WP04 - Tubulopathies


  • Identification of novel genes involved in causing or modifying tubular disorders
  • Development of a novel diagnostic tool for rapid complete screening of mutations and variants in known renal tubular disease genes
  • Use of reference -omics profiling and deep phenotyping to refine ontology and predict global progression processes
  • Functional characterization of mutated renal gene products (Functiomics )
  • Deep phenotyping of the SLC12A3 (Gitelman syndrome) carrier state
  • Development of preclinical disease models and large-scale in vivo drug discovery screens

Workpackage Description

The tubular segments of the kidney are lined by specialized epithelial cells which play an essential role in homeostasis by reabsorbing, secreting and activating solutes and thus fixing the final composition of urine. Multiple rare disorders have been described as affecting these specialized functions, leading to inappropriate renal losses of NaCl, calcium, magnesium, water and phosphate, hypertension and acid-base disturbances. These disorders are often affecting children and causing multi-systemic, life-threatening complications and  progression to renal failure. This workpackage includes eight European centers each involving experts in genetics, clinical nephrology (adult and pediatric), physiology and cell/molecular biology as well as epidemiology and technology developments in relation with inherited tubulopathies. The participants have been selected on the basis of skills (transgenic animal models, human genetics, registry, imaging) that were considered crucial to the success of this program, as well as their close links with academic hospitals and cohorts of patients. A major goal of the proposal will be the integration of databases and bio-resources that have been generated in previously funded EU programs with clinical and mechanistic informations generated, in order to help understanding the clinical heterogeneity of tubular diseases, reveal common pathways which will facilitate the update ontologies and lead to an appropriate portofolio of models necessary to support future clinical trials. These tools will aim to promote an immediate application in medical care through interactions with clinicians.

Objectives and tasks

Our project aims to identify genes involved in causing and modifying tubulopathies in a large collaborative cohort of patients with well-defined tubular disorders from the pediatric and adult age groups. Identification of these genes will enable a better diagnosis, inform prognosis and management of affected patients and provide a basis for the rational development of new treatments. Whilst several underlying disease genes have been identified, many more are yet to be discovered. A substantial proportion of patients affected by various defined tubular disorders do not have identifiable mutations in currently known disease genes, suggesting that the disease is caused by yet unknown “primary” disease genes. Moreover, variations in “secondary” disease genes may modify the phenotype. With the recent revolutionary progress in next generation sequencing techniques, we now have the opportunity to efficiently and quickly find these missing genes and directly translate all knowledge into clinical care. Based on the identity of the mutated genes, a multi-level approach will focus on the functional aspects of the identified proteins (“functiomics”). This approach will integrate proteomics and metabolomics data in order to better understand the role of these renal proteins and characterize the mechanisms of renal diseases, in conjunction with the clinical phenotype of the patients.

Cohorts of patients and available biobanking

Brussels, Zurich, EUNEFRON: specialized clinics and registries for proximal tubulopathies (cystinosis, Dent’s disease), TAL (uromodulin and FJHN), Bartter and Gitelman, NDI and Sjogren (O. Devuyst, C. Wagner). EUNEFRON worked closely with the CEMARA information system for rare diseases developed in Paris (C. Antignac, X. Jeunemaitre).

London (UCL and GOSH): Specialized clinics for renal tubulopathies and stones exist at Great Ormond Street Hospital for Children (D.Bockenhauer/ W. van’t Hoff/ R. Kleta) and the Royal Free Hospital (Drs. R. Unwin/ C. Laing) in London. Each clinic caters for more than 200 patients with over 400 visits annually. DNA samples from approximately 500 patients’ DNA so far have been collected with consent. Detailed clinical data covering the entire age-spectrum are available.

Nijmegen and Utrecht: Families with distal tubulopathies (Gitelman) and renal hypomagnesemia are available for sequencing at present in the departments of Human Genetics of the University Medical Centres in Nijmegen en Utrecht. Importantly, newly identified hypomagnesemia genes will subsequently be screened for mutations in  larger cohorts of hypomagnesemia  patients available within the consortium (N.V. Knoers)

Paris, HEGP: Large registry of various tubulopathies including Gitelman, dRTA, Bartter, PHA1 and PHA2 (X. Jeunemaitre, R. Vargas-Poussou).

Models in Zurich, Brussels, Paris, London and Nijmegen: at least 25 transgenic mouse lines, GFP mouse models, immortalized and primary cell cultures covering the specific nephron segments, as well as other animal models i.e. Zebrafish, Xenopus.

Contacts with patient organizations and the ERA-EDTA Working Group on Inherited Kidney Disorders.


Our network has access to several cohorts (Nijmegen/Utrecht, EUNEFRON, Paris HEGP, Brussels, London GOSH and UCL, Zurich) with well-defined tubulopathies that are in the process for screening the causatives genes.

