Molecular function predictions and diagnostic value analysis of plasma exosomal miRNAs in Hirschsprung's disease

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

Hirschsprung's disease (HSCR) is a congenital disorder characterized by the absence of ganglion cells in the colon, leading to various intestinal complications. The etiology of HSCR stems from complex genetic and environmental interactions, of which the intricate roles of non-coding RNAs (ncRNAs) are a key area of research. However, the roles of ncRNAs in the pathogenesis of HSCR have not been fully elucidated. In order to understand the variety of symptoms caused by HSCR and develop new therapeutic approaches, it is essential to understand the underlying biological genetic basis of HSCR. This review presents a comprehensive overview of the current understanding regarding the involvement of ncRNAs in HSCR, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). Additionally, it provides a summary of the molecular mechanisms through which ncRNAs regulate the expression of genes related to the proliferation, migration, and differentiation of intestinal neural crest cells, thereby contributing to the advancement of HSCR research.

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

Hirschsprung's disease (HSCR) is a rare developmental disorder in which enteric ganglia are missing along a portion of the intestine. HSCR has a complex inheritance, with RET as the major disease-causing gene. However, the pathogenesis of HSCR is still not completely understood. Therefore, we applied a computational approach based on multi-omics network characterization and clustering analysis for HSCR-related gene/miRNA identification and biomarker discovery. Protein-protein interaction (PPI) and miRNA-target interaction (MTI) networks were analyzed by DPClusO and BiClusO, respectively, and finally, the biomarker potential of miRNAs was computationally screened by miRNA-BD. In this study, a total of 55 significant gene-disease modules were identified, allowing us to propose 178 new HSCR candidate genes and two biological pathways. Moreover, we identified 12 key miRNAs with biomarker potential among 137 predicted HSCR-associated miRNAs. Functional analysis of new candidates showed that enrichment terms related to gene ontology (GO) and pathways were associated with HSCR. In conclusion, this approach has allowed us to decipher new clues of the etiopathogenesis of HSCR, although molecular experiments are further needed for clinical validations.

Up-Regulation of microRNA-424 Causes an Imbalance in AKT Phosphorylation and Impairs Enteric Neural Crest Cell Migration in Hirschsprung Disease

Insights into the role of microRNAs (miRNAs) in disease pathogenesis have made them attractive therapeutic targets, and numerous miRNAs have been functionally linked to Hirschsprung disease (HSCR), a life-threatening genetic disorder due to defective migration, proliferation, and colonization of enteric neural crest cells (ENCCs) in the gut. Recent studies have demonstrated that miR-424 strongly inhibits migration in a variety of cell types and its potential target RICTOR is essential for neural crest cell development. We therefore sought to interrogate how miR-424 and RICTOR contribute to the pathogenesis of HSCR. We utilized HSCR cases and human neural cells to evaluate the miR-424-mediated regulation of RICTOR and the downstream AKT phosphorylation. We further developed an ex vivo model to assess the effects of miR-424 on ENCC migration and proliferation. Then, single-cell atlases of gene expression in both human and mouse fetal intestines were used to determine the characteristics of RICTOR and AKT expression in the developing gut. Our findings demonstrate that miR-424 levels are markedly increased in the colonic tissues of patients with HSCR and that it regulates human neural cell migration by directly targeting RICTOR. Up-regulation of miR-424 leads to decreased AKT phosphorylation levels in a RICTOR-dependent manner, and this, in turn, impairs ENCC proliferation and migration in the developing gut. Interestingly, we further identified prominent RICTOR and AKT expressions in the enteric neurons and other types of enteric neural cells in human and mouse fetal intestines. Our present study reveals the role of the miR-424/RICTOR axis in HSCR pathogenesis and indicates that miR-424 is a promising candidate for the development of targeted therapies against HSCR.

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

Objective

Hirschsprung 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.

Methods

Based 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.

Results

We 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 (TP53 and TWIST1), 4 miRNAs (has-miR-107, has-miR-10b-5p, has-miR-659-3p, and has-miR-371a-5p), and 4 mRNAs (PIM3, CHUK, F2RL1, and CA1) 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).

Conclusion

This 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.

Plasma single-stranded DNA autoantibodies in the diagnosis of Hirschsprung’s disease

Background

Hirschsprung’s disease (HSCR) is a neonatal enteric nervous system (ENS) disease characterized by congenital enteric ganglion cell loss. The only treatment is aganglionic bowel segment resection and innervated bowel segment reconstruction. Delayed diagnosis and treatment cause postoperative complications such as intractable constipation and enterocolitis. Existing preoperative HSCR diagnostic methods have shortcomings such as false positives, radiation and invasiveness.

Methods

We used the robust linear model (RLM) for normalization and the M statistic for screening plasma human autoimmune antigen microarrays and quantitatively assessed single-stranded DNA (ssDNA) antibody levels with enzyme-linked immunosorbent assay (ELISA).

Results

The autoimmune antigen microarray revealed that autoantibodies were higher in HSCR plasma than in disease control (DC) and healthy control (HC) plasma. ssDNA antibodies in HSCR plasma were significantly higher than those in DC and HC plasma. Quantitative ssDNA antibody level detection in plasma by ELISA showed that HSCR (n = 32) was 1.3- and 1.7-fold higher than DC (n = 14) and HC (n = 25), respectively. ssDNA antibodies distinguished HSCR from non-HSCR (HC and DC), achieving an area under the curve (AUC) of 0.917 (95% CI, 0.8550–0.9784), with a sensitivity of 96.99% and a specificity of 74.63%.

Conclusion

ssDNA antibodies in plasma can serve as a diagnostic biomarker for HSCR in the clinic.

Hirschsprung's disease: key microRNAs and target genes

BACKGROUND

This study aimed to identify key microRNAs (miRNAs), pathways, and target genes mediating Hirschsprung's disease (HSCR) pathogenesis and identify the diagnostic potential of miRNAs.

METHODS

The Gene Expression Omnibus database and reverse transcription-quantitative PCR were used to compare miRNA expression between ganglionic and aganglionic colon tissues of children with HSCR, and the TAM 2.0 database was used to identify colon tissue-specific miRNAs. The StarBase database, TargetScan database, luciferase reporter, and western blot assays were used to analyze miRNA-messenger RNA interactions. OmicShare was used to perform functional and pathway enrichment analyses of the target genes. Migration assays were performed to validate the functions of the miRNAs.

RESULTS

The TAM 2.0 database analysis and reverse transcription-quantitative PCR showed that hsa-miR-192-5p, hsa-miR-200a-3p, and hsa-miR-200b-3p were colon tissue-specific and upregulated in aganglionic colon tissue compared to paired ganglionic colon tissue. These three miRNAs effectively reduced cell viability and migration. Luciferase reporter and western blot assays verified the direct interaction between these three miRNAs and the target genes of ZEB2 and FNDC3B. Furthermore, the plasma levels of these miRNAs were higher in HSCR patients than in non-HSCR patients.

CONCLUSIONS

Three plasma miRNAs (hsa-miR-192-5p, hsa-miR-200a-3p, and hsa-miR-200b-3p) are potential peripheral HSCR biomarkers.

IMPACT

The molecular mechanisms underlying HSCR are unclear. HSCR is most accurately diagnosed using rectal biopsy samples, and no consensus has been reached on the use of blood-based tests for HSCR diagnosis. Circulating miRNAs may be candidate diagnostic HSCR biomarkers because they are typically easily detectable, stable, and tissue-specific. Three plasma miRNAs (miR-200a-3p, miR-192-5p, and miR-200b-3p) are potential peripheral HSCR biomarkers.

