Identification of MicroRNAs by Microarray Analysis and Prediction of Target Genes Involved in Osteogenic Differentiation of Human Periodontal Ligament Stem Cells

microRNA-142-3p regulates osteogenic differentiation of human periodontal ligament stem cells via mediating SGK1

OBJECTIVE

Human periodontal ligament stem cells (hPDLSCs) refer to one kind of somatic stem cells that are capable of differentiating into multiple cell kinds and undergoing robust clonal self-renewal. This work was unearthed to elucidate the possible molecular mechanism of miR-142-3p in mediating osteogenic differentiation of hPDLSCs by targeting SGK1.

METHODS

The hPDLSCs were isolated, cultured, and identified. hPDLSCs were identified by immunofluorescence staining and multiple differentiation ability detection. Cell proliferation ability was assessed by CCK-8 assay. hPDLSCs were induced using osteogenic differentiation medium. ALP activity was detected by alkaline phosphatase (ALP) staining  and ALP activity assay, and mineralized nodule formation was determined by alizarin red staining. The expression levels of osteogenic differentiation marker proteins ALP, RUNX2, and OCN were measured by RT-qPCR. miR-142-3p candidate targets were obtained through bioinformatics analysis. The relationship between miR-142-3p and SKG1 was verified.

RESULTS

miR-142-3p in hPDLSCs after osteogenic induction was down-regulated. Elevated miR-142-3p restricted hPDLSCs proliferation, and diminished ALP activity and mineralized nodule formation, as well as the expression of ALP, RUNX2, and OCN, while miR-142-3p inhibition led to inverse results. miR-142-3p inhibited SKG1 expression. SKG1 overexpression promoted hPDLSC proliferation and osteogenic differentiation, and reversed the inhibitory function of miR-142-3p on hPDLSCs.

CONCLUSION

This study highlights that miR-142-3p represses osteogenic differentiation of hPDLSCs by reducing SGK1 expression.

Periodontal ligament fibroblasts-derived exosomes induced by PGE2 inhibit human periodontal ligament stem cells osteogenic differentiation via activating miR-34c-5p/SATB2/ERK

Several studies have confirmed that exosomes containing microRNAs (miRNAs) from the aseptic inflammatory microenvironment play an important role in bone remodeling. But the mechanism that induces changes in the osteogenic ability of periodontal ligament stem cells (PDLSCs) is still unclear. In the present study, the osteogenic function of periodontal ligament fibroblasts-derived exosomes induced by PGE₂ on PDLSCs was detected by real-time PCR, alizarin red assay and alkaline phosphatase staining. High-throughput miRNAs sequencing was used to reveal that miR-34c-5p in exosomes-PGE₂ was upregulated compared it in exosomes-normal. Real-time PCR and western blotting assay verified that overexpression of miR-34c-5p inhibited osteogenic differentiation, and reduced phosphorylation of ERK1/2. In addition, dual-luciferase reporter assay revealed that miR-34c-5p targeted special AT-rich sequence-binding protein 2 (SATB2). It was shown that exosomal miR-34c-5p inhibited osteogenic differentiation of PDLSCs via SATB2/ERK pathway.

Clinical Perspectives of Non-Coding RNA in Oral Inflammatory Diseases and Neuropathic Pain: A Narrative Review

Non-coding RNAs (ncRNAs) represent a research hotspot by playing a key role in epigenetic and transcriptional regulation of diverse biological functions and due to their involvement in different diseases, including oral inflammatory diseases. Based on ncRNAs’ suitability for salivary biomarkers and their involvement in neuropathic pain and tissue regeneration signaling pathways, the present narrative review aims to highlight the potential clinical applications of ncRNAs in oral inflammatory diseases, with an emphasis on salivary diagnostics, regenerative dentistry, and precision medicine for neuropathic orofacial pain.

Progress in the Study of Non-Coding RNAs in Multidifferentiation Potential of Dental-Derived Mesenchymal Stem Cells

For decades, the desire for tissue regeneration has never been quenched. Dental-derived mesenchymal stem cells (DMSCs), with the potential of self-renewal and multi-directional differentiation, have attracted much attention in this topic. Growing evidence suggests that non-coding RNAs (ncRNAs) can activate various regulatory processes. Even with a slight decrease or increase in expression, ncRNAs can weaken or even subvert cellular fate. Therefore, a systematic interpretation of ncRNAs that guide the differentiation of DMSCs into cells of other tissue types is urgently needed. In this review, we introduce the roles of ncRNAs in the differentiation of DMSCs, such as osteogenic differentiation, odontogenic differentiation, neurogenic differentiation, angiogenic differentiation and myogenic differentiation. Additionally, we illustrate the regulatory mechanisms of ncRNAs in the differentiation of DMSCs, such as epigenetic regulation, transcriptional regulation, mRNA modulation, miRNA sponges and signalling. Finally, we summarize the types and mechanisms of ncRNAs in the differentiation of DMSCs, such as let-7 family, miR-17∼92 family, miR-21, lncRNA H19, lncRNA ANCR, lncRNA MEG3, circRNA CDR1as and CircRNA SIPA1L1. If revealing the intricate relationship between ncRNAs and pluripotency of DMSCs 1 day, the application of DMSCs in regenerative medicine and tissue engineering will be improved. Our work could be an important stepping stone towards this future.

Comprehensive analysis of the long noncoding RNA-associated competitive endogenous RNA network in the osteogenic differentiation of periodontal ligament stem cells

BACKGROUD

The mechanism implicated in the osteogenesis of human periodontal ligament stem cells (PDLSCs) has been investigated for years. Previous genomics data analyses showed that long noncoding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) have significant expression differences between induced and control human PDLSCs. Competing for endogenous RNAs (ceRNA), as a widely studied mechanism in regenerative medicine, while rarely reported in periodontal regeneration. The key lncRNAs and their ceRNA network might provide new insights into molecular therapies of periodontal regeneration based on PDLSCs.

RESULTS

Two networks reflecting the relationships among differentially expressed RNAs were constructed. One ceRNA network was composed of 6 upregulated lncRNAs, 280 upregulated mRNAs, and 18 downregulated miRNAs. The other network contained 33 downregulated lncRNAs, 73 downregulated mRNAs, and 5 upregulated miRNAs. Functional analysis revealed that 38 GO terms and 8 pathways related with osteogenesis were enriched. Twenty-four osteogenesis-related gene-centred lncRNA-associated ceRNA networks were successfully constructed. Among these pathways, we highlighted MAPK and TGF-beta pathways that are closely related to osteogenesis. Subsequently, subnetworks potentially linking the GO:0001649 (osteoblast differentiation), MAPK and TGF-beta pathways were constructed. The qRT-PCR validation results were consistent with the microarray analysis.

CONCLUSION

We construct a comprehensively identified lncRNA-associated ceRNA network might be involved in the osteogenesis of PDLSCs, which could provide insights into the regulatory mechanisms and treatment targets of periodontal regeneration.

Bioinformatics Analysis Identified miR-584-5p and Key miRNA-mRNA Networks Involved in the Osteogenic Differentiation of Human Periodontal Ligament Stem Cells

Human periodontal ligament cells (PDLCs) play an important role in periodontal tissue stabilization and function. In the process of osteogenic differentiation of PDLSCs, the regulation of molecular signal pathways are complicated. In this study, the sequencing results of three datasets on GEO were used to comprehensively analyze the miRNA-mRNA network during the osteogenic differentiation of PDLSCs. Using the GSE99958 and GSE159507, a total of 114 common differentially expressed genes (DEGs) were identified, including 62 up-regulated genes and 52 down-regulated genes. GO enrichment analysis was performed. The up-regulated 10 hub genes and down-regulated 10 hub genes were screened out by protein-protein interaction network (PPI) analysis and STRING in Cytoscape. Similarly, differentially expressed miRNAs (DEMs) were selected by limma package from GSE159508. Then, using the miRwalk website, we further selected 11 miRNAs from 16 DEMs that may have a negative regulatory relationship with hub genes. In vitro RT-PCR verification revealed that nine DEMs and 18 hub genes showed the same trend as the RNA-seq results during the osteogenic differentiation of PDLSCs. Finally, using miR-584-5p inhibitor and mimics, it was found that miR-584-5p negatively regulates the osteogenic differentiation of PDLSCs in vitro. In summary, the present results found several potential osteogenic-related genes and identified candidate miRNA-mRNA networks for the further study of osteogenic differentiation of PDLSCs.

MiR-874-3p inhibits osteogenic differentiation of human periodontal ligament fibroblasts through regulating Wnt/β-catenin pathway

Background/purpose

Previous studies have shown that miR-874 is considered to be an important regulatory factor that participated in osteoclast differentiation. The role of miR-874-3p on osteoclast differentiation of human periodontal ligament fibroblast(hPDLF), however, is still unclear. This study was aimed to delve into the related molecular mechanism of miR-874-3p on hPDLF osteoclast differentiation.

Materials and methods

The qRT-PCR assays were applied to check miR-874-3p and WNT3A expression levels during the osteoclast differentiation of hPDLF. Alkaline phosphatase (ALP) activity assays and alizarin red staining assays were applied to appraise the degree of hPDLF osteoclast differentiation. Bioinformatics method and dual-luciferase reporter assay were employed together to anticipate and certify the interaction between miR-874-3p and WNT3A. Western blot assay was applied to examine the β-catenin and WNT3A expression in transfected hPDLF.

Results

In this study, the results indicated that the expression level of miR-874-3p was gradually down-regulated while WNT3A was concomitantly increased during osteogenic differentiation of hPDLF. Overexpression or knockdown of miR-874-3p would inhibit or promote WNT3A and β-catenin protein expression as well as osteogenic differentiation of hPDLF, respectively. Further research indicated that miR-874-3p directly regulated WNT3A expression via coupling with the 3′-UTR of WNT3A. Finally, upregulation of WNT3A expression levels rescues β-catenin expression levels and osteogenic differentiation of hPDLF inhibited by miR-874-3p was explored.

Conclusion

MiR-874-3p inhibits osteogenic differentiation of hPDLF through regulating Wnt/β-catenin pathway.

Research hotspots and trends of microRNA in periodontology and dental implantology: a bibliometric analysis

Background

Periodontal disease is a leading cause of tooth loss, and microRNA (miRNA) has been shown to regulate various biological processes. This study aimed to quantitatively analyze the literature related to miRNA in periodontology and dental implantology and summarize the research hotspots and trends in this field.

Methods

Literature records from 1985 to 2020 were obtained from the Web of Science Core Collection database. After manual selection, the data was used for cooperative network analysis, keyword co-occurrence analysis, and reference co-citation analysis and visualized by CiteSpace.

Results

A total of 287 papers were analyzed between 2007 and 2020, and more than 95% of them were published in the past decade. The largest number of publications were from China, followed by the USA and Japan. The direct cooperation among the productive institutions was not close. At present, most of the research belongs to the discipline of dentistry, oral surgery, cell biology, and molecular biology. Literature clusters generated by reference co-citation analysis and keyword co-occurrence network showed that previous studies mainly focused on four hotspots: periodontal ligament stem cells (PDLSCs), the pathological process of periodontitis, osteogenic differentiation/bone regeneration, and the competing endogenous RNA (ceRNA) network.

Conclusions

The therapeutic potential of miRNA in promoting bone formation and how the ceRNA network contributes to miRNA regulation at a deeper level have become the two main research trends of this field.

MALAT1 regulates osteogenic differentiation of human periodontal ligament stem cells through mediating miR-155-5p/ETS1 axis

BACKGROUND

Osteogenic differentiation of human periodontal ligament stem cells is essential to periodontal regeneration treatment for periodontitis. This study investigated the mechanism of lncRNAs-related osteogenic differentiation.

METHODS

Human periodontal ligament stem cells were extracted from human periodontal ligament and identified via flow cytometry. After being induced into osteogenic differentiation for three weeks using osteoblast inducing conditional media, human periodontal ligament stem cells were transfected with siRNA-MALAT1, or miR-155-5p inhibitor. Human periodontal ligament stem cells osteogenesis was observed by alkaline phosphatase staining, followed by alizarin red staining for evaluating mineralized nodes formation. Runt-related gene 2, collagen-1 and osteocalcin expressions were assessed by western blot and qRT-PCR.

RESULTS

MALAT1 expression was assumed a negative correlation with miR-155-5p expression which was dropping over time in differentiating human periodontal ligament stem cells. MALAT1 could bind with miR-155-5p, and E26 transformation specific-1 (ETS1) was the targeted gene of miR-155-5p. Silenced MALAT1 suppressed ALP activity and mineralized nodes formation and inhibited the expressions of runt-related gene 2, collagen-1 and osteocalcin in differentiating human periodontal ligament stem cells, while miR-155-5p inhibitor reversed the effect of si-MALAT1 on differentiation of human periodontal ligament stem cells.

CONCLUSION

MALAT1 modulated differentiation of human periodontal ligament stem cells via regulating miR-155-5p.

Downregulation of Prolactin-Induced Protein Promotes Osteogenic Differentiation of Periodontal Ligament Stem Cells

Background

Periodontal ligament stem cells (PDLSCs) are promising seed cells for bone tissue engineering and periodontal regeneration applications. However, the mechanism underlying the osteogenic differentiation process remains largely unknown. Previous reports showed that prolactin-induced protein (PIP) was upregulated after PDLSCs osteogenic induction. However, few studies have reported on the function of PIP in osteogenic differentiation. The purpose of the present study was to investigate the effect of PIP on osteogenic differentiation of PDLSCs.

Material/Methods

The expression pattern of PIP during PDLSCs osteogenic differentiation was detected and the effect of each component in the osteogenic induction medium on PIP was also tested by qRT-PCR. Then, the PIP knockdown cells were established using lentivirus. The knockdown efficiency was measured and the proliferation, apoptosis, and osteogenic differentiation ability were examined to determine the functional role of PIP on PDLSCs.

Results

QRT-PCR showed that PIP was sustainedly upregulated during the osteogenic induction process and the phenomenon was mainly caused by the stimulation of dexamethasone in the induction medium. CCK-8 and flow cytometer showed that knocking down PIP had no influence on proliferation and apoptosis of PDLSCs. ALP staining and activity, Alizarin Red staining, and western blot analysis demonstrated PIP knockdown enhanced the osteogenic differentiation and mineralization of PDLSCs.

Conclusions

PIP was upregulated after osteogenic induction; however, PIP knockdown promoted PDLSCs osteogenic differentiation. PIP might be a by-product of osteogenic induction, and downregulating of PIP might be a new target in bone tissue engineering applications.

