Congenital anomalies of the kidney and urinary tract (CAKUT)
UTRECHT UNIVERSITY
Identifying novel genes involved in congenital anomalies of the kidney and urinary tract
A thesis written at the University Medical Center
Utrecht, Utrecht, The Netherlands
Glenn van de Hoek
July 2013 – August 2013
University Medical Center Utrecht
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Glenn van de Hoek
Identifying novel genes involved in congenital anomalies of the kidney and urinary tract
Student: Glenn van de Hoek
Examiner: Dr. K. Y. Renkema
Second reviewer: Dr. R. H. Giles
Course:
University:
Cancer, Stem Cells and Developmental Biology
Utrecht University
Institute:
Thesis period:
University Medical Center Utrecht
01/07/2013 – 01/08/2013
Identifying novel genes involved in congenital anomalies of the kidney and urinary tract | 2
University Medical Center Utrecht
Contents
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Glenn van de Hoek
Introduction
Currently, over 200 different rare renal disease have been described and in some studies it is estimated that more than 10% of people have a kidney disorder, equaling the prevalence of
diabetes (1). Thanks to progress in organ replacement therapy, patients with inherited or
acquired kidney disorders rarely die when their disease progresses. However, this apparent advantage is frequently bought at the expense of severely compromised health with poor quality of life, and causes a tremendous cumulative cost burden to health care systems. This is most strikingly exemplified by children born with severe congenital nephropathies, who nowadays can and will be dialyzed from neonatal age onwards and thus face many decades of life with endstage renal disease (ESRD) with a high likelihood of altered physical, cognitive and psychosocial development. It should be emphasized that the major proportion of children and up to 20% of
adults progressing to renal replacement therapy suffer from rare kidney diseases (1).
The current diagnostic and therapeutic management of rare kidney diseases is highly unsatisfactory. We are typically unable to explain the underlying inherited or acquired abnormality responsible for the disease phenotype, predict the individual risk and rate of disease progression, or quantitate the risk of relatives to develop the same disorder. Although numerous abnormalities in genes involved in renal development, structure, and function have been identified in recent years, the genetic and molecular basis of disease is still unknown in the majority of patients. Even in patients with known genetic disease causes, individual risk prediction is limited by considerable phenotypic variability which is thought to be due to complex genetic disease transmission and/or gene-environment interaction. On the other hand, different initial events often converge to common pathways of disease progression. Neither the clinical heterogeneity within individual disorders nor the commonalities between clinically disparate kidney diseases are well understood, and clinically applicable technologies for the molecular characterization of diseases and their risk of progression are lacking. Specific therapies effectively targeting disease activity and progression are, with a few notable exceptions, unavailable or limited to poorly defined disease subgroups; in the latter cases, biomarkers predicting individual susceptibility to pharmacotherapy are lacking. Finally, the lack of suitable disease models for many kidney disorders is conceived as a major barrier to progress in therapeutic development.
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Hence, to consistently improve the medical management and health outcomes of patients with rare kidney diseases, major progress is needed in four areas of research:
1.
Identification of the genetic and environmental initiators, modifiers of disease, biomarkers, and their molecular pathways;
2.
Re-definition of diseases according to molecular signatures and mechanistic principles beyond phenotypic or morphological description;
3.
Development of rapid and reliable diagnostic tests and biomarkers to allow better identification of progression risks and monitoring of disease activity;
4.
Development and application of disease models suitable to screen for novel molecular
therapies.
Recent progress in -omics technologies has opened a window of opportunity for rapid substantial progress in each of these areas. Diseases of the kidney appear particularly suited to
-omics approaches due to the opportunity to examine molecular events in the end organ that is manifesting the disease: kidney biopsy, provides a unique opportunity to study intrarenal biological processes ex vivo using transcriptomic, proteomic and morphological approaches in diagnostics. Urine is a readily available non-invasive bio resource to study molecular readouts directly derived from the organ of interest, the kidney. Amniotic fluid, which is the fetal urine, allows prenatal epigenetic, proteomic and metabolomic profiling in the context of renal maldevelopment. Recent technological progress in exosome isolation from urine and amniotic fluid even has created the opportunity to study non-invasively cellular biomaterials originating from the diseased tissues. The availability of such samples greatly facilitates the development of biomarkers.
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Glenn van de Hoek
The EURenOmics consortium for research on rare kidney disease
The EURenOmics consortium ( www.eurenomics.eu
) was established to facilitate the collaborative research on kidney diseases within Europe and beyond, which ultimately should lead to the development of novel tools that allow for a more accurate diagnoses, a better prediction of disease course and increased efficacy of available treatments, and help to develop new and improved therapies for rare kidney disorders. The consortium consist of specialists in the fields of nephrology, clinical genetics, fundamental and translational science and –omics technologies, all devoted to improve the lives of patients with rare kidney disorders. Together with NEUROMICS (neuromuscular disorders) and the RD-CONNECT infrastructure platform,
EURenOmics is being funded by the European Seventh Framework Programme (FP7; http://cordis.europa.eu/fp7 ). The consortium consists of 18 academic institutions and 8 industrial partners (for a list of participants see supplementary table 1), which together have access to the largest rare renal disease cohort (over 12,000 patients), containing detailed clinical information and comprehensive biorepositores containing DNA, blood, urine, amniotic fluid and kidney tissue.
The consortium has identified five groups (termed work packages within the consortium) of rare kidney diseases with the urgent need and significant potential for diagnostic and therapeutic progress: 1) steroid-resistant nephrotic syndrome (SRNS), 2) membranous nephropathy (MN), 3) tubulopathies, 4) complement disorders, and 5) congenital anomalies of the kidney and urinary
tract (CAKUT). The consortium will apply a wide range of -omics technologies, innovative systems biology approaches and a plethora of in vitro, ex vivo and in vivo models to study disease mechanisms and to explore novel therapeutic approaches (see figure 1). It starts with the search for new genes causing, modifying or predisposing to individual disease phenotypes. Screening strategies will encompass next-generation sequencing of known genes, regulatory regions, exomes and whole genomes as appropriate in the individual disease conditions, application of cutting-edge bioinformatic tools for data mining, filtering and gene network analysis, and extensive genotype-phenotype analyses. In addition, novel epitopes/antigens and antibodies will be searched systematically in those disorders in which an auto-immune pathology is suspected.
The information obtained in these first steps, including the gene products of the newly identified
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University Medical Center Utrecht gene variants, as well as the mechanisms of auto-antibody formation, will be functionally characterized in vitro, ex vivo and in vivo. In parallel to the genetic and immunological studies, multilevel -omics profiling (mRNA, miRNA, peptidome/proteome, metabolome) in body fluids and/or renal tissues will be performed to identify unique molecular signatures associating with individual disease entities (deep phenotyping). These studies are anticipated to lead to the development and validation of novel diagnostic tools and bio-markers. Finally, suitable in vitro and in vivo models will be developed that allow high-throughput screening of compound libraries for novel therapeutic agents reversing or attenuating disease phenotypes.
In this review we wish to focus on CAKUT, and describe how we can use the ample expertise within the EURenOmics consortium to achieve our goals in understanding this disease. To enhance our knowledge on CAKUT, EURenOmics has set multiple goals to be achieved by the groups that are part of the CAKUT work package. They include:
1.
Identification of novel candidate genes and elucidating the complex genetics of CAKUT;
2.
Establishing the transcriptional networks driving renal development;
3.
Functional characterization of CAKUT genes using in vivo-morpholino knockdown, ex vivo organ cultures, gene-targeting approaches in animal models and iPSC;
4.
Develop and implement a novel DNA diagnostic tool for CAKUT.
