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Global microRNA expression profiling of mouse livers following ischemia-reperfusion injury at different stages. [miRNA]

ABSTRACT: Hepatic ischemia reperfusion injury is a dynamic process consisting of two stages: ischemia and reperfusion, and triggers a cascade of physiological and biochemical events. Given the important role of microRNAs in regulating gene expression, we analyzed gene expression changes in mouse livers at sham control, ischemia stage, and reperfusion stage. We generated global expression profiles of microRNA and mRNA genes in mouse livers subjected to ischemia reperfusion injury at the three stages, respectively. Comparison analysis showed that reperfusion injury had a distinct expression profile whereas the ischemia sample and the sham control were clustered together. Consistently, there are 69 differentially expressed microRNAs between the reperfusion sample and the sham control whereas 28 differentially expressed microRNAs between the ischemia sample and the sham control. We further identified two modes of microRNA expression changes in ischemia reperfusion injury. Functional analysis of both the differentially expressed microRNAs in the two modes and their target mRNAs revealed that ischemia injury impaired mitochondria function, nutrient consumption, and metabolism process. In contrast, reperfusion injury led to severe tissue inflammation that is predominantly an innate-immune response in the ischemia reperfusion process. Our staged analysis of gene expression profiles provides new insights into regulatory mechanisms of microRNAs in mouse hepatic ischemia reperfusion injury.

ORGANISM(S): Mus musculus

PROVIDER: GSE72314 | GEO | 2015/10/01

SECONDARY ACCESSION(S): PRJNA293735

REPOSITORIES: GEO

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Global microRNA expression profiling of mouse livers following ischemia-reperfusion injury at different stages. [mRNA]

Project description:Hepatic ischemia reperfusion injury is a dynamic process consisting of two stages: ischemia and reperfusion, and triggers a cascade of physiological and biochemical events. Given the important role of microRNAs in regulating gene expression, we analyzed gene expression changes in mouse livers at sham control, ischemia stage, and reperfusion stage. We generated global expression profiles of microRNA and mRNA genes in mouse livers subjected to ischemia reperfusion injury at the three stages, respectively. Comparison analysis showed that reperfusion injury had a distinct expression profile whereas the ischemia sample and the sham control were clustered together. Consistently, there are 69 differentially expressed microRNAs between the reperfusion sample and the sham control whereas 28 differentially expressed microRNAs between the ischemia sample and the sham control. We further identified two modes of microRNA expression changes in ischemia reperfusion injury. Functional analysis of both the differentially expressed microRNAs in the two modes and their target mRNAs revealed that ischemia injury impaired mitochondria function, nutrient consumption, and metabolism process. In contrast, reperfusion injury led to severe tissue inflammation that is predominantly an innate-immune response in the ischemia reperfusion process. Our staged analysis of gene expression profiles provides new insights into regulatory mechanisms of microRNAs in mouse hepatic ischemia reperfusion injury.

2015-10-01 | GSE72312 | GEO

Proteome analysis of membranes from renal ischemia-reperfusion injury mouse models.

Project description:Ischemia-reperfusion injury (IRI) is a well-known model for acute kidney injury (AKI). We applied proteomic analysis to detect membrane proteins from IRI mouse kidneys. The analysis set are composed of negative control (sham operation), samples of 4-hour after IRI, and samples of 8-hour IRI.

2021-09-30 | PXD020708 | JPOST Repository

MicroRNA Profiling in Ischemia-Reperfusion Injury of the Gracilis Muscle in Rats (miRNA data)

Project description:Profile the microRNA expression in the Gracilis muscle of rat after 4h ischemia and 24 h reperfusion Following 4 h of ischemia and subsequent reperfusion for 4 h of the gracilis muscles, the specimens were analyzed with an Agilent rat miRNA array to detect the expressed miRNAs in the experimental muscles compared to those from the sham-operated controls. Two-condition experiment, Gracilis muscle after 4h ischemia and reperfusion injury for 24 h v.s. Gracilis muscle (sham control), Biological replicates: 2 control replicates, 2 experiement replicates

2010-04-22 | E-GEOD-21405 | biostudies-arrayexpress

Expression data from lung tissues of minipig with left lung ischemia-reperfusion

Project description:Lung ischemia-reperfusion (I/R) injury remains one of the common complications after various cardiopulmonary surgeries. I-R injury represents one potentially maladaptive response of the innate immune system which is featured by an exacerbated sterile inflammatory response triggered by tissue damage. Thus, understanding the key components and processes involved in sterile inflammation during lung I-R injury is critical to alter care and extend survival for patients with acute lung injury. We constructed a minipig surgical model of transient unilateral left pulmonary artery occlusion without bronchial involvement to create ventilated lung I-R injury. Lung tissues from minipig with sham operation (one sample), left side lung tissues (the operated side)(one sample) and right side lung tissues (the non-operated side)(one sample) from minipig with lung ischemia-reperfusion were submitted for gene expression array analysis.

