Gene expression profile at single cell level of injured enthesis at 7 day post repair operation from wild type and Nlrp3 knockout mice
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ABSTRACT:
PROVIDER: PRJNA1115526 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29150162_1.fastq.gz | Fastqsanger.gz | |||
| SRR29150162_2.fastq.gz | Fastqsanger.gz | |||
| SRR29150163_1.fastq.gz | Fastqsanger.gz | |||
| SRR29150163_2.fastq.gz | Fastqsanger.gz | |||
| SRR29150164_1.fastq.gz | Fastqsanger.gz |
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Project description:The repair of injured enthesis remains clinically challenging in sports medicine. We have proved that the activation of Nlrp3 inflammasomes suppressed enthesis regeneration. So we used single cell RNA-seq to uncover the mechanisms by which Nlrp3 inflammasomes modulate enthesis regeneration
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Project description:The repair of injured enthesis remains a challenging clinical issue in sports medicine due to dysregulated inflammation and limited regenerative capability. Nevertheless, the mechanisms through which this dysregulated inflammation deteriorates the regenerative niche of enthesis remain unclear. Here, we found that Nlrp3 inflammasomes were activated in macrophages after enthesis injury and subsequently suppressed the regeneration. Nlrp3 inflammasomes generated a proinflammatory niche through an imbalance between the pro-inflammatory factor IL-1β and anti-inflammatory factors including IL-10 and IL-13. Mechanistically, IL-1β was identified as an inhibitory inflammation signaling in proinflammatory niche, reducing the differentiation and migration of stem cells. Moreover, the P2rx7 receptors were verified as an activation signal for Nlrp3 inflammasome post-injury, and conditional knockout of P2rx7 receptors on myeloid cells promoted enthesis regeneration. Together, these results illustrate that Nlrp3 inflammasome generates a proinflammatory niche to suppress enthesis regeneration, and demonstrate that the P2rx7/Nlrp3 inflammasome axis and IL-1β are promising niche-directed regenerative therapeutic targets for enthesis injury treatment.
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Project description:The innervation of skeletal myofibers exerts a crucial influence on the maintenance of muscle tone and normal operation, but little is known concerning atrophy and its underlying mechanisms in denervated muscle to date. Here, we reported that activated NOD-like receptor protein 3 (NLRP3) inflammasome with pyroptotic cell death occurred in denervated gastrocnemius in the mouse model of sciatic denervation. This damage causes interleukin 1 beta (IL-1β) release，facilitating the ubiquitin proteasome system (UPS) activation, which was responsible for muscle proteolysis. Conversely, genetic knock-out of muscular NLRP3 inhibited the pyroptosis-associated protein expression and ameliorate muscle atrophy significantly. Meanwhile, co-treatment with shRNA-NLRP3, also remarkably attenuated NLRP3 inflammasome activator (NIA)-induced C2C12 myotube pyroptosis and atrophy. Interestingly, we also observed a correlation between NLRP3 inflammasome activation and muscular apoptosis possibly via caspase 1 mediation after denervation. This work for the first time elucidates on the roles and mechanisms of NLRP3 inflammasome in skeletal muscle atrophy during denervation and suggests the potential contribution to the pathogenesis of neuromuscular diseases.
2022-12-29 | GSE201133 | GEO
Project description:In the present study, a defect was created in the patellar enthesis of a rat model, and treatment was provided using two versions of a biphasic silk fibroin scaffold showing two different transition morphology between the phases. The study included two scaffold-treated groups, two control groups, and one native/healthy group. For the scaffold-treated groups, the defect was treated by implanting one of the two versions of the biphasic scaffolds. One scaffold showed a mixed/interconnected transition zone between the tendon and bony part of the construct (S-MT) while the transition in the other scaffold was abrupt (S-AT). Two control groups were included. In the first group, a defect was created in the patellar enthesis and the tendon was sutured back over the defect and to the bone. In the second group, a transversal cut was performed at the tendon part of the enthesis and sutured back. Samples were collected (n=8) per group at two time points (4 weeks and 12 weeks) after the surgery. Healthy (contralateral) samples were used as reference. The Qiagen Osteogenesis Pathway-focused PCR array was utilized to profile the expression of relevant osteogenic, chondrogenic, and tenogenic genes in samples from healthy, injured and treated patellar entheses samples.
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Project description:Circulating transcriptional landscapes between pre-operation and post-operation plasma samples were compared using the Arraystar Human LncRNA Microarray V4 with probes for profiling of 40173 human lncRNAs and 20730mRNAs. Goal was to investigate the impact of tumor removal on circulating lncRNA and mRNA expression levels.
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Project description:Macrophages are exquisitely capable of sensing danger-associated molecular patterns (DAMPs) and orchestrating inflammatory response during tissue injury. Nonalcoholic steatohepatitis (NASH) represents an advanced stage of metabolic fatty liver disease that increases the risk for cirrhosis and liver cancer. Pathogenic mechanisms of NASH center on hepatocyte injury and the ensuing immune response within the liver microenvironment. However, the nature of DAMPs released by injured hepatocytes and how they shape the liver immune milieu remain largely unknown. Here we show that lipid droplets (LDs) released by injured fatty hepatocytes provide a potent signal that triggers monocyte infiltration and maturation into Trem2+ macrophages, recently described as NASH-associated macrophages (NAMs) or lipid- associated macrophages. LD treatment exacerbated liver injury in mice with diet-induced NASH. We identified Membrane spanning 4-domains a7 (Ms4a7) as a NAM-specific pathogenic factor that was strongly induced in mouse and human NASH. Ms4a7 inactivation ameliorated key aspects of diet-induced NASH pathologies in mice. At the mechanistic level, Ms4a7 physically interacts with NLR family pyrin domain containing 3 (NLRP3) and is required for endosomal NLRP3 inflammasome activation. These findings illustrate a crucial role of Ms4a7 in driving pro-inflammatory signaling in NASH liver. Surprisingly, LD treatments attenuated Ms4a7 expression and NLRP3 inflammasome activation in cultured macrophages. As such, LDs serve as a DAMP signal that balances the induction of Trem2+ macrophages and NLRP3 inflammasome activation in NASH liver
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Project description:Inflammasome, activated by pathogen-derived and host-derived danger signals, constitutes a multimolecular signaling complex that serves as a platform for caspase-1 (CASP1) activation and interleukin-1beta (IL1B) maturation. The activation of NLRP3 inflammasome requires two-step signals. The first “priming” signal (Signal 1) enhances gene expression of inflammasome components. The second “activation” signal (Signal 2) promotes the assembly of inflammasome components. Deregulated activation of NLRP3 inflammasome contributes to the pathological processes of Alzheimer’s disease (AD) and multiple sclerosis (MS). However, at present, the precise mechanism regulating NLRP3 inflammasome activation and deactivation remains largely unknown. By genome-wide gene expression profiling, we studied the molecular network of NLRP3 inflammasome activation-responsive genes in a human monocyte cell line THP-1 sequentially given two-step signals. We identified the set of 83 NLRP3 inflammasome activation-responsive genes. Among them, we found the NR4A nuclear receptor family NR4A1, NR4A2, and NR4A3, the EGR family EGR1, EGR2, and EGR3, the IkappaB family NFKBIZ, NFKBID, and NFKBIA as a key group of the genes that possibly constitute a negative feedback loop for shutting down inflammation following NLRP3 inflammasome activation. By molecular network analysis, we identified a complex network of NLRP3 inflammasome activation-responsive genes involved in cellular development and death, and immune and inflammatory responses, where transcription factors AP-1, NR4A, and EGR serve as a hub. Thus, NLRP3 inflammasome activation-responsive genes constitute the molecular network composed of a set of negative feedback regulators for prompt resolution of inflammation. To load the Signal 1 (S1), THP-1 cells were incubated for 3 hours in the culture medium with or without inclusion of 0.2 microgram/ml lipopolysaccharide (LPS). To load the Signal 2 (S2), they were incubated further for 2 hours in the culture medium with inclusion of 10 microM nigericin sodium salt dissolved in ethanol or the equal v/v% concentration of ethanol (vehicle), followed by processing for microarray analysis on Human Gene 1.0 ST Array (Affymetrix).
2014-07-01 | E-GEOD-58959 | biostudies-arrayexpress
Project description:LncRNAs played a crucial role in the cell growth, development and some diseases relating to central nerve system.This study suggest that with regulating the LncRNAs expression level we might design novel therapy for spinalcord injury. In this dataset, we profiled the expression pattern of LncRNAs by microarray method after spinal cord injury (SCI). Through Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis seek LncRNAs potential function in the repair of spinal cord injury. Fifteen samples were analyzed. In these sample, we divided into five groups (sham operation, 1 day post-injured, 3 days post-injured, 1 week post-injued and 3 weeks post-injured) and each group contained three mice.After RNA extraction,RNA form mice in the same group were mixed by equal mass for the preparation of microarray.Compared with spinal cord without injury, the differential expression level of LncRNAs had a few changes at 1day post-injury, reached the peak at 1 week after SCI, and subsequently declined until 3 weeks post-injury. Genes with an FDR≤0.05 and a fold-change ≥2 were selected. Subsequently we analysis the significant differential expression genes.
2015-09-01 | E-GEOD-67515 | biostudies-arrayexpress
Project description:Bleomycin-injured alveolospheres
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