-lncRNAs) between T1D and normal samples were analyzed. For the DE-mRNAs, the functional terms were enriched by DAVID tool, and the significant pathways were enriched using gene set enrichment analysis. The interactions among DE-lncRNAs, DE-miRNAs and DE-mRNAs were predicted using mirwalk and starbase. The lncRNA-miRNA-mRNA interaction network analysis was visualized by Cytoscape. The key genes in the interaction network were verified by quantitatively real-time PCR. Results In comparison to normal samples, 236 DE-mRNAs, 184 DE-lncRNAs, and 45 DE-miRNAs in T1D samples were identified. For the 236 DE-mRNAs, 16 Gene Ontology (GO)_biological process (BP) terms, four GO_cellular component (CC) terms, and 57 significant pathways were enriched. A network involving 36 DE-mRNAs, 8 DE- lncRNAs, and 15 DE-miRNAs was built, such as TRG-AS1—miR-23b/miR-423—PPM1L and GAS5—miR-320a/miR-23b/miR-423—SERPINA1 regulatory axises. Quantitatively real-time PCR successfully validated the expression levels of TRG-AS1- miR-23b -PPM1L and GAS5-miR-320a- SERPINA1. Conclusion TRG-AS1—miR-23b—PPM1L and GAS5—miR-320a—SERPINA1 regulatory axises might impact the pathogenesis of T1D.

Keywords

• Type 1 diabetes
• Long non-coding RNA
• mRNA
• microRNA
• Differential expression analysis
• Interaction network