2015-12-07 | E-GEOD-75560 | biostudies-arrayexpress

small RNA-Seq of rat kidney in a model of ischemic preconditioning/ischemia-reperfusion injury

Project description:Ischemic preconditioning is effective in limiting subsequent ischemic acute kidney injury in experimental models. microRNAs are an important class of post-transcriptional regulator and show promise as biomarkers of kidney injury. An evaluation was performed of the time- and dose-dependent effects of ischemic preconditioning in a rat model of functional (bilateral) ischemia-reperfusion injury. A short, repetitive sequence of ischemic preconditioning resulted in optimal protection from subsequent ischemia-reperfusion injury. A detailed characterization of microRNA expression in ischemic preconditioning/ischemia-reperfusion injury was performed by small RNA-Seq.

2021-12-31 | E-MTAB-9896 | biostudies-arrayexpress

Exiqon miRCURY microRNA array of rat kidney in a model of ischemic preconditioning/ischemia-reperfusion injury

2021-12-31 | E-MTAB-9900 | biostudies-arrayexpress

RealTime quantitative PCR of cardiac at risk area samples obtained from a mouse model of ischemia and reperfusion injury

Project description:Mice were exposed to cardiac ischemia/reperfusion injury and sacrificed after 1 or 4 days. Hearts were stained with Evans blu/TTC to isolate the at risk area. Hearts were divided into 1mm slices, the at risk area of any slice were pooled together before RNA extraction. Mice were divided into 3 different groups: Sham animals have been subjected to the surgical procedure without the induction of the ischemia and reperfusion injury and represent the control animals; LAD group is represented by animals subjected to the surgical procedure and the induction of the ischemia and reperfusion imjury; MLAD group is represented by animals subjected to the surgical procedure and the induction of the ischemia and reperfusion injury, followed by myriocin treatment (SLN/Myr) at the beginning of reperfusion.

2019-07-07 | GSE133913 | GEO

Potential Target Genes of MicroRNA-21 In Ischemia-Reperfusion Injury Of The Gracilis Muscle In Rats

Project description:Transcriptional profiling of rat gracilis muscle after ischemia 4h and reperfusion for 1d, 3d, 7d and 14d v.s. sham control, and correlate the downregulated transcripts to the computational predicted gene targets of ron-miR-21 Following 4 h of ischemia and subsequent reperfusion for 4 h of the gracilis muscles, three miRNAs (miR-21, miR-200c, and miR-205) of 350 tested rat miRNAs were found to have an increased expression in the miRNA array.The expression of the mRNA in the muscle specimens after 4 h of ischemia and reperfusion for 1, 3, 7, and 14 d were detected with the Agilent Whole Rat Genome 4 Ã 44 k oligo microarray. A combined approach using a computational prediction algorithm that included miRanda, PicTar, TargetScanS, MirTarget2, RNAhybrid, and the whole genome microarray experiment was performed by monitoring the mRNA:miRNA association to identify potential target genes. Four-condition experiment, Gracilis muscle after ischemia-reperfusion injury for 1d, 3d, 7d and 14d v.s.Gracilis muscle (sham control), Biological replicates: 1 control replicate, 1 experiement replicate (each condition).

2010-05-07 | E-GEOD-21406 | biostudies-arrayexpress

McDougal2017 - Metabolism in ischemic cardiomyocytes

Project description:Heart disease remains the leading cause of death globally. Although reperfusion following myocardial ischemia can prevent death by restoring nutrient flow, ischemia/reperfusion injury can cause significant heart damage. The mechanisms that drive ischemia/reperfusion injury are not well understood; currently, few methods can predict the state of the cardiac muscle cell and its metabolic conditions during ischemia. Here, we explored the energetic sustainability of cardiomyocytes, using a model for cellular metabolism to predict the levels of ATP following hypoxia. We modeled glycolytic metabolism with a system of coupled ordinary differential equations describing the individual metabolic reactions within the cardiomyocyte over time. Reduced oxygen levels and ATP consumption rates were simulated to characterize metabolite responses to ischemia. By tracking biochemical species within the cell, our model enables prediction of the cell’s condition up to the moment of reperfusion. The simulations revealed a distinct transition between energetically sustainable and unsustainable ATP concentrations for various energetic demands. Our model illustrates how even low oxygen concentrations allow the cell to perform essential functions. We found that the oxygen level required for a sustainable level of ATP increases roughly linearly with the ATP consumption rate. An extracellular O2 concentration of ~0.007 mM could supply basic energy needs in non-beating cardiomyocytes, suggesting that increased collateral circulation may provide an important source of oxygen to sustain the cardiomyocyte during extended ischemia. Our model provides a time-dependent framework for studying various intervention strategies to change the outcome of reperfusion.

2020-08-25 | BIOMD0000000961 | BioModels

Ablation of CaMKIIδ oxidation by CRISPR-Cas9 base editing as a therapeutic approach for cardiac disease

Project description:To develop a new therapeutic strategy for cardiac ischemia/reperfusion injury, we ablated the oxidative activation site of CaMKIIδ in the heart using CRISPR-Cas9 adenine base editing technology. Adult C57Bl6 mice were subjected to control surgery (IR-Sham, 3 biological replicates) or ischemia/reperfusion injury with either no injection (IR, 3 biological replicates), injection of a control virus (IR-Virus control, 3 biological replicates) or injection of a functional CaMKIIδ editing system (IR-Edit, 4 biological replicates). Five weeks after the surgery, hearts were harvested for RNA isolation and subsequent bulk RNA sequencing and gene expression profiling analysis.

2023-02-06 | GSE210494 | GEO

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