Project description:The interactions between RNA and protein within cellular signaling pathways, known as the interactome, have modulatory effects on RNA binding proteins (RBP’s) effector functions, which contribute to post-transcriptional control of inflammatory cytokine release in the innate immune response. Post-translational modifications (PTMs) have a regulatory effect on a protein’s effector function. Thus, investigating the effect of RNA-protein interactions can answer questions central to our understanding of cellular signaling. Global RNA sequencing was used to investigate the differentially expressed (DE) genes from baseline following induction with LPS. Shotgun proteomics along with SILAC labeling was used to quantify relative abundance and differential protein expression in response to LPS. To assess the proteins interacting with RNA after LPS induction, total RNA associated protein purification was utilized. Using the tandem MS approach and methodology mentioned above, we were able to identify a list of candidate RNA binding proteins. Global RNA sequencing provided a baseline transcriptomic profile as well as quantification of DE genes across a stimulation time course (0, 30, 60 minutes). To investigate the discordance between the transcriptome and proteome, we performed miRNA sequencing at 0,30,60, and 120 minutes of LPS stimulation to assess expression changes in LPS induced miRNA’s which may regulate the transcriptome. We then handpicked potential RBPs of immunological interest (Il1a, MARCKS, and Acod1). Interestingly, Il1a, MARCKS, and Acod1 were all highly DE compared to baseline in the RNA Seq results and displayed a tendency to disassociate from RNA as the LPS time course pursued. Il1a, MARCKS, and Acod1 can all directly regulate pro-inflammatory gene expression in macrophages. These RBPs could offer a new regulatory mechanism to tune their effector function, which could lead to new therapeutic innovations for disease pathologies these proteins are implicated in. This research was supported by the Intramural Research Program of NIAID, NIH.

Project description:Background. In experimental setting the concept of myocardial preconditioning-by hyperoxia has been introduced and different intracellular protective mechanisms and their effects have been described. To study whether similar protective phenotype can be induced by hyperoxia also in humans, gene expression profile after hyperoxic exposure was analyzed. Methods and Findings. Adult patients were randomized to be ventilated with either FiO2 0.4 (n=14) or 1.0 (n=10) for 60 minutes before coronary artery bypass grafting. A tissue sample from the right atrial appendage was taken for gene analysis and expression profile analysis on genome wide level by gene chip analysis was applied. Exposure to > 96% oxygen for 60 minutes significantly changed the expression of 20 different genes, including upregulation of two different humanins - MTRNR2L2 and MTRNR2L8, and activated a “cell survival” network as detected by Ingenuity Pathway Analyses. Conclusions. Administration of > 96% oxygen for 1 hour changes gene expression in the myocardium of the patients with coronary artery disease and may enhance cell survival capability. Background. In experimental setting the concept of myocardial preconditioning-by hyperoxia has been introduced and different intracellular protective mechanisms and their effects have been described. To study whether similar protective phenotype can be induced by hyperoxia also in humans, gene expression profile after hyperoxic exposure was analyzed. Methods and Findings. Adult patients were randomized to be ventilated with either FiO2 0.4 (n=14) or 1.0 (n=10) for 60 minutes before coronary artery bypass grafting. A tissue sample from the right atrial appendage was taken for gene analysis and expression profile analysis on genome wide level by gene chip analysis was applied. Exposure to > 96% oxygen for 60 minutes significantly changed the expression of 20 different genes, including upregulation of two different humanins - MTRNR2L2 and MTRNR2L8, and activated a “cell survival” network as detected by Ingenuity Pathway Analyses. Conclusions. Administration of > 96% oxygen for 1 hour changes gene expression in the myocardium of the patients with coronary artery disease and may enhance cell survival capability.

Project description:Background. In experimental setting the concept of myocardial preconditioning-by hyperoxia has been introduced and different intracellular protective mechanisms and their effects have been described. To study whether similar protective phenotype can be induced by hyperoxia also in humans, gene expression profile after hyperoxic exposure was analyzed. Methods and Findings. Adult patients were randomized to be ventilated with either FiO2 0.4 (n=14) or 1.0 (n=10) for 60 minutes before coronary artery bypass grafting. A tissue sample from the right atrial appendage was taken for gene analysis and expression profile analysis on genome wide level by gene chip analysis was applied. Exposure to > 96% oxygen for 60 minutes significantly changed the expression of 20 different genes, including upregulation of two different humanins - MTRNR2L2 and MTRNR2L8, and activated a “cell survival” network as detected by Ingenuity Pathway Analyses. Conclusions. Administration of > 96% oxygen for 1 hour changes gene expression in the myocardium of the patients with coronary artery disease and may enhance cell survival capability. Background. In experimental setting the concept of myocardial preconditioning-by hyperoxia has been introduced and different intracellular protective mechanisms and their effects have been described. To study whether similar protective phenotype can be induced by hyperoxia also in humans, gene expression profile after hyperoxic exposure was analyzed. Methods and Findings. Adult patients were randomized to be ventilated with either FiO2 0.4 (n=14) or 1.0 (n=10) for 60 minutes before coronary artery bypass grafting. A tissue sample from the right atrial appendage was taken for gene analysis and expression profile analysis on genome wide level by gene chip analysis was applied. Exposure to > 96% oxygen for 60 minutes significantly changed the expression of 20 different genes, including upregulation of two different humanins - MTRNR2L2 and MTRNR2L8, and activated a “cell survival” network as detected by Ingenuity Pathway Analyses. Conclusions. Administration of > 96% oxygen for 1 hour changes gene expression in the myocardium of the patients with coronary artery disease and may enhance cell survival capability. 24 samples, 14 controls and 10 with intervention

			Action	DRS
	SRR26965733_1.fastq.gz	Fastqsanger.gz
	SRR26965733_2.fastq.gz	Fastqsanger.gz
	SRR26965734_1.fastq.gz	Fastqsanger.gz
	SRR26965734_2.fastq.gz	Fastqsanger.gz
	SRR26965735_1.fastq.gz	Fastqsanger.gz

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Effect of stimulation with lipopolysaccharide (LPS) at 0,30, and 60 minutes on gene expression in immortalized mouse macrophages (IMM).

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