# Systems Biology Approach to Identify Transcriptome Reprogramming and Candidate MicroRNA Targets during the Progression of Polycystic Kidney Disease

 Title: Systems Biology Approach to Identify Transcriptome Reprogramming and Candidate MicroRNA Targets during the Progression of Polycystic Kidney Disease Author: Pandey, Priyanka; Qin, Shan; Ho, Jacqueline; Kreidberg, Jordan Alexander; Zhou, Jing Note: Order does not necessarily reflect citation order of authors. Citation: Pandey, Priyanka, Shan Qin, Jacqueline Ho, Jing Zhou, and Jordan Alexander Kreidberg. 2011. Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the progression of polycystic kidney disease. BMC Systems Biology 5:56. Full Text & Related Files: 3111376.pdf (2.162Mb; PDF) Abstract: Background: Autosomal dominant polycystic kidney disease (ADPKD) is characterized by cyst formation throughout the kidney parenchyma. It is caused by mutations in either of two genes, $$PKD1$$ and $$PKD2$$. Mice that lack functional $$Pkd1 (Pkd1^{-/-})$$, develop rapidly progressive cystic disease during embryogenesis, and serve as a model to study human ADPKD. Genome wide transcriptome reprogramming and the possible roles of micro-RNAs (miRNAs) that affect the initiation and progression of cyst formation in the $$Pkd1^{-/-}$$ have yet to be studied. miRNAs are small, regulatory non-coding RNAs, implicated in a wide spectrum of biological processes. Their expression levels are altered in several diseases including kidney cancer, diabetic nephropathy and PKD. Results: We examined the molecular pathways that modulate renal cyst formation and growth in the $$Pkd1^{-/-}$$ model by performing global gene-expression profiling in embryonic kidneys at days 14.5 and 17.5. Gene Ontology and gene set enrichment analysis were used to identify overrepresented signaling pathways in $$Pkd1^{-/-}$$ kidneys. We found dysregulation of developmental, metabolic, and signaling pathways (e.g. Wnt, calcium, $$TGF-\beta$$ and MAPK) in $$Pkd^{-/-}$$ kidneys. Using a comparative transcriptomics approach, we determined similarities and differences with human ADPKD: ~50% overlap at the pathway level among the mis-regulated pathways was observed. By using computational approaches (TargetScan, miRanda, microT and miRDB), we then predicted miRNAs that were suggested to target the differentially expressed mRNAs. Differential expressions of 9 candidate miRNAs, miRs-10a, -30a-5p, -96, -126-5p, -182, -200a, -204, -429 and -488, and 16 genes were confirmed by qPCR. In addition, 14 candidate miRNA:mRNA reciprocal interactions were predicted. Several of the highly regulated genes and pathways were predicted as targets of miRNAs. Conclusions: We have described global transcriptional reprogramming during the progression of PKD in the $$Pkd1^{-/-}$$ model. We propose a model for the cascade of signaling events involved in cyst formation and growth. Our results suggest that several miRNAs may be involved in regulating signaling pathways in ADPKD. We further describe novel putative miRNA:mRNA signatures in ADPKD, which will provide additional insights into the pathogenesis of this common genetic disease in humans. Published Version: doi:10.1186/1752-0509-5-56 Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111376 Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:8830765 Downloads of this work: