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An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease

ABSTRACT: We established and validated sequence capture based NGS testing approach for all genes known for cystic and polycystic kidney disease including PKD1. This setup overcomes the complication of unspecific capture of pseudogenes by applying a mapping algorithm efficiently and specifically aligning reads to the PKD1 locus.

PROVIDER: EGAS00001001003 | EGA |

REPOSITORIES: EGA

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An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease.

Eisenberger Tobias T Decker Christian C Hiersche Milan M Hamann Ruben C RC Decker Eva E Neuber Steffen S Frank Valeska V Bolz Hanno J HJ Fehrenbach Henry H Pape Lars L Toenshoff Burkhard B Mache Christoph C Latta Kay K Bergmann Carsten C

PloS one 20150203 2

Renal cysts are clinically and genetically heterogeneous conditions. Autosomal dominant polycystic kidney disease (ADPKD) is the most frequent life-threatening genetic disease and mainly caused by mutations in PKD1. The presence of six PKD1 pseudogenes and tremendous allelic heterogeneity make molecular genetic testing challenging requiring laborious locus-specific amplification. Increasing evidence suggests a major role for PKD1 in early and severe cases of ADPKD and some patients with a recess ...[more]

PMID: 25646624

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ena-DATASET-BIOSCIENTIA-04-12-2014-09:03:57:327-147 - samples

Project description:We established and validated a sequence capture based NGS testing approach for PKD1. The presence of six PKD1 pseudogenes and tremendous allelic heterogeneity make molecular genetic testing of PKD1 variants challenging. In the publication accompaying this dataset (An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease, Eisenberger et.al., PLoS one), we demonstrate that the applied standard mapping algorithm specifically aligns reads to the PKD1 locus and overcomes the complication of unspecific capture of pseudogenes. This dataset contains the raw PKD1 reads of all patients from the publication.

| EGAD00001001091 | EGA

Polycystic Kidney Disease Progression Expression Analysis

Project description:Polycystic Kidney Disease (PKD) is a genetic disease of the kidney characterized by the gradual replacement of normal kidney parenchyma by fluid-filled cysts and fibrotic tissue. Autosomal Dominant Polycystic Kidney Disease (ADPKD) is caused by mutations in the PKD1 or PKD2 gene. Here we present an RNASeq experiment designed to investigate the effect of a kidney specific and Tamoxifen inducible knockout of the Pkd1 gene in mice. The Pkd1cko mice were harvested at different time points 2-weeks, 3-weeks, 5-weeks, 10.5-weeks, 11-weeks and 15-weeks after gene inactivation.

2019-12-24 | E-MTAB-8086 | biostudies-arrayexpress

Adamts1 Promotes Cyst Expansion in Polycystic Kidney Disease

Project description:Autosomal dominant polycystic kidney disease (ADPKD) is characterized by mutations in either the PKD1 or PKD2 genes leading to progressive cyst growth and often ESKD. We have previously demonstrated that with loss of Pkd1 the tubules can enlarge without an increase in tubular cell numbers, suggesting that tubular basement membrane remodeling is important for cystic dilation. Here we compared the transcriptomes from inducible tubule-specific knock out of Pkd1 (PkdTKO) and the uninduced littermate mice kidneys as controls. RNA sequencing revealed significant upregulation of 17 metalloproteinases. Of these, A Disintegrin and Metalloproteinase with Thrombospondin Motif 1 (Adamts1), expressed primarily by the proximal tubule, is the most significantly upregulated following loss of Pkd1 expression. Upregulation of Adamts1 in PkdTKO kidneys correlated with a significant increase in the 70 kDa cleavage product of the V1 isoform of versican, which localized to the tubule basement membrane (TBM) and adjacent interstitial mononuclear cells. Simultaneous deletion of both Adamts1 and Pkd1 (P/ATKO) reduced Adamts1 expression levels by >90%, prevented V1 versican cleavage, and reduced interstitial macrophage accumulation and activation. P/ATKO mice demonstrated slower cystic enlargement, improved BUN and creatinine and better survival than did PkdTKO mice. In conclusion, preventing Adamts1 upregulation following loss of tubular Pkd1 expression effectively reduced macrophage accumulation and TBM remodeling, slowing cyst growth and preserving renal function.

2024-09-30 | GSE270531 | GEO

Tuning the 3D-microenvironment of reprogrammed tubule cells enhances biomimetic modeling of polycystic kidney disease.

