Integrated miRNA-mRNA Expression Profile Analysis Reveals a Role of miR-146a-3p/TRAF6 in Plasma from Gestational Diabetes Mellitus Patients

Abstract

BACKGROUND: By utilizing an integrative strategy, we screened noninvasive molecular markers for the early detection of GDM and constructed miRNA-mRNA regulatory networks associated with GDM.METHODS: A total of 3 microarray datasets (GSE98043, GSE19649 and GSE92772) of plasma samples comparing GDM pregnant women and healthy control pregnant women were downloaded from the GEO database. The GEO2R online platform was used to identify the differentially expressed genes (DEmRNAs) and the differentially expressed miRNAs (DEmiRNAs). The target genes of DEmiRNAs were identified using two independent and complementary types of information: computational target predictions and expression relationships. KEGG pathway annotation was performed for target genes and DEmiRNAs. An interaction network was constructed to identify hub genes of GDM. Another dataset (GSE92772) was used to externally verify the predictive ability of the hub genes. Gene set enrichment analysis (GSEA) was performed to explore the biological function of hub genes.RESULTS: A total of 264 DEmiRNAs and 1217 DEmRNAs were identified by comparing the microarray data of serum samples of GDM patients and healthy pregnant women. Hsa-miR-146a-3p ranked first because of its lowest P value and was selected for further analysis. A total of 47 target genes, including TRAF6, were shared between the computational target predictions and DEmRNAs and were identified as target genes of hsa-miR-146a-3p. Enrichment analysis indicated that GDM-related miRNAs were mainly enriched in the glypican pathway, proteoglycan syndecan-mediated signaling events, and syndecan-1-mediated signaling events. In addition, the glypican pathway was also one of the pathways regulated by hsa-miR-146a-3p. The interaction network analysis of DEmRNAs identified TRAF6, CASP8, PTPN6, and CHD3 as hub genes involved in the pathophysiological process of GDM. Next, these 4 hub genes were selected for independent external validation using the GSE19649 dataset. The expression of TRAF6, CASP8 and CHD3 in 8 pairs of GDM blood samples was confirmed to be higher than that in healthy pregnant women blood samples. However, the expression of PTPN6 in the blood samples of GDM patients was similar to that of healthy pregnant women blood samples. The AUC for predicting GDM was 0.813, 0.828, 0.813, and 0.703 for CHD3, PTPN6, and CASP8, respectively. GSEA showed that 9 hallmark gene sets of metabolism processes were enriched in TRAF6 function.CONCLUSIONS: Three hub genes, TRAF6, CASP8, and CHD3, were identified and independently externally validated as potential GDM noninvasive serum markers. Enrichment analysis indicated that GDM-related miRNAs were mainly enriched in the glypican pathway, proteoglycan syndecan-mediated signaling events, and syndecan-1-mediated signaling events. In addition, integrated miRNA-mRNA expression profile analysis showed that miR-146a-3p/TRAF6 might play a central role in the pathogenesis of gestational diabetes mellitus by involving the above pathways.