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Figure 1 Workflow of the EURenOmics consortium
The project is structured in seven work packages: WP1 (Management and Dissemination) will be responsible for monitoring and orchestrating the progress of the activities, providing logistic and administrative support to the partners, and interacting with EU authorities, patient advocacy groups, the media and general public. WP2 (steroid-resistant nephrotic syndrome; SRNS), WP3 (membranous nephropathy; MN), WP4 (tubulopathies), WP5 (complement disorders) and WP6 (congenital anomalies of the kidney and urinary tract; CAKUT) will carry out disease-oriented research plans. WP7 (integrative bioinformatics) will provide a central bioinformatics platform and utilize the full range of -omics data to address overarching mechanistic, diagnostic and therapeutic challenges at the systems biology level. The
WPs will proceed according to a cohesive overall strategy involving the following logical steps of implementation: (1) data harmonization and standardized clinical phenotyping, (2) gene/antigen identification, (3) ‘functiomics’, (4) integration of multilevel ‘-omics’ information (molecular phenotyping),
(5) diagnostic tool and biomarker development, (6) approaches to high-throughput drug screening.
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Congenital anomalies of the kidney and urinary tract (CAKUT)
Congenital anomalies of the kidney and urinary tract comprise a spectrum of structural malformations (see figure 2) encompassing renal agenesis, renal hypoplasia, cystic and non-cystic kidney dysplasia, duplex collecting system (DCS), ureteropelvic junction obstruction (UPJ),
megaureter, and vesicoureteral reflux (VUR) (2). CAKUT occurs in 3-6 per 1000 live births and is
responsible for 34-59% of chronic kidney disease, and 31% of all end-stage renal disease (ESRD)
cases in children in the US (3). However, the postnatal course of kidney function varies markedly
and currently cannot be predicted by phenotypic criteria. Hence, knowledge of the causes of
CAKUT and reliable molecular markers would be essential for early and correct diagnosis, prediction of the risk for progressive disease, and the consecutive tailoring of personalized strategies for pharmacological nephroprotection and timely surgical interventions. Whilst the
occurrence of syndromic phenotypes (4-6) and familial clustering (7-9) point to a major genetic
component, CAKUT disease traits often do not follow classical Mendelian inheritance patterns.
Its aetiology matches a range of monogenic towards complex inheritance patterns. Animal experiments have demonstrated that alterations in renal developmental genes encoding for transcription factors, growth factors, cell adhesion and polarity molecules, and components of the renin-angiotensin system can cause CAKUT, and expression studies implicate mislocalisation
and/or aberrant levels of these factors in mouse and human CAKUT (10-12).
Currently, it is thought that the origin of CAKUT lies in an aberrant development of the kidney, either through genetic influence or because of intrauterine obstruction of the urinary tract. In a healthy embryo, the kidney (also termed metanephros) develops through interaction of two different mesodermal tissues: the metanephric mesenchyme and the metanephric duct
Congenital anomalies of the kidney and urinary tract (CAKUT) comprises a spectrum of malformations including: renal agenesis, where either one (unilateral) or both (bilateral) fetal kidneys fail to develop.
Hypoplasia, a morphologically normal kidney with a reduced number of nephrons, or smaller nephrons.
Multicystic kidney dysplasia (MCKD), where the kidney harbors irregular cysts of different sizes, disrupting normal kidney function. Horseshoe kidney, a (often asymptomatic) condition where both kidneys are fused together. Duplex collecting system (DCS), two ureters drain from a single kidney. Ureteropelvic junction obstruction (UPJ), blockage of the junction between the ureter and the renal pelvis of the kidney, leading to hydronephrosis. And vesicoureteral reflux (VUR), where there is a backflow of urine from the bladder to the kidneys. Pictures are courtesy of Realexis Christofides .
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Figure 2 Overview of CAKUT phenotypes
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(derived from the Wolffian duct). Through inductive signals of both tissues, the metanephric duct buds off of the Wolffian duct (see figure 3), branching into the metanephric mesenchyme. There it continues branching into individual segments that ultimately evolve into the nephrons of the adult kidney. The Wolffian duct eventually develops into the ureter, connecting the kidney to the bladder. The interaction between the early metanephric tissues are most crucial for normal development of both kidney and urinary tract and its genetic regulation is therefore a target of
CAKUT. Several genes and signaling molecules that regulate the budding, branching and induction of kidney formation, have been identified and include Ret, Gdnf, Pax2, Bmp4, Six1,
Eya1, Foxc1 and many others (see figure 3). Interestingly, mutations in most of these genes have been found in CAKUT patients, as detailed below.
The Gdnf (glial-cell-line-derived neurothropic factor) – Ret pathway plays a central role in initiating the budding of the ureter and many renal developmental genes are directly or indirectly involved in its regulation. Gdnf is initially expressed by the metanephric mesenchyme where it binds to the receptor tyrosine kinase Ret, which is located on the Wolffian duct. This action of
Gdnf triggers the budding of the metanephric duct into the metanephric mesenchyme.
Consequently, absence of Gdnf or Ret most often leads to failure of ureteric bud formation
(however this is not always the case, indicating the presence of additional signals that are
redundant with Gdnf/Ret function(13)) in mice (14, 15) and in humans both GDNF and RET
mutations are associated with renal agenesis (16). The formation of a single, properly located
ureteric bud relies on the correct spatio-temporal expression of the Gdnf-Ret pathway, which is
regulated by a network of both activating and repressing (transcription) factors (17). One of the
positive Gdnf regulators is Pax2. Pax2, a homeobox transcription factor, can directly bind and
transcactivate the Gdnf promoter (18), resulting in Gdnf expression. In humans, mutations in
PAX2 are associated with autosomal dominant renal coloboma syndrome, a condition that is characterized mainly by congenital anomalies of the kidney and coloboma of the optic nerve. The renal complications of PAX2 patients often result in end-stage renal disease. This, together with the large frequency of PAX2 mutations found in CAKUT patients (a large European multicenter
study revealed that seven out of a 100 CAKUT patients harbored a PAX2 mutation (19)), stresses
the need for genetic PAX2 screening in all patients with severe kidney malformations associated
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Glenn van de Hoek with ESRD. One of the most important genes involved in kidney dysplasia, and a regulator of Pax2, is HNF1β (hepatocyte nuclear factor-1β). Although expressed in many different tissues (e.g. kidney, liver, pancreas), in the developing kidney HNF1β is specifically involved in maintaining
(among others) Gdnf-Ret and Pax2 (20). Dominant mutations in HNF1B are associated with renal
cysts and diabetes syndrome (RCAD) however are also identified with high frequency in children
with isolated renal malformations (21). Next to Pax2 and Hnf1B, Six1 and Eya1 are prominent
activators of Gdnf, and mutations in these genes have been linked to Branchiootorenal syndrome
(22, 23). In addition to these positive Gdnf regulators, several negative factors have been
identified. For example, Foxc1, normally expressed in the (murine) metanephric mesenchyme,
kinase signaling, specifically regulates RET expression in the Wolffian duct and the Bmp pathway is involved in regulating Gdnf – Ret pathway through the surrounding stromal mesenchyme.
Figure 3 molecular regulation of the developing kidney
The budding hypothesis: ectopic budding of the Wolffian duct (WD; a and c) results in a ectopia of the ureteral opening into the bladder (A, C) with consequent reflux or obstruction and dysplasia of the renal
tissue (modified from (28)). MM; metanephric mesenchyme, B; normal development. Genes regulating
formation the metanephros: schematic representation of some of the genes involved in the budding of the ureter into the metanephric mesenchyme during early kidney development. Arrows indicate epistatic relationshipds and/or direct control.
