Targeting an anchored phosphatase-deacetylase unit restores renal ciliary homeostasis

  1. Janani Gopalan
  2. Mitchell H Omar
  3. Ankita Roy
  4. Nelly M Cruz
  5. Jerome Falcone
  6. Kiana N Jones
  7. Katherine A Forbush
  8. Jonathan Himmelfarb
  9. Benjamin S Freedman
  10. John D Scott  Is a corresponding author
  1. University of Washington, United States
  2. University of Washington Medical Center, United States

Abstract

Pathophysiological defects in water homeostasis can lead to renal failure. Likewise, common genetic disorders associated with abnormal cytoskeletal dynamics in the kidney collecting ducts and perturbed calcium and cAMP signaling in the ciliary compartment contribute to chronic kidney failure. We show that collecting ducts in mice lacking the A-Kinase anchoring protein AKAP220 exhibit enhanced development of primary cilia. Mechanistic studies reveal that AKAP220-associated protein phosphatase 1 (PP1) mediates this phenotype by promoting changes in the stability of histone deacetylase 6 (HDAC6) with concomitant defects in actin dynamics. This proceeds through a previously unrecognized adaptor function for PP1 as all ciliogenesis and cytoskeletal phenotypes are recapitulated in mIMCD3 knock-in cells expressing a phosphatase-targeting defective AKAP220-ΔPP1 mutant. Pharmacological blocking of local HDAC6 activity alters cilia development and reduces cystogenesis in kidney-on-chip and organoid models. These findings identify the AKAP220-PPI-HDAC6 pathway as a key effector in primary cilia development.

Data availability

All data generated or analyzed during this study are included in the manuscript.

Article and author information

Author details

  1. Janani Gopalan

    Pharmacology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Mitchell H Omar

    Pharmacology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Ankita Roy

    senior scientist, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Nelly M Cruz

    Nephrology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Jerome Falcone

    Pharmacology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Kiana N Jones

    Nephrology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Katherine A Forbush

    Pharmacology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4825-4766
  8. Jonathan Himmelfarb

    Nephrology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Benjamin S Freedman

    Nephrology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. John D Scott

    Department of Pharmacology, University of Washington Medical Center, Seattle, United States
    For correspondence
    scottjdw@uw.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0367-8146

Funding

National Institutes of Health (5R01DK105542)

  • John D Scott

National Institute of Diabetes and Digestive and Kidney Diseases (1R01DK119192-01)

  • John D Scott

National Institutes of Health (T32 GM007270)

  • Janani Gopalan

National Institute of Diabetes and Digestive and Kidney Diseases (F32DK121415)

  • Mitchell H Omar

Lara Nowak Macklin Research Fund

  • Mitchell H Omar

National Institutes of Health (UG3TR002158)

  • Jonathan Himmelfarb

National Institutes of Health (R01DK117914)

  • Benjamin S Freedman

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

Reviewing Editor

  1. Jeremy F Reiter, University of California, San Francisco, United States

Version history

  1. Preprint posted: February 24, 2021 (view preprint)
  2. Received: February 24, 2021
  3. Accepted: July 11, 2021
  4. Accepted Manuscript published: July 12, 2021 (version 1)
  5. Version of Record published: July 20, 2021 (version 2)
  6. Version of Record updated: August 12, 2021 (version 3)

Copyright

© 2021, Gopalan 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

  • 964
    views
  • 126
    downloads
  • 5
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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. Janani Gopalan
  2. Mitchell H Omar
  3. Ankita Roy
  4. Nelly M Cruz
  5. Jerome Falcone
  6. Kiana N Jones
  7. Katherine A Forbush
  8. Jonathan Himmelfarb
  9. Benjamin S Freedman
  10. John D Scott
(2021)
Targeting an anchored phosphatase-deacetylase unit restores renal ciliary homeostasis
eLife 10:e67828.
https://doi.org/10.7554/eLife.67828

Share this article

https://doi.org/10.7554/eLife.67828

Further reading

    1. Biochemistry and Chemical Biology
    2. Plant Biology
    Henning Mühlenbeck, Yuko Tsutsui ... Cyril Zipfel
    Research Article

    Transmembrane signaling by plant receptor kinases (RKs) has long been thought to involve reciprocal trans-phosphorylation of their intracellular kinase domains. The fact that many of these are pseudokinase domains, however, suggests that additional mechanisms must govern RK signaling activation. Non-catalytic signaling mechanisms of protein kinase domains have been described in metazoans, but information is scarce for plants. Recently, a non-catalytic function was reported for the leucine-rich repeat (LRR)-RK subfamily XIIa member EFR (elongation factor Tu receptor) and phosphorylation-dependent conformational changes were proposed to regulate signaling of RKs with non-RD kinase domains. Here, using EFR as a model, we describe a non-catalytic activation mechanism for LRR-RKs with non-RD kinase domains. EFR is an active kinase, but a kinase-dead variant retains the ability to enhance catalytic activity of its co-receptor kinase BAK1/SERK3 (brassinosteroid insensitive 1-associated kinase 1/somatic embryogenesis receptor kinase 3). Applying hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis and designing homology-based intragenic suppressor mutations, we provide evidence that the EFR kinase domain must adopt its active conformation in order to activate BAK1 allosterically, likely by supporting αC-helix positioning in BAK1. Our results suggest a conformational toggle model for signaling, in which BAK1 first phosphorylates EFR in the activation loop to stabilize its active conformation, allowing EFR in turn to allosterically activate BAK1.

    1. Biochemistry and Chemical Biology
    2. Neuroscience
    Katarzyna Marta Zoltowska, Utpal Das ... Lucía Chávez-Gutiérrez
    Research Article

    Amyloid β (Aβ) peptides accumulating in the brain are proposed to trigger Alzheimer’s disease (AD). However, molecular cascades underlying their toxicity are poorly defined. Here, we explored a novel hypothesis for Aβ42 toxicity that arises from its proven affinity for γ-secretases. We hypothesized that the reported increases in Aβ42, particularly in the endolysosomal compartment, promote the establishment of a product feedback inhibitory mechanism on γ-secretases, and thereby impair downstream signaling events. We conducted kinetic analyses of γ-secretase activity in cell-free systems in the presence of Aβ, as well as cell-based and ex vivo assays in neuronal cell lines, neurons, and brain synaptosomes to assess the impact of Aβ on γ-secretases. We show that human Aβ42 peptides, but neither murine Aβ42 nor human Aβ17–42 (p3), inhibit γ-secretases and trigger accumulation of unprocessed substrates in neurons, including C-terminal fragments (CTFs) of APP, p75, and pan-cadherin. Moreover, Aβ42 treatment dysregulated cellular homeostasis, as shown by the induction of p75-dependent neuronal death in two distinct cellular systems. Our findings raise the possibility that pathological elevations in Aβ42 contribute to cellular toxicity via the γ-secretase inhibition, and provide a novel conceptual framework to address Aβ toxicity in the context of γ-secretase-dependent homeostatic signaling.