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Genome-wide transcriptome analysis of organotypic rafts derived from human papillomavirus type 16 infected primary keratinocytes [3D raft]

ABSTRACT: Genome-wide transcriptome analysis of organotypic rafts derived from human papillomavirus type 16 infected primary keratinocytes [3D raft]

PROVIDER: PRJNA574045 | ENA |

REPOSITORIES: ENA

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Genome-wide transcriptome analysis of organotypic rafts derived from human papillomavirus type 16 infected primary keratinocytes [3D raft]

Project description:HPV alters the host transcriptional program to establish infection and complete its lifecycle. Infection of keratinocytes has been difficult until our development of extracellular matrix (ECM) to cell transfer system that allows efficient infection of primary keratinocytes. Using this model, the transcriptional program of HPV infected keratinocytes grown in raft culture was analyzed by mRNA-seq.

2019-11-10 | GSE137964 | GEO

Racial dimorphism in transcriptomic response in human organotypic raft cultures

Project description:Keratinocyte ethnicity affects transcriptomic response of human organotypic raft cultures

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The effects of UVB and the organic osmolyte betaine on rat epidermal keratinocytes in an organotypic culture system

Project description:Betaine (trimethylglycine) is a non-toxic, highly water-soluble organic osmolyte widely used in skin care due to its assumed moisturizing and protective properties, but only few studies have addressed its specific effects in skin. Here, the cellular and molecular targets of betaine were analyzed by genome-wide expression analysis in organotypic cultures of rat epidermal keratinocytes (REK). In this model, we also examined whether betaine modifies the impacts of acute UVB exposure. The expression of several genes relevant to epidermal biology, proliferation/differentiation or malignancy as well as solute transport were verified by independent methods (qRT-PCR, western blotting). The data concerning changes in calcium metabolism after UVB exposure has been published separately (Bart et al., Br. J. Dermatol. 171:376-387, 2014). Organotypic cultures of rat epidermal keratinocytes (REK) were prepared by plating cells on a collagen-coated insert (submerged in medium), lifting the confluent cell layer to the air-liquid interface 3 days after plating. These 3D cultures were divided in four treatment groups with three replicates in each: control, betaine (10 mM), UVB (30 mJ/cm2) and betaine + UVB. Betaine was added to the cultures for 11 days, starting from day 4 until sample collection. UVB exposure was performed 24 h prior to sample collection for 2-week-old 3D cultures with a well-formed epidermal layer. For further details on the experimental set-up and characteristics of the UV source, please refer to Bart et al. (Br. J. Dermatol. 171:376-387, 2014) and Rauhala et al. (J. Biol. Chem. 288:17999-18012, 2013).

2015-10-26 | E-GEOD-63004 | biostudies-arrayexpress

Genome-wide transcriptome analysis of human papillomavirus type 16 infected primary keratinocytes [monolayer]

2019-11-10 | GSE137361 | GEO

Genome-wide transcriptome analysis of human papillomavirus type 16 infected primary keratinocytes

Project description:Genome-wide transcriptome analysis of human papillomavirus type 16 infected primary keratinocytes

| PRJNA574042 | ENA

Dissecting the functional selectivity of TGFβ signaling pathway components using genome engineered human organotypic skin models

Project description:Transforming growth factor β (TGFβ) signaling is essential in cell growth and differentiation. Yet, the role of the individual TGFβ signaling components in human tissue homeostasis and transformation is still incompletely understood. Here we dissected the importance of the core components in the TGFβ signaling pathway by CRISPR/Cas9 genome editing of human keratinocytes. The edited keratinocytes were used for human organotypic skin cultures and global quantitative proteomics and phosphoproteomics by mass spectrometry. Characterization of cells and human organotypic skin tissues showed control of epithelial differentiation by Smad4-dependent TGF signaling through cell cycle regulation and ECM expression. In contrast, we found that the combined Smad4 dependent and independent pathways, governed by TGFβRII, controls epithelial homeostasis and prevents invasive growth by blocking epithelial inflammation and activation of p38 and ERK signaling. The study provides a framework for exploration of signaling pathways in human 3D tissue models and with global phosphoproteomics.

2023-02-09 | PXD024935 | Pride

Esophageal progenitor cell plasticity; a 3D organotypic model of epithelial regeneration

Project description:Epithelial stem cells are capable of remarkable plasticity, facilitating efficient regenerative responses following damage. Here, we present a versatile model of ectopic niche regeneration that provides evidence of a switch in epithelial stem cell identity as a response to foreign microenvironmental signals. A combination of 3D organotypic cultures, 3D confocal imaging and Next-Generation Sequencing reveal events of epithelial plasticity during the reepithelialization of denuded stroma. In this study we perform a temporal analysis that provides new insights on the mechanisms driving cell fate flexibility in adult epithelial stem cells.

2023-12-14 | GSE163218 | GEO

Genome-wide transcriptome analysis of human papillomavirus type 16 infected primary keratinocytes [monolayer]

Project description:Genome-wide transcriptome analysis of human papillomavirus type 16 infected primary keratinocytes [monolayer]

| PRJNA565235 | ENA

Human Papillomavirus 16 E5 modulates the expression of host microRNAs

Project description:The effect of human papillomavirus 16 E5 oncogene on cellular gene expression in human epithelial cells was studied. Alterations in cellular gene expression due to human papillomavirus type 16 E5 oncogene were studied in triplicate microarray screens. Epithelial cells where E5 expression was induced for 0, 2, 4, 24, 48, 72 and 96h were compared to control cells.

2011-08-31 | E-GEOD-24908 | biostudies-arrayexpress

Human Papillomavirus 16 E5 modulates the expression of host microRNAs

Project description:The effect of human papillomavirus 16 E5 oncogene on cellular gene expression in human epithelial cells was studied.

2011-09-01 | GSE24908 | GEO