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Identification of novel CAKUT candidate genes
Previously, linkage analysis, association studies, and candidate gene approaches have
identified several genes and loci linked to human CAKUT pathogenesis (19, 29). For example,
linkage analysis in CAKUT families and association studies in large case-control studies have identified several genetic loci associated with non-syndromic familial CAKUT, yet no disease-
causing genes have been found in these loci, thus far (reviewed in (29)). For candidate gene
approaches, genes that were previously found in family studies, genes important for kidney development, genes causal for syndromal forms of CAKUT, or found implicated in CAKUT through animal models, are of interest (an overview of known causal CAKUT genes is shown in
supplementary table 2). However, most genes are only found implicated in a minority (1.9-20%)
of CAKUT cases (3). Thus, the cause of most CAKUT cases remains unknown. It is assumed that
CAKUT in these cases might be more complex in their aetiology, and are caused by a combination
of epigenetic mechanisms and environmental influences in genetically susceptible individuals(3).
Causative mutations in key renal developmental genes and polymorphisms in other genes, that might be part of a larger molecular kidney network, could collectively be required to lead to a
CAKUT phenotype. This oligogenic inheritance might in part explain the phenotypic diversity of
CAKUT and is therefore a key objective in our research effort to understand the mechanisms that dictate CAKUT pathogenesis. Application of multiple techniques including GWAS, exome and whole genome sequencing, on large carefully phenotyped patient cohorts will help in identifying the specific genetic determinants that underlie CAKUT etiology. NGS, and in particular wholeexome sequencing (WES), has revolutionized the efficacy of disease gene detection. It allows for massive parallel sequencing, generating millions of sequences concurrently at relatively low-cost
(compared to standard dye-terminator methods). Previously, WES has been used to identify
novel disease causing mutations for a variety of diseases, including CAKUT (30). To broaden our
understanding of genetics in CAKUT, the EURenOmics consortium currently aims to employ its experience in NGS approaches (in part by research groups in Utrecht and Paris) in combination with its access to large renal disease cohorts.
Exome sequencing, the targeted sequencing of the protein-coding part (1-2%) of the human genome, is a powerful, fast, and cost-effective tool that determines nearly all coding variation
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Glenn van de Hoek present in a patient’s genome in a single experiment. Targeted exome sequencing of specified genetic loci like co-segregating regions, homozygous stretches, or a subset of candidate genes, facilitates sequencing of a specific region with high coverage. The methodology involves enrichment of the genomic regions of interest and sequencing on next-generation sequencer platforms. Recent improvements, also widely and successfully conducted in Utrecht, have led to the implementation of an innovative barcode system for multiplexed genomic enrichment,
making high-throughput next generation sequencing more efficient (31). Data analysis of
sequencing variants comprises discrete filtering strategies, comparing DNA reads of patients with reference sequences from publically available databases (1000 genomes project, dbSNP, inhouse databases) to identify novel variants and the determination of overlapping variants among affected family members based on the assumed model of inheritance. Sequencing is followed by confirmation of the identified variants in the cases, their family members, and healthy control individuals by Sanger sequencing. Stratification of candidate genes involves predictions on gene function, sequence conservation, and potential impact of the variant on the protein, using annotation strategies (for example by Polyphen2, SIFT, and phyloP prediction programs).
Initially, focus will be on patients with a high likelihood of genetic disease including familial, syndromic, and severe bilateral cases. In families with sufficient power, linkage analysis or homozygosity mapping can be used, utilizing the powerful combination with targeted sequencing. EURenOmics is aiming to sequence the exomes of 100 cases and for most severe, sporadic cases we will apply case-parent trio sequencing. Sequencing both patient and parents greatly facilitates down-stream variant prioritization steps through filtering on inheritance pattern including dominant, recessive and de novo models. The information content made available by this technology will markedly increase the genetic knowledge base of rare kidney disease and ultimately advance clinical management.
Establishing the transcriptional networks driving renal development
The kidney represents one of the most complex organs of the human body and its development requires the tight control of proliferation, apoptosis, cellular movements and differentiation. This control is coordinated by a limited set of transcriptional regulators that form
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University Medical Center Utrecht complex networks of interactions, thus regulating a multitude of downstream target genes. Novel high-throughput approaches such as chromatin immunoprecipitation-sequencing (ChIP-Seq) allow mapping of transcription factor binding sites on a genome wide level. For ChIP-Seq, DNA fragments bound by a transcriptional regulator are immunoprecipitated with specific antibodies
and the precipitated fraction is sequenced using NGS techniques (32). Bioinformatic analysis
allows mapping the sequences back to the genome and thus reveals the precise location of
regulatory elements bound by a transcription factor in a cell type specific manner (33).
EURenOmics will exploit this novel technology for the systematic analysis of key transcription factors involved in kidney development and disease in mice and humans. Using this approach we expect to identify a molecular code that allows for prediction of direct targets of transcription factor complexes and lead to the discovery of molecular interactions and a description of events leading to the tissue specific activation of genes during kidney development and differentiation.
Importantly, identified regulatory elements will also represent candidate regions for mutations in patients suffering from renal disease and thus may help clarifying data obtained from sequence analysis.
Functional characterization of CAKUT genes
Numerous mutations and rare variants in renal developmental genes are expected to emerge from the exome screening of CAKUT patients. The functional relevance of individual genetic variants, alone or in combination, will require testing by efficient in vitro and in vivo models with potential for high-throughput analysis.
Mouse
- The mammalian metanephric mesenchyme can be cultured so that the developmental program of early nephrogenesis can be recapitulated under in vitro / ex vivo conditions. Mouse embryonic kidney culture provides a powerful way to investigate gene functions and mechanisms leading to altered kidney development in detail. The laboratory of
Dr. A. Schedl, INSERM, Nice (see supplementary table 1) has mastered an ex vivo culture model involving tissue dissociation and reaggregation of kidney precursor cells in which specific genes can be silenced by in vivo morpholino oligonucleotides or RNA interference (RNAi) approaches,
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or overexpressed by viral transduction (34). The effects of silencing or overexpression of
individual genes can be studied with high resolution light and epifluorescent microscopy in realtime and time-lapse mode and by optical projection tomography, providing spatial–temporal
characterization of nephrogenic induction and branching morphogenesis (35). This system allows
screening of candidate CAKUT genes in the mouse model at medium- to high-throughput efficiency. Transgenic mouse mutants will be developed to evaluate the functional characterization of selected genes of interest emerging from genomic screening studies in patient cohorts, for which suggestive evidence of functional relevance has been established in the ex vivo and lower-vertebrate model systems. The emphasis in the CAKUT work package will be initially
Figure 4 Functional characterization of CAKUT genes
A schematic overview of the different models for functional characterization of novel CAKUT candidate genes. In mice, mouse embryonic kidney cultures can be obtained through culturing cells of the metanephric mass (containing the metanephric mesenchyme; red) that is located on the posterior end of the nephrogenic cord (pink). These kidney cultures can then be exposed to overexpression or knock-down of the investigated genes and variants. In zebrafish, the embryonic kidney (pronephros) displays a highly conserved structural pattern containing a glomerulus (G), neck (N), proximal convoluted tubule (PCT), proximal straight tubule (PST), distal early (DE), corpuscle of Stannius (CS), distal late (DL), pronephric duct
(PD) and cloaca (C). The zebrafish embryo can be used for developmental tracking, expression analysis, target-selected mutagenesis and reconstitution assays. Picture courtesy of Dr. E. van Rooijen. In humans, novel developmental renal genes might contribute to the reprogramming of induced pluripotent stem cells (iPSC) to differentiated kidney cells. This would enhance personalized medicine as renal cells could be cultured from individual patients and used for drug screening and fundamental research.
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University Medical Center Utrecht on knockdown (morpholino) models in organ cultures (mouse kidney culture isolated at E11.5) to quickly evaluate the role of candidate genes in kidney development. Additional genetic models
(knockout or floxed mice) will be generated for a selected number of confirmed candidates to precisely dissect gene function.
Zebrafish
- Danio rerio (the zebrafish) has become an invaluable model to study inborn and
acquired renal disorders (36). Renal processes can be followed non-invasively in one and the
same fish over time. The zebrafish pronephros and adult kidney share individual functional segments of the human kidney nephron. Importantly, many molecular pathways essential to
kidney development/homeostasis and renal vascular morphogenesis are highly conserved (36,
39)) together with transgenic vasculature (kdrl:mcherry, red fluorescent endothelium (40)).
Where developmental tracking is necessary, characterization of the developmental stages of individual mesonephric nephrons and the temporal-spatial pattern of mesonephrogenesis can
be performed using double transgenic zebrafish lines (wt1b:GFP and pod:NTR-mCherry (41)).
Expression patterns of candidate CAKUT genes in healthy and unilaterally laser-ablated pronephros zebrafish embryos will be examined by in situ RNA hybridization. The availability of
experiments, morpholinos can be injected into embryos immediately following fertilization for a maximum 4-day long “knock-down” of the gene of choice. Finally, reconstitution assays can be used for functional testing of a human (missense) allele. In detail, morpholino’s are injected into wild-type embryos to knock down the endogenous zebrafish orthologue of the gene of interest.
At the same time one injects a plasmid (pCS2+) expressing the human WT or mutant allele of interest. Given that the morpholino alone delivers a phenotype, one can then score whether expression of the human WT orthologue rescues the phenotype within 4 days.
Human
- A promising novel approach to test the functional consequences of particular mutations within the ‘human model’ is provided by the emerging induced pluripotent stem cell
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(iPSC) technology. Recent preliminary studies have provided proof of principle that differentiated kidney cells can be generated from skin or tooth fibroblasts of patients with renal disorders and that the differentiation of the iPS cells can be also directed towards early kidney related cell
lineages (45). We plan to study the usefulness of this innovative technology by obtaining iPSC
from CAKUT patients. The knowledge acquired by identifying key transcription factors driving renal development should allow programming of early nephron progenitors towards those of early nephron related cell lineages, provided such genes alone or in combination are sufficient to program the iPSC to kidney cell differentiation and reveal primitive organ development.
Develop and implement a novel DNA diagnostic tool for CAKUT
Currently there are very few distinctive diagnostic markers for rare nephropathies. One of the primary objectives of the project is to generate rapid diagnostic tests and novel bio-markers for rare kidney diseases. Within the EURenOmics project, targeted ‘mini-genome’ kits capturing all known genes in each group of disorders will be developed, allowing for rapid genetic diagnosis by multiplex PCR and massive parallel sequencing for each disease. For CAKUT, this parallel sequencing strategy will be developed to screen the (limited amount of) known CAKUT genes in a cohort of CAKUT patients (n=2000 currently available). We will use the Ion Torrent platform
(Life Technologies) for fast detection of variants in targeted genes in collaboration with development of a multiplex PCR based high-throughput sequencing protocol. A first assay will involve 200 patients and 14 genes implicated in human CAKUT to date: PAX2, EYA1, SIX1, SIX5,
SALL1, HNF1B, UMOD, UPK3A, RET, ROBO2, GDNF, SOX9, SOX17, and BMP4. Novel CAKUT genes identified through next-generation sequencing techniques will be included after validation and characterization to design a complete “CAKUTOME” that will be used to screen the full cohort of
CAKUT patients for causative or predisposing mutations in a high-throughput fashion. We believe that the targeted kidney disease gene sequencing assays described above will speed up the provision of genetic diagnoses and ultimately the implementation within the clinic will be a major step towards personalized medicine in the field of nephrology.
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Impact
Comprehensive exome sequencing of large patient cohorts, followed by careful functional characterization of the identified genetic variants, is expected to substantially increase the list of genes causing monogenic congenital kidney disease. Moreover, exome sequencing is a powerful approach that could disclose complex genetic disease transmission involving variation in several genes. It is anticipated that the overall proportion of patients in whom an unambiguous genetic diagnosis can be made will increase markedly.
Furthermore, the development of targeted next-generation sequencing efforts that cover all genes associated with a particular disease or disease group will materialize the full clinical benefit of this new technology and overcome the limitations of current genetic diagnostics based on
Sanger sequencing, i.e. long analysis times and high costs. The final screening arrays emerging from the different work packages of EURenOmics will include all new disease genes that will be identified in the course of the EURenOmics project, and thus will cover the vast majority of genes involved in hereditary kidney disorders altogether. Hence, the resulting diagnostic products in their entirety will define a new era of genetic testing in the field of clinical nephrology, with immediate relevance for affected patients.
Conclusion
The recent collation of a large patient cohort encompassing the complete CAKUT spectrum
(29), the advent of next generation sequencing (NGS) and progress in bioinformatic
developmental gene network modeling have created the opportunity to identify novel genetic causes, characterize complex genotype-phenotype relationships and develop rapid and reliable gene diagnostic tools for CAKUT. The studies on CAKUT genetics will have important implications for affected patients and their families. The elucidation of the complex genetics of disease transmission through studies of exome-wide genetic variability will pave the way towards individualized and more effective genetic counseling of families affected by CAKUT.
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Supplement
Supplementary table 1 List of EURenOmics participants
Participant no.
1
Acronym
UKL-HD
Name of principal
Investigator
Franz Schaefer
2 INSERM 2a Corinne
Antignac
2b Pierre Ronco
Participant organization name
Universitätsklinikum
Heidelberg
Institut National de la
Santé et de la Recherche
Medicale
2c Xavier
Jeunemaître
2d Andreas Schedl
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
Country
Germany
France
UZH
IRFMN
UMCU
UMICH
HU
Bristol
RUNMC
UNIMAN
UCL
CSIC
UNN
Nine Knoers University Medical
Centre Utrecht
Matthias Kretzler University of Michigan
Fatih Ozaltin
Peter Mathieson
Jack Wetzels
Hacettepe University
Ankara
University of Bristol
Paul Brenchley
Robert Kleta
The
Netherlands
USA
Turkey
UK
Radboud University
Nijmegen Medical Center
The
Netherlands
University of Manchester UK
Santiago-Rodriguez de Cordoba
Tim Goodship
University College London UK
Centro de Investigaciones
Biologicas
Spain
Newcastle University UK
France AP-HP
HKI
Veronique
Fremeaux-Bacchi
Peter Zipfel
Assistance Publique -
Hopitaux de Paris
Leibniz Institute for
Natural Product Research and Infection Biology
KU Leuven Elena Levtchenko Katholieke Universiteit
Leuven
Germany
Belgium
Oulu Seppo Vainio
Genomatix Thomas Werner
MTBX
2e Joost Schanstra
Olivier Devuyst Universität Zürich
Giuseppe Remuzzi Istituto di Ricerche
Farmacologiche Mario
Negri
John Lindon
University of Oulu
Genomatix Software
GmbH
Metabometrix Limited
Switzerland
Italy
Finland
Germany
UK
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20
21
22
23
24
25
Multiplicom Jürgen Del-Favero Multiplicom, Inc.
PHG Dario Neri Philogen Srl
PHC
CBC
MOS
GABO:mi
André Brändli
Matthias Scheffler Comprehensive
Petra Zürbig
Birgit Fuchs
Philochem AG
Biomarker Center
Mosaïques
GABO:mi Gesellschaft für
Ablauforganisation: milliarium mbH & Co. KG
Belgium
Italy
Switzerland
Germany
Germany
Germany
26 KIT Urban Liebel Karlsruhe Institute of
Technology
Germany
In bold (participant no5.) is shown the current affiliation of the author of this report.
