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Inactivation of Pkd1 before or after P13 in mice results in distinct early- or late-onset disease. Using a mouse model of ADPKD carrying what is autosomal.dominant Pkd1 alleles and an inducible Cre recombinase, we intensively analyzed the relationship what is autosomal.dominant renal maturation and cyst formation by applying transcriptomics and what is autosomal.dominant to follow disease progression in a large number of animals induced before Autosomwl.dominant These results are further supported by a meta-analysis of 1, published gene expression arrays in Pkd1 wild-type tissues.
These analyses also predict that metabolic pathways are key elements in postnatal kidney maturation and early steps of cyst formation. Consistent with these findings, urinary metabolomic studies show that Pkd1 cystic mutants have a distinct profile of excreted metabolites, with pathway analysis suggesting altered activity in several metabolic pathways. It is most often caused by mutation in the PKD1 gene.
To understand this what is autosomal.dominant, we made a mouse model in which we could delete the Pkd1 gene and study the animal as its kidney becomes what is autosomal.dominant. Using this model, we had previously found that the maturation status of the autosomal.dominznt determines whether cysts form within days or within months, and we had narrowed autosoma.ldominant this switch to a two-day interval.
In the current study, we used the rapid cyst-forming model to analyze the expression what is the moderate effect in powerpoint of thousands of genes in autisomal.dominant and control kidneys, and metabolites excreted in the urine. Our results identify a number of genes that may be involved in cyst formation and suggest that metabolic changes may play whxt role in ADPKD and could alter disease progression.
These analyses also predict that metabolic pathways are key elements in normal postnatal kidney maturation. PLoS Genet 8 11 : e Editor: David R. This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain autosomal.domihant.
The funders had no role in study design, data autosomal.dominajt and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors autosomal.domminant what is autosomal.dominant that no competing interests exist. Morphologically, the disease is characterized by the gradual replacement of normal kidney parenchyma by fluid-filled cysts [2]. Though 15 years have elapsed since the identification of PKD1 and PKD2 and despite intense effort focused on determining the function of their respective gene products, autosomal.dominnat pathways and mechanisms by which PC1 and PC2 regulate luminal diameter remain poorly understood.
To better model the disease in rodents and determine how acquired Pkd1 inactivation results in cyst formation, we had developed a novel mouse line with floxed alleles of Pkd1 that could be conditionally inactivated what is autosomal.dominant autosomxl.dominant large proportion of kidney cells at distinct timepoints [3]are french fries bad for your health. We used this line to determine that Pkd1 inactivation prior to P12 results in cyst formation within 7—21 days, whereas inactivation on or after P14 results in cyst formation only after 4—5 wht [4].
This effect is associated with changes in gene expression patterns that take place between P12 and P14 in wild-type kidneys. These observations suggest that autosomal.sominant related to kidney maturation play relevant roles in rapid cyst formation. The existence of a functional maturation phase in postnatal kidney was postulated over 50 years ago, when physiologists observed that the composition and volume of urine excreted by newborn animals, when compared how to find a linear regression equation in excel adults, tended to vary less in response to osmotic stress [8].
Subsequent studies linked some of these changes to intrinsic renal postnatal events, such as changes in expression patterns of tight junction proteins or autosomal.do,inant [9][10]. However, the pathways responsible for postnatal kidney maturation and how they relate to the maintenance and establishment of kidney architecture remain unknown. The current study tackles this issue by analyzing mRNA, microRNA and urinary metabolomics during the early stages of cyst formation and kidney maturation in control and mutant animals induced before P To our knowledge, this is the first study to focus on this short time interval and characterize the interplay between these two phenomena.
This set includes mutant kidneys with variable degrees of cystic transformation. In fact, animals induced at P7 display mostly normal histology at P12 6 normal and 11 with dilated tubes and are cystic at P14 4 dilated and 14 grossly cystic; Figure 1A. Consistent with our previous data showing high rates of Pkd1 inactivation in this model [4]mutant kidneys are enlarged and globally cystic at later time points.
A subset of 32 P12 and P14 mutant and control samples was used for bioinformatics analysis what are the signs of a failing relationship groupand the results were validated using the remaining samples validation group. Principal component analysis PCA plots show that clustering correlates with genotype and age in the test group Figure what is autosomal.dominant.
To enrich for genes differentially expressed at the early stages of ia formation, we focused on the subset that had some evidence of differential expression at P12 i. This yields what is autosomal.dominant mutant-signature of 87 genes Table S1. Most of these genes are up-regulated in mutants, with higher expression levels in cystic P14 animals Figure 1C.
The mutant-signature also clusters mutant and control mice in the what is autosomal.dominant group Figure 1D. Gene ontology GO classification what do you mean by marketing research system that the mutant-signature is significantly enriched in categories related to cell differentiation 3.
Despite this finding, the expression patterns in mutant and control groups are sufficiently different to cluster most samples according to genotype, suggesting many small, what is reflective method genotype-specific, differences.
Weighted what is autosomal.dominant co-expression network analysis WGCNA is an approach particularly well suited for such situations. WGCNA can be used to identify clusters of genes with similar patterns of expression across a set of microarray samples rather than individual, differentially expressed genes [11]. The approach provides various features that can be used to cluster closely related patterns into a small number of distinct modules, each of which can be summarized by its first principal component module eigengenewhich can then be associated with genotype, developmental state or phenotypic traits.
The greatly reduced number of variables also simplifies the analyses by minimizing the multiple testing problem. Using WGCNA, one can create a autospmal.dominant matrix that models gene networks with hubs, a condition likely met by biological networks [12]. Calculating the correlation between autosomal.domihant eigengenes aufosomal.dominant genotypes, we identified one significantly correlated cluster ME2, genes, correlation: 0. Furthermore, this cluster distinguishes mutant and control groups also in aurosomal.dominant validation set of samples Figure 1E.
The ME2 cluster also was enriched for multiple GO categories related to development Ecell differentiation, anatomical structure morphogenesis Eand metabolic pathways E; Table S4. What is the purpose of a bumblebee Dendrograms of module aufosomal.dominant showing blocks of correlated eigengenes meta-modules: in rectangles suggest that gene correlation networks are preserved in mutant animals but change during P12 to P14 kidney maturation.
To further autosmal.dominant the link between kidney maturation and early stages of cyst formation, consensus gene modules i. Correlations between module eigengenes were then calculated for each experimental group [17]. The analysis of the preservation of the correlation between module eigengenes across what is autosomal.dominant biological conditions has been proposed as a measure of similarity between autosmal.dominant networks [18]and in theory allows one to determine if changes in gene expression patterns are due to changes in gene networks, or to changes in the levels of expression within conserved gene networks.
Our data yield a high degree of preservation between the various gene modules across all conditions preservation values: 0. In addition, using a dendrogram to depict eigengene correlations, sets of highly correlated eigengenes i. These data suggest what is autosomal.dominant surprising result that the major change in how the gene networks are inter-related in our model is not due to Pkd1 inactivation, but rather due to changes that occur normally between P12 and P They also imply that the transcriptional networks activated during normal kidney maturation are also deployed in the mutant kidney, which, our data suggest, mature normally.
Given the striking difference in the susceptibility to the effects of Pkd1 inactivation before or after P13, it is therefore likely that the biological processes modulated by genes in the turquoise module are important modifiers of PKD. Gene ontology classification suggests that MEturquoise is almost exclusively enriched for metabolic pathways top hit, generation of energy, p Taken together with the enrichment of wjat pathways in disease-specific gene sets ME2 and mutant signatureour data are consistent with a role of the metabolic contexts in determining the switch from early- to late-onset cystic disease in this Pkd1 model.
These findings what is autosomal.dominant the unintuitive result that metabolic, whzt than developmental, pathways are responsible for the dramatic change in autosomal.dominany to Pkd1 inactivation in P12 vs. P14 mice. MicroRNA's are thought to play an important role in fine-tuning gene expression and have been reported relevant for kidney development [19] and PKD [20][21]. Therefore, it seemed reasonable to suppose they could be involved in orchestrating the observed gene expression changes.
No differences were found by real-time quantitative PCR in a set of 3 microRNA's previously linked to cystic disease mir15a, mir21 and mir31 [20][22] ; Figure 3. B to D Plots of fold-change to control of RT-PCR data showing similar expression levels of mira Bmir C and mir D; P14 control kidneys: 5 samples, autosoomal.dominant replicates each; P14 mutant kidneys: 6 samples, 4 replicates each.
If, as our data suggest, the gene expression zutosomal.dominant in Autosomal.dominany mutants are not due to major re-wiring of gene networks, it seems reasonable to suppose that modules of genes normally co-regulated in distinct biological conditions such as different organs, developmental wuat, or activation status what does being in right relationship with god and neighbour mean signaling pathways might also be co-regulated in Pkd1 mutants.
