Gene expression data for keratinocyte grown on different substrates
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE272016 | GEO | 2025/09/11
REPOSITORIES: GEO
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Project description:Purpose: To identify the cellular processes upregulated in fibroblasts after treatment with selected protein(s) or E16.5 skin extract Methods: To explore the mechanism of extract-induced HF neogenesis, adult dermal fibroblasts were cultured in the presence of E16.5 extract or selected protein(s) for 3 days before being tested. Results: we determined how the exposure of adult fibroblasts to E16.5 extract, the selected protein mix or each of the selected proteins and compared the resultant transcriptomes with those of adult DP and embryonic dermal fibroblasts. Conclusions: Gene expression of adult fibroblasts exposed to E16.5 extract and selected proteins mix, the key DP signature genes became upregulated.
2016-08-10 | GSE85303 | GEO
Project description:Purpose: To identify the cellular processes upregulated in fibroblasts after treatment with selected protein(s) or E16.5 skin extract Methods: To explore the mechanism of extract-induced HF neogenesis, adult dermal fibroblasts were cultured in the presence of E16.5 extract or selected protein(s) for 3 days before being tested. Results: we determined how the exposure of adult fibroblasts to E16.5 extract, the selected protein mix or each of the selected proteins and compared the resultant transcriptomes with those of adult DP and embryonic dermal fibroblasts. Conclusions: Gene expression of adult fibroblasts exposed to E16.5 extract and selected proteins mix, the key DP signature genes became upregulated. Fibroblasts mRNA profiles of mouse with different treatments and adult DP and embryonic dermal fibroblasts were generated by next generation sequencing. SRA study accession: SRP081009; BioProject accession: PRJNA337890
2016-08-10 | E-GEOD-85303 | biostudies-arrayexpress
Project description:The current study was to determine the effects of Fibroblast Growth Factor 2 (FGF2) on the transcriptome of adult human dermal fibroblasts. Transcriptional profiles of adult human dermal fibroblasts grown in culture medium (with FGF2 or not) were compared. Comparison of the transcriptomes will allow to identify significantly differentially expressed genes exposure to FGF2, which in turn will allow for identification of the pathways affected by these factors in the human adult fibroblasts. Methods: Human dermal fibroblasts were FGF2 (10ng/ML) treatment for 48h hours. Then, the RNA was extracted for library construction Results: FGF2-responsive genes were significantly involved in ECM-receptor interaction, PI3K-Akt signaling and Hippo pathway.
2020-12-22 | GSE157071 | GEO
Project description:Re-activating quiescent adult epicardium represents a potential therapeutic approach for human cardiac regeneration. However, the exact molecular differences between inactive adult and active foetal epicardium are not known. Here, we combined foetal and adult human hearts for the first time using single-cell and single-nuclei RNA sequencing, and compared epicardial cells from both stages. We found a migratory fibroblast-like epicardial population only in the foetal heart and foetal epicardium expressed angiogenic gene programs, while the adult epicardium was solely mesothelial and immune-responsive. Furthermore, we predicted that adult hearts may still receive foetal epicardial paracrine communication, including WNT-signalling with endocardium, reinforcing the validity of regenerative strategies that administer or reactivate epicardial cells in situ. Finally, we explained graft efficacy of our human embryonic stem-cell derived epicardium model, by noting its similarity to human foetal epicardium. Overall, our study defines epicardial programs of regenerative angiogenesis absent in adult hearts, contextualises animal studies, and defines epicardial states required for effective human heart regeneration.
2022-10-31 | GSE216019 | GEO
Project description:This study is associated with the GEO accession GSE216019. Abstract from article: Re-activating quiescent adult epicardium represents a potential therapeutic approach for human cardiac regeneration. However, the exact molecular differences between inactive adult and active foetal epicardium are not known. Here, we combined foetal and adult human hearts for the first time using single-cell and single-nuclei RNA sequencing, and compared epicardial cells from both stages. We found a migratory fibroblast-like epicardial population only in the foetal heart and foetal epicardium expressed angiogenic gene programs, while the adult epicardium was solely mesothelial and immune-responsive. Furthermore, we predicted that adult hearts may still receive foetal epicardial paracrine communication, including WNT-signalling with endocardium, reinforcing the validity of regenerative strategies that administer or reactivate epicardial cells in situ. Finally, we explained graft efficacy of our human embryonic stem-cell derived epicardium model, by noting its similarity to human foetal epicardium. Overall, our study defines epicardial programs of regenerative angiogenesis absent in adult hearts, contextualises animal studies, and defines epicardial endpoints required for effective human heart regeneration.
2022-10-31 | GSE216177 | GEO
Project description:Haematopoietic stem and progenitor cells (HSPCs) in the foetus and adult possess distinct molecular landscapes that regulate cell fate and change their susceptibility to initiation and progression of haematopoietic malignancies. The proteomic programs that govern these differences remain elusive. In this study, we have utilized a mass spectrometry-based quantitative proteomics approach to comprehensively describe and compare the proteome of foetal and adult HSPCs. We found that the proteome of foetal HSPCs is relatively simple, characterized by proteins involved in cell cycle and cell proliferation, while their adult counterparts are defined by a larger set of proteins that are involved in more diverse cellular processes. These adult characteristics include an arsenal of proteins important for viral and bacterial defence, as well as protection against ROS-induced protein oxidation. Our further analyses of Type I interferon signalling shows that foetal HSPCs are sensitive to Interferon a (IFNa), which impairs their production of mature lymphoid cells, whereas stimulation with IFNa to the pregnant mother enhances the production of early progenitors from foetal HSCs. Our results provide new and important insights into the molecular landscape of foetal and adult haematopoiesis that advance our understanding of normal and malignant haematopoiesis during foetal and adult life.