Supplementary table 2 Overview of known monocausal CAKUT genes
Gene
AGT
Disease
OMIN
RTD
Chromosome
1p42
Rnal phenotype
Reduced number of proximal tubules, short proximal tubules without brush border, atrophic loops of Henle and collecting ducts, closely packed glomeruli, marked thickening and disorganization of interlobular and preglomerular arteries
AGTR1
AGTR2
ACE
BMP4
RTD
—
RTD
—
3p24
Xq22-q23
17q23.3
14q22-q23
Similar to AGT phenotype, PUV
UPJ obstruction, megaureter, MCDK hydronephrosis, PUV
Similar to AGT phenotype renal hypodysplasia, PUV
Renal hypodysplasia
BMP7,
Dlx5/Dlx6 p63
CDC5L
SHFM
#603273
—
3q27 Urethral malformations
Eya1
Fras1,
Fram2
FoxC1
BOR,
#113650
Fraser syndrome
—
46XX,t(6; 19),
(p21; q13.1)
Multicystic kidney dysplasia
8q12 Unilateral or bilateral renal agenesis renal hypodysplasia, VUR
4q21, 13q13.3 Renal agenesis/hypodysplasia
6p25 CAKUT
References
Identifying novel genes involved in congenital anomalies of the kidney and urinary tract | 22
University Medical Center Utrecht
Gata3
HNF1β/
TCF2
Pax2
Ren
Ret
HDR syndrome
#146255
RCAD
#137920
GCKD
#609886
Renal coloboma syndrome
RTD
Renal agenesis
#191830
—
—
—
MCDK2
10pter
17q12
10q24
17q23.3
10q11.2
Renal dysplasia
Renal hypodysplasia, cysts
Renal hypoplasia, VUR
Similar to AGT phenotype
Absence of the kidney and ureter
Robo2
Six2
Slit2
Umod
3p12.3
2p16-p15
4p15.2
16p12.3
VUR
Renal hypodysplasia
Hydroureter, supernumerary UBs
Cysts in distal tubules and collecting ducts, renal dysplasia
Renal agenesis/hypodysplasia
Multicystic kidney dysplasia
Upk3A
Usf2
—
—
22q13.31
46XX t(6;19),
(p21; q13.1)
XPNPEP3 NPHP-like nephropathy
22q13.2 Renal cysts and dysplasia
AGTR: angiotensin II receptor type 1, AGTR2: angiotensin II receptor type 2, ARPKD: autosomal-recessive polycystic kidney disease, ADPKD: autosomal-dominant polycystic kidney disease, UPJ: ureteropelvic junction, VUR: vesicoureteral reflux, PUV: posterior urethral valves, UPJ: ureteropelvic junction, MCDK: multicystic dysplastic kidney, PUV: posterior urethral valve, RTD: renal tubular dysgenesis, RCAD: renal cysts and diabetes, MODY: maturity-onset diabetes, GCKD: glomerulocystic kidney disease, and NPHP: nephronophthisis, X-prolyl aminopeptidase (aminopeptidase P) 3, putative.
23 |
Glenn van de Hoek
References
1.
2.
3.
4.
5.
6.
7.
8.
9.
M. T. James, B. R. Hemmelgarn, M. Tonelli, Early recognition and prevention of chronic kidney disease. Lancet 375, 1296-1309 (2010); published online EpubApr 10 (10.1016/S0140-
6736(09)62004-3).
M. Loane, H. Dolk, A. Kelly, C. Teljeur, R. Greenlees, J. Densem, E. W. Group, Paper 4: EUROCAT statistical monitoring: identification and investigation of ten year trends of congenital anomalies in Europe. Birth defects research. Part A, Clinical and molecular teratology 91 Suppl 1, S31-43
(2011); published online EpubMar (10.1002/bdra.20778).
I. V. Yosypiv, Congenital anomalies of the kidney and urinary tract: a genetic disorder?
International journal of nephrology 2012, 909083 (2012)10.1155/2012/909083).
Y. Horikawa, N. Iwasaki, M. Hara, H. Furuta, Y. Hinokio, B. N. Cockburn, T. Lindner, K. Yamagata,
M. Ogata, O. Tomonaga, H. Kuroki, T. Kasahara, Y. Iwamoto, G. I. Bell, Mutation in hepatocyte nuclear factor-1 beta gene (TCF2) associated with MODY. Nature genetics 17, 384-385 (1997); published online EpubDec (10.1038/ng1297-384).
S. Sanna-Cherchi, G. Caridi, P. L. Weng, F. Scolari, F. Perfumo, A. G. Gharavi, G. M. Ghiggeri,
Genetic approaches to human renal agenesis/hypoplasia and dysplasia. Pediatric nephrology 22,
1675-1684 (2007); published online EpubOct (10.1007/s00467-007-0479-1).
P. Sanyanusin, L. A. Schimmenti, L. A. McNoe, T. A. Ward, M. E. Pierpont, M. J. Sullivan, W. B.
Dobyns, M. R. Eccles, Mutation of the PAX2 gene in a family with optic nerve colobomas, renal anomalies and vesicoureteral reflux. Nature genetics 9, 358-364 (1995); published online EpubApr
(10.1038/ng0495-358).
P. Winyard, L. S. Chitty, Dysplastic kidneys. Seminars in fetal & neonatal medicine 13, 142-151
(2008); published online EpubJun (10.1016/j.siny.2007.10.009).
A. L. Schwaderer, C. M. Bates, K. M. McHugh, K. L. McBride, Renal anomalies in family members of infants with bilateral renal agenesis/adysplasia. Pediatric nephrology 22, 52-56 (2007); published online EpubJan (10.1007/s00467-006-0295-z).
R. A. Belk, D. F. Thomas, R. F. Mueller, P. Godbole, A. F. Markham, M. J. Weston, A family study and the natural history of prenatally detected unilateral multicystic dysplastic kidney. The Journal
of urology 167, 666-669 (2002); published online EpubFeb
10. A. Schedl, Renal abnormalities and their developmental origin. Nature reviews. Genetics 8, 791-
802 (2007); published online EpubOct (10.1038/nrg2205).
11. M. C. Hu, N. D. Rosenblum, Genetic regulation of branching morphogenesis: lessons learned from loss-of-function phenotypes. Pediatric research 54, 433-438 (2003); published online EpubOct
(10.1203/01.PDR.0000085170.44226.DB).
12. B. Rumballe, K. Georgas, L. Wilkinson, M. Little, Molecular anatomy of the kidney: what have we learned from gene expression and functional genomics? Pediatric nephrology 25, 1005-1016
(2010); published online EpubJun (10.1007/s00467-009-1392-6).
13. A. Schuchardt, V. D'Agati, V. Pachnis, F. Costantini, Renal agenesis and hypodysplasia in ret-k- mutant mice result from defects in ureteric bud development. Development 122, 1919-1929
(1996); published online EpubJun
14. M. W. Moore, R. D. Klein, I. Farinas, H. Sauer, M. Armanini, H. Phillips, L. F. Reichardt, A. M. Ryan,
K. Carver-Moore, A. Rosenthal, Renal and neuronal abnormalities in mice lacking GDNF. Nature
382, 76-79 (1996); published online EpubJul 4 (10.1038/382076a0).
15. A. Schuchardt, V. D'Agati, L. Larsson-Blomberg, F. Costantini, V. Pachnis, Defects in the kidney and enteric nervous system of mice lacking the tyrosine kinase receptor Ret. Nature 367, 380-383
(1994)10.1038/367380a0).
Identifying novel genes involved in congenital anomalies of the kidney and urinary tract | 24
University Medical Center Utrecht
16. F. Costantini, R. Shakya, GDNF/Ret signaling and the development of the kidney. BioEssays : news
and reviews in molecular, cellular and developmental biology 28, 117-127 (2006); published online
EpubFeb (10.1002/bies.20357).
17. M. Bouchard, Transcriptional control of kidney development. Differentiation; research in
biological diversity 72, 295-306 (2004); published online EpubSep (10.1111/j.1432-
0436.2004.07207001.x).
