Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

Abstract

Background: Long noncoding RNAs (lncRNAs) play an important role in the multiple differentiations of mesenchymal stem cells (MSCs). However, few studies have focused on the regulatory mechanism of lncRNAs in the odontogenic differentiation of human dental pulp stem cells (hDPSCs). Methods: hDPSCs were induced to differentiate into odontoblasts in vitro, and the expression profiles of lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) in differentiated and undifferentiated cells were obtained by microarray. Bioinformatics analyses including Gene Ontology (GO) analysis, pathway analysis, and binding site prediction were performed for functional annotation of lncRNA. miRNA/odontogenesis-related gene networks and lncRNA-associated ceRNA networks were constructed. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was used to verify the expression of selected genes. RNA fluorescence in situ hybridization (FISH), qRT-PCR, and western blot analysis were used to explore the location and function of lncRNA-G043225. Dual-luciferase reporter assay was performed to confirm the binding sites of miR-588 with G043225 and Fibrillin 1 (FBN1). Results:We identified 132 lncRNAs, 114 miRNAs, and 172 mRNAs were differentially expressed. GO analysis demonstrated that regulation of the neurogenic locus notch homolog (Notch), Wnt, and epidermal growth factor receptor (ERBB) signaling pathways and activation of mitogen-activated protein kinase (MAPK) activity were related to odontogenic differentiation. Pathway analysis indicated that the most significant pathway was the forkhead box O (FoxO) signaling pathway, which is related to odontogenic differentiation. Two odontogenesis-related genecentered lncRNA-associated ceRNA networks were successfully constructed. The qRT-PCR validation results were consistent with the microarray analysis. G043225 mainly locating in cytoplasm was proved to promote the odontogenic differentiation of hDPSCs via miR-588 and FBN1. (Continued on next page)Conclusion: This is the first study revealing lncRNA-associated ceRNA network during odontogenic differentiation of hDPSCs using microarray, and it could provide clues to explore the mechanism of action at the RNA-RNA level as well as novel treatments for dentin regeneration based on stem cells.

Epigenetic Regulation of Dental Pulp Stem Cell Fate

“…Through bioinformatics analyses, two lncRNA-associated ceRNA networks centered two odontogenic-related proteins, rhodopsin and Fibrillin 1 (FBN1), are found to be involved in the odontogenic differentiation of DPSCs. Further research reported that lncRNA G043225 improves the odontogenic differentiation by competitively inhibiting the repression activity of miR-588 on FBN1 as an endogenous miRNA sponge [ 178 ]. Besides, lncRNA H19 can upregulate S-adenosylhomocysteine (SAH), which is an inhibitor of S-adenosylmethionine-dependent methyltransferase, and downregulate DNA methylation levels [ 179 ].…”

Characterization of Odontogenic Differentiation from Human Dental Pulp Stem Cells Using TMT-Based Proteomic Analysis

“…Yoshiba et al found that FBN1 upregulation was accompanied by wound healing in dental pulp tissue [ 32 ]. Our previous study found that the mRNA and protein expression of FBN1 was increased during the odontogenic differentiation of DPSCs, and the lncRNA-G043225/miR-588/FBN1 axis was involved in the odontogenic differentiation of DPSCs [ 19 ]. TGF- β 2 was also identified to be an important regulator of DPSC differentiation [ 33 ].…”

“…This project was approved by the Ethics Committee of Nanfang Hospital, Southern Medical University. DPSCs isolated from the pulp tissue of these premolars were cultured in routine media as we described previously [ 19 ].…”

Hsa-miRNA-143-3p Regulates Differentiation of Human Stem Cells From The Apical Papilla Through Targeting Nuclear Factor I-C

“…SCAPs share many features with dental pulp stem cells but also feature their own specific mechanisms at cellular and molecular levels in the dental root formation [13] . Ample evidence suggests that microRNAs are necessary for maintaining homeostasis and proper functionality in many organs and are also implicated in tooth germ development, differentiation and regeneration of pulp-dentin complex and periodontal tissue [14,15] .…”