In vitro gene signature of cultured volar or nonvolar keratinocytes
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PROVIDER: PRJNA476919 | ENA |
REPOSITORIES: ENA
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Project description:How cell and tissue identity persist despite constant cell turnover is an important biologic question with cell therapy implications. While many mechanisms exist, we investigated the controls for site-specific gene expression in skin given its diverse structures and functions. For example, the transcriptome of in vivo palmoplantar (i.e. volar) epidermis is globally unique including Keratin 9 (KRT9). While volar fibroblasts have the capacity to induce KRT9 in non-volar keratinocytes, we demonstrate here that volar keratinocytes continue to express KRT9 in vitro solo-cultures. Despite this, KRT9 expression is lost with volar keratinocyte passaging, in spite of stable hypo-methylation of its promoter. Coincident with KRT9 loss is a gain of the primitive Keratin 7 and a signature of dsRNA sensing, including the dsRNA receptor DDX58. Exogenous dsRNA inhibits KRT9 expression in early passage volar keratinocytes or in vivo footpads of wild-type mice. Loss of DDX58 in passaged volar keratinocytes rescues KRT9 and inhibits KRT7 expression. Additionally, DDX58 null mice are resistant to the ability of dsRNA to inhibit KRT9 expression. These results demonstrate that the sensing of dsRNA is critical for loss of cell specific gene expression; our results have important implications of how dsRNA sensing is important outside of immune pathways. Keratinocytes were expanded from both the sole and the dorsum of the foot and at passage 4, RNA was extracted and sent for microarray analysis
2018-07-20 | GSE116047 | GEO
Project description:How cell and tissue identity persist despite constant cell turnover is an important biologic question with cell therapy implications. While many mechanisms exist, we investigated the controls for site-specific gene expression in skin given its diverse structures and functions. For example, the transcriptome of in vivo palmoplantar (i.e. volar) epidermis is globally unique including Keratin 9 (KRT9). While volar fibroblasts have the capacity to induce KRT9 in non-volar keratinocytes, we demonstrate here that volar keratinocytes continue to express KRT9 in vitro solo-cultures. Despite this, KRT9 expression is lost with volar keratinocyte passaging, in spite of stable hypo-methylation of its promoter. Coincident with KRT9 loss is a gain of the primitive Keratin 7 and a signature of dsRNA sensing, including the dsRNA receptor DDX58. Exogenous dsRNA inhibits KRT9 expression in early passage volar keratinocytes or in vivo footpads of wild-type mice. Loss of DDX58 in passaged volar keratinocytes rescues KRT9 and inhibits KRT7 expression. Additionally, DDX58 null mice are resistant to the ability of dsRNA to inhibit KRT9 expression. These results demonstrate that the sensing of dsRNA is critical for loss of cell specific gene expression; our results have important implications of how dsRNA sensing is important outside of immune pathways. Keratinocytes were expanded from the sole of the foot and at passage 4 or 8, RNA was harvested to identify unique transcripts
2018-07-20 | GSE116053 | GEO
Project description:In vitro gene signature of keratinocytes
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Project description:In vitro gene signature of volar keratinocytes at early vs late passage
| PRJNA476921 | ENA
Project description:In vitro gene signature of cultured adult keratinocytes stimulated by all trans retinoic acid (atRA) and/or Poly I:C
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Project description:We were interested in defining the gene signature of volar skin. Punch biopsies of skin were split into epidermis and dermis after dispase treatment. Epidermis was trypsinized and sorted for alpha 6 integrin positive basal layer keratinocytes We collected RNA from basal layer keratinocytes of soles and backs of feet and submitted for Affymetrix Exon arrays. 2 replicates of each site from distinct human donors were included; total of 4 samples analyzed
2013-07-03 | E-GEOD-39500 | biostudies-arrayexpress
Project description:We were interested in defining the gene signature of volar skin.
2013-07-03 | GSE39500 | GEO
Project description:Human epidermal keratinocytes undergo tightly controlled program of cell differentiation, leading to the formation of cornified envelope. Primary keratinocytes in vitro, under calcium stimulation mimic the differentiation program observed in vivo. Analysis of the transcription profile of two cell population, such as proliferating cells and differentiating cells helps to discover new genes implicated in that process and to understand the mechanisms of regulation of the keratinocyte differentiation. Primary human keratinocytes were cultured under proliferating (Day 0, sub-confluent cells) and differentiating (seven days of high calcium medium) conditions. As a source of cells, we used normal skin from different body sites: back, foreskin, palmoplantar. RNA extracted from cultured primary human keratinocytes were isolated from five different donors. We compared the expression profiles of proliferating versus differentiating keratinocytes.
2010-08-01 | E-GEOD-21413 | biostudies-arrayexpress
Project description:Cultured skin substitutes, prepared using keratinocytes, fibroblasts and biopolymers, can facilitate closure of massive burn wounds by increasing the availability of autologous tissue for grafting. However, because they contain only two cell types, skin substitutes cannot replace all of the functions of native human skin. To better understand the physiological and molecular differences between cultured skin substitutes and native skin, we undertook a comprehensive analysis of gene expression in native skin, cultured keratinocytes, cultured fibroblasts, and skin substitutes using Affymetrix gene chip microarrays. Goals: Our analysis focused on identifying gene signatures that were highly characteristic of each cell and tissue type, and those that are regulated by the formation of cultured skin substitute from the individual components. Normalization: We used a normalization and referencing strategy that consisted of BioConductor/RMA Express RMA processing of the entire series of cel files followed by a per gene normalization in which the median value of expression for each gene was derived from the cultured samples only, and this was used as a reference for all samples including the cultured skin substitute. This approach allowed for the identification of genes that were higher and lower-expressed in the cultured skin relative to the individual cell types that were also expressed strongly or weakly in normal skin relative to the median value established by the three cell types. Results Summary:We identified six major clusters of coordinately regulated genes that were the most differentially expressed between groups. These clusters correspond to biomarker pools representing expression signatures for native skin, fibroblasts, keratinocytes, and cultured skin. The expression analysis revealed that entire clusters of genes were either up-regulated or down-regulated upon combination of fibroblasts and keratinocytes in cultured skin grafts. Further, several categories of genes were overexpressed in cultured skin substitutes compared with native skin, including genes associated with hyperproliferative skin or activated keratinocytes. The observed pattern of expression indicates that cultured skin substitutes in vitro, which display a well-differentiated epidermal layer, exhibit skin-like differentiation relative to gene expression patterns in the individual cells. This consists of both the activation of normal skin signature genes and the suppression of keratinocyte and fibroblast signatures. There is also a signature consistent with a hyperproliferative phenotype similar to wounded native skin. Keywords: Cell interaction and co-culture response expression profile
2005-08-29 | GSE3204 | GEO
Project description:SAGE libraries from cultured, differentiated keratinocytes and human epidermis, both normal and affected by actinic keratosis Keywords = Keratinocyte, Epidermis, Homo sapiens, Actinic Keratosis, TNF alpha
2002-02-22 | GSE31 | GEO