Molecular Mapping of Keratinocyte Differentiation by Functional Gene Expression Profiling
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE26688 | GEO | 2013/12/15
SECONDARY ACCESSION(S): PRJNA136595
REPOSITORIES: GEO
Similar Datasets
Project description:Our goal was to establish a robust and reliable platform for the mapping of gene expression changes occurring during the process of keratinocyte differentiation. We hypothesized that a functional gene expression profiling approach capable of identifying the program of gene expression over time would facilitate more focused identification of relevant genes. To achieve this, we used the confluenceinduced differentiation (CID) model, a widely used and reliable method that in many aspects recapitulates in vivo differentiation of human epidermal keratinocytes (Paragh et al, 2010; Poumay and Pittelkow, 1995). Primary human keratinocytes from three donors were subjected to CID in separate cultures and harvested at successive time points including 2 days prior to reaching confluence (D(-2)), at the point of confluence (D(0)), as well as after reaching confluence (D(1), D(2) and D(3)). In order to minimize any donor and sample effects, the RNA samples were pooled at each time point and gene expression profiling was performed (Affymetrix U133 A & B). Secondary validation study was performed with three additional time observation arrayed in Affymetrix U133A2 platform for the 3 patient pool. The time observations were: D(-3),D(-2),D(-1),D(0),D(+1),D(+2),D(+3),D(+5).
2013-12-15 | E-GEOD-26688 | biostudies-arrayexpress
Project description:Disrupted skin barrier due to altered keratinocyte differentiation is common in pathologic conditions such as atopic dermatitis, ichthyosis and psoriasis. However, the molecular cascades governing keratinocyte terminal differentiation are still poorly understood. We have previously demostrated that a dominante mutation in ZNF750 leads to a clinical phenotype that reminiscent of psoriasis and seborrehic dermatitis. We defined ZNF750 as a nuclear effector that is atrongly activated in and essiential for keratinocyte terminal differentiation. ZNF750 knockdown in HaCaT keratinocytes markedly reduced the expression of epidermal late differentiation markers, including gene subsets of epidermal differentiation complex and skin barrier formation such as FLG, LOR, SPINK5, ALOX12B and DSG1, known to be mutated in various human skin diseases. Furthermore, ZNF750 over-expression in undifferentiated cells induced terminal differentiation genes. Thus, ZNF750 is a regulator of keratinocyte terminal differnetiation, and with its downstream targets can serve in future elucidation of therapeutics for common disease of skin barrier Gene expression analysis: To determine the differentaition signature for HaCaT keratinocytes, with ZNF750 gene silencing, total RNA was isolated in biologic triplicates from cells induced to differentiate for twelve days and hybridized to Affymerix Human Gene 1.0 ST arrays.
2012-09-24 | E-GEOD-38039 | biostudies-arrayexpress
Project description:Disrupted skin barrier due to altered keratinocyte differentiation is common in pathologic conditions such as atopic dermatitis, ichthyosis and psoriasis. However, the molecular cascades governing keratinocyte terminal differentiation are still poorly understood. We have previously demonstrated that a dominant mutation in ZNF750 leads to a clinical phenotype that reminiscent of psoriasis and seborrheic dermatitis. We defined ZNF750 as a nuclear effector that is strongly activated in and essential for keratinocyte terminal differentiation. ZNF750 knockdown in HaCaT keratinocytes markedly reduced the expression of epidermal late differentiation markers, including gene subsets of epidermal differentiation complex and skin barrier formation such as FLG, LOR, SPINK5, ALOX12B and DSG1, known to be mutated in various human skin diseases. Furthermore, ZNF750 over-expression in undifferentiated cells induced terminal differentiation genes. Thus, ZNF750 is a regulator of keratinocyte terminal differentiation, and with its downstream targets can serve in future elucidation of therapeutics for common disease of skin barrier
2012-09-24 | GSE38039 | GEO
Project description:Notch signaling promotes commitment of keratinocytes to differentiation and suppresses tumorigenesis. p63, a p53 family member, has been implicated in establishment of the keratinocyte cell fate and/or maintenance of epithelial self-renewal. Here we show that p63 expression is suppressed by Notch1 activation in both mouse and human keratinocytes through a mechanism independent of cell cycle withdrawal and requiring down-modulation of selected interferon-responsive genes, including IRF7 and/or IRF3. In turn, elevated p63 expression counteracts the ability of Notch1 to restrict growth and promote differentiation. p63 functions as a selective modulator of Notch1-dependent transcription and function, with the Hes-1 gene as one of its direct negative targets. Thus, a complex cross-talk between Notch and p63 is involved in the balance between keratinocyte self-renewal and differentiation. Keywords: Notch1, p63, keratinocyte differentiation, gene expression profiling
2006-07-08 | GSE5229 | GEO
Project description:Here we characterized the transcriptome and epigenome of control keratinocytes during differentiation. Epigenomic analyses showed that the temporal enrichment of p63 motifs in dynamic enhancers underscores the key role of p63 in orchestrating the enhancer landscape during keratinocyte differentiation. The cooperation between p63 and its co-regulating factors, such as RUNX1, is important for the finetuning of gene expression.
