Exploring the Molecular Mechanism of lncRNA–miRNA–mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft Palate

Abstract

Background Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common craniofacial birth defect. Growing evidence has demonstrated the competing endogenous RNA (ceRNA) hypothesis has played a role in the pathogenesis of NSCL/P. Here, we identified the important lncRNAs in NSCL/P and constructed a ceRNA regulatory network to predict their underlying functional mechanism. Methods Total RNA isolated from the peripheral blood samples were analyzed by the Human Clariom D Affymetrix platform and differentially expressed genes (DEGs) were identified. Using the limma package in R software, DEGs in the expression profile of GSE42589 were identified from Gene Expression Omnibus (GEO) database. Co-differentially expressed lncRNAs (co-DElncRNAs) were used to predict the microRNAs that may bind to them. Co-differentially expressed mRNAs (co-DEmRNAs) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The hub genes were screened using the cytohubba plug-in in Cytoscape. A ceRNA network was built to investigate the molecular mechanism underlying the etiology of NSCL/P. The expression levels of lncRNAs, miRNAs, and mRNAs in the network were assessed by quantitative real-time polymerase chain reaction (qRT-PCR). Results We found 116 DElncRNAs and 2955 DEmRNAs from the GSE42589 dataset, and 2626 DElncRNAs and 2771 DEmRNAs from the Human Clariom D gene chip. A network of co-DEmRNAs containing 3712 edges and 621 nodes were identified by PPI analysis. A ceRNA regulatory network comprising lncRNA USP17L6P, hsa-miR-449c-5p, and MYC was established. qRT-PCR results revealed significantly lower expression levels of lncRNA USP17L6P and c-Myc in NSCL/P tissues, while the expression level of hsa-miR-449c-5p was higher as compared to control samples ( p < 0.05). Conclusion The identified lncRNAs and the established ceRNA regulatory network provide novel insight into the pathogenesis of NSCL/P, therefore hold great promise in NSCL/P management in clinical practice.

LncRNA-NONMMUT100923.1 regulates mouse embryonic palatal shelf adhesion by sponging miR-200a-3p to modulate medial epithelial cell desmosome junction during palatogenesis

“…More importantly, increasing evidence has shown that the lncRNA can regulate maxillofacial diseases, including cleft palate. For example, lncRNAUSP17L6P has been shown to bind to miR-449c-5p and regulate its target genes in patients with non-syndromic cleft lip with or without cleft palate [ 30 ]. lncRNA Meg3 was reported to inhibit the proliferation of mouse embryonic palate mesenchymal cells by interacting with Smad2 protein [ 16 ] and lncRNA H19 can mediated cleft palate formation in mouse by targeting insulin-like growth factor 2 [ 31 ].…”

An Uncharacterised lncRNA Coded by the ASAP1 Locus Is Downregulated in Serum of Type 2 Diabetes Mellitus Patients

“…Moreover, the Pico assay is particularly suitable for the analysis of biological fluids because it requires a very low input mass of total RNA, which is often isolated from fluidic samples in very low quantities. Indeed, some reports analysed biofluids from humans for this purpose [28][29][30][31][32][33]. In this study, we performed transcriptomic analysis through the Clariom D platform on 24 samples obtained from 12 T2D patients and 12 unaffected individuals.…”

Differentially Expressed Circulating Long-Noncoding RNAS in Premature Infants with Respiratory Distress Syndrome

“…Background-adjustment, normalization, and log-transformation of signals intensity were performed with the Signal Space Transformation-Robust Multi-Array Average algorithm (RMA). Raw data were analyzed by the transcriptome analysis console (TAC) 4.0 software (Applied Biosystems, Foster City, CA, USA) awaiting further analysis [ 14 ] . The differentially expressed lncRNAs and mRNAs were screened according to the criteria of gene differential expression with |log2-fold change| (FC) more than 2 times and adjusted P <0.05.…”