In vitro gene signature of volar keratinocytes at early vs late passage
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA476921 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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:In vitro gene signature of cultured volar or nonvolar keratinocytes
| PRJNA476919 | ENA
Project description:Primary cells deficient for PDCD10/CCM3 do not enter senescence as control cells. Microarray analysis was performed in cells transduced with non-targeting shRNA and CCM3 shRNA at passage 7 (early passage) and passage 11 (late passage), when control cells are already senescent.
2014-04-10 | GSE54095 | GEO
Project description:Primary cells deficient for PDCD10/CCM3 do not enter senescence as control cells. Microarray analysis was performed in cells transduced with non-targeting shRNA and CCM3 shRNA at passage 7 (early passage) and passage 11 (late passage), when control cells are already senescent. Primary endothelial cells were transduced either with non-target shRNA or with CCM3 shRNA. RNA was extracted at passage 7 and passage 11
2014-04-10 | E-GEOD-54095 | biostudies-arrayexpress
Project description:The paracellular passage of ions in epithelial systems is dictated by the repertoire of tight junction (TJ) proteins, the number and architecture of apicolateral TJ strands, and the interaction of TJ proteins with the cytoskeleton. To investigate the relative contribution of these factors and to explore their regulation, we examined a passage number dependent phenotypic change in Madin Darby Canine Kidney (MDCK) cells iteratively passaged at low density in which dilution potentials of the monolayer abruptly decreased but transepithelial resistance (TER) progressively increased. Here, we report that the phenotypic transition involved a decrease surface expression of peanut agglutinin (PNA), a decrease in steady state levels of claudin-1 and a slight decrease in E-cadherin expression in the context of an apparently claudin-2-negative system. Late passage cells grew in more densely packed monolayers and exhibited characteristics of a competent, functional cultured monolayer including inducible vectorial ion transport in response to norepinephrine (NE) and sphere formation in three dimensional laminin gel culture. Microarray analysis of gene expression levels in early and late passage cells revealed an increase in transcript abundance for SGK and GLUT-3, and a reduction Id-3. The steady state protein expression levels of GLUT-3, however, were found to be equivalent. These findings suggest that the expression of claudin-2 in MDCK cells could be contingent on signaling via lateral cell contacts and that claudin-1, in the context of sustained claudin-8 expression, could function as a negative regulator of overall TER.
2010-02-13 | GSE14837 | GEO
Project description:Two strains of B. pertussis were serially passaged on plates in the laboratory. Global gene expression profiles were measured for passage 1 and late-passage cultures grown in Bvg+ and Bvg- environmental conditions.
2006-04-30 | E-TABM-59 | biostudies-arrayexpress
Project description:The paracellular passage of ions in epithelial systems is dictated by the repertoire of tight junction (TJ) proteins, the number and architecture of apicolateral TJ strands, and the interaction of TJ proteins with the cytoskeleton. To investigate the relative contribution of these factors and to explore their regulation, we examined a passage number dependent phenotypic change in Madin Darby Canine Kidney (MDCK) cells iteratively passaged at low density in which dilution potentials of the monolayer abruptly decreased but transepithelial resistance (TER) progressively increased. Here, we report that the phenotypic transition involved a decrease surface expression of peanut agglutinin (PNA), a decrease in steady state levels of claudin-1 and a slight decrease in E-cadherin expression in the context of an apparently claudin-2-negative system. Late passage cells grew in more densely packed monolayers and exhibited characteristics of a competent, functional cultured monolayer including inducible vectorial ion transport in response to norepinephrine (NE) and sphere formation in three dimensional laminin gel culture. Microarray analysis of gene expression levels in early and late passage cells revealed an increase in transcript abundance for SGK and GLUT-3, and a reduction Id-3. The steady state protein expression levels of GLUT-3, however, were found to be equivalent. These findings suggest that the expression of claudin-2 in MDCK cells could be contingent on signaling via lateral cell contacts and that claudin-1, in the context of sustained claudin-8 expression, could function as a negative regulator of overall TER. 3 biological replicates of early and late passage were run on Affymetrix chips. the replicates were averaged then compared.
2010-04-09 | E-GEOD-14837 | biostudies-arrayexpress
Project description:In vitro gene signature of keratinocytes
| PRJNA476916 | ENA
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