  1. We will use state-of-the-art genetic technology including classical linkage studies for familial cases, genome wide association studies, and next generation sequencing technology (including whole-exome sequencing) to unravel the genetic basis of tubulopathies in which the genetic defect has not yet been identified. Data analysis will involve appropriate filtering strategies using both dominant and recessive models and comparisons with reference exome data to identify additional candidate rare causal variants. Identified variants will be verified by targeted segregation analysis (Sanger Sequencing) in family members and controls. Importantly, newly identified genes will subsequently be screened for mutations in  larger cohorts of patients available within the consortium. The results will be linked with the individual phenotypes to reveal relevant statistical genotype-phenotype correlations.
  2. We plan to develop a novel and effective DNA diagnostic approach, applicable for renal tubulopathies. We aim to implement massive parallel sequencing, a high-throughput method that covers multiple genes concurrently in order to improve early diagnosis and genetic counselling in selected patients and their family members. In detail, after identification of novel disease genes, a sequencing strategy will be developed to screen all known disease genes at once in an individual. For all selected genes to be analyzed, the coding sequence, the promoter region, and other regulatory non-coding regions like splice site domains will be included.
  3. We will investigate the role of rare variants in the general population, using the influence of SLC12A3 on blood pressure, salt handling and metabolic syndrome as a paradigm. We have a large cohort of heterozygous carriers (parents or siblings of patients with Gitelman syndrome).
  4. We will characterize the miRs playing a role in the various tubular segments, with focus on the distal renal tubule. Generation and characterization of mouse models with nephron-specific depletion of the miR pool.
  5. We will perform collaborative studies on the functiomics of renal (transport) proteins, with in silico analysis and modeling, coupled to multiple assays and models to study the functional consequences of the mutated renal proteins. These assays include:
    1. functional activity measurements (i.e. patch clamp analysis, radio tracer uptake studies, enzymatic activity assays, promotor activity measurements);
    2. cell biological techniques to monitor the traffic of renal proteins;
      biochemical assays to understand processing and shedding of transmembrane proteins;
    3. studies of (mutated) proteins in animal models (mice, zebrafish and Xenopus embryos) and renal (primary) cell lines that exhibit many characteristics of the original renal cells. All nephron segments are covered by specific renal cell culture systems to study their functional behavior in the right environment. These models will facilitate library screens (missense mutants, storage diseases, etc…).
  6. We will seek to identify pathogenic autoantibodies in renal Sjogren syndrome, to decipher auto-immune mechanisms involved in tubular dysfunction. The project will use cutting-edge technology (protein microarrays, proteomics, phage display of random peptide libraries) to identify the antigens and autoantibodies that cause renal Sjögren’s. Patients cohorts are available through collaborations; animal and cellular models will be developed.
  7. We will use an unbiased approach to identify new loci and genes involved in tubular function: GWAS, exome sequencing coupled to deep urine phenotyping in genetic isolates and population-based studies.
  8. The investigations detailed above will be completed by deep phenotyping, involving specific assay and tools available in the network (biomarkers, auto-antibodies, proteomics in blood/urine/exosomes, …)

Expected outcomes

The expected outcomes of the project include:

  1. Identification and categorization of families with inherited tubular transport disorders
  2. Application of omics technologies to inherited tubular transport disorders:
    genomics of DNA samples including next generation sequencing
    - proteomics of samples (blood, kidney, urine/exosomes)
    - functiomics of identified affected / mutated / SNP’s containing genes
    - development of animal models including classic mouse, (TG rats ?), model organisms (Xenopus, Zebrafish)
  3. Towards personalized medicine of tubular transport disorders

Functiomics will facilitate to narrow the bridge between correlative data and causative data. Knowing the molecular mechanisms behind these rare renal diseases will also permit prenatal diagnostics. Identification of the involved signaling pathways behind the tubulopathies will allow to correct the pathophysiology. In addition, the identification of various targets in these affected pathways has a high diagnostic and prognostic value. Potentially mutations, SNPs in affected genes or affiliated target molecules would be beneficial to identify the disease at early onset.

Identification of primary and secondary kidney disease genes will dramatically enhance our understanding of tubulopathies (and more frequent disorders including hypertension, renal stone disease, CKD progression…). In the first instance it will allow diagnostic genetic testing for affected patients and their families. Importantly, identification of secondary (modifying) genetic variations in correlation with the clinical information will provide relevant data that inform patient management and prognosis.

Together, these data will provide a better understanding of the pathophysiology of tubulopathies and thus a platform for the rational discovery of novel treatments. It will allow the development of animal models for drug discovery and further study of pathophysiology.

Insight into the genetic origin of tubulopathies and the translation of knowledge of all identified genes  into an innovative high-throughput parallel sequencing method for DNA diagnostics, will of crucial benefit for patients and their relatives with respect to early detection, accurate diagnosis, and genetic counselling. 

Genetic testing for these disorders will also stimulate the design of personalized therapeutic intervention in the future, based on patient-specific genetic profiles.

WP Leader

Prof. Olivier Devuyst (Deputy: Rosa Vargas-Poussou)
University of Zurich