Identifying the potential transcriptional regulatory network in Hirschsprung disease by integrated analysis of microarray datasets

Abstract

ObjectiveHirschsprung disease (HSCR) is one of the common neurocristopathies in children, which is associated with at least 20 genes and involves a complex regulatory mechanism. Transcriptional regulatory network (TRN) has been commonly reported in regulating gene expression and enteric nervous system development but remains to be investigated in HSCR. This study aimed to identify the potential TRN implicated in the pathogenesis and diagnosis of HSCR.MethodsBased on three microarray datasets from the Gene Expression Omnibus database, the multiMiR package was used to investigate the microRNA (miRNA)–target interactions, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Then, we collected transcription factors (TFs) from the TransmiR database to construct the TF–miRNA–mRNA regulatory network and used cytoHubba to identify the key modules. Finally, the receiver operating characteristic (ROC) curve was determined and the integrated diagnostic models were established based on machine learning by the support vector machine method.ResultsWe identified 58 hub differentially expressed microRNAs (DEMis) and 16 differentially expressed mRNAs (DEMs). The robust target genes of DEMis and DEMs mainly enriched in several GO/KEGG terms, including neurogenesis, cell–substrate adhesion, PI3K–Akt, Ras/mitogen-activated protein kinase and Rho/ROCK signaling. Moreover, 2 TFs (TP53andTWIST1), 4 miRNAs (has-miR-107,has-miR-10b-5p,has-miR-659-3p, andhas-miR-371a-5p), and 4 mRNAs (PIM3,CHUK,F2RL1, andCA1) were identified to construct the TF–miRNA–mRNA regulatory network. ROC analysis revealed a strong diagnostic value of the key TRN regulons (all area under the curve values were more than 0.8).ConclusionThis study suggests a potential role of the TF–miRNA–mRNA network that can help enrich the connotation of HSCR pathogenesis and diagnosis and provide new horizons for treatment.

Bioinformatics Prediction for Network-Based Integrative Multi-Omics Expression Data Analysis in Hirschsprung Disease

“…Third, we found that 9 out of 31 DE miRNAs obtained after DE re-analysis of GSE77296 were present in our list of HSCR associated miRNAs (hsa-miR-142-3p, hsa-miR-148a-3p, hsa-miR-194-5p, hsa-miR-200a-3p, hsa-miR-200b-3p, hsa-miR-200c-3p, hsa-miR-222-3p, hsa-miR-338-3p and hsa-miR-429). Furthermore, we found that another nine of our predicted miRNAs were described as dysregulated in HSCR patients by other citing articles [30,[75][76][77] of the GSE77296 dataset (Table S6), while another ten predicted miR-NAs previously associated with HSCR (Table S6) were reported to have an altered expression in HSCR colon tissue by quantitative techniques [4,5,[78][79][80][81][82][83][84]. Altogether, 28 of our predicted miRNAs (20.44%) were described with a dysregulated expression in colon tissue of HSCR patients.…”

“…For this purpose, the HSCR miRNA expression profiles from the publicly available microarray dataset GSE77296 [30] was re-analyzed by GEO2R [43] and compared with our results. Moreover, the list of predicted miRNAs was compared with reported DE miRNAs obtained from the GSE77296 dataset [30] by other citing articles [30,[75][76][77]. Additionally, we performed a manual search of altered expression in HSCR colon tissue [4,5,[78][79][80][81][82][83][84] for the predicted miRNAs previously associated with HSCR.…”

The roles of non-coding RNAs in Hirschsprung's disease

“…This approach enriches our understanding of the transcriptomic landscape and reveals differentially expressed ncRNAs specific to HSCR tissues. Simultaneously, the deployment of bioinformatics tools for dissecting differential gene expression, pathway enrichment, and mapping out miRNAs-mRNAs, lncRNAs-miRNAs, and circRNAs-miRNAs interaction networks provides a clearer picture of pivotal ncRNAs and the precise pathways they influence [ 116 , 117 ]. The specific molecular mechanism is illustrated in Fig.…”