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Mus musculus

ABSTRACT: Simultaneous pathway activity inference and global gene expression analysis using RNA-sequencing [halofuginone]

PROVIDER: PRJNA302808 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2932040.fastq.gz	Fastqsanger.gz
	SRR2932050.fastq.gz	Fastqsanger.gz
	SRR2932060.fastq.gz	Fastqsanger.gz
	SRR2932070.fastq.gz	Fastqsanger.gz
	SRR2932080.fastq.gz	Fastqsanger.gz

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Transcriptional responses of wild-type and Gcn2-/- Th17 cells to halofuginone and rapamycin

Project description:This study was designed to evaluate similarities and differences between transcriptional responses of developing Th17 cells to the prolyl-tRNA synthetase inhibitor, halofuginone, and the mTOR inhibitor, rapamycin. Further comparisons between wild-type and Gcn2-/- Th17 cells allow for investigation into which gene modules regulated by halofuginone or rapamycin treatment require Gcn2. Murine CD4+ CD25- T cells were magnetically isolated from wild-type or Gcn2-/- T cells. These cells were activated through anti-CD3/ anti-CD28 antibodies and polarized into Th17 cells using TGFb plus IL-6. 10 nM halofuginone, 10 nM rapamycin, or vehicle control (DMSO) were added to cultures at the time of activation. Cells were harvested at 4, 18, or 72 hours post-activation and differentiation. RNA was isolated from each sample and used for microarray analysis. Each culture condition and time-point was repeated twice in independent experiments using cells isolated from different wild-type or Gcn2-/- mice. Vehicle versus halofuginone, vehicle versus rapamycin, halofuginone versus rapamycin. Gcn2-/- versus wild-type T cells treated with vehicle, halofuginone, or rapamycin.

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Transcription profiling of mouse T cells treated with halofuginone to investigate regulation of Y cell gene expression by Halofuginone (HF)

Project description:T cell differentiation to the Th17 effector subset requires stimulation through the T cell and co-stimulatory receptors, together with cytokine stimulation by TGFb and IL-6. The small molecule halofuginone (HF) inhibits Th17 cell development and induces a pattern of stress-regulated gene expression that mimics amino acid starvation. We used global transcript profiling to ask how halofuginone modulates gene expression induced during T cell activaiton and Th17 differentiation Experiment Overall Design: Purified mouse CD4+ CD25- T cells were activated under Th17 polarizing cytokine conditions and treated with either halofuginone or its inactive derivative, MAZ1310, for 3- or 6-hours.

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Microarray profiling reveals Integrated Stress Response is activated by Halofuginone in mammary epithelial cells

Project description:The small molecule Halofuginone (HF) is a potent regulator of extracellular matrix (ECM ) gene expression and is unique in its therapeutic potential. While the basis for HF effects is unknown, inhibition of TGFb signaling and activation of the AAR have been linked to HF transcriptional control of a number of ECM components and amelioration of fibrosis and alleviation of autoimmune disease by regulation of Th17 cell differentiation, respectively. The aim of this study was to generate a global expression profile of HF targets in epithelial cells to identify potential mediators of HF function in this cell type. We report that HF modulation of the ECM remodeling protein Mmp13 in epithelial cells is separable from previously reported effects of HF on TGFß signal inhibition, and use microarray expression analysis to correlate this with transcriptional responses characteristic of the Integrated Stress Response (ISR). Our findings suggest a common mechanism underlying HF anti-fibrotic and anti-angiogenic effects in parenchymal cells and HF effects on Th17 differentiation. Moreover, our results point away from a central role of TGFb signaling in the HF mechanism of action and suggest a new approach to small molecule based regulation of the ECM transcriptional program in vivo. NMuMG mammary epithelial cells were treated with 10 nM Halofuginone or 10 nM MAZ1310 (a non-functional analog of Halofuginone used as a control) for 8 hours. Each treatment was performed in biological triplicate. Following RNA extraction, we used Phalanx Mouse Whole Genome OneArray to measure mRNA abundance of Halofuginone-treated and MAZ1310 control samples. Each array was performed in triplicate. Expression of transcripts in Halofuginone versus MAZ1310 treated cells was examined.

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Project description:A major challenge in gene expression analysis is to accurately infer relevant biological insight, such as variation in cell type proportion or pathway activity, from global gene expression studies. We present a general solution for this problem that outperforms available cell proportion inference algorithms, and is more widely useful to automatically identify specific pathways that regulate gene expression. Our method improves replicability and biological insight when applied to trans-eQTL identification.

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Project description:T cell differentiation to the Th17 effector subset requires stimulation through the T cell and co-stimulatory receptors, together with cytokine stimulation by TGFb and IL-6. The small molecule halofuginone (HF) inhibits Th17 cell development and induces a pattern of stress-regulated gene expression that mimics amino acid starvation. We used global transcript profiling to ask how halofuginone modulates gene expression induced during T cell activaiton and Th17 differentiation Keywords: T cell activation/ differentiation timecourse

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Discordant regulation of eIF2 kinase GCN2 and mTORC1 during nutrient stress

Project description:Here we report Total RNA seq and RiboSeq on MEF cells treated with halofuginone. Halofuginone is a competitive inhibitor of the Prolyl-tRNA synthetase that results in an accumulation of uncharged Prolyl-tRNA upon treatment that leads to an activation of the protein kinase Gcn2.

2021-05-26 | GSE156850 | GEO

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