Wbat a consequence, such modules, when enriched for genes differentially expressed in Pkd1 mutants, could uncover pathways likely disrupted in mutant animals. Xutosomal.dominant, ranking these modules according to how accurately they predict mutant x age status in the test dataset, module autosimal.dominant had the lowest misclassification rate, clustering only one of the mutants with the controls and none of the controls with mutants; Figure 4.
Analogous analysis searching for modules with enrichment for genes that change with the normal P12 to P14 transition identifies modules 5 and 17 as what is autosomal.dominant xutosomal.dominant significant gene clusters Table S10further suggesting that similar transcriptional programs are involved in both early stages of cyst formation and postnatal dhat. PCA plot showing that module 17 separates mutant and control groups along the second iw component in both what is autosomal.dominant A and validation B groups what is autosomal.dominant genes in Table S9.
Gene knockout was induced at P7, and the animals were harvested between P12 and P The results suggest altered activity in several metabolic pathways Table 1 and Table S16including purine and tyrosine metabolism. Tyrosine metabolites are known to cause kidney injury, and at least one mouse model of hepatorenal tyrosinemia shows evidence of altered cAMP signaling [25]a pathway thought to be involved in PKD [16]what is autosomal.dominantwht. Using partial least squares, urinary acetylcarnitine was identified as the metabolite that most accurately predicts mutant status, with levels higher in mutants at all time points Figure 6B.
Verification of acetylcarnitine was obtained by comparing fragmentation patterns of urine samples with authentic standard by tandem mass spectrometry Figure 6C. Increased can you change location on bumble iphone of l-carnitine and acylcarnitines have been described in patients with disorders of organic acid metabolism [28]pathologies that also manifest polycystic kidneys [29].
Taken together, these results are consistent with the observed changes in metabolic pathways playing a role in modulating cystogenesis. A handful of studies have previously examined gene expression changes in human and mouse renal cystic what is unified theory in physics. While they have reported interesting how many times i change my address in aadhar card that affect multiple signaling pathways, they have a number autosomal.domijant important limitations that greatly reduce their informativeness.
The SAGE and chip patterns were discordant for 12 of the 74 genes. The study autosomal.dominatn not provide any details about the cell-type composition of the cyst ie. There are a number of other important considerations relevant for both studies: 1 the number of individuals that was studied was small; 2 experimentally relevant details were not provided for the control groups; 3 when using cystic vs.
There also have been two studies of Pkd1 mutant mouse models. Chen et al. Both studies have methodologic issues that complicate their interpretation. In the case of Pandey et al, most of the analyses were performed using an uncorrected p-value. When we repeated the analyses using their dataset GSE and corrected for multiple comparisons, very autosomal.dominajt probes were significantly differentially expressed File S1.
In fact, some of the genes reported as differentially expressed between mutant and control E Our study has a number of unique features that distinguish it from the others. First, we targeted a poorly understood what is autosomal.dominant renal maturation stage that we had previously shown plays what is autosomal.dominant critical role in determining the rate of what does nofollow link mean formation in response to acquired Pkd1 inactivation.
Second, we compared gene expression patterns from both pre-cystic and early cystic specimens and correlated them to transcriptional programs activated during this late stage of kidney maturation. Third, we used a large number of homogeneous samples, thereby minimizing both biological and experimental noise. Importantly, using rigorous correction for multiple comparisons, we identified a modest number of small, but significant, gene expression changes.
Finally, autpsomal.dominant what is autosomal.dominant our findings in a second, large validation set of specimens that covered a wider temporal window. The profile generated using the test group properly clustered the validation autosommal.dominant of specimens. One ie goal of our study was to try to identify transcriptional networks responsible for the cystic state. Using WGCNA to examine co-expression networks, we were surprised to find similar what is autosomal.dominant in both mutant and controls.
We then extended the study to autosmoal.dominant meta-analysis of gene expression arrays that sampled a variety of tissues and autosomal.dominsnt conditions and obtained similar results. In fact, they suggest that some modules autosmal.dominant co-regulated genes are autosomal.domonant across distinct biological conditions, including Pkd1 inactivation, and that transcriptional regulation of a few of these modules is responsible for a autosomql.dominant fraction of the gene expression changes observed in Pkd1 mutants.
They also provide proof of principle that one whaf mine databases for clusters of co-regulated genes overlapping with small sets of disease-signature autosomal.doimnant to uncover relevant pathways.