Integrative analysis of CAKUT multi-omics data

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) is the leading cause of childhood end-stage renal disease and a significant cause of chronic kidney disease in adults. Genetic and environmental factors are known to influence CAKUT development, but the currently known disease mechanism remains incomplete. Our goal is to identify affected pathways and networks in CAKUT, and thereby aid in getting a better understanding of its pathophysiology. Multi-omics experiments, including amniotic fluid miRNome, peptidome, and proteome analyses, can shed light on foetal kidney development in non-severe CAKUT patients compared to severe CAKUT cases. We performed FAIRification of these omics data sets to facilitate their integration with external data resources. Furthermore, we analysed and integrated the omics data sets using three different bioinformatics strategies. The three bioinformatics analyses provided complementary features, but all pointed towards an important role for collagen in CAKUT development. We published the three analysis strategies as containerized workflows. These workflows can be applied to other FAIR data sets and help gaining knowledge on other rare diseases.

Authors 13

1. Jumamurat R. Bayjanov

   Radboud University Nijmegen · Radboud University Medical Center

   Affiliation as printed

   Medical BioSciences department, Radboud University Medical Centre

   Medical BioSciences department, Radboud University Medical Centre, Nijmegen, The Netherlands

2. Cenna Doornbos

   Radboud University Nijmegen · Radboud University Medical Center

   Affiliation as printed

   Medical BioSciences department, Radboud University Medical Centre

   Medical BioSciences department, Radboud University Medical Centre, Nijmegen, The Netherlands

3. Ozan Özışık

   Inserm · Aix-Marseille Université

   Affiliation as printed

   Aix Marseille Univ, INSERM

   Aix Marseille Univ, INSERM, MMG, Marseille, France

4. Woosub Shin

   Maastricht University

   Affiliation as printed

   Department of Bioinformatics - BiGCaT, NUTRIM/MHeNs, Maastricht University

   Department of Bioinformatics - BiGCaT, NUTRIM/MHeNs, Maastricht University, Maastricht, The Netherlands

5. Núria Queralt-Rosiñach Aachen Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Department of Human Genetics, Leiden University Medical Center

   Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

6. Daphne Wijnbergen Aachen Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Department of Human Genetics, Leiden University Medical Center

   Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

7. Jean Sébastien Saulnier Blache

   Université Toulouse III - Paul Sabatier · Inserm · Institut des Maladies Métaboliques et Cardiovasculaires

   Affiliation as printed

   Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Cardiovascular and Metabolic Disease

   Université Toulouse III Paul-Sabatier

   Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Cardiovascular and Metabolic Disease, Toulouse, France

   Université Toulouse III Paul-Sabatier, Toulouse, France

8. Joost Peter Schanstra

   Université Toulouse III - Paul Sabatier · Inserm · Institut des Maladies Métaboliques et Cardiovasculaires

   Affiliation as printed

   Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Cardiovascular and Metabolic Disease

   Université Toulouse III Paul-Sabatier

   Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Cardiovascular and Metabolic Disease, Toulouse, France

   Université Toulouse III Paul-Sabatier, Toulouse, France

9. José M. Fernández

   Barcelona Supercomputing Center

   Affiliation as printed

   Barcelona Supercomputing Center (BSC)

   Barcelona Supercomputing Center (BSC), Barcelona, Spain

10. Rajaram Kaliyaperumal Aachen Department of Human Genetics

    Leiden University Medical Center

    Affiliation as printed

    Department of Human Genetics, Leiden University Medical Center

    Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

11. Anaı̈s Baudot

    Centre National de la Recherche Scientifique · Inserm · Aix-Marseille Université · Barcelona Supercomputing Center

    Affiliation as printed

    Aix Marseille Univ, INSERM

    Barcelona Supercomputing Center (BSC)

    CNRS

    Aix Marseille Univ, INSERM, MMG, Marseille, France

    Barcelona Supercomputing Center (BSC), Barcelona, Spain

    CNRS, Marseille, France

12. Peter A.C. ’t Hoen

    Radboud University Nijmegen · Radboud University Medical Center

    Affiliation as printed

    Medical BioSciences department, Radboud University Medical Centre

    Medical BioSciences department, Radboud University Medical Centre, Nijmegen, The Netherlands

13. Friederike Ehrhart corresponding

    Maastricht University

    Affiliation as printed

    Department of Bioinformatics - BiGCaT, NUTRIM/MHeNs, Maastricht University

    Department of Bioinformatics - BiGCaT, NUTRIM/MHeNs, Maastricht University, Maastricht, The Netherlands