Meta-analysis of molecular response of kidney to ischemia reperfusion injury for the identification of new candidate genes

BMC Nephrology

Shui Q Ye²  Hamid Rabb³  Li Q Zhang¹  Peixin Huang¹  Daniel P Heruth¹  Dilyara I Cheranova¹  Dmitry N Grigoryev² 

[1] Division of Experimental and Translational Genetics, Department of Pediatrics, Children’s Mercy Hospitals and Clinics, University of Missouri School of Medicine, Kansas City, MO, USA;Omics Analysis Unit, Core of Genetic Research, Division of Experimental and Translational Genetics, Department of Pediatrics, Children’s Mercy Hospitals and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA;Division of Nephrology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA

关键词: Meta-analysis;    Bioinformatics;    Ischemia reperfusion injury;    Kidney;   

Others  :  1082808
DOI  :  10.1186/1471-2369-14-231

 received in 2013-06-12, accepted in 2013-10-11,  发布年份 2013

【 摘 要 】

Background

Accumulated to-date microarray data on ischemia reperfusion injury (IRI) of kidney represent a powerful source for identifying new targets and mechanisms of kidney IRI. In this study, we conducted a meta-analysis of gene expression profiles of kidney IRI in human, pig, rat, and mouse models, using a new scoring method to correct for the bias of overrepresented species. The gene expression profiles were obtained from the public repositories for 24 different models. After filtering against inclusion criteria 21 experimental settings were selected for meta-analysis and were represented by 11 rat models, 6 mouse models, and 2 models each for pig and human, with a total of 150 samples. Meta-analysis was conducted using expression-based genome-wide association study (eGWAS). The eGWAS results were corrected for a rodent species bias using a new weighted scoring algorithm, which favors genes with unidirectional change in expression in all tested species.

Results

Our meta-analysis corrected for a species bias, identified 46 upregulated and 1 downregulated genes, of which 26 (55%) were known to be associated with kidney IRI or kidney transplantation, including LCN2, CCL2, CXCL1, HMOX1, ICAM1, ANXA1, and TIMP1, which justified our approach. Pathway analysis of our candidates identified “Acute renal failure panel” as the most implicated pathway, which further validates our new method. Among new IRI candidates were 10 novel (<5 published reports related to kidney IRI) and 11 new candidates (0 reports related to kidney IRI) including the most prominent candidates ANXA2, CLDN4, and TYROBP. The cross-species expression pattern of these genes allowed us to generate three workable hypotheses of kidney IRI, one of which was confirmed by an additional study.

Conclusions

Our first in the field kidney IRI meta-analysis of 150 microarray samples, corrected for a species bias, identified 10 novel and 11 new candidate genes. Moreover, our new meta-analysis correction method improved gene candidate selection by identifying genes that are model and species independent, as a result, function of these genes can be directly extrapolated to the disease state in human and facilitate translation of potential diagnostic or therapeutic properties of these candidates to the bedside.

【 授权许可】

   
2013 Grigoryev et al.; licensee BioMed Central Ltd.

【 图 表 】

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