2018-12-18 | GSE98483 | GEO
Project description:Keratinocytes are the major constituent of epithelial cells at mucosal surfaces and skin, which cover organs, internal cavities and the body. Traditionally, keratinocytes have been considered as an inert component of the multilayered epithelium to protect the subepithelial compartments from the pathogenic microorganisms, toxic stimuli and physical trauma. However, accumulated researches of the airway, gastrointestinal tract and skin have demonstrated that keratinocytes function in the development of the immune system, promotion of pathologic inflammation and even impose diverse decisions on immune cells. We used microarrays to detail the global gene expression of oral keratinocyte during oral adaptive immune response. Oral keratinocyte were collected at three time points (control, 48h and 96h) in oral adaptive immune response for RNA extraction and hybridization on Affymetrix microarrays
2011-03-19 | E-GEOD-28035 | biostudies-arrayexpress
Project description:Epidermis, a continuously self-renewing and differentiating organ, produces a protective stratum corneum that shields us from external chemical, physical and microbial threats. Epidermal differentiation is a multi-step process regulated by influences, some unknown, others insufficiently explored. Detachment of keratinocytes from the basement membrane is one such pro-differentiation stimulus. Here, we define the transcriptional changes during differentiation, especially those caused by detachment from the substratum. Using comprehensive transcriptional profiling, we revisited the effects of detachment as a differentiation signal to keratinocytes. We identified the genes regulated by detachment, the corresponding ontological categories and, using metaanalysis, compared the genes and categories to those regulated by other pro-differentiating stimuli. We identified 762 genes overexpressed in suspended keratinocyte, including known and novel differentiation markers, and 1427 in attached cells, including basal layer markers. Detachment induced epidermis development, cornification and desmosomal genes, but also innate immunity, proliferation inhibitors, transcription regulators and MAPKs; conversely the attached cells overexpressed cell cycle, anchoring, motility, splicing and mitochondrial genes, and both positive and negative regulators of apoptosis. Metaanalysis identified which detachment-regulated categories overlap with those induced by suprabasal location in vivo, by reaching confluency in vitro, and by inhibition of JUN kinases. Attached and in vivo basal cells shared overexpression of mitochondrial components. Interestingly, melanosome trafficking components were also overexpressed in the attached and in vivo basal keratinocytes. Reaching confluency did not affect adhesion and ECM proteins. Lipid metabolism and steroid metabolism were induced by confluency and by JNK inhibition, respectively. These results suggest that specific pro-differentiation signals induce specific features of the keratinization process, which are in vivo orchestrated into harmonious epidermal homeostasis. Human epidermal keratinocytes are grown in standard growth medium either attached in tissue culture plates, or suspended, in the same medium, in bacteriological plates. After 48 hrs, attached and suspended cultures were harvested and their transcriptomes compared.
2014-04-25 | E-GEOD-57045 | biostudies-arrayexpress
Project description:Ts keratinocyte has increased proliferation compare to WT keratinocyte upon TPA treatment. This result showed the different transcription regulation in Ts and WT keratinocyte upon TPA treatment. Total RNA extracted from WT or Ts keratinocytes, not treated or treated with TPA for 12 hours.
2013-06-01 | E-GEOD-40382 | biostudies-arrayexpress
Project description:This study identifies FSTL1 as key component of intiating keratinocyte migration in skin Total RNA from N/TERT-1 keratinocytes transfected with a non-targeting siRNA or Smartpool siRNA against FSTL1 were subjected to microarray analysis
2013-03-02 | E-GEOD-41615 | biostudies-arrayexpress
Project description:In epidermis, granular keratinocytes are responsible for the synthesis of a great number of proteins of high tissue-specificity, and required for the epidermal barrier establishment and the regulation of the desquamation process. This project aims at characterizing the physiopathological function of genes implicated in these processes, and in the short term, defining their expression level in the course of keratinocyte differentiation. Pangenomic oligonucleotide microarrays are used to compare their expression between two cell populations enriched in basal or granular keratinocytes (T1 and T4 fractions resp.), obtained by successive incubations in trypsin solution of six independent normal human epidermis samples. Real-time quantitative PCR experiments were further performed to ensure the validity of the profiling for each candidate gene identified from microarrays data, and results of this multitechnique approach will be the object of a forthcoming publication. These results will be the basis for a better understanding of dermatological hyperkeratotic pathologies. Within epidermis, keratinocytes achieve a differentiation program culminating in cornification, a programmed cell death required for the establishment of the barrier function. A complex genetic regulatory network underlies the numerous biochemical modifications taking place in the last living cells, the granular keratinocytes (GKs), but very few transcription factors specific from this process were identified. Here we describe a large-scale, multitechnique approach performed on cells purified from normal human epidermis, and mainly focused on identification of these regulators. We performed microarray experiments to compare gene expression in cell fractions enriched in granular or basal keratinocytes. These data, with in silico promoter analysis for 52 differentiation markers, and exploitation of an EST library from GKs, were filtered according to gene products’ known or putative function and ESTs number in UniGene database, and allowed identification of 298 candidates out of 3,662 genes potentially specific from the last differentiation steps. Half were detected for the first time in epidermis and quantified by quantitative real-time PCR. These genes are linked to various aspects of GKs function, including structural components, lipid metabolism and secretory apparatus, cell signaling, and regulation of transcription. Forty-nine new differentiation-associated genes were identified, and 38 transcription factors in 92 were positively or negatively regulated in the course of differentiation, therefore possibly involved in the final differentiation of GKs. These data give new leads to have a global view of the network involved in epidermal barrier function, and allow in the future a better understanding of several pathologies, including genodermatoses of unknown aetiology. Keywords: Cell type comparison Six independent samples of normal human epidermis were used for this study. For three samples, technical replicates (at the labelling step) were performed (ie AQQ003, AQQ005 and AQQ011 slides are dye-swaps of AQQ002, AQQ004 and AQQ010, respectively). Data from each pair of “swap arrays” were merged and considered as coming from three simple arrays (named AQQ002dw, AQQ004dw and AQQ010dw) for statistical analysis. For each slide, T4 is the test sample (total RNA from granular keratinocytes), and T1 the reference sample (total RNA from basal keratinocytes of the same subject), and both come from the same biological sample.
2010-08-31 | E-GEOD-13263 | biostudies-arrayexpress