Dataset Information

Multiple gene differential expression patterns in human ischemic liver: safe limit of warm ischemic time.

ABSTRACT: AIM:To investigate the multiple gene differential expression patterns in human ischemic liver and to produce the evidence about the hepatic ischemic safety time. METHODS:The responses of cells to hepatic ischemia and hypoxia at hepatic ischemia were analyzed by cDNA microarrary representing 4 000 different human genes containing 200 apoptotic correlative genes. RESULTS:There were lower or normal expression levels of apoptotic correlative genes during the periods of hepatic ischemia for 0-15 min, the maintenance homostatic genes were expressed significantly higher at the same time. But at the hepatic ischemia for 30 min, the expression levels of maintenance homeostatic genes were down-regulated, the expressions of many apoptotic correlative genes and nuclear transcription factors were activated and up-regulated. CONCLUSION:HIF-1, APAF-1, PCDC10, FBX5, DFF40, DFFA XIAP, survivin may be regarded as the signal genes to judge the degree of hepatic ischemic-hypoxic injure, and the apoptotic liver cell injury due to ischemia in different time limits. The safe limit of human hepatic warm ischemic time appears to be generally less then 30 min.

SUBMITTER: Lu QP

PROVIDER: S-EPMC4572350 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Multiple gene differential expression patterns in human ischemic liver: safe limit of warm ischemic time.

Lu Qi-Ping QP Cao Ting-Jia TJ Zhang Zhi-Yong ZY Liu Wei W

World journal of gastroenterology 20040701 14

<h4>Aim</h4>To investigate the multiple gene differential expression patterns in human ischemic liver and to produce the evidence about the hepatic ischemic safety time.<h4>Methods</h4>The responses of cells to hepatic ischemia and hypoxia at hepatic ischemia were analyzed by cDNA microarrary representing 4 000 different human genes containing 200 apoptotic correlative genes.<h4>Results</h4>There were lower or normal expression levels of apoptotic correlative genes during the periods of hepatic ...[more]

PMID: 15237451

Similar Datasets

Project description:BACKGROUND: Frequent pattern mining analysis applied on microarray dataset appears to be a promising strategy for identifying relationships between gene expression levels. Unfortunately, too many itemsets (co-expressed genes) are identified by this analysis method since it does not consider the importance of each gene within biological processes to a cellular response and does not take into account temporal properties under biological treatment-control matched conditions in a microarray dataset. RESULTS: We propose a method termed TIIM (Top-k Impactful Itemsets Miner), which only requires specifying a user-defined number k to explore the top k itemsets with the most significantly differentially co-expressed genes between 2 conditions in a time course. To give genes different weights, a table with impact degrees for each gene was constructed based on the number of neighboring genes that are differently expressed in the dataset within gene regulatory networks. Finally, the resulting top-k impactful itemsets were manually evaluated using previous literature and analyzed by a Gene Ontology enrichment method. CONCLUSIONS: In this study, the proposed method was evaluated in 2 publicly available time course microarray datasets with 2 different experimental conditions. Both datasets identified potential itemsets with co-expressed genes evaluated from the literature and showed higher accuracies compared to the 2 corresponding control methods: i) performing TIIM without considering the gene expression differentiation between 2 different experimental conditions and impact degrees, and ii) performing TIIM with a constant impact degree for each gene. Our proposed method found that several new gene regulations involved in these itemsets were useful for biologists and provided further insights into the mechanisms underpinning biological processes. The Java source code and other related materials used in this study are available at "http://websystem.csie.ncku.edu.tw/TIIM_Program.rar".

Project description:Ischemic acute kidney injury (AKI) has always been a hot and difficult research topic in the field of renal diseases. This study aims to illustrate the safe warm ischemia time of kidney and the molecular network characteristics and pathological features of mild to severe ischemia reperfusion kidney injury. We established varying degrees of renal injury due to different ischemia time (0 min, 16 min, 18 min, 20 min, 22 min, 24 min, 26 min, 28 min, and 30 min) on unilateral (left kidney) ischemia-reperfusion injury and contralateral (right kidney) resection (uIRIx) mouse model. Mice were sacrificed 24 h after uIRIx, blood samples were harvested to detect serum creatinine (Scr), and kidney tissue samples were harvested to perform Periodic Acid-Schiff (PAS) staining and RNA-Seq. Differentially expressed genes (DEGs) were identificated, time-dependent gene expression patterns and functional enrichment analysis were further performed. Finally, qPCR was performed to validated RNA-Seq results. Our results indicated that there was no absolute safe renal warm ischemia time, and every minute of ischemia increases kidney damage. Warm ischemia 26min or above in mice makes severe kidney injury, renal pathology and SCr were both significantly changed. Warm ischemia between 18 and 26 min makes mild kidney injury, with changes in pathology and renal molecular expression, while SCr did not change. No obvious pathological changes but significant differences in molecular expression were found less than 16min warm ischemia. There are two key time intervals in the process of renal ischemia injury, 0 min-16 min (short-term) and 26 min-28 min (long-term). Gene expression of immune-related pathways were most significantly down-regulated in short-term ischemia, while metabolism-related pathways were the mainly enriched pathway in long-term ischemia. Taken together, this study provides novel insights into safe renal artery occlusion time in partial nephrectomy, and is of great value for elucidating molecular network characteristics and pathological features of mild to severe ischemia reperfusion kidney injury, and key genes related to metabolism and immune found in this study also provide potential diagnostic and therapeutic biomarkers for AKI.

Dataset Information

Multiple gene differential expression patterns in human ischemic liver: safe limit of warm ischemic time.

Publications

Multiple gene differential expression patterns in human ischemic liver: safe limit of warm ischemic time.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets