MiRNA Nanostring Data on a Silk Scaffold model following CCI injury
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PROVIDER: PRJNA1176137 | ENA |
REPOSITORIES: ENA
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Project description:This study investigates the effects of controlled cortical impact (CCI), a form of traumatic brain injury (TBI), using a 3D silk scaffold cell culture model. Human induced neural stem cells (iNSCs), human induced astrocytes, and HMC3 microglial cells were seeded onto the silk scaffolds and allowed to grow under controlled conditions. A subset of these cell cultures was then subjected to CCI to simulate injury. The primary aim of the study was to assess the cellular and molecular response to CCI, particularly focusing on miRNA expression profiles. miRNA Nanostring technology was employed to quantify differential expression patterns associated with CCI exposure, providing insights into neuroinflammatory, regenerative, and apoptotic pathways impacted by the injury. These data contribute to a better understanding of miRNA's role as a biomarker for TBI and its potential involvement in cellular recovery and neuroprotection processes following traumatic injury.
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Project description:Human pluripotent stem cells (hPSCs) are intrinsically able to self-organize into cerebral organoids that mimic features of developing human brain tissue. These three-dimensional (3D) structures provide a unique opportunity to generate cytoarchitecture and cell-cell interactions reminiscent of human brain complexity in a dish. However, current in vitro brain organoid methodologies often result in intra-organoid variability, limiting their use in recapitulating later developmental stages as well as in disease modeling and drug discovery. In addition, cell stress and hypoxia resulting from long-term culture lead to incomplete maturation and cell death within the inner core. Here, we used a recombinant silk microfiber network as a scaffold to drive human PSCs to self-arrange into engineered cerebral organoids. Silk scaffolding promoted neuroectoderm formation and reduced heterogeneity of cellular organization within individual organoids. Bulk and single cell transcriptomics confirmed that silk cerebral organoids display more homogeneous and functionally mature neuronal properties than organoids grown in the absence of silk fibers. Furthermore, oxygen sensing analysis showed that silk scaffolds create more favorable growth and differentiation conditions by facilitating the delivery of oxygen and nutrients. Silk-engineering platform appears to reduce intra-organoid variability and enhances functional maturation during spontaneous self-patterning in human brain organoid differentiation.
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Project description:Human pluripotent stem cells (hPSCs) are intrinsically able to self-organize into cerebral organoids that mimic features of developing human brain tissue. These three-dimensional (3D) structures provide a unique opportunity to generate cytoarchitecture and cell-cell interactions reminiscent of human brain complexity in a dish. However, current in vitro brain organoid methodologies often result in intra-organoid variability, limiting their use in recapitulating later developmental stages as well as in disease modeling and drug discovery. In addition, cell stress and hypoxia resulting from long-term culture lead to incomplete maturation and cell death within the inner core. Here, we used a recombinant silk microfiber network as a scaffold to drive human PSCs to self-arrange into engineered cerebral organoids. Silk scaffolding promoted neuroectoderm formation and reduced heterogeneity of cellular organization within individual organoids. Bulk and single cell transcriptomics confirmed that silk cerebral organoids display more homogeneous and functionally mature neuronal properties than organoids grown in the absence of silk fibers. Furthermore, oxygen sensing analysis showed that silk scaffolds create more favorable growth and differentiation conditions by facilitating the delivery of oxygen and nutrients. Silk-engineering platform appears to reduce intra-organoid variability and enhances functional maturation during spontaneous self-patterning in human brain organoid differentiation.
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Project description:Gene expression profiling of human glioma cell line LN-308. Cells were treated with the mTOR inhibitor CCI-779 or irradiated with a single dose of 4 Gy or a combination of both. The objective of this studywas to evaluate CCI-779 as a radio-sensitizing agent and to elucidate the underlying mechanisms. Irradiated, CCI-779-, DMSO- (vehicle control) or combination treated LN-308 samples were hybridized against pooled untreated LN-308 samples as reference (CCI+Irradiation vs. Ref; CCI vs. Ref; DMSO+Irradiation vs Ref; DMSO vs. Ref).Three independent replicates were generated for each treatment and control, respectively.