Mesenchymal Stem Cell-Derived Exosomes: Applications in Regenerative Medicine

Exosomes are a type of extracellular vesicles, produced within multivesicular bodies, that are then released into the extracellular space through a merging of the multivesicular body with the plasma membrane. These vesicles are secreted by almost all cell types to aid in a vast array of cellular functions, including intercellular communication, cell differentiation and proliferation, angiogenesis, stress response, and immune signaling. This ability to contribute to several distinct processes is due to the complexity of exosomes, as they carry a multitude of signaling moieties, including proteins, lipids, cell surface receptors, enzymes, cytokines, transcription factors, and nucleic acids. The favorable biological properties of exosomes including biocompatibility, stability, low toxicity, and proficient exchange of molecular cargos make exosomes prime candidates for tissue engineering and regenerative medicine. Exploring the functions and molecular payloads of exosomes can facilitate tissue regeneration therapies and provide mechanistic insight into paracrine modulation of cellular activities. In this review, we summarize the current knowledge of exosome biogenesis, composition, and isolation methods. We also discuss emerging healing properties of exosomes and exosomal cargos, such as microRNAs, in brain injuries, cardiovascular disease, and COVID-19 amongst others. Overall, this review highlights the burgeoning roles and potential applications of exosomes in regenerative medicine.

Plasma-Derived Exosomal hsa-miR-4488 and hsa-miR-1228-5p: Novel Biomarkers for Dermatomyositis-Associated Interstitial Lung Disease with Anti-Melanoma Differentiation-Associated Protein 5 Antibody-Positive Subset

The present study is aimed at profiling circulating exosome-derived microRNAs (miRNAs/miRs) from patients with dermatomyositis (DM), in particular those complicated with interstitial lung disease (ILD) with anti-melanoma differentiation-associated protein 5 (MDA5) antibody-positive. Fifteen participants were enrolled, including five patients with DM complicated with ILDs prior to treatment with circulating anti-MDA5 antibody-positive status [DM-ILD-MDA5 Ab(+)], five DM patients without ILDs who were negative for 16 detectable myositis-specific antibodies [DM-nonILD-MSA16(-)], and five age- and gender-matched healthy donor controls (HCs). The characteristics of the exosomes extracted by Ribo™ Exosome Isolation Reagent were identified using transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and flow cytometry. Differentially expressed miRNAs, determined by next-generation deep sequencing, were identified through the criteria of ∣log2 fold change | ≥1 and P < 0.01. A total of 38 miRNAs were significantly upregulated in exosomes from patients with DM-ILD-MDA5 Ab(+) compared to those from HC, while 21 miRNAs were significantly downregulated. Compared to exosomes derived from patients with DM-nonILD-MSA16(-), 51 miRNAs were significantly upregulated and 33 miRNAs were significantly downregulated from patients with DM-ILD-MDA5 Ab(+). A total of 73 exosomal miRNAs were significantly differentially expressed between DM-nonILD-MSA16(-) and HC. In particular, two miRNAs, Homo sapiens- (hsa-) miR-4488 and hsa-miR-1228-5p, were common differentially expressed miRNAs among three comparisons. GO and KEGG analyses suggested that several pathways may contribute the pathogenesis of DM-ILD-MDA5 Ab(+) and DM-nonILD-MSA16(-), while PPI network analysis of hsa-miR-4488 and hsa-miR-1228-5p indicated that their predicted target genes, DExD-box helicase 39B and MDM2, may be involved in the mechanisms of DM-ILD-MDA5 Ab(+).

Literature review: enteric nervous system development, genetic and epigenetic regulation in the etiology of Hirschsprung's disease

Hirschsprung's disease (HSCR) is a developmental disorder of the enteric nervous system (ENS) derived from neural crest cells (NCCs), which affects their migration, proliferation, differentiation, or preservation in the digestive tract, resulting in aganglionosis in the distal intestine. The regulation of both NCCs and the surrounding environment involves various genes, signaling pathways, transcription factors, and morphogens. Therefore, changes in gene expression during the development of the ENS may contribute to the pathogenesis of HSCR.

This review discusses several mechanisms involved in the development of ENS, confirming that deviant genetic and epigenetic patterns, such as DNA methylation, histone modification, and microRNA (miRNA) regulation, can contribute to the development of neurocristopathy. Specifically, the epigenetic regulation of miRNA expression and its relationship to cellular interactions and gene activation through various major pathways in Hirschsprung's disease will be discussed.