Project description:Mutations in PKD1 cause Autosomal Dominant Polycystic Kidney Disease (ADPKD). To further investigate the impact of Pkd1 knockout on renal tubular cells, a direct reprogramming approach was applied. After direct reprogramming of mouse embryonic fibroblasts to induced renal tubular epithelial cells (iRECs), Pkd1 knockout iREC clones were generated by Cre-mediated recombination of floxed Pkd1 alleles. The knockout clones were compared to their corresponding wild type clones by RNA Sequencing and transcriptome profiling.

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Pkd1 and Pkd2 mRNA cis-inhibition drives polycystic kidney disease progression

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Epigenetic silencing of PKD1 in autosomal dominant polycystic kidney disease

Project description:ADPKD (Autosomal dominant polycystic kidney disease) is the most common inherited disorders and is characterized by growth of numerous cysts filled with fluid in the kidneys. Ultimately, it leads to kidney failure. The mutations of PKD1 and PKD2 account for approximately 85 and 15 percent of ADPKD, respectively. However, the mechanisms related to genetic mutation of PKD1 and PKD2 are still unclear. To investigate altered gene expression levels, Affymetrix microarray was performed using the kidney tissue from normal and ADPKD patients.

2012-02-16 | GSE35831 | GEO

Expression profiling of Pkd1cko mice: A model of Polycystic Kidney Disease

Project description:Polycystic Kidney Disease (PKD) is a genetic disease of the kidney characterized by the gradual replacement of normal kidney parenchyma by fluid-filled cysts and fibrotic tissue. Autosomal Dominant Polycystic Kidney Disease (ADPKD) is caused by mutations in the PKD1 or PKD2 gene. Here we present an RNASeq experiment designed to investigate the effect of a kidney specific and Tamoxifen inducible knockout of the Pkd1 gene in mice. 7 mice were grouped into two groups, 4 Tamoxifen treated mice which develop an adult onset Polycystic Kidney Disease phenotype and 3 untreated mice which have WT phenotype.

2016-06-01 | E-MTAB-4086 | biostudies-arrayexpress

Transcriptomic and metabolomic analysis of autosomal dominant polycystic kidney disease identifies HNF4α as a disease modifier

2012-11-29 | GSE32586 | GEO

Transcriptomic and metabolomic analysis of autosomal dominant polycystic kidney disease identifies HNF4α as a disease modifier

Project description:Autosomal Dominant Polycystic Kidney Disease (ADPKD; MIM ID’s 173900, 601313, 613095) leads to end stage kidney disease, caused by mutations in PKD1 or PKD2. Inactivation of Pkd1 before or after P13 in mice results in distinct early- or late-onset disease. Using a mouse model of ADPKD carrying floxed Pkd1 alleles disrupted using a tamoxifen-inducible Cre recombinase, transcriptomics and metabolomics were applied to follow disease progression in animals induced before P10. Network analysis suggests that Pkd1-cystogenesis does not cause developmental arrest and occurs in the context of gene networks similar to those that regulate/maintain normal kidney morphology/function. These analyses also predict metabolic pathways, notably those controlled by HNF4α, are key elements in postnatal kidney maturation and early steps of cyst formation. To test this hypothesis, metabolic networks were altered by inactivating Hnf4a and Pkd1. The Pkd1/Hnf4a double knock-out have significantly more cystic kidneys thus indicating that modulating metabolic pathways might be an effective therapeutic approach. We crossed fifth-generation C57/BL6 Pkd1cond mice to fifth-generation C57/BL6 tamoxifen-Cre (B6.Cg-Tg(Cre/Esr1)5Amc/J mice (stock 004682), Jackson Laboratories) and C57/BL6 congenic B6.129S4-Gt(ROSA)26Sortm1Sor/J (stock 003474, Jackson Laboratories) to produce Pkd1 conditional mice with TamCre (mutant) or without TamCre (control). We induced Cre recombinase activity in mice < 10 days of age by intraperitoneally injecting nursing mothers with tamoxifen (10 mg/40 g) , and harvested kidney samples of control and mutant (34 and 36 animals, respectively) between the ages of 11 and 24 days. Postprocessed files (expression p value<0.05; quantile normalized; merged and corrected for batch-effect using COMBAT) linked below as supplementary files.

2012-11-29 | E-GEOD-32586 | biostudies-arrayexpress

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Project description:We report the findings of deletion of the miR17 binding motif from Pkd1 mRNA

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