18. P. D. Brophy, L. Ostrom, K. M. Lang, G. R. Dressler, Regulation of ureteric bud outgrowth by Pax2dependent activation of the glial derived neurotrophic factor gene. Development 128, 4747-4756
(2001); published online EpubDec
19. S. Weber, V. Moriniere, T. Knuppel, M. Charbit, J. Dusek, G. M. Ghiggeri, A. Jankauskiene, S. Mir,
G. Montini, A. Peco-Antic, E. Wuhl, A. M. Zurowska, O. Mehls, C. Antignac, F. Schaefer, R. Salomon,
Prevalence of mutations in renal developmental genes in children with renal hypodysplasia: results of the ESCAPE study. Journal of the American Society of Nephrology : JASN 17, 2864-2870
(2006); published online EpubOct (10.1681/ASN.2006030277).
20. L. Lokmane, C. Heliot, P. Garcia-Villalba, M. Fabre, S. Cereghini, vHNF1 functions in distinct regulatory circuits to control ureteric bud branching and early nephrogenesis. Development 137,
347-357 (2010); published online EpubJan (10.1242/dev.042226).
21. T. Ulinski, S. Lescure, S. Beaufils, V. Guigonis, S. Decramer, D. Morin, S. Clauin, G. Deschenes, F.
Bouissou, A. Bensman, C. Bellanne-Chantelot, Renal phenotypes related to hepatocyte nuclear factor-1beta (TCF2) mutations in a pediatric cohort. Journal of the American Society of Nephrology
: JASN 17, 497-503 (2006); published online EpubFeb (10.1681/ASN.2005101040).
22. S. Abdelhak, V. Kalatzis, R. Heilig, S. Compain, D. Samson, C. Vincent, D. Weil, C. Cruaud, I. Sahly,
M. Leibovici, M. Bitner-Glindzicz, M. Francis, D. Lacombe, J. Vigneron, R. Charachon, K. Boven, P.
Bedbeder, N. Van Regemorter, J. Weissenbach, C. Petit, A human homologue of the Drosophila eyes absent gene underlies branchio-oto-renal (BOR) syndrome and identifies a novel gene family.
Nature genetics 15, 157-164 (1997); published online EpubFeb (10.1038/ng0297-157).
23. R. G. Ruf, P. X. Xu, D. Silvius, E. A. Otto, F. Beekmann, U. T. Muerb, S. Kumar, T. J. Neuhaus, M. J.
Kemper, R. M. Raymond, Jr., P. D. Brophy, J. Berkman, M. Gattas, V. Hyland, E. M. Ruf, C. Schwartz,
E. H. Chang, R. J. Smith, C. A. Stratakis, D. Weil, C. Petit, F. Hildebrandt, SIX1 mutations cause branchio-oto-renal syndrome by disruption of EYA1-SIX1-DNA complexes. Proceedings of the
National Academy of Sciences of the United States of America 101, 8090-8095 (2004); published online EpubMay 25 (10.1073/pnas.0308475101).
24. T. Kume, K. Deng, B. L. Hogan, Murine forkhead/winged helix genes Foxc1 (Mf1) and Foxc2 (Mfh1) are required for the early organogenesis of the kidney and urinary tract. Development 127, 1387-
1395 (2000); published online EpubApr
25. U. Grieshammer, M. Le, A. S. Plump, F. Wang, M. Tessier-Lavigne, G. R. Martin, SLIT2-mediated
ROBO2 signaling restricts kidney induction to a single site. Developmental cell 6, 709-717 (2004); published online EpubMay
26. W. Lu, A. M. van Eerde, X. Fan, F. Quintero-Rivera, S. Kulkarni, H. Ferguson, H. G. Kim, Y. Fan, Q.
Xi, Q. G. Li, D. Sanlaville, W. Andrews, V. Sundaresan, W. Bi, J. Yan, J. C. Giltay, C. Wijmenga, T. P. de Jong, S. A. Feather, A. S. Woolf, Y. Rao, J. R. Lupski, M. R. Eccles, B. J. Quade, J. F. Gusella, C. C.
Morton, R. L. Maas, Disruption of ROBO2 is associated with urinary tract anomalies and confers risk of vesicoureteral reflux. American journal of human genetics 80, 616-632 (2007); published online EpubApr (10.1086/512735).
27. S. Zu, Z. Bartik, S. Zhao, U. Sillen, A. Nordenskjold, Mutations in the ROBO2 and SLIT2 genes are rare causes of familial vesico-ureteral reflux. Pediatric nephrology 24, 1501-1508 (2009); published online EpubAug (10.1007/s00467-009-1179-9).
25 |
Glenn van de Hoek
28. S. Weber, Novel genetic aspects of congenital anomalies of kidney and urinary tract. Current opinion in pediatrics 24, 212-218 (2012); published online EpubApr
(10.1097/MOP.0b013e32834fdbd4).
29. K. Y. Renkema, P. J. Winyard, I. N. Skovorodkin, E. Levtchenko, A. Hindryckx, C. Jeanpierre, S.
Weber, R. Salomon, C. Antignac, S. Vainio, A. Schedl, F. Schaefer, N. V. Knoers, E. M. Bongers, E. consortium, Novel perspectives for investigating congenital anomalies of the kidney and urinary tract (CAKUT). Nephrology, dialysis, transplantation : official publication of the European Dialysis
and Transplant Association - European Renal Association 26, 3843-3851 (2011); published online
EpubDec (10.1093/ndt/gfr655).
30. S. Sanna-Cherchi, R. V. Sampogna, N. Papeta, K. E. Burgess, S. N. Nees, B. J. Perry, M. Choi, M.
Bodria, Y. Liu, P. L. Weng, V. J. Lozanovski, M. Verbitsky, F. Lugani, R. Sterken, N. Paragas, G. Caridi,
A. Carrea, M. Dagnino, A. Materna-Kiryluk, G. Santamaria, C. Murtas, N. Ristoska-Bojkovska, C.
Izzi, N. Kacak, B. Bianco, S. Giberti, M. Gigante, G. Piaggio, L. Gesualdo, D. Kosuljandic Vukic, K.
Vukojevic, M. Saraga-Babic, M. Saraga, Z. Gucev, L. Allegri, A. Latos-Bielenska, D. Casu, M. State,
F. Scolari, R. Ravazzolo, K. Kiryluk, Q. Al-Awqati, V. D. D'Agati, I. A. Drummond, V. Tasic, R. P. Lifton,
G. M. Ghiggeri, A. G. Gharavi, Mutations in DSTYK and dominant urinary tract malformations. The
New England journal of medicine 369, 621-629 (2013); published online EpubAug 15
(10.1056/NEJMoa1214479).
31. M. Harakalova, M. Mokry, B. Hrdlickova, I. Renkens, K. Duran, H. van Roekel, N. Lansu, M. van
Roosmalen, E. de Bruijn, I. J. Nijman, W. P. Kloosterman, E. Cuppen, Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing. Nature protocols 6, 1870-1886 (2011); published online EpubDec
(10.1038/nprot.2011.396).
32. R. D. Hawkins, G. C. Hon, B. Ren, Next-generation genomics: an integrative approach. Nature
reviews. Genetics 11, 476-486 (2010); published online EpubJul (10.1038/nrg2795).
33. J. Rougemont, F. Naef, Computational analysis of protein-DNA interactions from ChIP-seq data.
Methods in molecular biology 786, 263-273 (2012)10.1007/978-1-61779-292-2_16).
34. M. Unbekandt, J. A. Davies, Dissociation of embryonic kidneys followed by reaggregation allows the formation of renal tissues. Kidney international 77, 407-416 (2010); published online EpubMar
(10.1038/ki.2009.482).
35. V. Veikkolainen, F. Naillat, A. Railo, L. Chi, A. Manninen, P. Hohenstein, N. Hastie, S. Vainio, K.
Elenius, ErbB4 modulates tubular cell polarity and lumen diameter during kidney development.
Journal of the American Society of Nephrology : JASN 23, 112-122 (2012); published online
EpubJan (10.1681/ASN.2011020160).
36. L. Ebarasi, A. Oddsson, K. Hultenby, C. Betsholtz, K. Tryggvason, Zebrafish: a model system for the study of vertebrate renal development, function, and pathophysiology. Current opinion in nephrology and hypertension 20, 416-424 (2011); published online EpubJul
(10.1097/MNH.0b013e3283477797).
37. E. van Rooijen, E. E. Voest, I. Logister, J. Bussmann, J. Korving, F. J. van Eeden, R. H. Giles, S.
Schulte-Merker, von Hippel-Lindau tumor suppressor mutants faithfully model pathological hypoxia-driven angiogenesis and vascular retinopathies in zebrafish. Disease models &
mechanisms 3, 343-353 (2010); published online EpubMay-Jun (10.1242/dmm.004036).
38. J. Xie, H. Yin, T. D. Nichols, J. A. Yoder, J. M. Horowitz, Sp2 is a maternally inherited transcription factor required for embryonic development. The Journal of biological chemistry 285, 4153-4164
(2010); published online EpubFeb 5 (10.1074/jbc.M109.078881).
39. J. Horsfield, A. Ramachandran, K. Reuter, E. LaVallie, L. Collins-Racie, K. Crosier, P. Crosier,
Cadherin-17 is required to maintain pronephric duct integrity during zebrafish development.
Mechanisms of development 115, 15-26 (2002); published online EpubJul
Identifying novel genes involved in congenital anomalies of the kidney and urinary tract | 26
University Medical Center Utrecht
40. Y. Wang, M. S. Kaiser, J. D. Larson, A. Nasevicius, K. J. Clark, S. A. Wadman, S. E. Roberg-Perez, S.
C. Ekker, P. B. Hackett, M. McGrail, J. J. Essner, Moesin1 and Ve-cadherin are required in endothelial cells during in vivo tubulogenesis. Development 137, 3119-3128 (2010); published online EpubSep (10.1242/dev.048785).
41. W. Zhou, F. Hildebrandt, Inducible podocyte injury and proteinuria in transgenic zebrafish. Journal
of the American Society of Nephrology : JASN 23, 1039-1047 (2012); published online EpubJun
(10.1681/ASN.2011080776).
42. E. Wienholds, F. van Eeden, M. Kosters, J. Mudde, R. H. Plasterk, E. Cuppen, Efficient targetselected mutagenesis in zebrafish. Genome research 13, 2700-2707 (2003); published online
EpubDec (10.1101/gr.1725103).
43. X. Meng, M. B. Noyes, L. J. Zhu, N. D. Lawson, S. A. Wolfe, Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nature biotechnology 26, 695-701 (2008); published online EpubJun (10.1038/nbt1398).
44. V. M. Bedell, Y. Wang, J. M. Campbell, T. L. Poshusta, C. G. Starker, R. G. Krug, 2nd, W. Tan, S. G.
Penheiter, A. C. Ma, A. Y. Leung, S. C. Fahrenkrug, D. F. Carlson, D. F. Voytas, K. J. Clark, J. J. Essner,
S. C. Ekker, In vivo genome editing using a high-efficiency TALEN system. Nature 491, 114-118
(2012); published online EpubNov 1 (10.1038/nature11537).
45. S. D. Ricardo, B. Song, J. Niclis, A. L. Laslett, P. G. Kerr, Induced pluripotent stem cells from patients with genetic kidney disease: Applications for disease modeling and therapeutic screening. ASN
Annual Meeting, Philadelphia, (2011).
46. O. Gribouval, M. Gonzales, T. Neuhaus, J. Aziza, E. Bieth, N. Laurent, J. M. Bouton, F. Feuillet, S.
Makni, H. Ben Amar, G. Laube, A. L. Delezoide, R. Bouvier, F. Dijoud, E. Ollagnon-Roman, J. Roume,
M. Joubert, C. Antignac, M. C. Gubler, Mutations in genes in the renin-angiotensin system are associated with autosomal recessive renal tubular dysgenesis. Nature genetics 37, 964-968
(2005); published online EpubSep (10.1038/ng1623).
47. M. Lacoste, Y. Cai, L. Guicharnaud, F. Mounier, Y. Dumez, R. Bouvier, F. Dijoud, M. Gonzales, J.
Chatten, A. L. Delezoide, L. Daniel, M. Joubert, N. Laurent, J. Aziza, T. Sellami, H. B. Amar, C. Jarnet,
A. M. Frances, F. Daikha-Dahmane, A. Coulomb, T. J. Neuhaus, B. Foliguet, P. Chenal, P.
Marcorelles, J. M. Gasc, P. Corvol, M. C. Gubler, Renal tubular dysgenesis, a not uncommon autosomal recessive disorder leading to oligohydramnios: Role of the Renin-Angiotensin system.
Journal of the American Society of Nephrology : JASN 17, 2253-2263 (2006); published online
EpubAug (10.1681/ASN.2005121303).
48. L. Peruzzi, F. Lombardo, A. Amore, E. Merlini, G. Restagno, L. Silvestro, T. Papalia, R. Coppo, Low renin-angiotensin system activity gene polymorphism and dysplasia associated with posterior urethral valves. The Journal of urology 174, 713-717 (2005); published online EpubAug
(10.1097/01.ju.0000164739.13408.e2).
49. H. Nishimura, E. Yerkes, K. Hohenfellner, Y. Miyazaki, J. Ma, T. E. Hunley, H. Yoshida, T. Ichiki, D.
Threadgill, J. A. Phillips, 3rd, B. M. Hogan, A. Fogo, J. W. Brock, 3rd, T. Inagami, I. Ichikawa, Role of the angiotensin type 2 receptor gene in congenital anomalies of the kidney and urinary tract,
CAKUT, of mice and men. Molecular cell 3, 1-10 (1999); published online EpubJan
50. H. Hahn, S. E. Ku, K. S. Kim, Y. S. Park, C. H. Yoon, H. I. Cheong, Implication of genetic variations in congenital obstructive nephropathy. Pediatric nephrology 20, 1541-1544 (2005); published online
EpubNov (10.1007/s00467-005-1999-1).
51. L. Rigoli, R. Chimenz, C. di Bella, E. Cavallaro, R. Caruso, S. Briuglia, C. Fede, C. D. Salpietro,
Angiotensin-converting enzyme and angiotensin type 2 receptor gene genotype distributions in
Italian children with congenital uropathies. Pediatric research 56, 988-993 (2004); published online EpubDec (10.1203/01.PDR.0000145252.89427.9E).
27 |
Glenn van de Hoek
52. A. Stankovic, M. Zivkovic, M. Kostic, J. Atanackovic, Z. Krstic, D. Alavantic, Expression profiling of the AT2R mRNA in affected tissue from children with CAKUT. Clinical biochemistry 43, 71-75
(2010); published online EpubJan (10.1016/j.clinbiochem.2009.09.009).
53. S. Weber, J. C. Taylor, P. Winyard, K. F. Baker, J. Sullivan-Brown, R. Schild, T. Knuppel, A. M.
Zurowska, A. Caldas-Alfonso, M. Litwin, S. Emre, G. M. Ghiggeri, A. Bakkaloglu, O. Mehls, C.
Antignac, E. Network, F. Schaefer, R. D. Burdine, SIX2 and BMP4 mutations associate with anomalous kidney development. Journal of the American Society of Nephrology : JASN 19, 891-
903 (2008); published online EpubMay (10.1681/ASN.2006111282).
54. K. Suzuki, R. Haraguchi, T. Ogata, O. Barbieri, O. Alegria, M. Vieux-Rochas, N. Nakagata, M. Ito, A.
A. Mills, T. Kurita, G. Levi, G. Yamada, Abnormal urethra formation in mouse models of splithand/split-foot malformation type 1 and type 4. European journal of human genetics : EJHG 16,
36-44 (2008); published online EpubJan (10.1038/sj.ejhg.5201925).