Key Markers and Epigenetic Modifications of Dental-Derived Mesenchymal Stromal Cells

As a novel research hotspot in tissue regeneration, dental-derived mesenchymal stromal cells (MSCs) are famous for their accessibility, multipotent differentiation ability, and high proliferation. However, cellular heterogeneity is a major obstacle to the clinical application of dental-derived MSCs. Here, we reviewed the heterogeneity of dental-derived MSCs firstly and then discussed the key markers and epigenetic modifications related to the proliferation, differentiation, immunomodulation, and aging of dental-derived MSCs. These messages help to control the composition and function of dental-derived MSCs and thus accelerate the translation of cell therapy into clinical practice.

The Role of Noncoding RNAs in Osteogenic Differentiation of Human Periodontal Ligament Stem Cells

Chronic inflammatory diseases, including periodontitis, are the most common causes of bone tissue destruction. Periodontitis often leads to loss of connective tissue homeostasis and reduced alveolar bone levels. Human periodontal ligament stem cells (PDLSCs), a population of multipotent stem cells derived from periodontal ligament tissues, are considered as candidate cells for the regeneration of alveolar bone and periodontal tissues. Periodontitis impairs the osteogenic differentiation of human PDLSCs. Noncoding RNAs (ncRNAs), including long noncoding RNA (lncRNA), microRNA (miRNA), and circular RNA (circRNA), have been proposed as vital regulators influencing several differentiation processes including bone regeneration. Still, the molecular mechanisms of ncRNAs regulating osteogenic differentiation of human PDLSCs remain poorly understood. Exploring the influence of ncRNAs in the process of osteogenic differentiation of human PDLSCs may provide novel therapeutic strategies for tissue regeneration as the regeneration of the lost periodontium is the ultimate goal of periodontal therapy.

Dynamic proteomic profiling of human periodontal ligament stem cells during osteogenic differentiation

Background

Human periodontal ligament stem cells (hPDLSCs) are ideal seed cells for periodontal regeneration. A greater understanding of the dynamic protein profiles during osteogenic differentiation contributed to the improvement of periodontal regeneration tissue engineering.

Methods

Tandem Mass Tag quantitative proteomics was utilized to reveal the temporal protein expression pattern during osteogenic differentiation of hPDLSCs on days 0, 3, 7 and 14. Differentially expressed proteins (DEPs) were clustered and functional annotated by Gene Ontology (GO) terms. Pathway enrichment analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes database, followed by the predicted activation using Ingenuity Pathway Analysis software. Interaction networks of redox-sensitive signalling pathways and oxidative phosphorylation (OXPHOS) were conducted and the hub protein SOD2 was validated with western blotting.

Results

A total of 1024 DEPs were identified and clustered in 5 distinctive clusters representing dynamic tendencies. The GO enrichment results indicated that proteins with different tendencies show different functions. Pathway enrichment analysis found that OXPHOS was significantly involved, which further predicted continuous activation. Redox-sensitive signalling pathways with dynamic activation status showed associations with OXPHOS to various degrees, especially the sirtuin signalling pathway. SOD2, an important component of the sirtuin pathway, displays a persistent increase during osteogenesis. Data are available via ProteomeXchange with identifier PXD020908.

Conclusion

This is the first in-depth dynamic proteomic analysis of osteogenic differentiation of hPDLSCs. It demonstrated a dynamic regulatory mechanism of hPDLSC osteogenesis and might provide a new perspective for research on periodontal regeneration.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13287-020-02123-6.

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

Background

The repair of dental pulp injury relies on the odontogenic differentiation of dental pulp stem cells (DPSCs). To better understand the odontogenic differentiation of DPSCs and identify proteins involved in this process, tandem mass tags (TMTs) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) were applied to compare the proteomic profiles of induced and control DPSCs.

Methods

The proteins expressed during osteogenic differentiation of human DPSCs were profiled using the TMT method combined with LC-MS/MS analysis. The identified proteins were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Then, a protein-protein interaction (PPI) network was constructed. Two selected proteins were confirmed by western blotting (WB) analysis.

Results

A total of 223 proteins that were differentially expressed were identified. Among them, 152 proteins were significantly upregulated and 71 were downregulated in the odontogenic differentiation group compared with the control group. On the basis of biological processes in GO, the identified proteins were mainly involved in cellular processes, metabolic processes, and biological regulation, which are connected with the signaling pathways highlighted by KEGG pathway analysis. PPI networks showed that most of the differentially expressed proteins were implicated in physical or functional interaction. The protein expression levels of FBN1 and TGF-β2 validated by WB were consistent with the proteomic analysis.

Conclusions

This is the first proteomic analysis of human DPSC odontogenesis using a TMT method. We identified many new differentially expressed proteins that are potential targets for pulp-dentin complex regeneration and repair.

Proteomic profiling of various human dental stem cells - a systematic review

BACKGROUND

The proteomic signature or profile best describes the functional component of a cell during its routine metabolic and survival activities. Additional complexity in differentiation and maturation is observed in stem/progenitor cells. The role of functional proteins at the cellular level has long been attributed to anatomical niches, and stem cells do not deflect from this attribution. Human dental stem cells (hDSCs), on the whole, are a combination of mesenchymal and epithelial coordinates observed throughout craniofacial bones to pulp.

