scholarly journals Time series clustering of mRNA and lncRNA expression during osteogenic differentiation of periodontal ligament stem cells

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5214 ◽  
Author(s):  
Yunfei Zheng ◽  
Xiaobei Li ◽  
Yiping Huang ◽  
Lingfei Jia ◽  
Weiran Li
Keyword(s):  
Stem Cells ◽  
Time Series ◽  
Osteogenic Differentiation ◽  
Periodontal Ligament ◽  
Osteoblast Differentiation ◽  
Expression Patterns ◽  
Rna Seq ◽  
Periodontal Ligament Stem Cells ◽  
Specific Expression ◽  
Qrt Pcr

Background Long noncoding RNAs (lncRNAs) are regulatory molecules that participate in biological processes such as stem cell differentiation. Periodontal ligament stem cells (PDLSCs) exhibit great potential for the regeneration of periodontal tissue and the formation of new bone. However, although several lncRNAs have been found to be involved in the osteogenic differentiation of PDLSCs, the temporal transcriptomic landscapes of mRNAs and lncRNAs need to be mapped to obtain a complete picture of osteoblast differentiation. In this study, we aimed to characterize the time-course expression patterns of lncRNAs during the osteogenic differentiation of PDLSCs and to identify the lncRNAs that are related to osteoblastic differentiation. Methods We cultured PDLSCs in an osteogenic medium for 3, 7, or 14 days. We then used RNA sequencing (RNA-seq) to analyze the expression of the coding and non-coding transcripts in the PDLSCs during osteogenic differentiation. We also utilized short time-series expression miner (STEM) to describe the temporal patterns of the mRNAs and lncRNAs. We then performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses to assess the biological relevance of genes in each profile, and used quantitative real-time PCR (qRT-PCR) to validate the differentially expressed mRNAs and lncRNAs that were associated with osteoblast differentiation. Lastly, we performed a knock down of two lncRNAs, MEG8, and MIR22HG, and evaluated the expression of osteogenic markers. Results When PDLSCs were differentiated to osteoblasts, mRNAs associated with bone remodeling, cell differentiation, and cell apoptosis were upregulated while genes associated with cell proliferation were downregulated. lncRNAs showed stage-specific expression, and more than 200 lncRNAs were differentially expressed between the undifferentiated and osteogenically differentiated PDLSCs. Using STEM, we identified 25 temporal gene expression profiles, among which 14 mRNA and eight lncRNA profiles were statistically significant. We found that genes in pattern 12 were associated with osteoblast differentiation. The expression patterns of osteogenic mRNAs (COL6A1, VCAN, RRBP1, and CREB3L1) and lncRNAs (MEG8 and MIR22HG) were consistent between the qRT-PCR and RNA-seq results. Moreover, the knockdown of MEG8 and MIR22HG significantly decreased the expression of osteogenic markers (runt-related transcription factor 2 and osteocalcin). Discussion During the osteogenic differentiation of PDLSCs, both mRNAs and lncRNAs showed stage-specific expression. lncRNAs MEG8 and MIR22HG showed a high correlation with osteoblastogenesis. Our results can be used to gain a more comprehensive understanding of the molecular events regulating osteoblast differentiation and the identification of functional lncRNAs in PDLSCs.

scholarly journals Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12091
Author(s):  
Wenyan Kang ◽  
Lingqian Du ◽  
Qianyu Liang ◽  
Rui Zhang ◽  
Chunxu Lv ◽  
...  
Keyword(s):  
Stem Cells ◽  
Osteogenic Differentiation ◽  
Signaling Pathways ◽  
Periodontal Ligament ◽  
Stromal Cell ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Gene Set Enrichment Analysis ◽  
Periodontal Ligament Stem Cells ◽  
Stromal Cell Derived Factor

