Identification of diagnostic biomarkers in patients with gestational diabetes mellitus based on transcriptome gene expression and methylation correlation analysis

• Published in: Reproductive biology and endocrinology Vol. 17; no. 1; p. 112
• Main Authors: Li, Enchun, Luo, Tengfei, Wang, Yingjun
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 27.12.2019; BioMed Central; BMC
• Subjects: Adult; Analysis; Biochemistry; Biological markers; Biomarkers; Biomarkers - analysis; Care and treatment; Correlation analysis; Datasets; Deoxyribonucleic acid; Diabetes mellitus; Diabetes Mellitus, Type 1 - genetics; Diabetes, Gestational - diagnosis; Diabetes, Gestational - genetics; Diagnosis; Diagnostic markers; DNA; DNA Methylation; Epigenesis, Genetic - genetics; Epigenetic inheritance; Epigenetics; Female; GDM; Gene expression; Gene Expression Profiling; Gene Expression Regulation; Genes; Genetic screening; Gestational diabetes; Humans; Immune System; Immunization; Medical diagnosis; Medical research; Messenger RNA; Metabolic disorders; Methylation; Network architectures; Pathway; Pregnancy; Promoter Regions, Genetic - genetics; Reproducibility of Results; RNA; SVM; Womens health; GDM; SVM; Methylation; Diagnostic markers; Pathway
• ISSN: 1477-7827; 1477-7827
• DOI: 10.1186/s12958-019-0556-x

Gestational diabetes mellitus (GDM) has a high prevalence in the period of pregnancy. However, the lack of gold standards in current screening and diagnostic methods posed the biggest limitation. Regulation of gene expression caused by DNA methylation plays an important role in metabolic diseases. In this study, we aimed to screen GDM diagnostic markers, and establish a diagnostic model for predicting GDM. First, we acquired data of DNA methylation and gene expression in GDM samples (N = 41) and normal samples (N = 41) from the Gene Expression Omnibus (GEO) database. After pre-processing the data, linear models were used to identify differentially expressed genes (DEGs). Then we performed pathway enrichment analysis to extract relationships among genes from pathways, construct pathway networks, and further analyzed the relationship between gene expression and methylation of promoter regions. We screened for genes which are significantly negatively correlated with methylation and established mRNA-mRNA-CpGs network. The network topology was further analyzed to screen hub genes which were recognized as robust GDM biomarkers. Finally, the samples were randomly divided into training set (N = 28) and internal verification set (N = 27), and the support vector machine (SVM) ten-fold cross-validation method was used to establish a diagnostic classifier, which verified on internal and external data sets. In this study, we identified 465 significant DEGs. Functional enrichment analysis revealed that these genes were associated with Type I diabetes mellitus and immunization. And we constructed an interactional network including 1091 genes by using the regulatory relationships of all 30 enriched pathways. 184 epigenetics regulated genes were screened by analyzing the relationship between gene expression and promoter regions' methylation in the network. Moreover, the accuracy rate in the training data set was increased up to 96.3, and 82.1% in the internal validation set, and 97.3% in external validation data sets after establishing diagnostic classifiers which were performed by analyzing the gene expression profiles of obtained 10 hub genes from this network, combined with SVM. This study provided new features for the diagnosis of GDM and may contribute to the diagnosis and personalized treatment of GDM.