Gene expression after liver transplantation
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ABSTRACT:
PROVIDER: PRJNA794075 | ENA |
REPOSITORIES: ENA
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Project description:We have studied the genes activated in human liver transplantation to identify potential target genes for the prevention or treatment of related injuries. In a first protocol, in order to evaluate the effect of Ischemia-Reperfusion Injury (IRI) on gene expression profile, we compared gene expression levels in transplanted-reperfused livers versus basal values in donor livers, identifying 795 genes significantly modified in human liver after transplantation. Some genes are likely to be completely activated by IRI, as they are not expressed at all in basal livers. In a second protocol, in order to identify gene dysregulations already present in donor livers, which might affect gene expression profile after transplantation, gene expression evaluated in the first study was compared to control livers (espression data retrieved from ArrayExpress database). About 900 genes in donor livers are dysregulated if compared to the control condition. At least 400 of them remain dysregulated or become more and more dysregulated after transplantation.
2009-10-01 | GSE14951 | GEO
Project description:To determine the circRNA expression profile in hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation, we uesed circRNA microArray analysis form Arraystar to examine the expression of circRNAs and circRNAs in hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation.
2020-04-10 | GSE119748 | GEO
Project description:We have studied the genes activated in human liver transplantation to identify potential target genes for the prevention or treatment of related injuries. In a first protocol, in order to evaluate the effect of Ischemia-Reperfusion Injury (IRI) on gene expression profile, we compared gene expression levels in transplanted-reperfused livers versus basal values in donor livers, identifying 795 genes significantly modified in human liver after transplantation. Some genes are likely to be completely activated by IRI, as they are not expressed at all in basal livers. In a second protocol, in order to identify gene dysregulations already present in donor livers, which might affect gene expression profile after transplantation, gene expression evaluated in the first study was compared to control livers (espression data retrieved from ArrayExpress database). About 900 genes in donor livers are dysregulated if compared to the control condition. At least 400 of them remain dysregulated or become more and more dysregulated after transplantation. For the first protocol, two biopsies were collected from each liver: 1 biopsy before explantation from the donor, immediately after opening, before ice was applied, and 1 biopsy about 2-3 hours after liver reperfusion in the recipient organism. Gene expression of 5 transplanted livers was compared to that of 5 donor livers. In the second protocol gene expression both of transplanted and donor livers was compared to gene expression data from 5 control livers retrieved from ArrayExpress repository SAMPLE ID: E-AFMX-11. This dataset is part of the TransQST collection.
2009-10-01 | E-GEOD-14951 | biostudies-arrayexpress
Project description:The clear benefits of ischemic preconditioning (IPC) in reducing ischemia reperfusion injury (IRI) remain indistinct in human liver transplantation. To further understand the mechanistic aspects of IPC in human deceased donor liver transplantation (DDLT), we performed microarray analyses to determine global gene expression profiles associated with IPC administration. Donor and recipient characteristics in both groups were comparable. Clinical data from our study subset and larger trial were similar. IPC increased expression of 10 transcripts at either time point with roles in: antioxidant defenses, immunological response, lipid biosynthesis, and xenobiotic metabolism. IPC decreased the expression of 1 cell development related transcript. Conclusions: 1) IPC in DDLT increased the expression of antioxidant transcripts similar to studies in animal IPC, anesthetic, and remote IPC. 2) IPC increased expression of lipogenic transcripts, which may be relevant to the clinically observed increased IRI in our IPC group. 3) Our microarray findings support our clinical observations and are compatible with the varied outcomes of hepatic IPC studies in human liver transplantation.
2009-04-01 | GSE15480 | GEO
Project description:INTRODUCTION Ischemia and reperfusion injury (IRI)-elicited tissue injury contributes to morbidity and mortality in a wide range of pathologies, including myocardial infarction, ischemic stroke, acute kidney injury, trauma, circulatory arrest 1. Ischemia-reperfusion injury is also a major challenge during organ transplantation and cardiothoracic, vascular and general surgery 1. IRI, one of the biggest challenges for organ transplantation, continues to be a vital source of morbidity among recipients, especially in liver transplantation 2. With the enlarging shortage of available donor livers, the increased use of extended criteria donor grafts further increases IRI, adversely affecting both short-term and long-term outcomes of graft and patient survival 3. Numerous studies have investigated the benefits of pharmacological, heat shock, and ischemic preconditioning interventions aimed at decreasing liver IRI 4. However, the benefit was limited. Our center has been making great effort in conquering IRI and have developed a novel surgical technique called ischemia-free liver transplantation 5. It is an ultimate method to overcome IRI in liver transplantation, but there is still a long way to popularize it. As a result, it is still of great significance to study IRI and identify the core genes in the process and the underlying mechanism. Comprehensive bioinformatics analysis has been increasingly important as a method to study various pathological and physiological condition 6. By enrolling multiple omics or combining different types of omics, comprehensive bioinformatics analysis was able to recognize key factors that could have potentially pathogenic impact such as gene expression, protein function, and downstream pathways. With the rapid development of high-throughput sequencing technologies, several transcriptomic datasets on IRI of liver transplantation have become available in the Gene Expression Omnibus (GEO) database. Herein, we recruited 3 GEO datasets to conduct comprehensive analysis with the GEO dataset from our center. Moreover, we performed the first proteome of liver tissues to study liver IRI. Then the transcriptome and proteome were used for combined analysis to reveal key factors in liver IRI.