Stromal cell-derived factor-1 (SDF-1) and Exendin-4 (EX-4) play beneficial roles in promoting periodontal ligament stem cells (PDLSCs) osteogenic differentiation, while the detailed mechanism has not been clarified. In this study, we aimed to evaluate the biological mechanism of SDF-1 and EX-4 alone or synergistic application in regulating PDLSCs differentiation by RNA-sequencing (RNA-seq). A total of 110, 116 and 109 differentially expressed genes (DEGs) were generated in osteogenic medium induced PDLSCs treated by SDF-1, EX-4, and SDF-1+EX-4, respectively. The DEGs in SDF-1 group were enriched in signal transduction related signaling pathways; the DEGs in EX-4 group were enriched in metabolism and biosynthesis-related pathways; and the DEGs generated in SDF-1+EX-4 group were mainly enriched in RNA polymerase II transcription, cell differentiation, chromatin organization, protein phosphorylation pathways. Based on Venn analysis, a total of 37 specific DEGs were identified in SDF-1+EX-4 group, which were mainly enriched in negative regulation of autophagy and cellular component disassembly signaling pathways. Short time-series expression miner (STEM) analysis grouped all expressed genes of PDLSCs into 49 clusters according to the dynamic expression patterns and 25 genes, including NRSN2, CHD9, TUBA1A, distributed in 10 gene clusters in SDF-1+EX-4 treated PDLSCs were significantly up-regulated compared with the SDF-1 and EX-4 alone groups. The gene set enrichment analysis indicated that SDF-1 could amplify the role of EX-4 in regulating varied signaling pathways, such as type II diabetes mellitus and insulin signaling pathways; while EX-4 could aggravate the effect of SDF-1 on PDLSCs biological roles via regulating primary immunodeficiency, tight junction signaling pathways. In summary, our study confirmed that SDF-1 and EX-4 combined application could enhance PDLSCs biological activity and promote PDLSCs osteogenic differentiation by regulating the metabolism, biosynthesis and immune-related signaling pathways.

scholarly journals Upregulating the Expression of LncRNA ANRIL Promotes Osteogenesis via the miR-7-5p/IGF-1R Axis in the Inflamed Periodontal Ligament Stem Cells

2021 ◽  
Vol 9 ◽  
Author(s):  
Minxia Bian ◽  
Yan Yu ◽  
Yuzhi Li ◽  
Zhou Zhou ◽  
Xiao Wu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Western Blot ◽  
Osteogenic Differentiation ◽  
Periodontal Ligament ◽  
Luciferase Reporter ◽  
Periodontal Ligament Stem Cells ◽  
Alizarin Red ◽  
Qrt Pcr ◽  
Non Coding Rna ◽  
Protein Expressions

BackgroundLong non-coding RNA (lncRNA) antisense non-coding RNA in the INK4 locus (ANRIL) is a base length of about 3.8 kb lncRNA, which plays an important role in several biological functions including cell proliferation, migration, and senescence. This study ascertained the role of lncRNA ANRIL in the senescence and osteogenic differentiation of inflamed periodontal ligament stem cells (iPDLSCs).MethodsHealthy periodontal ligament stem cells (hPDLSCs) and iPDLSCs were isolated from healthy/inflamed periodontal ligament tissues, respectively. The proliferation abilities were determined by CCK-8, EdU assay, and flow cytometry (FCM). The methods of Western blot assay (WB), quantitative real-time polymerase chain reaction (qRT-PCR), alizarin red staining, alkaline phosphatase (ALP) staining, ALP activity detection, and immunofluorescence staining were described to determine the biological influences of lncRNA ANRIL on iPDLSCs. Senescence-associated (SA)-β-galactosidase (gal) staining, Western blot analysis, and qRT-PCR were performed to determine cell senescence. Dual-luciferase reporter assays were conducted to confirm the binding of lncRNA ANRIL and miR-7-5-p, as well as miR-7-5p and insulin-like growth factor receptor (IGF-1R).ResultsHPDLSCs and iPDLSCs were isolated and cultured successfully. LncRNA ANRIL and IGF-1R were declined, while miR-7-5p was upregulated in iPDLSCs compared with hPDLSCs. Overexpression of ANRIL enhanced the osteogenic protein expressions of OSX, RUNX2, ALP, and knocked down the aging protein expressions of p16, p21, p53. LncRNA ANRIL could promote the committed differentiation of iPDLSCs by sponging miR-7-5p. Upregulating miR-7-5p inhibited the osteogenic differentiation of iPDLSCs. Further analysis identified IGF-1R as a direct target of miR-7-5p. The direct binding of lncRNA ANRIL and miR-7-5p, miR-7-5p and the 3′-UTR of IGF-1R were verified by dual-luciferase reporter assay. Besides, rescue experiments showed that knockdown of miR-7-5p reversed the inhibitory effect of lncRNA ANRIL deficiency on osteogenesis of iPDLSCs.ConclusionThis study disclosed that lncRNA ANRIL promotes osteogenic differentiation of iPDLSCs by regulating the miR-7-5p/IGF-1R axis.

scholarly journals Effects of Naringin on Proliferation and Osteogenic Differentiation of Human Periodontal Ligament Stem Cells In Vitro and In Vivo

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Lihua Yin ◽  
Wenxiao Cheng ◽  
Zishun Qin ◽  
Hongdou Yu ◽  
Zhanhai Yu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Osteogenic Differentiation ◽  
Periodontal Ligament ◽  
Trabecular Structure ◽  
Control Group ◽  
Periodontal Ligament Stem Cells ◽  
Expression Levels ◽  
Proliferation And Differentiation