55. P. M. Groenen, G. Vanderlinden, K. Devriendt, J. P. Fryns, W. J. Van de Ven, Rearrangement of the human CDC5L gene by a t(6;19)(p21;q13.1) in a patient with multicystic renal dysplasia. Genomics
49, 218-229 (1998); published online EpubApr 15 (10.1006/geno.1998.5254).
56. P. Saisawat, V. Tasic, V. Vega-Warner, E. O. Kehinde, B. Gunther, R. Airik, J. W. Innis, B. E. Hoskins,
J. Hoefele, E. A. Otto, F. Hildebrandt, Identification of two novel CAKUT-causing genes by massively parallel exon resequencing of candidate genes in patients with unilateral renal agenesis.
Kidney international 81, 196-200 (2012); published online EpubJan (10.1038/ki.2011.315).
57. S. Jadeja, I. Smyth, J. E. Pitera, M. S. Taylor, M. van Haelst, E. Bentley, L. McGregor, J. Hopkins, G.
Chalepakis, N. Philip, A. Perez Aytes, F. M. Watt, S. M. Darling, I. Jackson, A. S. Woolf, P. J.
Scambler, Identification of a new gene mutated in Fraser syndrome and mouse myelencephalic blebs. Nature genetics 37, 520-525 (2005); published online EpubMay (10.1038/ng1549).
58. T. Nakano, F. Niimura, K. Hohenfellner, E. Miyakita, I. Ichikawa, Screening for mutations in BMP4 and FOXC1 genes in congenital anomalies of the kidney and urinary tract in humans. The Tokai
journal of experimental and clinical medicine 28, 121-126 (2003); published online EpubOct
59. H. Van Esch, P. Groenen, M. A. Nesbit, S. Schuffenhauer, P. Lichtner, G. Vanderlinden, B. Harding,
R. Beetz, R. W. Bilous, I. Holdaway, N. J. Shaw, J. P. Fryns, W. Van de Ven, R. V. Thakker, K.
Devriendt, GATA3 haplo-insufficiency causes human HDR syndrome. Nature 406, 419-422 (2000); published online EpubJul 27 (10.1038/35019088).
60. T. H. Lindner, P. R. Njolstad, Y. Horikawa, L. Bostad, G. I. Bell, O. Sovik, A novel syndrome of diabetes mellitus, renal dysfunction and genital malformation associated with a partial deletion of the pseudo-POU domain of hepatocyte nuclear factor-1beta. Human molecular genetics 8,
2001-2008 (1999); published online EpubOct
61. J. Martinovic-Bouriel, A. Benachi, M. Bonniere, N. Brahimi, C. Esculpavit, N. Morichon, M.
Vekemans, C. Antignac, R. Salomon, F. Encha-Razavi, T. Attie-Bitach, M. C. Gubler, PAX2 mutations in fetal renal hypodysplasia. American journal of medical genetics. Part A 152A, 830-835 (2010); published online EpubApr (10.1002/ajmg.a.33133).
62. M. A. Skinner, S. D. Safford, J. G. Reeves, M. E. Jackson, A. J. Freemerman, Renal aplasia in humans is associated with RET mutations. American journal of human genetics 82, 344-351 (2008); published online EpubFeb (10.1016/j.ajhg.2007.10.008).
63. H. J. Cordell, R. Darlay, P. Charoen, A. Stewart, A. M. Gullett, H. J. Lambert, S. Malcolm, S. A.
Feather, T. H. Goodship, A. S. Woolf, R. B. Kenda, J. A. Goodship, U. V. S. Group, Whole-genome linkage and association scan in primary, nonsyndromic vesicoureteric reflux. Journal of the
American Society of Nephrology : JASN 21, 113-123 (2010); published online EpubJan
(10.1681/ASN.2009060624).
64. A. M. Bertoli-Avella, M. L. Conte, F. Punzo, B. M. de Graaf, G. Lama, A. La Manna, C. Polito, C.
Grassia, B. Nobili, P. F. Rambaldi, B. A. Oostra, S. Perrotta, ROBO2 gene variants are associated
Identifying novel genes involved in congenital anomalies of the kidney and urinary tract | 28
University Medical Center Utrecht with familial vesicoureteral reflux. Journal of the American Society of Nephrology : JASN 19, 825-
831 (2008); published online EpubApr (10.1681/ASN.2007060692).
65. T. C. Hart, M. C. Gorry, P. S. Hart, A. S. Woodard, Z. Shihabi, J. Sandhu, B. Shirts, L. Xu, H. Zhu, M.
M. Barmada, A. J. Bleyer, Mutations of the UMOD gene are responsible for medullary cystic kidney disease 2 and familial juvenile hyperuricaemic nephropathy. Journal of medical genetics 39, 882-
892 (2002); published online EpubDec
66. E. Benetti, G. Caridi, M. D. Vella, L. Rampoldi, G. M. Ghiggeri, L. Artifoni, L. Murer, Immature renal structures associated with a novel UMOD sequence variant. American journal of kidney diseases :
the official journal of the National Kidney Foundation 53, 327-331 (2009); published online
EpubFeb (10.1053/j.ajkd.2008.08.020).
67. D. Jenkins, M. Bitner-Glindzicz, L. Thomasson, S. Malcolm, S. A. Warne, S. A. Feather, S. E.
Flanagan, S. Ellard, C. Bingham, L. Santos, M. Henkemeyer, A. Zinn, L. A. Baker, D. T. Wilcox, A. S.
Woolf, Mutational analyses of UPIIIA, SHH, EFNB2 and HNF1beta in persistent cloaca and associated kidney malformations. Journal of pediatric urology 3, 2-9 (2007); published online
EpubFeb (10.1016/j.jpurol.2006.03.002).
68. P. Hu, F. M. Deng, F. X. Liang, C. M. Hu, A. B. Auerbach, E. Shapiro, X. R. Wu, B. Kachar, T. T. Sun,
Ablation of uroplakin III gene results in small urothelial plaques, urothelial leakage, and vesicoureteral reflux. The Journal of cell biology 151, 961-972 (2000); published online EpubNov
27
69. P. M. Groenen, E. Garcia, P. Debeer, K. Devriendt, J. P. Fryns, W. J. Van de Ven, Structure, sequence, and chromosome 19 localization of human USF2 and its rearrangement in a patient with multicystic renal dysplasia. Genomics 38, 141-148 (1996); published online EpubDec 1 (
70. J. F. O'Toole, Y. Liu, E. E. Davis, C. J. Westlake, M. Attanasio, E. A. Otto, D. Seelow, G. Nurnberg, C.
Becker, M. Nuutinen, M. Karppa, J. Ignatius, J. Uusimaa, S. Pakanen, E. Jaakkola, L. P. van den
Heuvel, H. Fehrenbach, R. Wiggins, M. Goyal, W. Zhou, M. T. Wolf, E. Wise, J. Helou, S. J. Allen, C.
A. Murga-Zamalloa, S. Ashraf, M. Chaki, S. Heeringa, G. Chernin, B. E. Hoskins, H. Chaib, J. Gleeson,
T. Kusakabe, T. Suzuki, R. E. Isaac, L. M. Quarmby, B. Tennant, H. Fujioka, H. Tuominen, I. Hassinen,
H. Lohi, J. L. van Houten, A. Rotig, J. A. Sayer, B. Rolinski, P. Freisinger, S. M. Madhavan, M. Herzer,
F. Madignier, H. Prokisch, P. Nurnberg, P. K. Jackson, H. Khanna, N. Katsanis, F. Hildebrandt,
Individuals with mutations in XPNPEP3, which encodes a mitochondrial protein, develop a nephronophthisis-like nephropathy. The Journal of clinical investigation 120, 791-802 (2010); published online EpubMar (10.1172/JCI40076).
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