2022-02-23 | PXD010812 | Pride
Project description:The clear benefits of ischemic preconditioning (IPC) in reducing ischemia reperfusion injury (IRI) remain indistinct in human liver transplantation. To further understand the mechanistic aspects of IPC in human deceased donor liver transplantation (DDLT), we performed microarray analyses to determine global gene expression profiles associated with IPC administration. Donor and recipient characteristics in both groups were comparable. Clinical data from our study subset and larger trial were similar. IPC increased expression of 10 transcripts at either time point with roles in: antioxidant defenses, immunological response, lipid biosynthesis, and xenobiotic metabolism. IPC decreased the expression of 1 cell development related transcript. Conclusions: 1) IPC in DDLT increased the expression of antioxidant transcripts similar to studies in animal IPC, anesthetic, and remote IPC. 2) IPC increased expression of lipogenic transcripts, which may be relevant to the clinically observed increased IRI in our IPC group. 3) Our microarray findings support our clinical observations and are compatible with the varied outcomes of hepatic IPC studies in human liver transplantation. We conducted a nested sub-study in 12/101 subjects enrolled in a prospective randomized trial of 10 min IPC in DDLT during 2003-2006. Liver biopsies were performed at the end of cold storage and at 90 minutes after allograft reperfusion. Six biopsy pairs from both IPC and No IPC (STD) groups within a narrow donor risk index range were selected. Total RNA was extracted and hybridized with Affymetrix GeneChip Human Gene 1.0 ST Array. IPC effects were examined by comparing IPC vs. STD at both time points. Transcripts whose expression changed 2-fold with p<0.05 were considered significant.
2010-05-20 | E-GEOD-15480 | biostudies-arrayexpress
Project description:Brain death donor liver is an important organ source for liver transplantation.The liver injury after brain death donor liver transplantation is serious and the mechanism is unknown.In order to explore the role of lncRNAs and circRNAs expression profile and their biological functions in liver injury after brain death and liver transplantation, lncRNA and mRNA microarray expression profile were tested in the liver after brain death and normal liver transplantation.And this study lays a foundation for future studies on the potential role of lncRNAs in liver injury after brain death donor liver transplantation. To determine the LncRNA expression profile in hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation, we uesed LncRNA microArray analysis form Arraystar to examine the expression of LncRNAs and circRNAs in hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation.
2021-08-06 | GSE118182 | GEO
Project description:Liver tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation.
| PRJNA490174 | ENA
Project description:Introduction: Hepatic cell transplantation offers an alternative to orthotopic liver transplantation for chronic liver disease. We previously demonstrated that fetal rat hepatocytes durably persist and proliferate when transplanted to an injured adult liver. To identify mechanisms underlying fetal hepatocyte repopulation, we profiled gene expression and histone post-translational modifications (hPTM) of post-transplantation fetal colonies and surrounding liver, as well as those of primary fetal and adult hepatocytes. Methods: Using the DPPIV rat model, we transplanted and traced fetal hepatocytes into adult hosts. At 10 months after transplantation, we used laser capture microscopy to isolate fetal-derived colonies and surrounding adult host tissue. RNA and histones were extracted from laser captured tissue and isolated hepatocytes for RNA-seq and quantitation of hPTM. Results: Principal component analysis of RNA-seq results discriminated between fetal-derived colonies and surrounding adult host tissue. We identified 953 differentially expressed genes, many of which were significantly overexpressed in pre-transplant fetal hepatocytes relative to adult hepatocytes. This gene set included a disproportionate number of genes encoding ion transmembrane transporters. Proteomic analyses identified 13 distinct marks on Histone H3 whose relative abundance differed significantly between fetal-derived colonies and adult host tissue. Of these 13 marks, 11 had abundance profiles similar to those of fetal hepatocytes. Conclusions: A distinct gene expression and epigenetic profile seen in pre-transplant fetal cells is retained for at least 10 months following transplantation. Ontological and pathway analysis indicates activation of ion transporters, which may relate to the growth advantage of transplanted fetal cells.
2023-04-27 | GSE201757 | GEO