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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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			Action	DRS
	SRR10181180_1.fastq.gz	Fastqsanger.gz
	SRR10181180_2.fastq.gz	Fastqsanger.gz
	SRR10181181_1.fastq.gz	Fastqsanger.gz
	SRR10181181_2.fastq.gz	Fastqsanger.gz
	SRR10181182_1.fastq.gz	Fastqsanger.gz

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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.

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Racial dimorphism in transcriptomic response in human organotypic raft cultures

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mRNA expression data from keratinocytes with disorganized lipid raft structures (by cholesterol depletion by methyl-beta-cyclodextrin)

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mRNA expression data from keratinocytes with disorganized lipid raft structures (by cholesterol depletion by methyl-beta-cyclodextrin)

Project description:Lipid rafts are cholesterol-rich cell signaling platforms and their physiological role can be explored by cholesterol depletion. To dress a global picture of transcriptional changes ongoing after lipid raft disruption, we performed whole-genome expression profiling in epidermal keratinocytes, a cell type which synthesizes its cholesterol in situ. We used microarrays to identify transcriptional changes in gene expression of cholesterol-depleted keratinocytes. Cholesterol depletion by methyl-beta-cyclodextrin disrupts the organization of lipid rafts, which are cholesterol- and sphingolipid-rich membrane microdomains. Transcript levels were measured in autocrine confluent cultures of normal human epidermal keratinocytes were either left untreated (Ctrl), cholesterol-depleted for 1h with 7.5mM methyl-beta-cyclodextrin (MBCD), or mock cholesterol-depleted for 1h with 7.5mM cholesterol-charged methyl-beta-cyclodextrin complexes (MBCD/chol) (Mock cholesterol depletion is a suppementary negative control as this treatment does not extract cholesterol from cell membranes). Samples are analysed either immediately after the treatment (R0h) or after recovery times of 1h (R1h) respectively 8h (R8h). in total 9 samples are analysed and no replicates are performed.

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Racial dimorphism in transcriptomic response in human organotypic raft cultures

Project description:Racial dimorphism in transcriptomic response in human organotypic raft cultures

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Ovarian Cancer Lipid raft proteomics and role of OPCML

Project description:ipid rafts are dynamic membrane micro-domains that orchestrate molecular interactions and are implicated in cancer development. To understand potential role of tumor suppressor OPCML on the altered dynamics of lipid raft residing proteins, we performed quantitative (SILAC) proteomics experiment. We recently found that OPCML negatively regulates a subset of receptor tyrosine kinases (RTKs) by altering their recycling and ubiquitin-mediated degradation via sequestration to lipid rafts; however, the molecular mechanism linking OPCML tumor suppressor expression to altered RTK trafficking remains unclear. Here we performed a quantitative lipid raft proteomics study to dissect raft-mediated mechanism of OPCML-regulated tumor suppression. We also examined raft-associated mechanism of OPCML P95R, a common mutation resulting in substitution of proline to arginine at position 95, mediated regulation of adhesion potential of tumors.

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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

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A sensitive S-trap-based approach to the analysis of T-cell raft proteome

Project description:The development of sensitive technologies for T cell-raft proteomics is highly challenging. We explored an innovative strategy, based on suspension trapping (S-trap) sample preparation. Mouse splenocytes were subjected to negative immunoselection for T cell preparation. Rafts were isolated by a detergent-free method and Optiprep gradient ultracentrifugation. Flotillin-1-, LAT- and cholesterol-rich microdomains were subjected to proteomic analysis through an optimized protocol based on S-Trap and high pH fractionation, followed by nano-LC-MS/MS. We identified 2680 proteins in the raft-rich fraction and established a database of 894 bona fide T cell-raft proteins. We performed a differential analysis on the raft-rich fraction from non-stimulated vs. anti-CD3/CD28 TCR-stimulated T cells. Our results revealed 42 proteins present in one condition and absent in the other, such as Akt2 and Nck1. For the first time a proteomic analysis is performed on rafts from ex-vivo T cells obtained from individual mice, before and after TCR activation. Our results show an increased specificity and sensitivity of the proposed method.

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