AIM

To specify the proteomic profile and compare each type of hDSC with other mesenchymal stem cells (MSCs) of various niches. Furthermore, we analyzed the characteristics of the microenvironment and preconditioning changes associated with the proteomic profile of hDSCs and their influence on committed lineage differentiation.

METHODS

Literature searches were performed in PubMed, EMBASE, Scopus, and Web of Science databases, from January 1990 to December 2018. An extra inquiry of the grey literature was completed on Google Scholar, ProQuest, and OpenGrey. Relevant MeSH terms (PubMed) and keywords related to dental stem cells were used independently and in combination.

RESULTS

The initial search resulted in 134 articles. Of the 134 full-texts assessed, 96 articles were excluded and 38 articles that met the eligibility criteria were reviewed. The overall assessment of hDSCs and other MSCs suggests that differences in the proteomic profile can be due to stem cellular complexity acquired from varied tissue sources during embryonic development. However, our comparison of the proteomic profile suffered inconsistencies due to the heterogeneity of various hDSCs. We believe that the existence of a heterogeneous population of stem cells at a given niche determines the modalities of regeneration or tissue repair. Added prominences to the differences present between various hDSCs have been reasoned out.

CONCLUSION

Systematic review on proteomic studies of various hDSCs are promising as an eye-opener for revisiting the proteomic profile and in-depth analysis to elucidate more refined mechanisms of hDSC functionalities.

Downregulating microRNA-152-3p promotes the viability and osteogenic differentiation of periodontal ligament stem cells via targeting integrin alpha 5

OBJECTIVE

The aim of this study was to investigate the role of microRNA-152-3p (miR-152-3p) in the osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs).

DESIGN

HPDLSCs were isolated and identified using immunofluorescence staining, and their osteogenic differentiation capability was evaluated by alkaline phosphatase staining and Alizarin Red staining. HPDLSC viability was measured using cell counting kit-8. alkaline phosphatase level in hPDLSCs was measured by enzyme-linked immunosorbent assay. Target gene and potential binding sites between miR-152-3p and integrin alpha 5 (ITGA5) were predicted using TargetScan and confirmed by dual-luciferase reporter assay. Relative expressions of miR-152-3p and factors related to hPDLSC osteogenic differentiation were measured by quantitative real-time polymerase chain reaction and Western blot as needed.

RESULTS

Collected cells were observed and identified as hPDLSCs. MiR-152-3p expression was downregulated during hPDLSC osteogenic differentiation in a time-dependent manner, and downregulating miR-152-3p promoted cell viability, enhanced alkaline phosphatase level, and increased the expressions of genes related to hPDLSC osteogenic differentiation. ITGA5 was the target gene of miR-152-3p and ITGA5 expression was upregulated during osteogenic differentiation in a time-dependent manner. Silencing ITGA5 partially reversed the effects of downregulating miR-152-3p on hPDLSCs.

CONCLUSION

Downregulating miR-152-3p may promote hPDLSC viability and osteogenic differentiation via targeting ITGA5, and have potential effects on periodontal and alveolar bone regeneration.

Identification of regulatory mRNA and microRNA for differentiation into cementoblasts and periodontal ligament cells

OBJECTIVE

Periodontitis causes periodontal tissue destruction and results in physiological tooth dysfunction. Therefore, periodontal regeneration is ideal therapy for periodontitis. Mesenchymal stem cells (MSCs) are useful for periodontal regenerative therapy as they can differentiate into periodontal cells; however, the underlying regulatory mechanism is unclear. In this study, we attempted to identify regulatory genes involved in periodontal cell differentiation and clarify the differentiation mechanism for effective periodontal regenerative therapy.

BACKGROUND

The cementum and periodontal ligament play important roles in physiological tooth function. Therefore, cementum and periodontal ligament regeneration are critical for periodontal regenerative therapy. Mesenchymal stem cell transplantation can be a common periodontal regenerative therapy because these cells have multipotency and self-renewal ability, which induces new cementum or periodontal ligament formation. Moreover, MSCs can differentiate into cementoblasts. Cementoblast- or periodontal ligament cell-specific proteins have been reported; however, it is unclear how these proteins are regulated. MicroRNA (miRNA) can also act as a key regulator of MSC function. Therefore, in this study, we identified regulatory genes involved in cementoblast or periodontal cell differentiation and commitment.

METHODS

Human MSCs (hMSCs), cementoblasts (HCEM), and periodontal ligament cells (HPL cells) were cultured, and mRNA or miRNA expression was evaluated. Additionally, cementoblast-specific genes were overexpressed or suppressed in hMSCs and their expression levels were investigated.

RESULTS

HCEM and HPL cells expressed characteristic genes, of which we focused on ets variant 1 (ETV1), miR-628-5p, and miR-383 because ETV1 is a differentiation-related transcription factor, miR-628-5p was the second-highest expressed gene in HCEM and lowest expressed gene in HPL cells, and miR-383 was the highest expressed gene in HCEM. miR-628-5p and miR-383 overexpression in hMSCs regulated ETV1 mRNA expression, and miR-383 overexpression downregulated miR-628-5p expression. Moreover, miR-383 suppression decreased miR-383 expression and enhanced ETV1 mRNA expression, but miR-383 suppression also decreased miR-628-5p. Furthermore, silencing of ETV1 expression in hMSCs regulated miR-628-5p and miR-383 expression. Concerning periodontal cell commitment, miR-628-5p, miR-383, and ETV1 regulated the expression of HCEM- or HPL cell-related genes by adjusting the expression of these miRNAs.

CONCLUSION

HCEM and HPL cells show characteristic mRNA and miRNA profiles. In particular, these cells have specific miR-383, miR-628-5p, and ETV1 expression patterns, and these genes interact with each other. Therefore, miR-383, miR-628-5p, and ETV1 are key genes involved in cementogenesis or HPL cell differentiation.

[Functions of non-coding RNAs in the osteogenic differentiation of human periodontal ligament-derived cells]

Human periodontal ligament-derived cells serve as an important source of seeding cells in periodontal regenerative medicine, and their osteogenic potential is closely related to alveolar bone repair and periodontal regeneration. Non-coding RNA (ncRNA), such as microRNA, long non-coding RNA, and circular RNA, play important roles in the regu-lation of osteogenic genes in human periodontal ligament-derived cells. In this review, we summarize the target genes, path-ways, and functions of the ncRNA network during osteogenic differentiation of periodontal ligament-derived cells.

Overview of noncoding RNAs involved in the osteogenic differentiation of periodontal ligament stem cells

Periodontal diseases are infectious diseases that are characterized by progressive damage to dental support tissue. The major goal of periodontal therapy is to regenerate the periodontium destroyed by periodontal diseases. Human periodontal ligament (PDL) tissue possesses periodontal regenerative properties, and periodontal ligament stem cells (PDLSCs) with the capacity for osteogenic differentiation show strong potential in clinical application for periodontium repair and regeneration. Noncoding RNAs (ncRNAs), which include a substantial portion of poly-A tail mature RNAs, are considered “transcriptional noise.” Recent studies show that ncRNAs play a major role in PDLSC differentiation; therefore, exploring how ncRNAs participate in the osteogenic differentiation of PDLSCs may help to elucidate the underlying mechanism of the osteogenic differentiation of PDLSCs and further shed light on the potential of stem cell transplantation for periodontium regeneration. In this review paper, we discuss the history of PDLSC research and highlight the regulatory mechanism of ncRNAs in the osteogenic differentiation of PDLSCs.

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

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 gene-centered 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.

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.

Long non-coding RNA FER1L4 promotes osteogenic differentiation of human periodontal ligament stromal cells via miR-874-3p and vascular endothelial growth factor A

Background

Periodontal ligament stromal cells (PDLSCs) are ideal cell sources for periodontal tissue repair and regeneration, but little is known about what determines their osteogenic capacity. Long non-coding RNAs (lncRNAs) are important regulatory molecules at both transcriptional and post-transcriptional levels. However, their roles in the osteogenic differentiation of PDLSCs are still largely unknown.

Methods

The expression of lncRNA Fer-1-like family member 4 (FER1L4) during the osteogenic differentiation of PDLSCs was detected by quantitative reverse transcription polymerase chain reaction. Overexpression or knockdown of FER1L4 was used to confirm its regulation of osteogenesis in PDLSCs. Alkaline phosphatase and Alizarin red S staining were used to detect mineral deposition. Dual luciferase reporter assays were used to analyze the binding of miR-874-3p to FER1L4 and vascular endothelial growth factor A (VEGFA). Bone regeneration in critical-sized calvarial defects was assessed in nude mice. New bone formation was analyzed by micro-CT, hematoxylin and eosin staining, Masson’s trichrome staining, and immunohistochemical analyses.

Results

FER1L4 levels increased gradually during consecutive osteogenic induction of PDLSCs. Overexpression of FER1L4 promoted the osteogenic differentiation of PDLSCs, as revealed by alkaline phosphatase activity, Alizarin red S staining, and the expression of osteogenic markers, whereas FER1L4 knockdown inhibited these processes. Subsequently, we identified a predicted binding site for miR-874-3p on FER1L4 and confirmed a direct interaction between them. Wild-type FER1L4 reporter activity was significantly inhibited by miR-874-3p, whereas mutant FER1L4 reporter was not affected. MiR-874-3p inhibited osteogenic differentiation and reversed the promotion of osteogenesis in PDLSCs by FER1L4. Moreover, miR-874-3p targeted VEGFA, a crucial gene in osteogenic differentiation, whereas FER1L4 upregulated the expression of VEGFA. In vivo, overexpression of FER1L4 led to more bone formation compared to the control group, as demonstrated by micro-CT and the histologic analyses.

Conclusion

FER1L4 positively regulates the osteogenic differentiation of PDLSCs via miR-874-3p and VEGFA. Our study provides a promising target for enhancing the osteogenic potential of PDLSCs and periodontal regeneration.

Noncoding RNAs: new insights into the odontogenic differentiation of dental tissue-derived mesenchymal stem cells

Odontoblasts are cells that contribute to the formation of the dental pulp complex. The differentiation of dental tissue-derived mesenchymal stem cells into odontoblasts comprises many factors and signaling pathways. Noncoding RNAs (ncRNAs), comprising a substantial part of poly-A tail mature RNAs, are considered “transcriptional noise.” Emerging evidence has shown that ncRNAs have key functions in the differentiation of mesenchymal stem cells. In this review, we discussed two major types of ncRNAs, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), in terms of their role in the odontogenic differentiation of dental tissue-derived stem cells. Recent findings have demonstrated important functions for miRNAs and lncRNAs in odontogenic differentiation. It is expected that ncRNAs will become promising therapeutic targets for dentin regeneration based on stem cells.

Role of a novel race-related tumor suppressor microRNA located in frequently deleted chromosomal locus 8p21 in prostate cancer progression

The prostate cancer (PCa) genome is characterized by deletions of chromosome 8p21-22 region that increase significantly with tumor grade and are associated with poor prognosis. We proposed and validated a novel, paradigm-shifting hypothesis that this region is associated with a set of microRNA genes-miR-3622, miR-3622b, miR-383-that are lost in PCa and play important mechanistic roles in PCa progression and metastasis. Extending our hypothesis, in this study, we evaluated the role of a microRNA gene located in chromosome 8p-miR-4288-by employing clinical samples and cell lines. Our data suggests that (i) miR-4288 is widely downregulated in primary prostate tumors and cell lines; (ii) miR-4288 expression is lost in metastatic castration-resistant PCa; (ii) miR-4288 downregulation is race-related PCa alteration that is prevalent in Caucasian patients and not in African Americans; (iii) in Caucasians, miR-4288 was found to be associated with increasing tumor grade and high serum prostate-specific antigen, suggesting that miR-4288 downregulation/loss may be associated with tumor progression specifically in Caucasians; (iv) miR-4288 possess significant potential as a molecular biomarker to predict aggressiveness/metastasis; and (v) miR-4288 is anti-proliferative, is anti-invasive and inhibits epithelial-to-mesenchymal transition; and (vi) miR-4288 directly represses expression of metastasis/invasion-associated genes MMP16 and ROCK1. Thus, the present study demonstrates a tumor suppressor role for a novel miRNA located with a frequently lost region in PCa, strengthening our hypothesis that this locus is causally related to PCa disease progression via loss of microRNA genes. Our study suggests that miR-4288 may be a novel biomarker and therapeutic target, particularly in Caucasians.

Role of microRNAs in osteogenesis of stem cells

Osteogenic differentiation is a controlled developmental process in which external and internal factors including cytokines, growth factors, transcription factors (TFs), signaling pathways and microRNAs (miRNAs) play important roles. Various stimulatory and inhibitory TFs contribute to osteogenic differentiation and are responsible for bone development. In addition, cross-talk between several complex signaling pathways regulates the osteogenic differentiation of some stem cells. Although much is known about regulatory genes and signaling pathways in osteogenesis, the role of miRNAs in osteogenic differentiation still needs to be explored. miRNAs are small, approximately 22 nucleotides, single-stranded nonprotein coding RNAs which are abundant in many mammalian cell types. They paly significant regulated roles in various biological processes and serve as promising biomarkers for disease states. Recently, emerging evidence have shown that miRNAs are the key regulators of osteogenesis of stem cells. They may endogenously regulate osteogenic differentiation of stem cells through direct targeting of positive or negative directors of osteogenesis and depending on the target result in the promotion or inhibition of osteogenic differentiation. This review aims to provide a general overview of miRNAs participating in osteogenic differentiation of stem cells and explain their regulatory effect based on the genes targeted with these miRNAs.

Assessment of microRNA-144-5p and its putative targets in inflamed gingiva from chronic periodontitis patients

BACKGROUND AND OBJECTIVE

This study aimed to discover the distinctive MicroRNAs (miRNA) functioning in the pathogenesis of periodontal inflammation, which might be potential therapy targets of chronic periodontitis.

MATERIAL AND METHODS

miRNA profiles of human inflamed gingival tissue from three previous microarrays were re-analysed. Gingival tissues were collected for the validation of overlapping miRNAs, and a network was constructed to show regulatory connection between overlapping miRNAs and periodontitis-associated target genes. Potential miRNAs were screened based on their expression levels and predicted target genes. Correlation analysis and binding site prediction were conducted to reveal the relationship between the potential miRNAs and their target genes.

RESULTS

miR-144-5p, found to be upregulated in all three studies, showed the greatest upregulation (P < 0.0001). Another 16 miRNAs (10 upregulated and six downregulated) overlapped between any two of the three studies. All overlapping miRNAs had expected expression levels except for miR-203 during validation. Ten miRNAs (six upregulated and four downregulated) were found to have periodontal inflammation-associated targets. Cyclooxygenase 2 (COX2) and interleukin-17F (IL17F), predicted target genes of upregulated miR-144-5p, showed significant decreases and were negatively correlated with miR-144-5p in the periodontitis group (r = -0.742 for COX2, r = -0.615 for IL17F).

