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Updated: Jun 2, 2026
MicroRNA In situ Hybridization for Formalin Fixed Kidney Tissues
Published on: November 30, 2013
Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the
Priyanka Pandey1, Shan Qin, Jacqueline Ho
1Department of Medicine, Children's Hospital Boston; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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.
Insights
Researchers studied gene expression in a mouse model of Autosomal dominant polycystic kidney disease (ADPKD). They identified key signaling pathways and potential micro-RNA (miRNA) targets involved in cyst development, offering new insights into ADPKD pathogenesis.
Area of Science:
- Genomics and Molecular Biology
- Developmental Biology
- Genetics
Background:
- Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder causing kidney cyst formation.
- Mutations in PKD1 or PKD2 genes cause ADPKD.
- The Pkd1⁻/⁻ mouse model exhibits rapid, embryonic cystic kidney disease, valuable for studying human ADPKD.
Purpose of the Study:
- To investigate global transcriptome reprogramming in the Pkd1⁻/⁻ mouse model.
- To identify signaling pathways and micro-RNAs (miRNAs) involved in ADPKD cystogenesis.
- To compare molecular findings between the mouse model and human ADPKD.
Main Methods:
- Global gene-expression profiling of embryonic Pkd1⁻/⁻ kidneys.
- Gene Ontology and gene set enrichment analysis to identify dysregulated pathways.
- Computational prediction of miRNA targets and validation of candidate miRNAs and genes by qPCR.
Main Results:
- Dysregulation of developmental, metabolic, and signaling pathways (Wnt, calcium, TGF-β, MAPK) in Pkd1⁻/⁻ kidneys.
- Approximately 50% pathway overlap observed between the mouse model and human ADPKD.
- Differential expression of 9 candidate miRNAs and 16 genes confirmed, with predicted miRNA:mRNA interactions.
Conclusions:
- Global transcriptional changes occur during PKD progression in the Pkd1⁻/⁻ model.
- A signaling cascade model for cyst formation and growth is proposed.
- Novel miRNA:mRNA signatures identified in ADPKD offer insights into disease pathogenesis.
