Development of gene expression signatures for SOX2 overexpressing human dental pulp stem cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE73548 | GEO | 2015/09/30
SECONDARY ACCESSION(S): PRJNA297283
REPOSITORIES: GEO
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Project description:To evaluate the miRNA and mRNA expression profiles (miRNOME) we identified miRNAs during in vitro osteogenic differentiation of human dental pulp stem cells (DPSC). The DPSCs were cultured in the DMEM + beta-glycerol phosphate, ascorbic acid and dexamethasone for 2 dias to 21days. The microRNA or mRNA expression profiling during the differentiation process was analyzed through hybridizations with Agilent miRNA-microarray (8x15K format).
2014-11-28 | E-MTAB-3077 | biostudies-arrayexpress
Project description:Dental stem cells isolated from oral tissues have been shown to provide with high proliferation ability and multi-lineage differentiation potential. Although the dental stem cells possess the potential of nerve regeneration, the specific expression profile of dental pulp stem cells (DPSCs) and periodontal ligament stem cells (PDLSCs) are still unclear. Here, DPSCs and PDLSCs, collected from the same tooth with 3 donors, were tested for high-throughput protein profiles by combining two-dimensional gel proteomics and TMT-based proteomics.
2021-06-10 | PXD021997 | Pride
Project description:Chromatin accessibility is key epigenomic regulatory mechanisms of transcription. Herein, to profile open chromatin maps and transcriptional feature associated with odontogenic tropism of dental pulp stem cells (DPSCs), we conducted integrative analysis of epigenomic alteration and transcriptome changes during odontogenic differentiation of DPSCs. DPSCs were long-term cultured in odontogenic induction medium to evaluate differentiation abilities. ATAC-seq and RNA-seq samples were collected before and after the 9-day culture. One of the day 9 specific-super-enhancer was constructed in ALPL (Alkaline Phosphatase, Biomineralization Associated) intragenic region in which all the day 9-specific open chromatin peaks were included and BMP-mediated Smad binding element are specifically accumulated. These results suggest that the specific local chromatin regions were selectively opened and, particularly, super-enhancers were constructed, which was able to guide differentiative transcriptional factors such as Smad1/4 to their target gene loci in differentiating DPSCs; hence, epigenetic modifications such as histone deacetylase (HDACs) inhibitor application have therapeutic potential for DPSCs-induced dentin/pulp regeneration.
2023-09-29 | GSE244058 | GEO
Project description:Chromatin accessibility is key epigenomic regulatory mechanisms of transcription. Herein, to profile open chromatin maps and transcriptional feature associated with odontogenic tropism of dental pulp stem cells (DPSCs), we conducted integrative analysis of epigenomic alteration and transcriptome changes during odontogenic differentiation of DPSCs. DPSCs were long-term cultured in odontogenic induction medium to evaluate differentiation abilities. ATAC-seq and RNA-seq samples were collected before and after the 9-day culture. One of the day 9 specific-super-enhancer was constructed in ALPL (Alkaline Phosphatase, Biomineralization Associated) intragenic region in which all the day 9-specific open chromatin peaks were included and BMP-mediated Smad binding element are specifically accumulated. These results suggest that the specific local chromatin regions were selectively opened and, particularly, super-enhancers were constructed, which was able to guide differentiative transcriptional factors such as Smad1/4 to their target gene loci in differentiating DPSCs; hence, epigenetic modifications such as histone deacetylase (HDACs) inhibitor application have therapeutic potential for DPSCs-induced dentin/pulp regeneration.
2023-09-29 | GSE244057 | GEO
Project description:To evaluate the miRNA and mRNA expression profiles (miRNOME and transcriptome) we reconstructed networks identifying miRNAs and mRNA during in vitro osteogenic differentiation of human dental pulp stem cells (DPSC). The DPSCs were cultured in the DMEM + beta-glycerol phosphate, ascorbic acid and dexamethasone for 2 to 21 days. The microRNA or mRNA expression profiling during the differentiation process was analyzed through hybridizations with Agilent miRNA-microarray (8x15K format) or whole-human genome Agilent microarray (4x44K format).
2014-11-13 | E-MTAB-3010 | biostudies-arrayexpress
Project description:Lineage commitment and tumorigenesis specify adult stem cells from different tissues or organs. To gain insight into the mechanism of this programming, phenotypic, functional and transcriptome analyses were performed in mesenchymal stem cells derived from human dental pulp (DPSCs) and bone marrow (BMSCs). DPSCs and BMSCs had similar morphologies and flow cytometric profiles, and were capable of tri-lineage differentiation into osteoblast, adipocyte and chondocyte. However, compared with BMSCs, DPSCs increased in osteogenic potential, decreased in adipogenic potential, and formed dentin-pulp-like complexes in vivo. Genome-wide RNA-seq and differential expression analysis revealed that signalings such as, phosphatase and tensin homolog (PTEN)/PI3K/AKT pathway, and cancer-related pathway were different in both cells. Differential PTEN expression, higher in DPSCs than BMSCs, was responsible for the lineage commitment and tumorigenesis differences in both cells. Besides, BMSCs decreased in PTEN DNA methylation compared to DPSCs, which was mediated by increased DNA (cytosine-5) methyltransferase 3B (DNMT3B) expression. Furthermore, histone methyltransferase G9a mediated repressive epigenetic mark H3K9Me2 was selectively enriched in BMSCs. Moreover, DPSCs were more resistant to oncogenic transformation than BMSCs. To link lineage commitment with tumorigenesis, we demonstrated that DPSCs were more resistant to oncogenic transformation than BMSCs and PTEN deficiency increased the sensitivity of DPSCs for tumorigenic transformation. The results help understanding the roles of the epigenetic factors in lineage commitment and tumorigenesis and also for therapeutic uses of adult stem cells.
2019-03-17 | GSE105145 | GEO
Project description:We report screening of genes differentially expressed in cells isolated from immature and mature third molar teeth. Among them, a homeobox transcription factor, distal-less homeobox 4 (DLX4) was highly expressed in immature human dental pulp cells, and significantly enhanced iPSC colony formation in combination with OCT3/4, SOX2, and KLF4 to the level comparable with that using classical combination of Yamanaka's factors, OCT3/4, SOX2, KLF4, and c-MYC.
2014-12-25 | GSE52853 | GEO
Project description: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 proteome profiles of induced and control DPSCs. 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 analysis. Then a protein-protein interaction (PPI) network was constructed. Two selected proteins were confirmed by western blot (WB) analysis. 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 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 TMT analysis. 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.
2021-09-09 | PXD021279 | Pride
Project description:Purpose: The goals of this study are to compare differentially expressed genes in young dental pulp stem cells to the aging dental pulp stem cells and to predict key regular factors. Methods: mRNA and ncRNA profiles of young and aging dental pulp stem cells were generated by deep sequencing, using BGISEQ-500 platform (BGI-Shenzhen, China). The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Agilent Technologies 2100 system and real-time quantitative PCR (QPCR) (TaqMan Probe). Results:After filtering out adaptor-related and low-quality sequences, 669 million clean reads in mRNA Library were generated. Clean reads was mapped to genome sequence with the mapping ratio from 88.54% to 97.61%. A total of 230487 mRNAs was obtained including 123724 known mRNAs and 106763 novel mRNAs respectively; In addition, we detected 177880 lncRNAs，139743 and 38137 were known and novel. For correlation analysis, the coefficient we obtained were all greater than 0.90, indicating a high biological correlation Conclusions: Our study represents the first detailed analysis of differentially expressed genes in aging and young dental pulp stem cells, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that hsa-miR-6724-5p may be a key node in the aging process of DPSCs, and its target genes was involved in the dopaminergic synapse
2021-11-28 | GSE185751 | GEO
Project description:Gene expression analysis data of human permanent dental pulp tissues
2016-11-22 | GSE75644 | GEO