Tissue specific human fibroblast differential expression based on RNAsequencing analysis
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PROVIDER: PRJNA590132 | ENA |
REPOSITORIES: ENA
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Project description:Background:Physical forces, such as mechanical stress, are essential for tissue homeostasis and influence geneexpression of cells. In particular, the fibroblast has demonstrated sensitivity to extracellular matrices with assumedadaptation upon various mechanical loads. The purpose of this study was to compare the vocal fold fibroblastgenotype, known for its unique mechanically stressful tissue environment, with cellular counterparts at various otheranatomic locales to identify differences in functional gene expression profiles. Results:By using RNA-seq technology, we identified differentially expressed gene programs (DEseq2) among sevennormal human fibroblast primary cell lines from healthy cadavers, which included: vocal fold, trachea, lung, abdomen,scalp, upper gingiva, and soft palate. Unsupervised gene expression analysis yielded 6216 genes differentially expressedacross all anatomic sites. Hierarchical cluster analysis revealed grouping based on anatomic site origin rather thandonor, suggesting global fibroblast phenotype heterogeneity. Sex and age-related effects were negligible. Functionalenrichment analyses based on separate post-hoc 2-group comparisons revealed several functional themes within thevocal fold fibroblast related to transcription factors for signaling pathways regulating pluripotency of stem cells andextracellular matrix components such as cell signaling, migration, proliferation, and differentiation potential. Conclusions:Human fibroblasts display a phenomenon of global topographic differentiation, which is maintained inisolation via in vitro assays. Epigenetic mechanical influences on vocal fold tissue may play a role in uniquely modellingand maintaining the local environmental cellular niche during homeostasis with vocal fold fibroblasts distinctlyspecialized related to their anatomic positional and developmental origins established during embryogenesis.
2019-11-19 | GSE140523 | GEO
Project description:BackgroundPhysical forces, such as mechanical stress, are essential for tissue homeostasis and influence gene expression of cells. In particular, the fibroblast has demonstrated sensitivity to extracellular matrices with assumed adaptation upon various mechanical loads. The purpose of this study was to compare the vocal fold fibroblast genotype, known for its unique mechanically stressful tissue environment, with cellular counterparts at various other anatomic locales to identify differences in functional gene expression profiles.ResultsBy using RNA-seq technology, we identified differentially expressed gene programs (DEseq2) among seven normal human fibroblast primary cell lines from healthy cadavers, which included: vocal fold, trachea, lung, abdomen, scalp, upper gingiva, and soft palate. Unsupervised gene expression analysis yielded 6216 genes differentially expressed across all anatomic sites. Hierarchical cluster analysis revealed grouping based on anatomic site origin rather than donor, suggesting global fibroblast phenotype heterogeneity. Sex and age-related effects were negligible. Functional enrichment analyses based on separate post-hoc 2-group comparisons revealed several functional themes within the vocal fold fibroblast related to transcription factors for signaling pathways regulating pluripotency of stem cells and extracellular matrix components such as cell signaling, migration, proliferation, and differentiation potential.ConclusionsHuman fibroblasts display a phenomenon of global topographic differentiation, which is maintained in isolation via in vitro assays. Epigenetic mechanical influences on vocal fold tissue may play a role in uniquely modelling and maintaining the local environmental cellular niche during homeostasis with vocal fold fibroblasts distinctly specialized related to their anatomic positional and developmental origins established during embryogenesis.
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2013-11-12 | E-GEOD-44303 | biostudies-arrayexpress
Project description:Combinatorial knock down of LHX9, OSR1, PRRX1, TWIST2, fibroblast specific transcription factors and adipogenic induction by medium change induce transdifferentiation from fibroblast to adipocyte. Adipogenesis from meshencymal stem cell (MSC) and human preadipocyte (PreADP) were used for general reference of adipogenesis.
2013-11-12 | GSE44303 | GEO
Project description:In vitro fibroblast gene expression - tissue comparison
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Project description:Fibroblast Activation Protein (FAP) is a cell-surface transmembrane-anchored anchored dimeric protease. This unique constitutively active serine protease has both dipeptidyl aminopeptidase and endopeptidase activities, and can hydrolyse post-proline bonds. FAP expression is very low in adult organs, but is greatly up regulated by activated fibroblasts in sites of tissue remodelling, including fibrosis, atherosclerosis, arthritis and tumours. Primary mouse embryonic fibroblasts (MEF) were isolated from FAP gene knockout (GKO) embryos, immortalised and then transduced to express either enzyme active or inactive FAP. The cell secretomes were analysed using degradomic and proteomic techniques. Terminal Amine Isotopic Labelling of Substrates based degradomics identified cleavage sites in collagens, many other extracellular matrix (ECM) and associated proteins, and lysyl oxidase-like-1, CCL2, IL13, C1qT6 and CSF-1 that were confirmed in vitro. In addition, differential metabolic labelling coupled with quantitative proteomic analysis also implicated FAP in ECM-cell interactions, as well as with coagulation and wound healing associated proteins. FAP GKO plasma exhibited slower that wildtype clotting times. This study greatly enhances the understanding of the roles of FAP through a significant expansion of the substrate repertoire of this protease and identifying downstream effects of its activity that support roles in pathological processes.
2018-12-19 | PXD004754 | Pride
Project description:Transcriptional profiling of chicken embryo fibroblast (CEF) cells comparing CEF derived immortal chicken embryo fibroblast cell line (DF-1). Goal was to determine differentially expressed genes of CEF which were changed responding DF-1.
2011-05-12 | GSE29257 | GEO