This study is to explore the osteogenesis potential of the human periodontal ligament stem cells (hPDLSCs) induced by naringin in vitro and in vitro. The results confirmed that 1 μM naringin performs the best effect and a collection of bone-related genes (RUNX2,COL1A2, OPN, and OCN) had significantly higher expression levels compared to the control group. Furthermore, a typical trabecular structure was observed in vivo, surrounded by a large amount of osteoblasts. These results demonstrated that naringin, at a concentration of 1 μM, can efficiently promote the proliferation and differentiation of hPDLSCs both in vitro and in vivo.

scholarly journals Azithromycin Promotes the Osteogenic Differentiation of Human Periodontal Ligament Stem Cells after Stimulation with TNF-α

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Tingting Meng ◽  
Ying Zhou ◽  
Jingkun Li ◽  
Meilin Hu ◽  
Xiaomeng Li ◽  
...  
Keyword(s):  
Stem Cells ◽  
Alkaline Phosphatase ◽  
Osteogenic Differentiation ◽  
Alkaline Phosphatase Activity ◽  
Periodontal Ligament ◽  
Caspase 3 ◽  
Caspase 8 ◽  
Periodontal Ligament Stem Cells ◽  
Alizarin Red ◽  
Induced Apoptosis

Background and Objective. This study investigated the effects and underlying mechanisms of azithromycin (AZM) treatment on the osteogenic differentiation of human periodontal ligament stem cells (PDLSCs) after their stimulation with TNF-α in vitro. Methods. PDLSCs were isolated from periodontal ligaments from extracted teeth, and MTS assay was used to evaluate whether AZM and TNF-α had toxic effects on PDLSCs viability and proliferation. After stimulating PDLSCs with TNF-α and AZM, we analyzed alkaline phosphatase staining, alkaline phosphatase activity, and alizarin red staining to detect osteogenic differentiation. Real-time quantitative polymerase chain reaction (RT-qPCR) analysis was performed to detect the mRNA expression of osteogenic-related genes, including RUNX2, OCN, and BSP. Western blotting was used to measure the NF-κB signaling pathway proteins p65, phosphorylated p65, IκB-α, phosphorylated IκB-α, and β-catenin as well as the apoptosis-related proteins caspase-8 and caspase-3. Annexin V assay was used to detect PDLSCs apoptosis. Results. TNF-α stimulation of PDLSCs decreased alkaline phosphatase and alizarin red staining, alkaline phosphatase activity, and mRNA expression of RUNX2, OCN, and BSP in osteogenic-conditioned medium. AZM enhanced the osteogenic differentiation of PDLSCs that were stimulated with TNF-α. Western blot analysis showed that β-catenin, phosphorated p65, and phosphorylated IκB-α protein expression decreased in PDLSCs treated with AZM. In addition, pretreatment of PDLSCs with AZM (10 μg/ml, 20 μg/ml) prevented TNF-α-induced apoptosis by decreasing caspase-8 and caspase-3 expression. Conclusions. Our results showed that AZM promotes PDLSCs osteogenic differentiation in an inflammatory microenvironment by inhibiting the WNT and NF-κB signaling pathways and by suppressing TNF-α-induced apoptosis. This suggests that AZM has potential as a clinical therapeutic for periodontitis.

scholarly journals MicroRNA-21 regulates Osteogenic Differentiation of Periodontal Ligament Stem Cells by targeting Smad5

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Fulan Wei ◽  
Shuangyan Yang ◽  
Qingyuan Guo ◽  
Xin Zhang ◽  
Dapeng Ren ◽  
...  
Keyword(s):  
Stem Cells ◽  
Osteogenic Differentiation ◽  
Periodontal Ligament ◽  
Periodontal Ligament Stem Cells

scholarly journals Zein/gelatin/nanohydroxyapatite nanofibrous scaffolds are biocompatible and promote osteogenic differentiation of human periodontal ligament stem cells

2019 ◽  
Vol 7 (5) ◽  
pp. 1973-1983 ◽  
Author(s):  
Qianmin Ou ◽  
Yingling Miao ◽  
Fanqiao Yang ◽  
Xuefeng Lin ◽  
Li-Ming Zhang ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Stem Cells ◽  
Bone Tissue Engineering ◽  
Osteogenic Differentiation ◽  
Bone Tissue ◽  
Tissue Regeneration ◽  
Periodontal Ligament ◽  
Periodontal Ligament Stem Cells ◽  
Nanofibrous Scaffolds

In bone tissue engineering, it is important for biomaterials to promote the osteogenic differentiation of stem cells to achieve tissue regeneration.

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