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Project description:Bi-layer silk fibroin (BLSF) scaffolds represent an emerging technology in the development of acellular biomaterials for esophageal repair. Their therapeutic potential is attributed to their robust mechanical properties, elasticity, and low immunogenicity. However, the underlying molecular mechanisms of scaffold-mediated wound healing processes in the esophagus remain unclear. Previous research has identified signaling cascades involved in neoepithelial regeneration in a rat model of onlay esophagoplasty with BLSF grafts, including c-MET, TrkA, and PI3K-Akt signaling. Interestingly, these pro-survival signaling cascades are largely governed by DNA methylation (DNAme). Such findings motivate us to apply reduced-representation bisulfite sequencing (RRBS) to characterize the temporal dynamics of DNAme in host and regenerated tissues up to 1 week post-operation. Globally, we observe hypermethylation at post-surgical repair timepoints and an inverse correlation between DNAme and the expression levels of differentially expressed proteins during regeneration. Site-specific hypomethylation targets genes associated with immune activation, which may be indicative of immune cell infiltration at the surgical implant site, while site-specific hypermethylation appears to target PI3K-Akt signaling. Our work provides mechanistic insight into the molecular processes governing esophageal regeneration, which can motivate therapeutic innovations toward temporal modulation of tissue regeneration during scaffold-mediated esophageal repair via epigenetic regulators that target key pathways.
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Project description:Clinical Pharmacogenomics study. Renal Cell Carcinoma subjects were treated with CCI-779 and peripheral blood mononuclear cells were profiled over time of treatment. Population pharmacokinetics of CCI-779: Correlations to safety and pharmacogenomics responses in patients with advanced renal cancer. Clin Pharm Therapeutics Dec 2004 Keywords: other
2004-12-01 | GSE1982 | GEO
Project description:Spider silk proteins are synthesized in the silk-producing glands, where the spidroins are produced, stored and processed into a solid fiber from a crystalline liquid solution. Despite great interest in the spider silk properties, that make this material suitable for biomedical and biotechnological applications, the mechanism of formation and spinning of the silk fibers has not been fully elucidated; and no combination of proteomic and transcriptomic study has been carried out so far in the spider silk-producing glands. Nephila clavipes is an attractive orb-web spider to investigate the spinning process of silk production, given the properties of strength, elasticity and biocompatibility of their silk fibers. Thus, considering that the combination of proteomic and transcriptomic analysis may reveal an extensive repertoire of novel proteins involved in the silk spinning process, and in order to facilitate and enable proteomics in this non-model organism, the current study aims to construct a high quality reference mRNA-derived protein database that could be used to identify tissue specific expression patterns in spider silk glands. Next-generation sequencing has offered a powerful and cost-efficient technique for the generation of transcriptomic datasets in non-model species using diverse platforms such as the Illumina HiSeq, Roche 454, Pacific Biosystems, and Applied Biosystems SOLiD; In the current study, the Illumina HiSeq 2000 platform will be used to generate a N. clavipes spider silk glands transcriptome-based protein database. The transcriptome data generated in this study will provide a comprehensive and valuable genomic resource for future research of the group of spider silk-producing glands, in order to improve our understanding of the overall mechanism of action involved in production, secretion, storage, transport, protection and conformational changes of spidroins during the spinning process, and prey capture; and the results may be relevant for scientists in material Science, biology, biochemistry, and environmental scientists.
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Project description:To investigate the role of DNA methylation in modulating chronic neuropathic pain (NPP), and identify possible target genes of DNA methylation involved in this process. The chronic constriction injury (CCI) induced NPP model was used. The Arraystar Rat RefSeq Promoter Arrays were used to identify the methylation profiles at the genome-wide level in the DNA promoter regions of the lumbar spinal cord in rats 14 Days following CCI surgery. The underlying genes with differential methylation were then identified and submitted to Gene Ontology and pathway analysis. Methyl-DNA immunoprecipitation quantitative PCR (MeDIP-qPCR) and quantitative reverse transcription-PCR (RT‒qPCR) were used to confirm gene methylation and expression.
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