CONCLUSION

This re-analysis of miRNA signatures has implied the potential regulatory mechanism of miR-144-5p and its potential for exploring alternative therapeutic approaches, especially those that use miRNA delivery systems to treat chronic periodontitis. Nevertheless, further study based on larger sample size and homogenous cells is needed to reveal the exact roles of miRNAs in chronic periodontitis.

MicroRNA-543 functions as an osteogenesis promoter in human periodontal ligament-derived stem cells by inhibiting transducer of ERBB2, 2

BACKGROUND AND OBJECTIVE

Previous research has indicated that altered expression of microRNAs (miRNAs) is in connection with osteogenesis of human periodontal ligament-derived stem cells (hPDLSCs). We investigated the mechanisms by which miR-543 promotes osteogenic differentiation of hPDLSCs.

MATERIAL AND METHODS

First, the expression of miR-543 in hPDLSCs cultured with or without an osteogenic inductive cocktail was explored. Then, the function of miR-543 during osteogenesis of hPDLSCs was investigated by overexpressing and inhibiting miR-543. Next, 3 databases were used to predict target genes of miR-543 and a luciferase report was used to validate the direct regulation of miR-543 on the target gene. Further, a rescue experiment using co-transfection of miR-543 mimic and target mimic was performed to evaluate whether overexpressing the target gene could partly rescue the efficiency of overexpressing miR-543 on osteogenesis in hPDLSCs.

RESULTS

miR-543 was upregulated during osteogenic differentiation of hPDLSCs. Functional experiments showed that overexpressing miR-543 could enhance osteogenesis, while inhibiting miR-543 resulted in reduced formation of mineralized nodules. The transducer of ERBB2, 2 (TOB2) was identified as a target gene of miR-543 and luciferase report revealed that miR-543 interacts directly with the 3'-untranslated repeat sequence of TOB2 mRNA. Overexpression of miR-543 inhibited the expression of TOB2 in both mRNA and protein levels while inhibiting miR-543 increased. Furthermore, the rescue experiment confirmed the promotional role of miR-543 TOB2 expression could be abrogated by overexpressing TOB2, which also had the effect of reducing osteogenic differentiation.

CONCLUSION

Our research confirmed that miR-543 is a promoter of osteogenesis in hPDLSCs, acting by inhibiting its target gene TOB2, which suggests that miR-543 may be a potential therapy for bone loss in periodontitis.

Identification and integrated analysis of differentially expressed lncRNAs and circRNAs reveal the potential ceRNA networks during PDLSC osteogenic differentiation

Background

Researchers have been exploring the molecular mechanisms underlying the control of periodontal ligament stem cell (PDLSC) osteogenic differentiation. Recently, long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) were shown to function as competitive endogenous RNAs (ceRNAs) to regulate the effect of microRNAs (miRNAs) on their target genes during cell differentiation. However, comprehensive identification and integrated analysis of lncRNAs and circRNAs acting as ceRNAs during PDLSC osteogenic differentiation have not been performed.

Results

PDLSCs were derived from healthy human periodontal ligament and cultured separately with osteogenic induction and normal media for 7 days. Cultured PDLSCs were positive for STRO-1 and CD146 and negative for CD31 and CD45. Osteo-induced PDLSCs showed increased ALP (alkaline phosphatase) activity and up-regulated expression levels of the osteogenesis-related markers ALP, Runt-related transcription factor 2 and osteocalcin. Then, a total of 960 lncRNAs and 1456 circRNAs were found to be differentially expressed by RNA sequencing. The expression profiles of eight lncRNAs and eight circRNAs were measured with quantitative real-time polymerase chain reaction and were shown to agree with the RNA-seq results. Furthermore, the potential functions of lncRNAs and circRNAs as ceRNAs were predicted based on miRanda and were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. In total, 147 lncRNAs and 1382 circRNAs were predicted to combine with 148 common miRNAs and compete for miRNA binding sites with 744 messenger RNAs. These mRNAs were predicted to significantly participate in osteoblast differentiation, the MAPK pathway, the Wnt pathway and the signaling pathways regulating pluripotency of stem cells. Among them, lncRNAs coded as TCONS_00212979 and TCONS_00212984, as well as circRNA BANP and circRNA ITCH, might interact with miRNA34a and miRNA146a to regulate PDLSC osteogenic differentiation via the MAPK pathway.

Conclusions

This study comprehensively identified lncRNAs/circRNAs and first integrated their potential ceRNA function during PDLSC osteogenic differentiation. These findings suggest that specific lncRNAs and circRNAs might function as ceRNAs to promote PDLSC osteogenic differentiation and periodontal regeneration.

Electronic supplementary material

The online version of this article (10.1186/s12863-017-0569-4) contains supplementary material, which is available to authorized users.