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Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the progression of polycystic kidney disease.

Pandey P, Qin S, Ho J, Zhou J, Kreidberg JA - BMC Syst Biol (2011)

Bottom Line: We found dysregulation of developmental, metabolic, and signaling pathways (e.g. Wnt, calcium, TGF-β and MAPK) in Pkd1⁻/⁻ kidneys.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medicine, Children's Hospital Boston; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.

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-β and MAPK) in Pkd1⁻/⁻ 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.

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qPCR analysis of miRNAs in PKD at embryonic age 17. Expression of 9 miRNAs (miR-10a, miR-126-5p, miR-200a, miR-204, miR-429, miR-488, miR-96, miR-182 and miR-30a-5p), predicted to target significantly regulated genes at E17.5 was evaluated using miRNA-qPCR assays. (A) miR-10a, miR-126-5p, miR-200a, miR-204 and miR-429 were down-regulated in Pkd1-/- kidneys. (B) miR-488, miR-96, miR-182 and miR-30a-5p were up-regulated in Pkd1-/- kidneys. '*' significantly different at p-value < 0.05.
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Figure 8: qPCR analysis of miRNAs in PKD at embryonic age 17. Expression of 9 miRNAs (miR-10a, miR-126-5p, miR-200a, miR-204, miR-429, miR-488, miR-96, miR-182 and miR-30a-5p), predicted to target significantly regulated genes at E17.5 was evaluated using miRNA-qPCR assays. (A) miR-10a, miR-126-5p, miR-200a, miR-204 and miR-429 were down-regulated in Pkd1-/- kidneys. (B) miR-488, miR-96, miR-182 and miR-30a-5p were up-regulated in Pkd1-/- kidneys. '*' significantly different at p-value < 0.05.

Mentions: Computational identification of a large number of miRNA-mRNA target interactions suggested that the expression of miRNAs might also change during the progression of PKD. We tested this hypothesis by determining the differential expression of 9 miRNAs (mmu-miR-10a, mmu-miR-30a-5p, mmu-miR-96, mmu-miR-126-5p, mmu-miR-182, mmu-miR-200a, mmu-miR-204, mmu-miR-429, and mmu-miR-488) between WT and Pkd1-/- genotypes at E14.5 and E17.5 (Figures 7 and 8). These nine miRNAs are expressed in kidney [48], but have not been previously associated with ADPKD. In our computational analysis, two or more tools predicted them as targets for differentially expressed genes at E14.5 and E17.5. The significance of changes in relative expression of miRNAs among the two groups was tested by Student's t-test, and a cutoff of 1.2 fold [49] and P ≤ 0.05 was used to determine the differential miRNA accumulation.


Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the progression of polycystic kidney disease.

Pandey P, Qin S, Ho J, Zhou J, Kreidberg JA - BMC Syst Biol (2011)

qPCR analysis of miRNAs in PKD at embryonic age 17. Expression of 9 miRNAs (miR-10a, miR-126-5p, miR-200a, miR-204, miR-429, miR-488, miR-96, miR-182 and miR-30a-5p), predicted to target significantly regulated genes at E17.5 was evaluated using miRNA-qPCR assays. (A) miR-10a, miR-126-5p, miR-200a, miR-204 and miR-429 were down-regulated in Pkd1-/- kidneys. (B) miR-488, miR-96, miR-182 and miR-30a-5p were up-regulated in Pkd1-/- kidneys. '*' significantly different at p-value < 0.05.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3111376&req=5

Figure 8: qPCR analysis of miRNAs in PKD at embryonic age 17. Expression of 9 miRNAs (miR-10a, miR-126-5p, miR-200a, miR-204, miR-429, miR-488, miR-96, miR-182 and miR-30a-5p), predicted to target significantly regulated genes at E17.5 was evaluated using miRNA-qPCR assays. (A) miR-10a, miR-126-5p, miR-200a, miR-204 and miR-429 were down-regulated in Pkd1-/- kidneys. (B) miR-488, miR-96, miR-182 and miR-30a-5p were up-regulated in Pkd1-/- kidneys. '*' significantly different at p-value < 0.05.
Mentions: Computational identification of a large number of miRNA-mRNA target interactions suggested that the expression of miRNAs might also change during the progression of PKD. We tested this hypothesis by determining the differential expression of 9 miRNAs (mmu-miR-10a, mmu-miR-30a-5p, mmu-miR-96, mmu-miR-126-5p, mmu-miR-182, mmu-miR-200a, mmu-miR-204, mmu-miR-429, and mmu-miR-488) between WT and Pkd1-/- genotypes at E14.5 and E17.5 (Figures 7 and 8). These nine miRNAs are expressed in kidney [48], but have not been previously associated with ADPKD. In our computational analysis, two or more tools predicted them as targets for differentially expressed genes at E14.5 and E17.5. The significance of changes in relative expression of miRNAs among the two groups was tested by Student's t-test, and a cutoff of 1.2 fold [49] and P ≤ 0.05 was used to determine the differential miRNA accumulation.

Bottom Line: We found dysregulation of developmental, metabolic, and signaling pathways (e.g. Wnt, calcium, TGF-β and MAPK) in Pkd1⁻/⁻ kidneys.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medicine, Children's Hospital Boston; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.

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-β and MAPK) in Pkd1⁻/⁻ 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.

Show MeSH
Related in: MedlinePlus