Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA361395 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5178060_1.fastq.gz | Fastqsanger.gz | |||
| SRR5178060_2.fastq.gz | Fastqsanger.gz | |||
| SRR5178061_1.fastq.gz | Fastqsanger.gz | |||
| SRR5178061_2.fastq.gz | Fastqsanger.gz | |||
| SRR5178062_1.fastq.gz | Fastqsanger.gz |
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Project description:Periodontitis can impair the osteogenic differentiation of human periodontal mesenchymal stem cells, but the underlying molecular mechanisms are still poorly understood. Long noncoding RNAs (lncRNAs) have been demonstrated to play significant roles under both physiologic and pathological conditions. We performed comprehensive lncRNAs profiling by lncRNA microarray to identify differentially expressed long noncoding RNA expression between Periodontal ligament stem cells from healthy Periodontal tissue and periodontal ligament stem cells from inflammatory periodontal tissue. Our analysis identified 233 lncRNAs and 423 mRNAs that were differently expressed (fold change >2.0, p-value < 0.05) between the two groups of cells. The GO analysis revealed that the significantly down-regulated biological processes included multicellular organismal process, developmental process and multicellular organismal development and the significantly up-regulated biological processes included cellular process, biological regulation and response to stimulus in periodontal ligament stem cells from inflammatory periodontal tissue. The Pathway analysis revealed that the differentially expressed mRNAs may involved in Focal adhesion, ECM-receptor interaction, Bacterial invasion of epithelial cells, Long-term depression, Circadian entrainment and HIF-1 signaling pathway. Two-condition experiment, periodontal ligament stem cells from healthy periodontal tissue (hPDLSCs) vs. periodontal ligament stem cells from inflammatory periodontal tissue (pPDLSCs), Biological replicates: 3 control replicates (hPDLSCs), 3 testing replicates (pPDLSCs).
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Project description:To explore the lncRNA landscape of periodontal ligament stem cells (PDLSCs) subjected to compressive force.
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Project description:Periodontitis can impair the osteogenic differentiation of human periodontal mesenchymal stem cells, but the underlying molecular mechanisms are still poorly understood. Long noncoding RNAs (lncRNAs) have been demonstrated to play significant roles under both physiologic and pathological conditions. We performed comprehensive lncRNAs profiling by lncRNA microarray to identify differentially expressed long noncoding RNA expression between Periodontal ligament stem cells from healthy Periodontal tissue and periodontal ligament stem cells from inflammatory periodontal tissue. Our analysis identified 233 lncRNAs and 423 mRNAs that were differently expressed (fold change >2.0, p-value < 0.05) between the two groups of cells. The GO analysis revealed that the significantly down-regulated biological processes included multicellular organismal process, developmental process and multicellular organismal development and the significantly up-regulated biological processes included cellular process, biological regulation and response to stimulus in periodontal ligament stem cells from inflammatory periodontal tissue. The Pathway analysis revealed that the differentially expressed mRNAs may involved in Focal adhesion, ECM-receptor interaction, Bacterial invasion of epithelial cells, Long-term depression, Circadian entrainment and HIF-1 signaling pathway.
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Project description:Periodontal disease is a chronic inflammatory condition that destroys tooth-supporting tissues, particularly alveolar bone and the periodontal ligament, and effective regenerative therapies remain limited. While the role of metabolic-epigenomic crosstalk in determining cell fate is well established, the specific mechanism by which a tricarboxylic acid (TCA) cycle metabolite can modulate chromatin regulation to promote periodontal regeneration remains to be elucidated. The impact of one TCA-cycle metabolite, alpha-ketoglutarate (α-KG), was examined in human periodontal ligament fibroblasts cultured under osteogenic induction and profiled by ALP assays, RT-qPCR, analyses of multiple histone modifications, ATAC-seq, and RNA-seq. α-KG increased ALP activity and up-regulated genes associated with osteogenesis and the extracellular matrix (ECM). ATAC-seq revealed minimal genome-wide accessibility changes, whereas histone analyses showed reduced H3K27me3, consistent with an epigenetic mechanism that does not require extensive chromatin opening. The RNA-seq identified α-KG-induced 14 genes upregulated, including multiple components of the OGN-OMD-PLAP1/ASPN-ECM2 locus, supporting an osteogenic/ECM transcriptional program. In a mouse periodontal regeneration model, oral administration of α-KG enhanced alveolar bone regeneration and reduced H3K27me3 signals and collagen-rich tissue organization within the periodontal ligament space. These findings identify α-KG as a metabolite-driven epigenetic modulator that alleviates H3K27me3-mediated repression and supports periodontal regeneration.
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Project description:Periodontal disease is a chronic inflammatory condition that destroys tooth-supporting tissues, particularly alveolar bone and the periodontal ligament, and effective regenerative therapies remain limited. While the role of metabolic-epigenomic crosstalk in determining cell fate is well established, the specific mechanism by which a tricarboxylic acid (TCA) cycle metabolite can modulate chromatin regulation to promote periodontal regeneration remains to be elucidated. The impact of one TCA-cycle metabolite, alpha-ketoglutarate (α-KG), was examined in human periodontal ligament fibroblasts cultured under osteogenic induction and profiled by ALP assays, RT-qPCR, analyses of multiple histone modifications, ATAC-seq, and RNA-seq. α-KG increased ALP activity and up-regulated genes associated with osteogenesis and the extracellular matrix (ECM). ATAC-seq revealed minimal genome-wide accessibility changes, whereas histone analyses showed reduced H3K27me3, consistent with an epigenetic mechanism that does not require extensive chromatin opening. The RNA-seq identified α-KG-induced 14 genes upregulated, including multiple components of the OGN-OMD-PLAP1/ASPN-ECM2 locus, supporting an osteogenic/ECM transcriptional program. In a mouse periodontal regeneration model, oral administration of α-KG enhanced alveolar bone regeneration and reduced H3K27me3 signals and collagen-rich tissue organization within the periodontal ligament space. These findings identify α-KG as a metabolite-driven epigenetic modulator that alleviates H3K27me3-mediated repression and supports periodontal regeneration.
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Project description:The pre-occlusal eruption brings the rat molars into functional occlusion, which implicates tensional strains during mastication. We hypothesized that upon establishment of occlusion, the periodontal ligament undergoes cell and extracellular matrix maturation to adopt to this mechanical function. We thus aimed to characterize the protein content and changes in expression levels of tensionally relevant extracellular matrix components in the periodontal ligament between the eruption and newly established occlusion in rat molars. Twelve Wistar male rats were divided into 3 groups based on eruption and occlusal stages: covering the pre-occlusal stages at time of eruption, the first day of occlusion and 1 week after occlusion. We employed laser capture microdissection to obtain samples of the periodontal ligament at three regions, cervical, apical and subapical. The proteome was screened with Tandem Mass Tag 10-plexTM mass spectrometry and the expression of key proteins were confirmed by immunofluorescence. Differential expression of matrisome proteins was seen in the cervical and the apical region. Downregulation of pro-metabolic proteins, such as apolipoproteins implicated in lipid transport was observed. Alpha-fetoprotein, a stem cell marker, was also downregulated indicating cell differentiation and PDL maturation. Upregulated proteins were components of the extracellular matrix, involving several proteoglycans and glycoproteins and the matrisome was thus further analyzed. Periostin appeared around collagen α-1 (III) fibers and its expression was particularly strong on Sharpey’s fibers. This co-localization coincided with organization of collagen fibers in direction of the occlusal forces. Establishment of occlusion coincides with cellular differentiation and the maturation of the extracellular matrix of the periodontal ligament, as seen by downregulation of the stem cell marker Alpha-fetoprotein and apolipoproteins, and the progressive accumulation of collagen type III fibers, proteoglycans, glycoproteins. The increase in collagen fiber associates periostin may reflect a physiological response to enforce cell-ECM contacts during PDL maturation.
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