Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1170301 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30911700.fastq.gz | Fastqsanger.gz | |||
| SRR30911701.fastq.gz | Fastqsanger.gz | |||
| SRR30911702.fastq.gz | Fastqsanger.gz | |||
| SRR30911703.fastq.gz | Fastqsanger.gz | |||
| SRR30911704.fastq.gz | Fastqsanger.gz |
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Project description:The fracture hematoma that forms between the broken fragments of bone serves as a natural fibrin scaffold. However, there is no data regarding the differences between the micro-architectural and biological properties of hematomas formed in normally healing, delayed healing, and non-healing bone defects. Mimicking these three conditions in the rat femur, we demonstrate clear differences in fibrin clot morphology, which directly affect the gene expression pattern. Specifically, RNA-sequencing reveals that the expression of essential osteogenic genes in normally healing defects are significantly up-regulated, whereas in delayed and non-healing defects they are down-regulated. Surprisingly, there were no substantial differences between delayed and non-healing defects. Most importantly, this study demonstrates that the healing outcome has already been determined at the earliest stage of bone healing. These findings could be used to develop biomaterial scaffolds mimicking the micro-architectural properties of normally healing fracture hematoma as a treatment strategy for bone defects. The hypothesis of this study was that the micro-architectural properties of the initially formed hematoma has a significant effect on the regulation of the biological process at the fracture site, which ultimately determines the outcome of bone healing. Three different healing models were investigated - normally healing, delayed healing, and non-healing defects. The results demonstrated that the intrinsic micro-architectural properties of hematomas between those groups varied distinctly in terms of fiber diameter, porosity, and density of the formed fibrin network. Those differences influenced biological responses, as evidenced by a higher expression of osteogenic genes in normally healing compared to delayed and non-healing defects, and the failed activation of BMP-2 in non-healing defects. More importantly, our results demonstrate healing outcomes are already determined at the initial (hematoma) stage of bone healing.
2023-11-01 | GSE161315 | GEO
Project description:Elevated bone resorption and diminished bone formation have been recognized as the primary features of glucocorticoid-associated skeletal disorders. However, the direct effects of excess glucocorticoids on bone turnover remains unclear. Here, we explored the outcomes of exogenous glucocorticoid treatment on bone loss and delayed fracture healing in mice and found that reduced bone turnover was a dominant feature, resulting in a net loss of bone mass. We investigated the single-cell gene expression profiles of these two models. In the glucocorticoid-induced bone loss model, we sequenced the cell population digested from the bone surface. In the glucocorticoid-associated fracture healing model, we sequenced the cell population digested from the callus. Overall, the cell population on the bone surface was predominantly composed of hematopoietic cells, while only a small fraction represented the bone progenitor cells. In the fracture healing model, the callus contained a significant number of osteogenic and osteoclastic lineage cells. We primarily analyzed the gene expression of functional genes in the fracture healing model and characterized the metabolic profiles. These data provide insights into the multifactorial metabolic mechanisms by which glucocorticoids generate skeletal disorders.
2024-03-12 | GSE261072 | GEO
Project description:Background: Dicalcium cilicate (C2S) is a potent biomaterial for bone regeneration application. Circular RNA (circRNAs) plays crucial role in osteogenic differentiation of mesenchymal stem cells (MSCs) and bone defect healing. In this study, we aim to elucidate the differential expression of circ_RNAs and mRNAs in C2S-treated MSCs, the role of circ_1983 in C2S-mediated bone regeneration, and its mechanism. Methods: The effect of C2S on osteogenic differentiation of mice bone marrow-derived MSCs (BMSCs) and rat cranial bone defect healing were analyzed. Differential expression of circ-RNAs and mRNAs in C2S-treated BMSCs were profiled by RNA-sequencing. The interaction between circ_1983 and miR-6931 was confirmed by pull-down and dual luciferase reporter assays. ceRNA function of circ_1983 via sponging miR-6931 and targeting Gas7 mRNA expression in BMSCs was analyzed by miRanda (http://www.microrna.org/microrna/). Role of circ_1983 in C2S-induced osteogenic differentiation of BMSCs was analyzed by shRNA-mediated knockdown of circ_1983. Results: C2S enhanced osteogenic differentiation of BMSCs and bone defect healing. CircRNAs (total 1384) and mRNAs (total 1725) were differentially upregulated in C2S-treated BMSCs. Upregulated circRNAs and ceRNA-interaction networks were associated with osteogenesis-related signaling pathways, i.e. MAPK, PI3K-Akt. RNA-sequencing and qRT-PCR results confirmed upregulation of circ_1983 in C2S-tretaed BMSCs. Circ_1983 showed ceRNA effect by sponging miR-6931 and overexpressing Gas mRNA that enhanced Runx2 expression and promoted osteogenic differentiation of BMSCs. Knockdown of circ_1983 inhibited the C2S-induced osteogenic differentiation of BMSCs. Interpretation: C2S-induced circ_1983 upregulation in BMSCs sponges miR-6931 and targets Gas7 gene to enhance Runx2 expression thereby promotes osteogenic differentiation and bone regeneration.
2021-04-12 | GSE140273 | GEO
Project description:Approximately 10% of fractures that occur in the United States annually will not heal without intervention. This figure is rising due to an aging population and a rise in conditions that impair bone healing. Current treatments can be marginally effective, costly, and some have adverse effects. A safe and manufacturable material that mimics anabolic bone is the holy grail of bone tissue engineering, but achieving this is challenging. Adult stem cells, especially mesenchymal stem cells (MSCs), are excellent candidates for engineering bone, but the lack of reproducibility due to donor variation and culture protocols have hindered progress in this area. Herein, we describe an MSC line generated from induced pluripotent stem cells with remarkable osteogenic properties. The cells can be induced to generate large amounts of osteogenic extracellular matrix (ihMatrix) under monolayer culture conditions. When pure ihMatrix is implanted into calvarial defects in mice, it has intrinsic osteogenic activity that significantly surpasses the efficacy of bone morphogenic protein 2 resulting in complete healing of defects in 4 weeks through a mechanism of action mediated in part by collagen VI and XII. Based on these findings, we propose that ihMatrix could represent a superior replacement for the current gold standards, autograft and BMP products, used commonly in bone tissue engineering.
2020-07-02 | PXD016017 | Pride
Project description:Delayed fracture healing or the complete failure of bone tissue to heal (non-union) occurs with high incidence and in certain populations, such as the elderly or diabetics, the fracture incidence is even higher due to a reduced ability to form new osteoblasts, leading to less efficient bone regeneration. New therapies are needed to improve fracture management, but the molecular mechanisms governing bone healing and stem/progenitor cell proliferation and differentiation remain poorly understood. Leucine-rich repeat-containing G-protein coupled receptors are implicated in regenerating tissues with well-defined stem cell niches in stem cell-reliant organs. Using global Lgr6-null mice we recently demonstrated that Lgr6 is necessary for maintaining bone volume during adulthood and in fracture repair. Rspondins are the major ligands for Lgrs; Rspo-Lgr interaction increases cWnt signaling by preventing the turnover of Frizzled receptors. Intriguingly, we demonstrate that in Lgr6-null osteogenic cultures, cWnt-beta catenin signaling is not diminished. We performed RNA sequencing on bone marrow-derived osteogenic cultures from Lgr6-null mice and analyzed published single-cell RNA sequencing datasets to explore the molecular mechanisms regulating impaired osteogenesis and to identify cell-specific expression of Lgr6 in the bone environment. Our findings suggest that Lgr6 likely mediates osteogenesis through the Bmp pathway.
2024-12-31 | GSE235758 | GEO
Project description:The mechanisms of obesity and type 2 diabetes (T2D)-associated impaired fracture healing are poorly studied. In a murine model of T2D reflecting both hyperinsulinemia induced by high fat diet (HFD) and insulinopenia induced by treatment with streptozotocin (STZ), we examined bone healing in a tibia cortical bone defect. A delayed bone healing was observed during hyperinsulinemia as newly formed bone was reduced by – 28.4±7.7% and was associated with accumulation of marrow adipocytes at the defect site +124.06±38.71%, and increased density of SCA1+ (+74.99± 29.19%) but not Runx2+osteoprogenitor cells. We also observed increased in reactive oxygen species production (+101.82± 33.05%), senescence gene signature (≈106.66± 34.03%) and LAMIN B1- senescent cell density (+225.18± 43.15%), suggesting accelerated senescence phenotype. During insulinopenia, a more pronounced delayed bone healing was observed with decreased newly formed bone to -34.9± 6.2% which was inversely correlated with glucose levels (R2=0.48, p<0.004) and callus adipose tissue area (R2=0.3711, p<0.01). Finally, to investigate the relevance to human physiology, we observed that sera from obese and T2D patients exerted inhibitory effects on osteoblastic and enhanced adipocyte differentiation of human bone marrow stromal stem cells. Our data demonstrate that T2D exerts negative effects on bone healing through inhibition of osteoblast differentiation of skeletal stem cells and induction of accelerated bone senescence and that the hyperglycaemia per se and not just insulin levels is detrimental for bone healing.
2021-10-01 | GSE180504 | GEO
Project description:The regeneration of craniofacial bones of the mammalian skeleton necessitates the action of both intrinsic and extrinsic inductive factors from multiple cell types, which function in a hierarchical and temporal fashion to control the differentiation of osteogenic progenitors. Single-cell transcriptomics of developing mouse cranial suture recently identified a suture mesenchymal progenitor population with tendon- or ligament-associated gene expression profile previously uncharacterized. Here, we developed a Mohawk homeobox (MkxCG;R26RtdT) reporter mouse, finding that this teno-ligamentous gene identifies a cranial suture resident cell population within the adult mouse that gives rise to calvarial osteoblasts and osteocytes overtime during homeostatic conditions. Single cell RNA-Sequencing (scRNA-Seq) demonstrated that Mkx+ suture cells demonstrate a stem-like phenotype with expression of teno-ligamentous genes. Bone injury with Mkx+ cell ablation showed delayed bone healing. Remarkably, Mkx gene played a critical role as an osteo-inhibitory factor in cranial suture cells, as knockdown or knockout resulted in increased osteogenic differentiation. Furthermore, in vivo local deletion of Mkx in Mkx floxed mice resulted in robustly increased calvarial defect repair. Finally, we observed that mechanical stretch dynamically regulates Mkx expression in turn regulating calvarial cell osteogenesis. Overall, we identify Mkx+ cells within the suture mesenchyme as a progenitor cell population for adult craniofacial bones required for bone repair and Mkx itself as mechanical stretch responsive gene which functions to prevent osteogenic differentiation within the stem cell niche.
2024-06-13 | GSE246238 | GEO