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An avb3 integrin checkpoint is critical for efficient TH2 cytokine polarisation and potentiating antigen-specific immunity [RNA-seq]

ABSTRACT: An avb3 integrin checkpoint is critical for efficient TH2 cytokine polarisation and potentiating antigen-specific immunity [RNA-seq]

PROVIDER: PRJNA896642 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22135226.fastq.gz	Fastqsanger.gz
	SRR22135227.fastq.gz	Fastqsanger.gz
	SRR22135228.fastq.gz	Fastqsanger.gz
	SRR22135229.fastq.gz	Fastqsanger.gz
	SRR22135230.fastq.gz	Fastqsanger.gz

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Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation [CRISPRscr]

Project description:T helper 2 (TH2) cells play critical roles in protective immunity against parasitic helminth infections and in tissue repair. However, misdirected TH2 cell responses promote allergy and asthma. Using whole-genome CRISPR-Cas9 screens in developing TH2 cells we defined a functional TH2ome for TH2 differentiation and validated a diverse array of molecules not previously linked to TH2 cell development and function. Strikingly, we discovered that integrin avb3 plays a key and previously unappreciated role in the differential polarisation of TH2 cells and their type 2 cytokine expression. Conversely, we did not identify the LFA-1 integrin which mediates inside-out signalling following TCR ligation as part of the T cell synapse and preferentially promotes TH1 differentiation. We find that TH2 cell expression of integrin avb3 is required for the formation of TH2 cell clusters that exhibit enhanced T cell activation, promoting proliferation and TH2 cell differentiation, and thereby potentiating antigen-driven TH2 cell responses.

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Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation [RNA-seq I]

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An avb3 integrin checkpoint is critical for efficient TH2 cytokine polarisation and potentiating antigen-specific immunity [RNA-seq]

Project description:To investigate the role of avb3 integrin in TH2 immunity. We performed gene expression profiling analysis using control vs av-KO TH cells.

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An avb3 integrin checkpoint is critical for efficient TH2 cytokine polarisation and potentiating antigen-specific immunity [ChIP-seq]

Project description:To investigate the role of avb3 integrin in TH2 immunity. We performed gene expression profiling analysis using control vs av-KO TH cells.

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An avb3 integrin checkpoint is critical for efficient TH2 cytokine polarisation and potentiating antigen-specific immunity [ChIP-seq]

Project description:An avb3 integrin checkpoint is critical for efficient TH2 cytokine polarisation and potentiating antigen-specific immunity [ChIP-seq]

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Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation.

Project description:Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation.

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Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation [CRISPRscr]

Project description:Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation [CRISPRscr]

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Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation [RNA-seq I]

Project description:Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation [RNA-seq I]

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Integrin a5, aV, and aVb3 in zebrafish embryos at the 12 somite stage

Project description:Integrins are a major class of heterodimeric adhesion receptors composed of an a and b subunit that mediate cell adhesion to the extracellular matrix (ECM). The extracellular matrix protein fibronectin is important for early vertebrate development, and Integrin a5b1 and aVb3 are the two primary fibronectin receptors. To better define the integrin – ECM protein network at 10-13 somite stage of zebrafish development, we performed co-immunoprecipitation and Mass Spectrometry (MS) based proteomics using FLAG-tagged Integrin a5, aV, and aVb3 expressed in maternal zygotic a5 mutant (MZa5-/-) embryos. We found that Integrin a5b1 and aVb1 are the functional fibronectin receptors, whereas Integrin aVb3 displayed low affinity to both fibronectins (Fn1a and Fn1b). In addition, basement membrane ligands Laminins (lama1, lamb1a, lamc1) are roughly equal in all three datasets while Thrombospondins (thbs3b, thbs4b) and cartilage oligomeric matrix protein (comp/thbs5) are found exclusively in the aV dataset. Our results suggest a diverse role of aV class integrins in ECM protein recruitment.

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The Effects of avb3 Integrin Signaling on the Transcriptome of an Immortalized Line of Human Trabecular Meshwork Cells (TM-1)

Project description:Purpose: To study the effects of overexpressing either a wild type (WT) or a constitutively active (CA) avb3 integrin on the transcriptome of an immortalied line of human trabecular meshwork cells. Methods: RNA was collected from four samples each of control cells expressing an empty vector (EV), cells overexpressing a WT avb3 integrin (WTb3) or a CA avb3 (CAb3) integrin. All cells had been cultured at confluence for 24 hr in 1%FBS-containing medium. RNA libraries were prepared using 1µg of RNA/sample with the TruSeq RNA sample preparation kit and sequenced on four lanes of an Illumina HiSeq 2500 System. Quality control was performed on the sequencing reads using fastq and skewer trimming software was used to preprocess raw fastq files. A quality control pipeline was then applied and each RNA-Seq sample was subsequently normalized by the method of trimmed mean M-values prior to DGE analysis using EdgeR. Results: 5,186 genes had significantly altered expression (p<0.05) in WTb3 cells compared to EV cells (2,645 upregulated vs 2541 downregulated); 8,249 genes had significantly altered expression (p<0.05) in CAb3 cells compared to EV cells (4,094 upregulated vs 4,255 downregulated). However, 6,999 genes had significantly altered expression (p<0.05) in WTb3 cells vs CAb3 cells (3,524 upregulated vs 3,475 downregulated). Conclusions: Overexpressing of both a WT avb3 and a constitutively active avb3 integrin caused signficant alterations in the transcriptome of immortalized TM-1 cells, however constitutive activation of avb3 signaling had a more pronounced effect on the TM-1 transcriptome than did mere overexpression of the integrin.

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