2017-12-12 | PXD006876 | Pride
Project description:Aberrant production of extracellular matrix (ECM) from dermal fibroblasts drives fibrotic skin diseases, which significantly affect the quality of patients’ lives. Current treatment options for skin fibrosis remain limited or ineffective; therefore, new antifibrotic strategies are urgently needed. Gaining insights into molecular control of ECM production could lead to the identification of new therapeutic targets. Recent studies suggest Zinc Finger 469 (ZNF469) as a positive regulator for ECM production; however, its role in skin fibrosis has not been investigated. In this study, we found that knockdown of ZNF469 impaired proliferation, migration, and contraction in human dermal fibroblasts. More importantly, depletion of ZNF469 significantly caused a reduction in collagen production. RNA-sequence analysis of ZNF469-knockdown cells revealed significant suppression of several ECM genes and genes involved in the process of collagen biosynthesis, suggesting ZNF469 as a key regulator of ECM production. To find the clinical relevance, we examined expression of ZNF469 by reanalyzing public bulk and single-cell RNA-sequence data sets of hypertrophic scars and keloids as a representation of skin fibrosis. The RNA sequence of bulk tissues showed that hypertrophic scar and keloid tissues had higher levels of ZNF469 and that ZNF469 and ECM genes were positively correlated. Single-cell RNA sequence of keloid scars revealed restricted expression of ZNF469 in the fibroblast population. Further analysis of fibroblast subpopulations showed specific expression of ZNF469 in mesenchymal fibroblasts, a subpopulation that has been demonstrated to be crucial for collagen overexpression in keloids. Psuedotime analysis indicated ZNF469 as a pioneering factor to establish the mesenchymal fibroblast subpopulation. Supporting this finding, we observed downregulation of various mesenchymal fibroblast markers from our RNA sequence results of ZNF469-depleted dermal fibroblasts, suggesting ZNF469 as a crucial factor for maintaining mesenchymal phenotypes. Finally, to explore the therapeutic potential of ZNF469, we silenced it in human keloid fibroblasts and demonstrated that its depletion reduced proliferation, migration, contraction, and collagen production. Moreover, expression of key mesenchymal fibroblast markers was significantly downregulated in ZNF469-knockdown keloid fibroblasts. Together, we illustrated that ZNF469 promoted the ECM production in dermal fibroblasts and could serve as a novel target for treating skin fibrosis.
2025-11-13 | GSE290035 | GEO
Project description:Adult human dermal fibroblasts reside in vivo under low oxygen tension. Thus, low oxygen culture conditions represent a physiological state for adult human dermal fibroblasts. We have also previously shown that low oxygen and addition of basic fibroblast growth factor (FGF2) lead to prolonged life-span of adult human dermal fibroblasts. Therefore, we set to determine effects of low oxygen and FGF2 on the gene expression signature of adult human dermal fibroblasts. This global analysis will allow identification of genes affected and pathways regulated by low oxygen and FGF2.
2016-12-21 | GSE60580 | GEO
Project description:Idiopathic pulmonary fibrosis (IPF) is a fatal fibrotic lung disease characterized by impaired fibroblast clearance, accumulation, and excessive extracellular matrix (ECM) protein production. Wilms' Tumor 1 (WT1), a transcription factor, is selectively upregulated in IPF fibroblasts. However, the mechanisms by which WT1 contributes to fibroblast accumulation and ECM production remain unknown. Here, we investigated the heterogeneity of WT1-expressing fibroblasts using single-nucleus RNA sequencing on the distal lung tissues of IPF patients and healthy controls. WT1 was selectively upregulated in a subset of IPF fibroblasts that co-expressed several pro-survival genes. Both the loss-of-function and gain-of-function studies support the idea that WT1 functions as a positive regulator of multiple pro-survival genes to impair apoptotic clearance and promote ECM production. In support, fibroblast-specific overexpression of WT1 augmented fibroproliferation, myofibroblast accumulation, and ECM production during bleomycin-induced pulmonary fibrosis in both young and old mice. Together, these findings identify WT1 as a potential therapeutic target to attenuate fibroblast expansion, and ECM production in the distal areas of fibrosing lungs.
2025-05-27 | GSE279404 | GEO
Project description:Skin aging is a physiological problem that remains a concern. Studies have demonstrated that the dermal extracellular matrix (ECM) plays important roles in skin aging; however, changes in ECM characteristics and molecules that are secreted to the extracellular space and involved in the formation of dermal matrix from birth to aging remain unclear. Furthermore, it is not understood how the ECM microenvironment supports the functions of skin development across different age groups. We used a decellularization method and matrisome analysis to compare the composition, expression, and function of the dermal ECM in neonate, teenage, adult, and elderly skin. We found that the collagens, glycoproteins, proteoglycans, and regulatory factors that support skin development and function together with these core ECM proteins were differentially expressed at different ages. We also identified ECM expression markers during the process of skin development. Our results systematically revealed the characteristics of ECM synthesis, response to growth factors, water conservation, anti-oxidation, and the ability of the ECM to support epidermal stem cell growth via the basement membrane in young skin, as well as the characteristics of response to wound repair and fungal invasion in aging skin.
2022-11-28 | PXD016440 |