Understanding Kidney Disease: Toward the Integration of Regulatory Networks Across Species
Section snippets
Systems Approaches to Rodent Models of Kidney Pathophysiology
Because of its size, ease of handling, and relative susceptibility to genetic manipulation, the laboratory mouse has become perhaps the major mammalian model of kidney disease over the past few years. The mouse is also genetically and physiologically similar to human beings, and the mouse genome has been sequenced and annotated to a high standard, second only to that of human beings.1, 2 Systems approaches have been applied to the study of kidney diseases in the mouse in several disease models.
Comprehensive Strategy of Network Integration: Tool for Approximate Subgraph Matching of Large Queries Efficiently for Effective Integration of Knowledge from Cross-Species Studies
In addition to the strategies described previously, a more sophisticated use of cross-species gene expression studies compares complex regulatory networks across species for conserved network structures. To best define the shared transcriptional networks between human beings and a mouse model of human nephropathies, an index-based method, a Tool for Approximate Subgraph Matching of Large Queries Efficiently (TALE),23 can be applied. Species-specific transcriptional networks are built using
Web-Based Tools for Effective Integration of Knowledge From Cross-Species Studies
Large sets of genomic and EST-based expression data in various species are more and more accessible to the public, although often these data are stored in heterogeneous formats and scattered over a multitude of species-specific databases (Zebrafish Information Network [ZFIN] for zebrafish,24, 25 Berkeley Drosophila Genome Project [BDGP]26 and Flybase27, 28, 29, 30 for Drosophila, the Gene Expression Database [GXD],31, 32, 33 EMAGE,34, 35, 36 and the GenitoUrinary Development Molecular Anatomy
Outlook
Although we have concentrated our review on mouse models of kidney disease, nonrodent models such as the zebrafish, Danio rerio, the fruitfly, Drosophila melanogaster, and the toad, Xenopus laevis also should be considered for systems biology approaches because they have some advantages over rodent models, including smaller size, shorter generation time, high repopulation rate, and greater ease of genetic manipulation. Kidney systems biology researchers have not yet taken full advantage of
Acknowledgements
The authors thank Viji Nair, Celine Berthier, Markus Bitzer, Felix Eichinger, Sebastian Martini, and Subramaniam Pennathur for insightful discussion and critical reading of the manuscript.
References (50)
- et al.
Cancer gene discovery in mouse and man
Biochim Biophys Acta
(2009) - et al.
Glomerulus-specific mRNA transcripts and proteins identified through kidney expressed sequence tag database analysis
Kidney Int
(2007) - et al.
Gene expression profiling of anti-GBM glomerulonephritis model: the role of NF-kappaB in immune complex kidney disease
Kidney Int
(2004) - et al.
Gene expression profiling in the remnant kidney model of wild type and kinin B1 and B2 receptor knockout mice
Kidney Int
(2007) - et al.
Renal gene and protein expression signatures for prediction of kidney disease progression
Am J Pathol
(2009) - et al.
The quest for orthologs: finding the corresponding gene across genomes
Trends Genet
(2008) - et al.
Comparative gene expression analysis of zebrafish and mammals identifies common regulators in hematopoietic stem cells
Blood
(2010) - et al.
Maximizing mouse cancer models
Nat Rev Cancer
(2007) - et al.
The glomerular transcriptome and a predicted protein-protein interaction network
J Am Soc Nephrol
(2008) - et al.
Large-scale identification of genes implicated in kidney glomerulus development and function
EMBO J
(2006)
A panoramic view of gene expression in the human kidney
Proc Natl Acad Sci U S A
Gene expression in the normal adult human kidney assessed by complementary DNA microarray
Mol Biol Cell
Gene expression profiling analysis in nephrology: towards molecular definition of renal disease
Clin Exp Nephrol
Gene expression analysis in renal biopsies
Nephrol Dial Transplant
Gene expression analysis of human renal biopsies: recent developments towards molecular diagnosis of kidney disease
Curr Opin Nephrol Hypertens
Molecular profiling of diabetic mouse kidney reveals novel genes linked to glomerular disease
Diabetes
The role of aldosterone blockade in murine lupus nephritis
Arthritis Res Ther
Serum and urinary biomarker signatures for rapid preclinical in vivo assessment of CDK inhibition as a therapeutic approach for PKD
Cell Cycle
Kallikrein genes are associated with lupus and glomerular basement membrane-specific antibody-induced nephritis in mice and humans
J Clin Invest
Mouse models of diabetic nephropathy
J Am Soc Nephrol
Enhanced expression of Janus kinase-signal transducer and activator of transcription pathway members in human diabetic nephropathy
Diabetes
Characterization of susceptibility of inbred mouse strains to diabetic nephropathy
Diabetes
Impact of genetic background on nephropathy in diabetic mice
Am J Physiol
Rosiglitazone reduces renal and plasma markers of oxidative injury and reverses urinary metabolite abnormalities in the amelioration of diabetic nephropathy
Am J Physiol
Cited by (3)
Structural and physiological changes of the kidney with age and its impact on chronic conditions and COVID-19
2023, Ageing Research ReviewsDesign of the nephrotic syndrome study network (NEPTUNE) to evaluate primary glomerular nephropathy by a multidisciplinary approach
2013, Kidney InternationalCitation Excerpt :Emerging systems biology approaches will be used to define associations between these multiphasic and interrelated genome-scale profiles and the detailed clinical and structural phenotypes. The NEPTUNE study will establish a core molecular data set containing genetic profiles and renal tissue, compartment-specific, genome-wide mRNA expression data to facilitate multidisciplinary and transdisciplinary research exploration along the genotype–phenotype continuum.10-13 The NEPTUNE core data sets will provide a foundation to link mechanistic information with clinical disease presentation, and link molecular information from model systems to human NS data sets.
Microarray applications in nephrology with special focus on transplantation
2012, Journal of Nephrology