Transcriptome analysis of periodontal tissue response after immediate replantation and delayed replantation
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ABSTRACT:
PROVIDER: PRJNA726416 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14368750.fastq.gz | Fastqsanger.gz | |||
| SRR14368751.fastq.gz | Fastqsanger.gz | |||
| SRR14368752.fastq.gz | Fastqsanger.gz | |||
| SRR14368753.fastq.gz | Fastqsanger.gz | |||
| SRR14368754.fastq.gz | Fastqsanger.gz |
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Project description:Objective: This study aimed to identify the transcriptome profiles from periodontal tissues of replanted teeth and evaluate the functional differences of transcriptomes between immediate replantation and delayed replantation in a rat teeth avulsion animal model. Background: In dental avulsion, the prognosis of replanted teeth is hardly favorable in delayed replantation. After tooth replantation, complex inflammatory responses occur to return homeostasis in periodontal tissue. Various types of cytokines are produced in inflammatory microenvironment and these cytokines determine the periodontal tissue responses. Methods: Maxillary first molars of Sprague–Dawley rats were extracted and exposed to dry environment, then replanted. The animals were divided into two groups according to extra–oral time: immediate replantation group (dry for 5 min) and delayed replantation (dry for 60 min). Either 3 or 7 days after replantation, the animals were sacrificed. The palatal gingival tissues were harvested for mRNA–sequencing. Hallmark gene set enrichment analysis were performed to predict the function of transcriptomes. Normalized enrichment score (NES) was generated to determine the functional differences between the groups. Results: Hallmark gene sets enriched in delayed replantation at 3 days were oxidative phosphorylation (NES=2.82, q < 0.001) and TNF–α signaling via NF–κB pathway (NES= 1.52, q=0.034). At 7 days, TNF–α signaling via NF–κB pathway (NES=–1.82, q=0.002), angiogenesis (NES=–1.66, q =0.01), and TGF–β signaling pathway (NES=–1.46, q=0.051) were negatively highlighted in delayed replantation compared to immediate replantation. Conclusions: Transcriptome profiles were significantly different between immediate replantation and delayed replantation. The responses of periodontal tissues were associated with TNF–α signaling via NF–κB pathway. However, the enrichment score of this pathway were changed with time–dependent manner between immediate replantation and delayed replantation.
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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: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 Ehlers–Danlos syndrome (pEDS) is a rare, distinct hereditary disorder characterized by early onset periodontal destruction, tissue fragility and joint hypermobility. pEDS is caused by mutant variants of C1R (and C1S) genes, which encode the C1s (and C1s) subunits of the first component of the classical complement pathway. Abberant serine protease activation will result in C4 cleavage and local complement cascade activation, as well as other possible consequences. Although multiple studies have investigated the genetic variant analysis of pEDS, the transcriptome profiles of pEDS remain unknown. To better understand the pathomechanism underlying the clinical manifestation of pEDS and to identify novel molecular targets that may expand treatment strategies, our study performed transcriptome profiling by RNA sequencing of patient-derived monocytes from 2 pEDS patients and 3 normal controls. Genes related to periodontal host defense, inflammatory response, skin disease and vascular development were significantly enriched. Furthermore, we identified genes that may be involved in the pathogenesis of periodontal destruction and pretibial pigmentation of pEDS. Overall, our study presents the first pEDS transcriptomics data, revealing distinct molecular features in monocytes of periodontal Ehlers–Danlos syndrome, and serves as a tool to better understand the disease.
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Project description:Periodontal tissue supports teeth in the alveolar bone socket via fibrous attachment of the periodontal ligament (PDL). The PDL contains many stromal cell types, including osteoblasts, cementoblasts, periodontal fibroblasts, and stem/progenitor cells. However, the characteristics and lineage hierarchy of each cell type remain poorly defined. Here we present a single-cell atlas of PDL, highlighting diverse cell populations in PDL.
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Project description:PurposeIn dental avulsion, delayed replantation usually has an uncertain prognosis. After tooth replantation, complex inflammatory responses promote a return to periodontal tissue homeostasis. Various types of cytokines are produced in the inflammatory microenvironment, and these cytokines determine the periodontal tissue response. This study aimed to identify the gene expression profiles of replanted teeth and evaluate the functional differences between immediate and delayed replantation.MethodsMaxillary molars from Sprague-Dawley rats were extracted, exposed to a dry environment, and then replanted. The animals were divided into 2 groups according to the extra-oral time: immediate replantation (dry for 5 minutes) and delayed replantation (dry for 60 minutes). Either 3 or 7 days after replantation, the animals were sacrificed. Periodontal soft tissues were harvested for mRNA sequencing. Hallmark gene set enrichment analysis was performed to predict the function of gene-gene interactions. The normalized enrichment score (NES) was calculated to determine functional differences.ResultsThe hallmark gene sets enriched in delayed replantation at 3 days were oxidative phosphorylation (NES=2.82, Q<0.001) and tumor necrosis factor-alpha (TNF-α) signaling via the nuclear factor kappa light chain enhancer of activated B cells (NF-κB) pathway (NES=1.52, Q=0.034). At 7 days after delayed replantation, TNF-α signaling via the NF-κB pathway (NES=-1.82, Q=0.002), angiogenesis (NES=-1.66, Q=0.01), and the transforming growth factor-beta signaling pathway (NES=-1.46, Q=0.051) were negatively highlighted.ConclusionsDifferentially expressed gene profiles were significantly different between immediate and delayed replantation. TNF-α signaling via the NF-κB pathway was marked during the healing process. However, the enrichment score of this pathway changed in a time-dependent manner between immediate and delayed replantation.
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