Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA243056 | ENA |
REPOSITORIES: ENA
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Project description:In addition to satisfying the metabolic demands of cells, mitochondrial metabolism helps regulate immune cell function. To date, such cell-intrinsic metabolic-immunologic cross-talk has only been described operating in cells of the immune system. Here we show that epidermal cells utilize fatty acid β-oxidation to fuel their contribution to the immune response during cutaneous inflammation. By live imaging metabolic and immunological processes within intact zebrafish embryos during cutaneous inflammation, we uncover a mechanism where elevated β-oxidation-fueled mitochondria-derived reactive oxygen species within epidermal cells helps guide matrix metalloproteinase-driven leukocyte recruitment. This mechanism requires the activity of a zebrafish homolog of the mammalian mitochondrial enzyme, Immunoresponsive gene 1. This study describes the first example of metabolic reprogramming operating within a non-immune cell type to help control its contribution to the immune response. Targeting of this metabolic-immunologic interface within keratinocytes may prove useful in treating inflammatory dermatoses. In this study, Affymetrix Zebrafish Genome Arrays were used to identify zebrafish Irg1l (a homolog of mammalian IRG1) as a gene up-regulated in response to Salmonella infection. The microarray analysis compared 4 day post fertilisation (dpf) dissected larval zebrafish trunks (approximately 50) that had been injected at 2 dpf with either: (i) PBS (as a negative control) or (ii) live Salmonella enterica serovar Typhimurium bacteria. The study was performed in triplicate.
2014-04-01 | E-GEOD-56365 | biostudies-arrayexpress
Project description:In addition to satisfying the metabolic demands of cells, mitochondrial metabolism helps regulate immune cell function. To date, such cell-intrinsic metabolic-immunologic cross-talk has only been described operating in cells of the immune system. Here we show that epidermal cells utilize fatty acid β-oxidation to fuel their contribution to the immune response during cutaneous inflammation. By live imaging metabolic and immunological processes within intact zebrafish embryos during cutaneous inflammation, we uncover a mechanism where elevated β-oxidation-fueled mitochondria-derived reactive oxygen species within epidermal cells helps guide matrix metalloproteinase-driven leukocyte recruitment. This mechanism requires the activity of a zebrafish homolog of the mammalian mitochondrial enzyme, Immunoresponsive gene 1. This study describes the first example of metabolic reprogramming operating within a non-immune cell type to help control its contribution to the immune response. Targeting of this metabolic-immunologic interface within keratinocytes may prove useful in treating inflammatory dermatoses. In this study, Affymetrix Zebrafish Genome Arrays were used to identify zebrafish Irg1l (a homolog of mammalian IRG1) as a gene up-regulated in response to Salmonella infection.
2014-04-01 | GSE56365 | GEO
Project description:The goal of this study is to compare transcriptome profilings of liver from Mettl3 flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice. Gene ontology analysis showed that the dowregulated genes were associated with monocarboxylic acid metabolic process, small molecule catabolic process, fatty acid metabolic process, cofactor metabolic process, organic acid catabolic process, and lipid biosynthetic process, whereas the upregulated genes were associated with leukocyte migration, cell chemotaxis, leukocyte cell-cell adhesion, positive regulation of cytokine production and defense response to other organism. KEGG pathway analysis showed that the downregulated genes were associated with Steroid hormone biosynthesis, Peroxisome, Chemical carcinogenesis, proteasome, Oxidative phosphorylation and Non-alcoholic fatty liver disease (NAFLD), whereas the upregulated genes were associated with Cell adhesion molecules (CAMs), Staphylococcus aureus infection, Viral protein interaction with cytokine and cytokine receptor, and Chemokine signaling pathway.
2023-03-12 | GSE214371 | GEO
Project description:Matrix metalloproteinase-9 in chronic lymphocytic leukemia
| PRJNA312827 | ENA
Project description:Epidermal function is maintained through a continuous process called epidermal homeostasis, in which keratinocytes gradually differentiate from proliferating stem cells to dead corneocytes that shed off the skin. We investigated the metabolic rewiring that occur during keratinocyte differentiation. We analyzed endometabolome, exometabolome and transcriptome during differentiating in vitro under high calcium conditions. Using network-based computational approaches, we found that proliferating keratinocytes gain energy through branched-chain amino acid-fueled TCA cycle that is shut down during differentiation. Upon differentiation, metabolism is repurposed to serve two main purposes. First, to form the epidermal barrier. Specifically, glucose and nucleotides are utilized for the formation of the lipid-enriched hydrophobic extracellular matrix, the transformation from keratinocytes to corneocytes and their cross-linking. Second, we found active regulation of metabolites with signaling functions during differentiation including hydrocortisone, sphingosines, and exonucleotides. Functional relevance of these findings was tested experimentally by 14 metabolic perturbations that were inferred by our analysis, and effectively affected keratinocytes differentiation and proliferation. Overall, this work provides an integrated and mechanistic analysis of the metabolic underpinnings that sustain epidermal function.
2020-01-01 | GSE136375 | GEO
Project description:Mouse hair follicles undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by hair follicle stem cells (HFSCs). We used RNA-seq to identify SOX9-dependent transcriptional changes and ChIP-seq to identify SOX9-bound genes in HF-SCs. Telogen quiescent hair follicle stem cells (HFSCs) and intefollicular epidermal cells (IFE) were FACS-purified for ChIP-sequcencing and HFSCs for RNA-Sequencing
2014-01-28 | E-GEOD-54424 | biostudies-arrayexpress
Project description:In order to investigate the underlying molecular mechanism of Yki-regulated tracheal progenitor migration and proliferation, genomic chromatin immunoprecipitation (ChIP-seq) was performed to identify loci bound by Yki in trachea.The peaks we observed included multiple Yki binding sites in the promoter and intronic regions of expanded (ex) and Diap1, which are well-characterized direct target genes of Yki. Other Yki targets are regulators in cell migration, cell cycle, and cell adhesion, and include hnt, which is a regulator of cell cycle in follicle cells.Yki occupancy was also pronounced in the promoter region of two heparan sulfate proteoglycans (HSPGs), Dally and Dally-like protein (Dlp) , which together with Ex and Diap1 belong to the cell migration GO cluster. Significant ChIP-seq peaks were observed in the region of N-cadherin (Ncad), a cell adhesion molecule that promotes cell migration and Matrix metalloproteinase-1 (MMP-1), a component of the extracellular matrix. Together, these results suggest that Yki activates various targets that function in cell cycle, cell migration and cell adhesion.
2022-04-22 | GSE184856 | GEO
Project description:Tumors and tumor surrounding tissues produce multiple growth factors that influence tumor cell behavior via different signal transduction pathways. Growth factors like transforming growth factor beta (TGFβ) and epidermal growth factor (EGF) were shown to induce proliferation, migration and invasion in different cell models. Both factors are frequently overexpressed in cancer and will often act in combination. Although both factors are being used as rational targets in clinical oncology, similarities and differences of their contributions to cancer cell migration and invasion are not fully understood. Here we compared the impact of TGFβ, EGF and the combination of both factors on A549 cells. Both factors stimulated A549 migration to a similar extent but with a different kinetic and the combination had an additive effect. While EGF-induced migration depended on activation of the mitogen-activated protein kinase (MAPK) pathway, this pathway was dispensable for TGFβ-induced migration despite a strong activation by TGFβ. Proteome analysis revealed an overlap in expression patterns of migration-related proteins and associated gene ontology (GO) terms by TGFβ and EGF but only TGFβ induced the expression of epithelial to mesenchymal transition (EMT)-related proteins like matrix metalloproteinase 2 (MMP2). EGF in contrast, made no major contribution to EMT marker expression on either the protein or the transcript level. In line with these expression patterns, EGF was unable to increase invasion of A549 cells on its own and failed to enhance TGFβ-induced invasion. Overall, these data suggest that TGFβ and EGF may partly compensate each other for stimulation of cell migration but abrogation of TGFβ signaling may be more suitable for antagonizing invasion.
2021-04-08 | PXD023024 | Pride
Project description:Bacterial profiling of Arabidopsis Matrix Metalloproteinase-5 mutant during drought
| PRJNA658104 | ENA
Project description:In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. Absence or deregulation of RICs leads to excessive extracellular matrix deposition and regeneration defects.
2023-11-30 | GSE245318 | GEO