Analysis of the genomic architecture of a complex trait locus in hypertensive rat models links Tmem63c to kidney damage

  1. Angela Schulz
  2. Nicola Victoria Müller
  3. Nina Anne van de Lest
  4. Andreas Eisenreich
  5. Martina Schmidbauer
  6. Andrei Barysenka
  7. Bettina Purfürst
  8. Anje Sporbert
  9. Theodor Lorenzen
  10. Alexander M Meyer
  11. Laura Herlan
  12. Anika Witten
  13. Frank Rühle
  14. Weibin Zhou
  15. Emile de Heer
  16. Marion Scharpfenecker
  17. Daniela Panáková  Is a corresponding author
  18. Monika Stoll
  19. Reinhold Kreutz  Is a corresponding author
  1. Charité - Universitätsmedizin Berlin, Germany
  2. Leiden University Medical Center, Netherlands
  3. Westfälische Wilhelms University, Germany
  4. Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Germany
  5. Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Germany
  6. Duke University School of Medicine, United States

Abstract

Unraveling the genetic susceptibility of complex diseases such as chronic kidney disease remains challenging. Here, we used inbred rat models of kidney damage associated with elevated blood pressure for the comprehensive analysis of a major albuminuria susceptibility locus detected in these models. We characterized its genomic architecture by congenic substitution mapping, targeted next generation sequencing, and compartment-specific RNA sequencing analysis in isolated glomeruli. This led to prioritization of transmembrane protein Tmem63c as a novel potential target. Tmem63c is differentially expressed in glomeruli of allele-specific rat models during onset of albuminuria. Patients with focal segmental glomerulosclerosis exhibited specific TMEM63C loss in podocytes. Functional analysis in zebrafish revealed a role for tmem63c in mediating the glomerular filtration barrier function. Our data demonstrate that integrative analysis of the genomic architecture of a complex trait locus is a powerful tool for identification of new targets such as Tmem63c for further translational investigation.

Data availability

The genomic and transcriptomic data from this publication have been deposited to the NCBI curated repositories, GEO, and SRA, and assigned the identifier SubmissionID: SUB2950675 and BioProject ID: PRJNA398197 (DNA-Seq) and accession GSE102546 (RNA-Seq).

The following data sets were generated

Article and author information

Author details

  1. Angela Schulz

    Institute of Clinical Pharmacology and Toxicology, Charité - Universitätsmedizin Berlin, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4576-8035
  2. Nicola Victoria Müller

    Institute of Clinical Pharmacology and Toxicology, Charité - Universitätsmedizin Berlin, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7261-830X
  3. Nina Anne van de Lest

    Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  4. Andreas Eisenreich

    Institute of Clinical Pharmacology and Toxicology, Charité - Universitätsmedizin Berlin, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Martina Schmidbauer

    Institute of Clinical Pharmacology and Toxicology, Charité - Universitätsmedizin Berlin, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Andrei Barysenka

    Genetic Epidemiology, Institute for Human Genetics, Westfälische Wilhelms University, Münster, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Bettina Purfürst

    Core Facility Electron Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Anje Sporbert

    Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  9. Theodor Lorenzen

    Institute of Clinical Pharmacology and Toxicology, Charité - Universitätsmedizin Berlin, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Alexander M Meyer

    Electrochemical Signaling in Development and Disease, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  11. Laura Herlan

    Institute of Clinical Pharmacology and Toxicology, Charité - Universitätsmedizin Berlin, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  12. Anika Witten

    Genetic Epidemiology, Institute for Human Genetics, Westfälische Wilhelms University, Münster, Germany
    Competing interests
    The authors declare that no competing interests exist.
  13. Frank Rühle

    Genetic Epidemiology, Institute for Human Genetics, Westfälische Wilhelms University, Münster, Germany
    Competing interests
    The authors declare that no competing interests exist.
  14. Weibin Zhou

    Center for Human Disease Modeling, Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Emile de Heer

    Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  16. Marion Scharpfenecker

    Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  17. Daniela Panáková

    Electrochemical Signaling in Development and Disease, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
    For correspondence
    daniela.panakova@mdc-berlin.de
    Competing interests
    The authors declare that no competing interests exist.
  18. Monika Stoll

    Department of Genetic Epidemiology, Westfälische Wilhelms University, Münster, Germany
    Competing interests
    The authors declare that no competing interests exist.
  19. Reinhold Kreutz

    Institute of Clinical Pharmacology and Toxicology, Charité - Universitätsmedizin Berlin, Berlin, Germany
    For correspondence
    reinhold.kreutz@charite.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4818-211X

Funding

Deutsche Hochdruckliga

  • Reinhold Kreutz

Deutsche Forschungsgemeinschaft (DFG KR 1152-3-1)

  • Reinhold Kreutz

Helmholtz-Gemeinschaft (VH-NG-736)

  • Daniela Panáková

European Commission (WNT/CALCIUM IN HEART-322189)

  • Daniela Panáková

Deutsche Forschungsgemeinschaft (SCHU 2604/1-1)

  • Angela Schulz

Deutsche Forschungsgemeinschaft (Project number 394046635 - SFB 1365)

  • Reinhold Kreutz

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All experimental work in rat models was performed in accordance with the guidelines of the Charité-Universitätsmedizin Berlin and the local authority for animal protection (Landesamt für Gesundheit und Soziales, Berlin, Germany) for the use of laboratory animals. The registration numbers for the rat experiments are G 0255/09 and T 0189/02. Zebrafish were bred, raised and maintained in accordance with the guidelines of the Max Delbrück Center for Molecular Medicine and the local authority for animal protection (Landesamt für Gesundheit und Soziales, Berlin, Germany) for the use of laboratory animals, and followed the 'Principles of Laboratory Animal Care' (NIH publication no. 86-23, revised 1985) as well as the current version of German Law on the Protection of Animals.

Human subjects: All biopsy samples were handled and analyzed anonymously in accordance with the Dutch National Ethics Guidelines (Code for Proper Secondary Use of Human Tissue, Dutch Federation of Medical Scientific Societies). Because this study concerned retrospectively collected anonymized material, no informed consent was necessary following the Dutch National Ethics Guidelines. This study is in agreement with the Declaration of Helsinki and the Department of Health and Human Services Belmont Report and the use of the patient biopsies was approved by the medical ethical committee of the LUMC (registration number G16.110).

Reviewing Editor

  1. Tim Aitman, University of Edinburgh, United Kingdom

Publication history

  1. Received: September 16, 2018
  2. Accepted: March 20, 2019
  3. Accepted Manuscript published: March 22, 2019 (version 1)
  4. Version of Record published: April 23, 2019 (version 2)

Copyright

© 2019, Schulz et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,382
    Page views
  • 228
    Downloads
  • 13
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Angela Schulz
  2. Nicola Victoria Müller
  3. Nina Anne van de Lest
  4. Andreas Eisenreich
  5. Martina Schmidbauer
  6. Andrei Barysenka
  7. Bettina Purfürst
  8. Anje Sporbert
  9. Theodor Lorenzen
  10. Alexander M Meyer
  11. Laura Herlan
  12. Anika Witten
  13. Frank Rühle
  14. Weibin Zhou
  15. Emile de Heer
  16. Marion Scharpfenecker
  17. Daniela Panáková
  18. Monika Stoll
  19. Reinhold Kreutz
(2019)
Analysis of the genomic architecture of a complex trait locus in hypertensive rat models links Tmem63c to kidney damage
eLife 8:e42068.
https://doi.org/10.7554/eLife.42068

Further reading

    1. Genetics and Genomics
    2. Neuroscience
    Hayeon Sung, Anoumid Vaziri ... Monica Dus
    Research Article

    Diet profoundly influences brain physiology, but how metabolic information is transmuted into neural activity and behavior changes remains elusive. Here, we show that the metabolic enzyme O-GlcNAc Transferase (OGT) moonlights on the chromatin of the D. melanogaster gustatory neurons to instruct changes in chromatin accessibility and transcription that underlie sensory adaptations to a high-sugar diet. OGT works synergistically with the Mitogen Activated Kinase/Extracellular signal Regulated Kinase (MAPK/ERK) rolled and its effector stripe (also known as EGR2 or Krox20) to integrate activity information. OGT also cooperates with the epigenetic silencer Polycomb Repressive Complex 2.1 (PRC2.1) to decrease chromatin accessibility and repress transcription in the high-sugar diet. This integration of nutritional and activity information changes the taste neurons’ responses to sugar and the flies’ ability to sense sweetness. Our findings reveal how nutrigenomic signaling generates neural activity and behavior in response to dietary changes in the sensory neurons.

    1. Genetics and Genomics
    2. Evolutionary Biology
    Zane Kliesmete, Lucas Esteban Wange ... Wolfgang Enard
    Research Article

    Brain size and cortical folding have increased and decreased recurrently during mammalian evolution. Identifying genetic elements whose sequence or functional properties co-evolve with these traits can provide unique information on evolutionary and developmental mechanisms. A good candidate for such a comparative approach is TRNP1, as it controls proliferation of neural progenitors in mice and ferrets. Here, we investigate the contribution of both regulatory and coding sequences of TRNP1 to brain size and cortical folding in over 30 mammals. We find that the rate of TRNP1 protein evolution (ω) significantly correlates with brain size, slightly less with cortical folding and much less with body size. This brain correlation is stronger than for >95% of random control proteins. This co-evolution is likely affecting TRNP1 activity, as we find that TRNP1 from species with larger brains and more cortical folding induce higher proliferation rates in neural stem cells. Furthermore, we compare the activity of putative cis-regulatory elements (CREs) of TRNP1 in a massively parallel reporter assay and identify one CRE that likely co-evolves with cortical folding in Old World monkeys and apes. Our analyses indicate that coding and regulatory changes that increased TRNP1 activity were positively selected either as a cause or a consequence of increases in brain size and cortical folding. They also provide an example how phylogenetic approaches can inform biological mechanisms, especially when combined with molecular phenotypes across several species.