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Lizotte F, Rousseau M, Denhez B, Lévesque D, Guay A, Liu H, Moreau J, Higgins S, Sabbagh R, Susztak K, Boisvert FM, Côté AM, Geraldes P. Deletion of protein tyrosine phosphatase SHP-1 restores SUMOylation of podocin and reverses the progression of diabetic kidney disease. Kidney Int 2023; 104:787-802. [PMID: 37507049 DOI: 10.1016/j.kint.2023.06.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/03/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]
Abstract
Both clinical and experimental data suggest that podocyte injury is involved in the onset and progression of diabetic kidney disease (DKD). Although the mechanisms underlying the development of podocyte loss are not completely understood, critical structural proteins such as podocin play a major role in podocyte survival and function. We have reported that the protein tyrosine phosphatase SHP-1 expression increased in podocytes of diabetic mice and glomeruli of patients with diabetes. However, the in vivo contribution of SHP-1 in podocytes is unknown. Conditional podocyte-specific SHP-1-deficient mice (Podo-SHP-1-/-) were generated to evaluate the impact of SHP-1 deletion at four weeks of age (early) prior to the onset of diabetes and after 20 weeks (late) of diabetes (DM; Ins2+/C96Y) on kidney function (albuminuria and glomerular filtration rate) and kidney pathology. Ablation of the SHP-1 gene specifically in podocytes prevented and even reversed the elevated albumin/creatinine ratio, glomerular filtration rate progression, mesangial cell expansion, glomerular hypertrophy, glomerular basement membrane thickening and podocyte foot process effacement induced by diabetes. Moreover, podocyte-specific deletion of SHP-1 at an early and late stage prevented diabetes-induced expression of collagen IV, fibronectin, transforming growth factor-β, transforming protein RhoA, and serine/threonine kinase ROCK1, whereas it restored nephrin, podocin and cation channel TRPC6 expression. Mass spectrometry analysis revealed that SHP-1 reduced SUMO2 post-translational modification of podocin while podocyte-specific deletion of SHP-1 preserved slit diaphragm protein complexes in the diabetic context. Thus, our data uncovered a new role of SHP-1 in the regulation of cytoskeleton dynamics and slit diaphragm protein expression/stability, and its inhibition preserved podocyte function preventing DKD progression.
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Affiliation(s)
- Farah Lizotte
- Research Center of the Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Marina Rousseau
- Research Center of the Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Benoit Denhez
- Research Center of the Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dominique Lévesque
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Andréanne Guay
- Research Center of the Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - HongBo Liu
- Renal, Electrolyte, and Hypertension Division, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Genetics Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie Moreau
- Research Center of the Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sarah Higgins
- Division of Nephrology, Department of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Robert Sabbagh
- Department of Surgery, Université de Sherbrooke, Québec, Canada
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Genetics Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Anne Marie Côté
- Research Center of the Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada; Division of Nephrology, Department of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Pedro Geraldes
- Research Center of the Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada; Division of Endocrinology, Department of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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Späth MR, Hoyer-Allo KJR, Seufert L, Höhne M, Lucas C, Bock T, Isermann L, Brodesser S, Lackmann JW, Kiefer K, Koehler FC, Bohl K, Ignarski M, Schiller P, Johnsen M, Kubacki T, Grundmann F, Benzing T, Trifunovic A, Krüger M, Schermer B, Burst V, Müller RU. Organ Protection by Caloric Restriction Depends on Activation of the De Novo NAD+ Synthesis Pathway. J Am Soc Nephrol 2023; 34:772-792. [PMID: 36758124 PMCID: PMC10125653 DOI: 10.1681/asn.0000000000000087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 01/10/2023] [Indexed: 02/11/2023] Open
Abstract
SIGNIFICANCE STATEMENT AKI is a major clinical complication leading to high mortality, but intensive research over the past decades has not led to targeted preventive or therapeutic measures. In rodent models, caloric restriction (CR) and transient hypoxia significantly prevent AKI and a recent comparative transcriptome analysis of murine kidneys identified kynureninase (KYNU) as a shared downstream target. The present work shows that KYNU strongly contributes to CR-mediated protection as a key player in the de novo nicotinamide adenine dinucleotide biosynthesis pathway. Importantly, the link between CR and NAD+ biosynthesis could be recapitulated in a human cohort. BACKGROUND Clinical practice lacks strategies to treat AKI. Interestingly, preconditioning by hypoxia and caloric restriction (CR) is highly protective in rodent AKI models. However, the underlying molecular mechanisms of this process are unknown. METHODS Kynureninase (KYNU) knockout mice were generated by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and comparative transcriptome, proteome and metabolite analyses of murine kidneys pre- and post-ischemia-reperfusion injury in the context of CR or ad libitum diet were performed. In addition, acetyl-lysin enrichment and mass spectrometry were used to assess protein acetylation. RESULTS We identified KYNU as a downstream target of CR and show that KYNU strongly contributes to the protective effect of CR. The KYNU-dependent de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis pathway is necessary for CR-associated maintenance of NAD+ levels. This finding is associated with reduced protein acetylation in CR-treated animals, specifically affecting enzymes in energy metabolism. Importantly, the effect of CR on de novo NAD+ biosynthesis pathway metabolites can be recapitulated in humans. CONCLUSIONS CR induces the de novo NAD+ synthesis pathway in the context of IRI and is essential for its full nephroprotective potential. Differential protein acetylation may be the molecular mechanism underlying the relationship of NAD+, CR, and nephroprotection.
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Affiliation(s)
- Martin R. Späth
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - K. Johanna R. Hoyer-Allo
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Lisa Seufert
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christina Lucas
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Theresa Bock
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Institute of Genetics, University of Cologne, Cologne, Germany
| | - Lea Isermann
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Medical Faculty, Institute for Mitochondrial Diseases and Aging, University of Cologne, Cologne, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Susanne Brodesser
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jan-Wilm Lackmann
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Katharina Kiefer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Felix C. Koehler
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Katrin Bohl
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Michael Ignarski
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Petra Schiller
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Marc Johnsen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Torsten Kubacki
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Franziska Grundmann
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Aleksandra Trifunovic
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Medical Faculty, Institute for Mitochondrial Diseases and Aging, University of Cologne, Cologne, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Marcus Krüger
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Institute of Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Volker Burst
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Emergency Department, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
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Ermanoska B, Asselbergh B, Morant L, Petrovic-Erfurth ML, Hosseinibarkooie S, Leitão-Gonçalves R, Almeida-Souza L, Bervoets S, Sun L, Lee L, Atkinson D, Khanghahi A, Tournev I, Callaerts P, Verstreken P, Yang XL, Wirth B, Rodal AA, Timmerman V, Goode BL, Godenschwege TA, Jordanova A. Tyrosyl-tRNA synthetase has a noncanonical function in actin bundling. Nat Commun 2023; 14:999. [PMID: 36890170 PMCID: PMC9995517 DOI: 10.1038/s41467-023-35908-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 01/06/2023] [Indexed: 03/10/2023] Open
Abstract
Dominant mutations in tyrosyl-tRNA synthetase (YARS1) and six other tRNA ligases cause Charcot-Marie-Tooth peripheral neuropathy (CMT). Loss of aminoacylation is not required for their pathogenicity, suggesting a gain-of-function disease mechanism. By an unbiased genetic screen in Drosophila, we link YARS1 dysfunction to actin cytoskeleton organization. Biochemical studies uncover yet unknown actin-bundling property of YARS1 to be enhanced by a CMT mutation, leading to actin disorganization in the Drosophila nervous system, human SH-SY5Y neuroblastoma cells, and patient-derived fibroblasts. Genetic modulation of F-actin organization improves hallmark electrophysiological and morphological features in neurons of flies expressing CMT-causing YARS1 mutations. Similar beneficial effects are observed in flies expressing a neuropathy-causing glycyl-tRNA synthetase. Hence, in this work, we show that YARS1 is an evolutionary-conserved F-actin organizer which links the actin cytoskeleton to tRNA-synthetase-induced neurodegeneration.
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Affiliation(s)
- Biljana Ermanoska
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Bob Asselbergh
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, 2610, Antwerp, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium
| | - Laura Morant
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
| | - Maria-Luise Petrovic-Erfurth
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
| | - Seyyedmohsen Hosseinibarkooie
- Institute of Human Genetics; Center for Molecular Medicine Cologne; Center for Rare Diseases Cologne, University Hospital of Cologne; University of Cologne, 50931, Cologne, Germany
- Division of Endocrinology and Metabolism and Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Ricardo Leitão-Gonçalves
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
- Frontiers Media SA, Lausanne, Switzerland
| | - Leonardo Almeida-Souza
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
- Helsinki Institute of Life Science, Institute of Biotechnology & Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Sven Bervoets
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Litao Sun
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangdong, China
| | - LaTasha Lee
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL, 33458, USA
- Center for Social and Clinical Research, National Minority Quality Forum, Washington, DC, USA
| | - Derek Atkinson
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Akram Khanghahi
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
| | - Ivaylo Tournev
- Department of Neurology, Medical University-Sofia, 1431, Sofia, Bulgaria
- Department of Cognitive Science and Psychology, New Bulgarian University, 1618, Sofia, Bulgaria
| | | | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000, Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, 3000, Leuven, Belgium
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Brunhilde Wirth
- Institute of Human Genetics; Center for Molecular Medicine Cologne; Center for Rare Diseases Cologne, University Hospital of Cologne; University of Cologne, 50931, Cologne, Germany
| | - Avital A Rodal
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Vincent Timmerman
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium
| | - Bruce L Goode
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Tanja A Godenschwege
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL, 33458, USA
| | - Albena Jordanova
- Center for Molecular Neurology, VIB, University of Antwerp, 2610, Antwerpen, Belgium.
- Department of Biomedical Sciences, University of Antwerp, 2610, Antwerpen, Belgium.
- Department of Medical Chemistry and Biochemistry, Medical University-Sofia, 1431, Sofia, Bulgaria.
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Lausecker F, Koehler S, Fresquet M, Naylor RW, Tian P, Wanner N, Braun F, Butt L, Huber TB, Lennon R. Integrating basic science with translational research: the 13th International Podocyte Conference 2021. Kidney Int 2022; 102:708-719. [PMID: 35964799 PMCID: PMC9386279 DOI: 10.1016/j.kint.2022.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/30/2022]
Abstract
The 13th International Podocyte Conference was held in Manchester, UK, and online from July 28 to 30, 2021. Originally planned for 2020, this biannual meeting was postponed by a year because of the coronavirus disease 2019 (COVID-19) pandemic and proceeded as an innovative hybrid meeting. In addition to in-person attendance, online registration was offered, and this attracted 490 conference registrations in total. As a Podocyte Conference first, a day for early-career researchers was introduced. This premeeting included talks from graduate students and postdoctoral researchers. It gave early career researchers the opportunity to ask a panel, comprising academic leaders and journal editors, about career pathways and the future for podocyte research. The main meeting over 3 days included a keynote talk and 4 focused sessions each day incorporating invited talks, followed by selected abstract presentations, and an open panel discussion. The conference concluded with a Patient Day, which brought together patients, clinicians, researchers, and industry representatives. The Patient Day was an interactive and diverse day. As well as updates on improving diagnosis and potential new therapies, the Patient Day included a PodoArt competition, exercise and cooking classes with practical nutrition advice, and inspirational stories from patients and family members. This review summarizes the exciting science presented during the 13th International Podocyte Conference and demonstrates the resilience of researchers during a global pandemic.
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Affiliation(s)
- Franziska Lausecker
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Sybille Koehler
- Biomedical Sciences, University of Edinburgh, Edinburgh, UK; III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maryline Fresquet
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Richard W Naylor
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Pinyuan Tian
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Nicola Wanner
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabian Braun
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Linus Butt
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
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5
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BIG Modulates Stem Cell Niche and Meristem Development via SCR/SHR Pathway in Arabidopsis Roots. Int J Mol Sci 2022; 23:ijms23126784. [PMID: 35743225 PMCID: PMC9224481 DOI: 10.3390/ijms23126784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/18/2022] Open
Abstract
BIG, a regulator of polar auxin transport, is necessary to regulate the growth and development of Arabidopsis. Although mutations in the BIG gene cause severe root developmental defects, the exact mechanism remains unclear. Here, we report that disruption of the BIG gene resulted in decreased quiescent center (QC) activity and columella cell numbers, which was accompanied by the downregulation of WUSCHEL-RELATED HOMEOBOX5 (WOX5) gene expression. BIG affected auxin distribution by regulating the expression of PIN-FORMED proteins (PINs), but the root morphological defects of big mutants could not be rescued solely by increasing auxin transport. Although the loss of BIG gene function resulted in decreased expression of the PLT1 and PLT2 genes, genetic interaction assays indicate that this is not the main reason for the root morphological defects of big mutants. Furthermore, genetic interaction assays suggest that BIG affects the stem cell niche (SCN) activity through the SCRSCARECROW (SCR)/SHORT ROOT (SHR) pathway and BIG disruption reduces the expression of SCR and SHR genes. In conclusion, our findings reveal that the BIG gene maintains root meristem activity and SCN integrity mainly through the SCR/SHR pathway.
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UBR4/POE facilitates secretory trafficking to maintain circadian clock synchrony. Nat Commun 2022; 13:1594. [PMID: 35332162 PMCID: PMC8948264 DOI: 10.1038/s41467-022-29244-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/02/2022] [Indexed: 11/08/2022] Open
Abstract
Ubiquitin ligases control the degradation of core clock proteins to govern the speed and resetting properties of the circadian pacemaker. However, few studies have addressed their potential to regulate other cellular events within clock neurons beyond clock protein turnover. Here, we report that the ubiquitin ligase, UBR4/POE, strengthens the central pacemaker by facilitating neuropeptide trafficking in clock neurons and promoting network synchrony. Ubr4-deficient mice are resistant to jetlag, whereas poe knockdown flies are prone to arrhythmicity, behaviors reflective of the reduced axonal trafficking of circadian neuropeptides. At the cellular level, Ubr4 ablation impairs the export of secreted proteins from the Golgi apparatus by reducing the expression of Coronin 7, which is required for budding of Golgi-derived transport vesicles. In summary, UBR4/POE fulfills a conserved and unexpected role in the vesicular trafficking of neuropeptides, a function that has important implications for circadian clock synchrony and circuit-level signal processing. Although ubiquitin ligases are known to control clock protein degradation, their other roles in clock neurons are unclear. Here the authors report that UBR4 promotes export of neuropeptides from the Golgi for axonal trafficking, which is important for circadian clock synchrony in mice and flies.
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Bracci N, de la Fuente C, Saleem S, Pinkham C, Narayanan A, García-Sastre A, Balaraman V, Richt JA, Wilson W, Kehn-Hall K. Rift Valley fever virus Gn V5-epitope tagged virus enables identification of UBR4 as a Gn interacting protein that facilitates Rift Valley fever virus production. Virology 2022; 567:65-76. [PMID: 35032865 PMCID: PMC8877469 DOI: 10.1016/j.virol.2021.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/15/2021] [Accepted: 12/31/2021] [Indexed: 02/03/2023]
Abstract
Rift Valley fever virus (RVFV) is an arbovirus that was first reported in the Rift Valley of Kenya which causes significant disease in humans and livestock. RVFV is a tri-segmented, negative-sense RNA virus consisting of a L, M, and S segments with the M segment encoding the glycoproteins Gn and Gc. Host factors that interact with Gn are largely unknown. To this end, two viruses containing an epitope tag (V5) on the Gn protein in position 105 or 229 (V5Gn105 and V5Gn229) were generated using the RVFV MP-12 vaccine strain as a backbone. The V5-tag insertion minimally impacted Gn functionality as measured by replication kinetics, Gn localization, and antibody neutralization assays. A proteomics-based approach was used to identify novel Gn-binding host proteins, including the E3 ubiquitin-protein ligase, UBR4. Depletion of UBR4 resulted in a significant decrease in RVFV titers and a reduction in viral RNA production.
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Affiliation(s)
- Nicole Bracci
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University,National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Cynthia de la Fuente
- The National Institutes of Health, National Institute of Allergy and Infectious Diseases, DEA,National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Sahar Saleem
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Chelsea Pinkham
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | | | - Velmurugan Balaraman
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University
| | - William Wilson
- National Bio and Agro-Defense Facility, Agricultural Research Service, USDA
| | - Kylene Kehn-Hall
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University,National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University,Center for Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University,Corresponding Author: Kylene Kehn-Hall, Ph.D., Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Integrated Life Sciences Building, 1981 Kraft Drive, Blacksburg, VA 24060 USA,
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8
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Butt L, Unnersjö-Jess D, Höhne M, Hahnfeldt R, Reilly D, Rinschen MM, Plagmann I, Diefenhardt P, Brähler S, Brinkkötter PT, Brismar H, Blom H, Schermer B, Benzing T. Super-Resolution Imaging of the Filtration Barrier Suggests a Role for Podocin R229Q in Genetic Predisposition to Glomerular Disease. J Am Soc Nephrol 2022; 33:138-154. [PMID: 34853150 PMCID: PMC8763184 DOI: 10.1681/asn.2020060858] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/07/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Diseases of the kidney's glomerular filtration barrier are a leading cause of end stage renal failure. Despite a growing understanding of genes involved in glomerular disorders in children, the vast majority of adult patients lack a clear genetic diagnosis. The protein podocin p.R229Q, which results from the most common missense variant in NPHS2, is enriched in cohorts of patients with FSGS. However, p.R229Q has been proposed to cause disease only when transassociated with specific additional genetic alterations, and population-based epidemiologic studies on its association with albuminuria yielded ambiguous results. METHODS To test whether podocin p.R229Q may also predispose to the complex disease pathogenesis in adults, we introduced the exact genetic alteration in mice using CRISPR/Cas9-based genome editing (PodR231Q ). We assessed the phenotype using super-resolution microscopy and albuminuria measurements and evaluated the stability of the mutant protein in cell culture experiments. RESULTS Heterozygous PodR231Q/wild-type mice did not present any overt kidney disease or proteinuria. However, homozygous PodR231Q/R231Q mice developed increased levels of albuminuria with age, and super-resolution microscopy revealed preceding ultrastructural morphologic alterations that were recently linked to disease predisposition. When injected with nephrotoxic serum to induce glomerular injury, heterozygous PodR231Q/wild-type mice showed a more severe course of disease compared with Podwild-type/wild-type mice. Podocin protein levels were decreased in PodR231Q/wild-type and PodR231Q/R231Q mice as well as in human cultured podocytes expressing the podocinR231Q variant. Our in vitro experiments indicate an underlying increased proteasomal degradation. CONCLUSIONS Our findings demonstrate that podocin R231Q exerts a pathogenic effect on its own, supporting the concept of podocin R229Q contributing to genetic predisposition in adult patients.
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Affiliation(s)
- Linus Butt
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - David Unnersjö-Jess
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Robert Hahnfeldt
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Dervla Reilly
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Markus M. Rinschen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,III Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ingo Plagmann
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Paul Diefenhardt
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Sebastian Brähler
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Paul T. Brinkkötter
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Hans Blom
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne and University Hospital Cologne, Cologne, Germany,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne and University Hospital Cologne, Cologne, Germany,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
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9
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Koehler S, Odenthal J, Ludwig V, Jess DU, Höhne M, Jüngst C, Grawe F, Helmstädter M, Janku JL, Bergmann C, Hoyer PF, Hagmann HHH, Walz G, Bloch W, Niessen C, Schermer B, Wodarz A, Denholm B, Benzing T, Iden S, Brinkkoetter PT. Scaffold polarity proteins Par3A and Par3B share redundant functions while Par3B acts independent of atypical protein kinase C/Par6 in podocytes to maintain the kidney filtration barrier. Kidney Int 2021; 101:733-751. [PMID: 34929254 DOI: 10.1016/j.kint.2021.11.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/08/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022]
Abstract
Glomerular diseases are a major cause for chronic kidney disorders. In most cases podocyte injury is causative for disease development. Cytoskeletal rearrangements and morphological changes are hallmark features of podocyte injury and result in dedifferentiation and loss of podocytes. Here, we establish a link between the Par3 polarity complex and actin regulators necessary to establish and maintain podocyte architecture by utilizing mouse and Drosophila models to characterize the functional role of Par3A and Par3B and its fly homologue Bazooka in vivo. Only simultaneous inactivation of both Par3 proteins caused a severe disease phenotype. Rescue experiments in Drosophila nephrocytes revealed atypical protein kinase C (aPKC)-Par6 dependent and independent effects. While Par3A primarily acts via aPKC-Par6, Par3B function was independent of Par6. Actin-associated synaptopodin protein levels were found to be significantly upregulated upon loss of Par3A/B in mouse podocytes. Tropomyosin2, which shares functional similarities with synaptopodin, was also elevated in Bazooka depleted nephrocytes. The simultaneous depletion of Bazooka and Tropomyosin2 resulted in a partial rescue of the Bazooka knockdown phenotype and prevented increased Rho1, a member of a GTPase protein family regulating the cytoskeleton. The latter contribute to the nephrocyte phenotype observed upon loss of Bazooka. Thus, we demonstrate that Par3 proteins share a high functional redundancy but also have specific functions. Par3A acts in an aPKC-Par6 dependent way and regulates RhoA-GTP levels, while Par3B exploits Par6 independent functions influencing synaptopodin localization. Hence, Par3A and Par3B link elements of polarity signaling and actin regulators to maintain podocyte architecture.
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Affiliation(s)
- Sybille Koehler
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Biomedical Sciences, University of Edinburgh, Edinburgh, Scotland, UK.
| | - Johanna Odenthal
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Vivian Ludwig
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - David Unnersjö Jess
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Christian Jüngst
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Ferdi Grawe
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Molecular Cell Biology, Institute I for Anatomy, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Martin Helmstädter
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Johanna L Janku
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Carsten Bergmann
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany; Department of Medicine, Nephrology, University Hospital Freiburg, Germany
| | - Peter F Hoyer
- Klinik für Kinderheilkunde 2, Zentrum für Kinder- und Jugendmedizin, Universitätsklinikum Essen, Essen, Germany
| | - H H Henning Hagmann
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Gerd Walz
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Wilhelm Bloch
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiovascular Research and Sport Medicine, German Sport University Cologne, Cologne, Germany
| | - Carien Niessen
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Department of Dermatology, University Hospital of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Andreas Wodarz
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Molecular Cell Biology, Institute I for Anatomy, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Barry Denholm
- Biomedical Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Thomas Benzing
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sandra Iden
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Institute for Cell and Developmental Biology, Saarland University, Homburg/Saar, Germany
| | - Paul T Brinkkoetter
- Department II of Internal Medicine; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
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10
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Hunt LC, Schadeberg B, Stover J, Haugen B, Pagala V, Wang YD, Puglise J, Barton ER, Peng J, Demontis F. Antagonistic control of myofiber size and muscle protein quality control by the ubiquitin ligase UBR4 during aging. Nat Commun 2021; 12:1418. [PMID: 33658508 PMCID: PMC7930053 DOI: 10.1038/s41467-021-21738-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/08/2021] [Indexed: 01/31/2023] Open
Abstract
Sarcopenia is a degenerative condition that consists in age-induced atrophy and functional decline of skeletal muscle cells (myofibers). A common hypothesis is that inducing myofiber hypertrophy should also reinstate myofiber contractile function but such model has not been extensively tested. Here, we find that the levels of the ubiquitin ligase UBR4 increase in skeletal muscle with aging, and that UBR4 increases the proteolytic activity of the proteasome. Importantly, muscle-specific UBR4 loss rescues age-associated myofiber atrophy in mice. However, UBR4 loss reduces the muscle specific force and accelerates the decline in muscle protein quality that occurs with aging in mice. Similarly, hypertrophic signaling induced via muscle-specific loss of UBR4/poe and of ESCRT members (HGS/Hrs, STAM, USP8) that degrade ubiquitinated membrane proteins compromises muscle function and shortens lifespan in Drosophila by reducing protein quality control. Altogether, these findings indicate that these ubiquitin ligases antithetically regulate myofiber size and muscle protein quality control.
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Affiliation(s)
- Liam C Hunt
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bronwen Schadeberg
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jared Stover
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benard Haugen
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Vishwajeeth Pagala
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason Puglise
- College of Health & Human Performance Applied Physiology & Kinesiology, University of Florida, Gainesville, FL, USA
| | - Elisabeth R Barton
- College of Health & Human Performance Applied Physiology & Kinesiology, University of Florida, Gainesville, FL, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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11
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Rinschen MM, Saez-Rodriguez J. The tissue proteome in the multi-omic landscape of kidney disease. Nat Rev Nephrol 2020; 17:205-219. [PMID: 33028957 DOI: 10.1038/s41581-020-00348-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Kidney research is entering an era of 'big data' and molecular omics data can provide comprehensive insights into the molecular footprints of cells. In contrast to transcriptomics, proteomics and metabolomics generate data that relate more directly to the pathological symptoms and clinical parameters observed in patients. Owing to its complexity, the proteome still holds many secrets, but has great potential for the identification of drug targets. Proteomics can provide information about protein synthesis, modification and degradation, as well as insight into the physical interactions between proteins, and between proteins and other biomolecules. Thus far, proteomics in nephrology has largely focused on the discovery and validation of biomarkers, but the systematic analysis of the nephroproteome can offer substantial additional insights, including the discovery of mechanisms that trigger and propagate kidney disease. Moreover, proteome acquisition might provide a diagnostic tool that complements the assessment of a kidney biopsy sample by a pathologist. Such applications are becoming increasingly feasible with the development of high-throughput and high-coverage technologies, such as versatile mass spectrometry-based techniques and protein arrays, and encourage further proteomics research in nephrology.
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Affiliation(s)
- Markus M Rinschen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark. .,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. .,Department of Chemistry, Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research, La Jolla, CA, USA.
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, and Heidelberg University Hospital, Bioquant, Heidelberg, Germany.,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
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12
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Recognition of nonproline N-terminal residues by the Pro/N-degron pathway. Proc Natl Acad Sci U S A 2020; 117:14158-14167. [PMID: 32513738 DOI: 10.1073/pnas.2007085117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Eukaryotic N-degron pathways are proteolytic systems whose unifying feature is their ability to recognize proteins containing N-terminal (Nt) degradation signals called N-degrons, and to target these proteins for degradation by the 26S proteasome or autophagy. GID4, a subunit of the GID ubiquitin ligase, is the main recognition component of the proline (Pro)/N-degron pathway. GID4 targets proteins through their Nt-Pro residue or a Pro at position 2, in the presence of specific downstream sequence motifs. Here we show that human GID4 can also recognize hydrophobic Nt-residues other than Pro. One example is the sequence Nt-IGLW, bearing Nt-Ile. Nt-IGLW binds to wild-type human GID4 with a K d of 16 μM, whereas the otherwise identical Nt-Pro-bearing sequence PGLW binds to GID4 more tightly, with a K d of 1.9 μM. Despite this difference in affinities of GID4 for Nt-IGLW vs. Nt-PGLW, we found that the GID4-mediated Pro/N-degron pathway of the yeast Saccharomyces cerevisiae can target an Nt-IGLW-bearing protein for rapid degradation. We solved crystal structures of human GID4 bound to a peptide bearing Nt-Ile or Nt-Val. We also altered specific residues of human GID4 and measured the affinities of resulting mutant GID4s for Nt-IGLW and Nt-PGLW, thereby determining relative contributions of specific GID4 residues to the GID4-mediated recognition of Nt-Pro vs. Nt-residues other than Pro. These and related results advance the understanding of targeting by the Pro/N-degron pathway and greatly expand the substrate recognition range of the GID ubiquitin ligase in both human and yeast cells.
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13
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Five enzymes of the Arg/N-degron pathway form a targeting complex: The concept of superchanneling. Proc Natl Acad Sci U S A 2020; 117:10778-10788. [PMID: 32366662 DOI: 10.1073/pnas.2003043117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Arg/N-degron pathway targets proteins for degradation by recognizing their N-terminal (Nt) residues. If a substrate bears, for example, Nt-Asn, its targeting involves deamidation of Nt-Asn, arginylation of resulting Nt-Asp, binding of resulting (conjugated) Nt-Arg to the UBR1-RAD6 E3-E2 ubiquitin ligase, ligase-mediated synthesis of a substrate-linked polyubiquitin chain, its capture by the proteasome, and substrate's degradation. We discovered that the human Nt-Asn-specific Nt-amidase NTAN1, Nt-Gln-specific Nt-amidase NTAQ1, arginyltransferase ATE1, and the ubiquitin ligase UBR1-UBE2A/B (or UBR2-UBE2A/B) form a complex in which NTAN1 Nt-amidase binds to NTAQ1, ATE1, and UBR1/UBR2. In addition, NTAQ1 Nt-amidase and ATE1 arginyltransferase also bind to UBR1/UBR2. In the yeast Saccharomyces cerevisiae, the Nt-amidase, arginyltransferase, and the double-E3 ubiquitin ligase UBR1-RAD6/UFD4-UBC4/5 are shown to form an analogous targeting complex. These complexes may enable substrate channeling, in which a substrate bearing, for example, Nt-Asn, would be captured by a complex-bound Nt-amidase, followed by sequential Nt modifications of the substrate and its polyubiquitylation at an internal Lys residue without substrate's dissociation into the bulk solution. At least in yeast, the UBR1/UFD4 ubiquitin ligase interacts with the 26S proteasome, suggesting an even larger Arg/N-degron-targeting complex that contains the proteasome as well. In addition, specific features of protein-sized Arg/N-degron substrates, including their partly sequential and partly nonsequential enzymatic modifications, led us to a verifiable concept termed "superchanneling." In superchanneling, the synthesis of a substrate-linked poly-Ub chain can occur not only after a substrate's sequential Nt modifications, but also before them, through a skipping of either some or all of these modifications within a targeting complex.
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14
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Musante L, Bontha SV, La Salvia S, Fernandez-Piñeros A, Lannigan J, Le TH, Mas V, Erdbrügger U. Rigorous characterization of urinary extracellular vesicles (uEVs) in the low centrifugation pellet - a neglected source for uEVs. Sci Rep 2020; 10:3701. [PMID: 32111925 PMCID: PMC7048852 DOI: 10.1038/s41598-020-60619-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/30/2020] [Indexed: 02/07/2023] Open
Abstract
Urinary extracellular vesicles (uEVs) provide bio-markers for kidney and urogenital diseases. Centrifugation is the most common method used to enrich uEVs. However, a majority of studies to date have focused on the ultracentrifugation pellet, potentially losing a novel source of important biomarkers that could be obtained at lower centrifugation. Thus, the aim of this study is to rigorously characterize for the first time uEVs in the low speed pellet and determine the minimal volume of urine required for proteomic analysis (≥9.0 mL urine) and gene ontology classification identified 75% of the protein as extracellular exosomes. Cryo-Transmission Electron Microscopy (≥3.0 mL urine) provided evidence of a heterogeneous population of EVs for size and morphology independent of uromodulin filaments. Western blot detected several specific uEV kidney and EV markers (≥4.5 mL urine per lane). microRNAs quantification by qPCR was possible with urine volume as low as 0.5 mL. Particle enumeration with tunable resistive pulse sensing, nano particles tracking analysis and single EV high throughput imaging flow cytometry are possible starting from 0.5 and 3.0 mL of urine respectively. This work characterizes a neglected source of uEVs and provides guidance with regard to volume of urine necessary to carry out multi-omic studies and reveals novel aspects of uEV analysis such as autofluorescence of podocyte origin.
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Affiliation(s)
- Luca Musante
- Division of Nephrology and Center for Immunity, Inflammation and Regenerative Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Sai Vineela Bontha
- Transplant Research Institute, James D. Eason Transplant Institute, School of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sabrina La Salvia
- Division of Nephrology and Center for Immunity, Inflammation and Regenerative Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Angela Fernandez-Piñeros
- Transplant Research Institute, James D. Eason Transplant Institute, School of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Joanne Lannigan
- School of Medicine, Flow Cytometry Core, University of Virginia, Charlottesville, VA, USA
| | - Thu H Le
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, USA
| | - Valeria Mas
- Transplant Research Institute, James D. Eason Transplant Institute, School of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Uta Erdbrügger
- Division of Nephrology and Center for Immunity, Inflammation and Regenerative Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA.
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15
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Koehler S, Kuczkowski A, Kuehne L, Jüngst C, Hoehne M, Grahammer F, Eddy S, Kretzler M, Beck BB, Höhfeld J, Schermer B, Benzing T, Brinkkoetter PT, Rinschen MM. Proteome Analysis of Isolated Podocytes Reveals Stress Responses in Glomerular Sclerosis. J Am Soc Nephrol 2020; 31:544-559. [PMID: 32047005 DOI: 10.1681/asn.2019030312] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Understanding podocyte-specific responses to injury at a systems level is difficult because injury leads to podocyte loss or an increase of extracellular matrix, altering glomerular cellular composition. Finding a window into early podocyte injury might help identify molecular pathways involved in the podocyte stress response. METHODS We developed an approach to apply proteome analysis to very small samples of purified podocyte fractions. To examine podocytes in early disease states in FSGS mouse models, we used podocyte fractions isolated from individual mice after chemical induction of glomerular disease (with Doxorubicin or LPS). We also applied single-glomerular proteome analysis to tissue from patients with FSGS. RESULTS Transcriptome and proteome analysis of glomeruli from patients with FSGS revealed an underrepresentation of podocyte-specific genes and proteins in late-stage disease. Proteome analysis of purified podocyte fractions from FSGS mouse models showed an early stress response that includes perturbations of metabolic, mechanical, and proteostasis proteins. Additional analysis revealed a high correlation between the amount of proteinuria and expression levels of the mechanosensor protein Filamin-B. Increased expression of Filamin-B in podocytes in biopsy samples from patients with FSGS, in single glomeruli from proteinuric rats, and in podocytes undergoing mechanical stress suggests that this protein has a role in detrimental stress responses. In Drosophila, nephrocytes with reduced filamin homolog Cher displayed altered filtration capacity, but exhibited no change in slit diaphragm structure. CONCLUSIONS We identified conserved mechanisms of the podocyte stress response through ultrasensitive proteome analysis of human glomerular FSGS tissue and purified native mouse podocytes during early disease stages. This approach enables systematic comparisons of large-scale proteomics data and phenotype-to-protein correlation.
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Affiliation(s)
- Sybille Koehler
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Biomedical Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Alexander Kuczkowski
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Lucas Kuehne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Christian Jüngst
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Martin Hoehne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Florian Grahammer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Eppendorf, Hamburg, Germany
| | - Sean Eddy
- Division of Nephrology, Department of Internal Medicine, and
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, and.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Bodo B Beck
- Department of Human Genetics, University Hospital Cologne, Cologne, Germany
| | - Jörg Höhfeld
- Cell Biology, University of Bonn, Bonn, Germany; and
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Paul T Brinkkoetter
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany;
| | - Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; .,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California
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16
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BENZING THOMAS. MOLECULAR DESIGN OF THE KIDNEY FILTRATION BARRIER. TRANSACTIONS OF THE AMERICAN CLINICAL AND CLIMATOLOGICAL ASSOCIATION 2020; 131:125-139. [PMID: 32675853 PMCID: PMC7358502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Kidneys are the central regulators of organismal homeostasis. These organs filter enormous amounts of fluid from plasma; excrete toxic waste products; maintain salt, water, and volume balance; coordinate blood pressure regulation; and maintain the acid-base equilibrium essential for life. Although it has been known for decades that renal glomeruli serve as the site of plasma ultrafiltration and urine production, both the molecular design and function of the kidney filtration barrier have remained elusive. Indeed, the past two decades have witnessed enormous breakthroughs in our fundamental understanding of kidney filtration and the critical role that podocytes, specialized terminally differentiated epithelial cells at the glomerular capillaries, fulfill in the function of the kidney filtration barrier. Here we discuss recent advances in this field that will change the way we think about plasma ultrafiltration in health and proteinuria as a manifestation of glomerular diseases.
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Affiliation(s)
- THOMAS BENZING
- Correspondence and reprint requests: Thomas Benzing, MD, Department II of Internal Medicine, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany+ 49 221 4784480, 49 221 4785959
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17
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Abstract
BACKGROUND Recently, pathogenic alleles within ubiquitin N-recognin domain-containing E3 ligase 4 (UBR4) gene have been shown to be associated with Hirschsprung disease (HSCR). We determined the UBR4 expressions in Indonesian HSCR patients. METHODS We analyzed the UBR4 expressions in the colons of HSCR patient and anorectal malformation (ARM) patient as control by real-time polymerase chain reaction (qPCR). RESULTS Thirty-seven patients with non-syndromic HSCR and eighteen controls were involved in this study. qPCR revealed that the UBR4 expression was strongly decreased (0.77-fold) in the ganglionic group of patients with HSCR compared to the control group with ARM (ΔCT 2.43 ± 0.36 vs. 2.05 ± 0.69; p = 0.009), whereas the UBR4 expression was also significantly reduced (0.79-fold) in the aganglionic group of patients with HSCR compared to the control group with ARM (ΔCT 2.39 ± 0.46 vs. 2.05 ± 0.69; p = 0.044). However, the UBR4 expression change was not associated with gender (p = 0.35 and 0.80), nor with degree of aganglionosis both in ganglionic and aganglionic colons (p = 0.72 and 0.73), respectively. CONCLUSION Our study demonstrates that expression of UBR4 is decreased in both aganglionic and ganglionic colon of HSCR patients.
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18
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Rinschen MM, Palygin O, Guijas C, Palermo A, Palacio-Escat N, Domingo-Almenara X, Montenegro-Burke R, Saez-Rodriguez J, Staruschenko A, Siuzdak G. Metabolic rewiring of the hypertensive kidney. Sci Signal 2019; 12:12/611/eaax9760. [PMID: 31822592 DOI: 10.1126/scisignal.aax9760] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hypertension is a persistent epidemic across the developed world that is closely associated with kidney disease. Here, we applied a metabolomic, phosphoproteomic, and proteomic strategy to analyze the effect of hypertensive insults on kidneys. Our data revealed the metabolic aspects of hypertension-induced glomerular sclerosis, including lipid breakdown at early disease stages and activation of anaplerotic pathways to regenerate energy equivalents to counter stress. For example, branched-chain amino acids and proline, required for collagen synthesis, were depleted in glomeruli at early time points. Furthermore, indicators of metabolic stress were reflected by low amounts of ATP and NADH and an increased abundance of oxidized lipids derived from lipid breakdown. These processes were specific to kidney glomeruli where metabolic signaling occurred through mTOR and AMPK signaling. Quantitative phosphoproteomics combined with computational modeling suggested that these processes controlled key molecules in glomeruli and specifically podocytes, including cytoskeletal components and GTP-binding proteins, which would be expected to compete for decreasing amounts of GTP at early time points. As a result, glomeruli showed increased expression of metabolic enzymes of central carbon metabolism, amino acid degradation, and lipid oxidation, findings observed in previously published studies from other disease models and patients with glomerular damage. Overall, multilayered omics provides an overview of hypertensive kidney damage and suggests that metabolic or dietary interventions could prevent and treat glomerular disease and hypertension-induced nephropathy.
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Affiliation(s)
- Markus M Rinschen
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA.,Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Cologne 50931, Germany
| | - Oleg Palygin
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Carlos Guijas
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA
| | - Amelia Palermo
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA
| | - Nicolas Palacio-Escat
- COMBINE-Joint Research Center for Computational Biomedicine RWTH Aachen University, Aachen 52074, Germany.,Institute of Computational Biomedicine, Bioquant, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg 69120, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg 69120, Germany
| | - Xavier Domingo-Almenara
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA
| | - Rafael Montenegro-Burke
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA
| | - Julio Saez-Rodriguez
- COMBINE-Joint Research Center for Computational Biomedicine RWTH Aachen University, Aachen 52074, Germany.,Institute of Computational Biomedicine, Bioquant, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg 69120, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory and Heidelberg University, Heidelberg 69120, Germany
| | - Alexander Staruschenko
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA. .,Clement J. Zablocki VA Medical Center, Milwaukee, WI 53295, USA
| | - Gary Siuzdak
- Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA.
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19
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Rinschen MM, Gödel M, Grahammer F, Zschiedrich S, Helmstädter M, Kretz O, Zarei M, Braun DA, Dittrich S, Pahmeyer C, Schroder P, Teetzen C, Gee H, Daouk G, Pohl M, Kuhn E, Schermer B, Küttner V, Boerries M, Busch H, Schiffer M, Bergmann C, Krüger M, Hildebrandt F, Dengjel J, Benzing T, Huber TB. A Multi-layered Quantitative In Vivo Expression Atlas of the Podocyte Unravels Kidney Disease Candidate Genes. Cell Rep 2019; 23:2495-2508. [PMID: 29791858 PMCID: PMC5986710 DOI: 10.1016/j.celrep.2018.04.059] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/07/2018] [Accepted: 04/15/2018] [Indexed: 12/31/2022] Open
Abstract
Damage to and loss of glomerular podocytes has been identified as the culprit lesion in progressive kidney diseases. Here, we combine mass spectrometry-based proteomics with mRNA sequencing, bioinformatics, and hypothesis-driven studies to provide a comprehensive and quantitative map of mammalian podocytes that identifies unanticipated signaling pathways. Comparison of the in vivo datasets with proteomics data from podocyte cell cultures showed a limited value of available cell culture models. Moreover, in vivo stable isotope labeling by amino acids uncovered surprisingly rapid synthesis of mitochondrial proteins under steady-state conditions that was perturbed under autophagy-deficient, disease-susceptible conditions. Integration of acquired omics dimensions suggested FARP1 as a candidate essential for podocyte function, which could be substantiated by genetic analysis in humans and knockdown experiments in zebrafish. This work exemplifies how the integration of multi-omics datasets can identify a framework of cell-type-specific features relevant for organ health and disease. Deep proteome and transcriptome analyses of native podocytes unravel druggable targets Static and dynamic proteomics uncover features of podocyte identity and proteostasis Candidate genes for nephrotic syndrome were predicted based on multi-omic integration FARP1 is a previously unreported candidate gene for human proteinuric kidney disease
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, 50931 Cologne, Germany.
| | - Markus Gödel
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Florian Grahammer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Stefan Zschiedrich
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Martin Helmstädter
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Oliver Kretz
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Mostafa Zarei
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg, Germany; Center for Systems Biology (ZBSA), Albert Ludwigs University, 79104 Freiburg, Germany
| | - Daniela A Braun
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sebastian Dittrich
- Department II of Internal Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Caroline Pahmeyer
- Department II of Internal Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Patricia Schroder
- Department of Medicine/Nephrology, Hannover Medical School, 30625 Hannover, Germany; Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04609, USA
| | - Carolin Teetzen
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - HeonYung Gee
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04609, USA; Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ghaleb Daouk
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Martin Pohl
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Medical Center and Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Elisa Kuhn
- Center for Human Genetics, Bioscientia, 55218 Ingelheim, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, 50931 Cologne, Germany
| | - Victoria Küttner
- Department for Neuroanatomy, University of Freiburg, 79104 Freiburg, Germany; Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg, Germany; Department of Dermatology, Medical Center - University of Freiburg, 79106 Freiburg, Germany
| | - Melanie Boerries
- Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert Ludwigs University Freiburg, 79106 Freiburg, Germany; German Cancer Consortium (DKTK), 79106 Freiburg, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert Ludwigs University Freiburg, 79106 Freiburg, Germany; Lübeck Institute for Experimental Dermatology (LIED), University of Lübeck, 23562 Lübeck, Germany
| | - Mario Schiffer
- Department of Medicine/Nephrology, Hannover Medical School, 30625 Hannover, Germany; Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04609, USA
| | - Carsten Bergmann
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Center for Human Genetics, Bioscientia, 55218 Ingelheim, Germany
| | - Marcus Krüger
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joern Dengjel
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg, Germany; Center for Systems Biology (ZBSA), Albert Ludwigs University, 79104 Freiburg, Germany; Department of Dermatology, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; BIOSS Centre for Biological Signaling Studies, Albert Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, 50931 Cologne, Germany.
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg, Germany; Center for Systems Biology (ZBSA), Albert Ludwigs University, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Albert Ludwigs University Freiburg, 79104 Freiburg, Germany.
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20
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Lu XY, Liu BC, Cao YZ, Song C, Su H, Chen G, Klein JD, Zhang HX, Wang LH, Ma HP. High glucose reduces expression of podocin in cultured human podocytes by stimulating TRPC6. Am J Physiol Renal Physiol 2019; 317:F1605-F1611. [PMID: 31566428 DOI: 10.1152/ajprenal.00215.2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The transient receptor potential canonical 6 (TRPC6) channel and podocin are colocalized in the glomerular slit diaphragm as an important complex to maintain podocyte function. Gain of TRPC6 function and loss of podocin function induce podocyte injury. We have previously shown that high glucose induces apoptosis of podocytes by activating TRPC6; however, whether the activated TRPC6 can alter podocin expression remains unknown. Western blot analysis and confocal microscopy were used to examine both expression levels of TRPC6, podocin, and nephrin and morphological changes of podocytes in response to high glucose. High glucose increased the expression of TRPC6 but reduced the expression of podocin and nephrin, in both cultured human podocytes and type 1 diabetic rat kidneys. The decreased podocin was diminished in TRPC6 knockdown podocytes. High glucose elevated intracellular Ca2+ in control podocytes but not in TRPC6 knockdown podocytes. High glucose also elevated the expression of a tight junction protein, zonula occludens-1, and induced the redistribution of zonula occludens-1 and loss of podocyte processes. These data together suggest that high glucose reduces protein levels of podocin by activating TRPC6 and induces morphological changes of cultured podocytes.
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Affiliation(s)
- Xiao-Yu Lu
- Department of Neurology, the Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China.,Department of Physiology, Emory University School of Medicine, Atlanta, Georgia
| | - Bing-Chen Liu
- Department of Physiology, Emory University School of Medicine, Atlanta, Georgia.,Department of Cardiology, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Yu-Ze Cao
- Department of Neurology, the Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China.,Department of Neurology, Peking Union Medical College Hospital, Beijing, People's Republic of China
| | - Chang Song
- Department of Neurology, the Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China.,Department of Physiology, Emory University School of Medicine, Atlanta, Georgia
| | - Hua Su
- Department of Physiology, Emory University School of Medicine, Atlanta, Georgia
| | - Guangping Chen
- Department of Physiology, Emory University School of Medicine, Atlanta, Georgia
| | - Janet D Klein
- Department of Medicine, Renal Division, Emory University School of Medicine, Atlanta, Georgia
| | - Hui-Xue Zhang
- Department of Neurology, the Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Li-Hua Wang
- Department of Neurology, the Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - He-Ping Ma
- Department of Physiology, Emory University School of Medicine, Atlanta, Georgia
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21
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An integrative approach to cisplatin chronic toxicities in mice reveals importance of organic cation-transporter-dependent protein networks for renoprotection. Arch Toxicol 2019; 93:2835-2848. [PMID: 31493026 DOI: 10.1007/s00204-019-02557-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/02/2019] [Indexed: 12/11/2022]
Abstract
Cisplatin (CDDP) is one of the most important chemotherapeutic drugs in modern oncology. However, its use is limited by severe toxicities, which impair life quality after cancer. Here, we investigated the role of organic cation transporters (OCT) in mediating toxicities associated with chronic (twice the week for 4 weeks) low-dose (4 mg/kg body weight) CDDP treatment (resembling therapeutic protocols in patients) of wild-type (WT) mice and mice with OCT genetic deletion (OCT1/2-/-). Functional and molecular analysis showed that OCT1/2-/- mice are partially protected from CDDP-induced nephrotoxicity and peripheral neurotoxicity, whereas ototoxicity was not detectable. Surprisingly, proteomic analysis of the kidneys demonstrated that genetic deletion of OCT1/2 itself was associated with significant changes in expression of proinflammatory and profibrotic proteins which are part of an OCT-associated protein network. This signature directly regulated by OCT consisted of three classes of proteins, viz., profibrotic proteins, proinflammatory proteins, and nutrient sensing molecules. Consistent with functional protection, CDDP-induced proteome changes were more severe in WT mice than in OCT1/2-/- mice. Laser ablation-inductively coupled plasma-mass spectrometry analysis demonstrated that the presence of OCT was not associated with higher renal platinum concentrations. Taken together, these results redefine the role of OCT from passive membrane transporters to active modulators of cell signaling in the kidney.
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22
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Melnykov A, Chen SJ, Varshavsky A. Gid10 as an alternative N-recognin of the Pro/N-degron pathway. Proc Natl Acad Sci U S A 2019; 116:15914-15923. [PMID: 31337681 PMCID: PMC6689949 DOI: 10.1073/pnas.1908304116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In eukaryotes, N-degron pathways (formerly "N-end rule pathways") comprise a set of proteolytic systems whose unifying feature is their ability to recognize proteins containing N-terminal degradation signals called N-degrons, thereby causing degradation of these proteins by the 26S proteasome or autophagy. Gid4, a subunit of the GID ubiquitin ligase in the yeast Saccharomyces cerevisiae, is the recognition component (N-recognin) of the GID-mediated Pro/N-degron pathway. Gid4 targets proteins by recognizing their N-terminal Pro residues or a Pro at position 2, in the presence of distinct adjoining sequence motifs. Under conditions of low or absent glucose, cells make it through gluconeogenesis. When S. cerevisiae grows on a nonfermentable carbon source, its gluconeogenic enzymes Fbp1, Icl1, Mdh2, and Pck1 are expressed and long-lived. Transition to a medium containing glucose inhibits the synthesis of these enzymes and induces their degradation by the Gid4-dependent Pro/N-degron pathway. While studying yeast Gid4, we identified a similar but uncharacterized yeast protein (YGR066C), which we named Gid10. A screen for N-terminal peptide sequences that can bind to Gid10 showed that substrate specificities of Gid10 and Gid4 overlap but are not identical. Gid10 is not expressed under usual (unstressful) growth conditions, but is induced upon starvation or osmotic stresses. Using protein binding analyses and degradation assays with substrates of GID, we show that Gid10 can function as a specific N-recognin of the Pro/N-degron pathway.
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Affiliation(s)
- Artem Melnykov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Shun-Jia Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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23
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Hunt LC, Stover J, Haugen B, Shaw TI, Li Y, Pagala VR, Finkelstein D, Barton ER, Fan Y, Labelle M, Peng J, Demontis F. A Key Role for the Ubiquitin Ligase UBR4 in Myofiber Hypertrophy in Drosophila and Mice. Cell Rep 2019; 28:1268-1281.e6. [PMID: 31365869 PMCID: PMC6697171 DOI: 10.1016/j.celrep.2019.06.094] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 05/07/2019] [Accepted: 06/26/2019] [Indexed: 12/31/2022] Open
Abstract
Skeletal muscle cell (myofiber) atrophy is a detrimental component of aging and cancer that primarily results from muscle protein degradation via the proteasome and ubiquitin ligases. Transcriptional upregulation of some ubiquitin ligases contributes to myofiber atrophy, but little is known about the role that most other ubiquitin ligases play in this process. To address this question, we have used RNAi screening in Drosophila to identify the function of > 320 evolutionarily conserved ubiquitin ligases in myofiber size regulation in vivo. We find that whereas RNAi for some ubiquitin ligases induces myofiber atrophy, loss of others (including the N-end rule ubiquitin ligase UBR4) promotes hypertrophy. In Drosophila and mouse myofibers, loss of UBR4 induces hypertrophy via decreased ubiquitination and degradation of a core set of target proteins, including the HAT1/RBBP4/RBBP7 histone-binding complex. Together, this study defines the repertoire of ubiquitin ligases that regulate myofiber size and the role of UBR4 in myofiber hypertrophy.
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Affiliation(s)
- Liam C Hunt
- Division of Developmental Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jared Stover
- Division of Developmental Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Benard Haugen
- Division of Developmental Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Timothy I Shaw
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yuxin Li
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Vishwajeeth R Pagala
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Elisabeth R Barton
- College of Health & Human Performance Applied Physiology & Kinesiology, University of Florida, 124 Florida Gym, 1864 Stadium Road, Gainesville, FL 32611, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Myriam Labelle
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabio Demontis
- Division of Developmental Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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24
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25
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Späth MR, Bartram MP, Palacio-Escat N, Hoyer KJR, Debes C, Demir F, Schroeter CB, Mandel AM, Grundmann F, Ciarimboli G, Beyer A, Kizhakkedathu JN, Brodesser S, Göbel H, Becker JU, Benzing T, Schermer B, Höhne M, Burst V, Saez-Rodriguez J, Huesgen PF, Müller RU, Rinschen MM. The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury. Kidney Int 2018; 95:333-349. [PMID: 30522767 DOI: 10.1016/j.kint.2018.08.037] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 07/24/2018] [Accepted: 08/16/2018] [Indexed: 01/18/2023]
Abstract
Acute kidney injury (AKI) leads to significant morbidity and mortality; unfortunately, strategies to prevent or treat AKI are lacking. In recent years, several preconditioning protocols have been shown to be effective in inducing organ protection in rodent models. Here, we characterized two of these interventions-caloric restriction and hypoxic preconditioning-in a mouse model of cisplatin-induced AKI and investigated the underlying mechanisms by acquisition of multi-layered omic data (transcriptome, proteome, N-degradome) and functional parameters in the same animals. Both preconditioning protocols markedly ameliorated cisplatin-induced loss of kidney function, and caloric restriction also induced lipid synthesis. Bioinformatic analysis revealed mRNA-independent proteome alterations affecting the extracellular space, mitochondria, and transporters. Interestingly, our analyses revealed a strong dissociation of protein and RNA expression after cisplatin treatment that showed a strong correlation with the degree of damage. N-degradomic analysis revealed that most posttranscriptional changes were determined by arginine-specific proteolytic processing. This included a characteristic cisplatin-activated complement signature that was prevented by preconditioning. Amyloid and acute-phase proteins within the cortical parenchyma showed a similar response. Extensive analysis of disease-associated molecular patterns suggested that transcription-independent deposition of amyloid P-component serum protein may be a key component in the microenvironmental contribution to kidney damage. This proof-of-principle study provides new insights into the pathogenesis of cisplatin-induced AKI and the molecular mechanisms underlying organ protection by correlating phenotypic and multi-layered omics data.
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Affiliation(s)
- Martin R Späth
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Malte P Bartram
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Nicolàs Palacio-Escat
- COMBINE-Joint Research Center for Computational Biomedicine RWTH Aachen University, Aachen, Germany
| | - K Johanna R Hoyer
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Cedric Debes
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Christina B Schroeter
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Amrei M Mandel
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Franziska Grundmann
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Giuliano Ciarimboli
- Department of Experimental Nephrology, University Hospital of Münster, Münster, Germany
| | - Andreas Beyer
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Jayachandran N Kizhakkedathu
- Department of Pathology, Centre for Blood Research, The University of British Columbia, British Columbia, Vancouver, Canada; Laboratory Medicine, Department of Chemistry, The University of British Columbia, British Columbia, Vancouver, Canada
| | - Susanne Brodesser
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Heike Göbel
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Jan U Becker
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Volker Burst
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Julio Saez-Rodriguez
- COMBINE-Joint Research Center for Computational Biomedicine RWTH Aachen University, Aachen, Germany; Faculty of Medicine Bioquant, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany.
| | - Markus M Rinschen
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany.
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26
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Erzhi Formula Extracts Reverse Renal Injury in Diabetic Nephropathy Rats by Protecting the Renal Podocytes. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 2018:1741924. [PMID: 30210570 PMCID: PMC6126112 DOI: 10.1155/2018/1741924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/28/2018] [Accepted: 08/05/2018] [Indexed: 12/18/2022]
Abstract
Podocytes injury was a crucial factor resulting in diabetic nephropathy (DN). Erzhi formula extract (EZF) was a clinical effective Chinese medicine on DN, but its mechanism was unclear. In this study, the main compounds of EZF and their pharmacokinetics in rat were detected by HPLC-MS/MS. And then, blood glucose, urine protein, renal index, renal microstructural (HE/PAS staining), inflammatory factors (IL-β, TNF-α, IL-6), and protein/mRNA expression related to the function of podocyte (CD2AP and Podocin) in DN rats were investigated after the oral administration of EZF. The concentrations of specnuezhenide and wedelolactone in rat kidney were 7.19 and 0.057 mg/kg, respectively. The Tmax of specnuezhenide and wedelolactone were 2.0 and 1.50 h, respectively. Their Cmax were, respectively, 30.24 ± 2.68 and 6.39 ± 0.05 μg/L. Their AUC(0-∞) were 123.30 ± 2.68 and 16.56 ± 0.98 μg/L⁎h, respectively. Compared with the model group, the blood glucose and the 24-hour urinary protein were significantly decreased (P < 0.05) after 16 weeks' treatment of EZF. The expressions of Podocin and CD2AP protein/mRNA were increased (P < 0. 05). The deteriorate of glomerular morphology was alleviated under the treatment of EZF. EZF prominently decreased the levels of inflammatory factors (P < 0.05). MDA was significantly decreased (P < 0.05) with the significant increase of SOD activity (P < 0.05) in EZF groups. All the results proved that EZF repaired glomerular mesangial matrix, protected renal tubule, and improved renal function in DN rats by upregulating the expression of Podocin and CD2AP protein/mRNA in podocytes.
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27
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Kim ST, Lee YJ, Tasaki T, Mun SR, Hwang J, Kang MJ, Ganipisetti S, Yi EC, Kim BY, Kwon YT. The N-recognin UBR4 of the N-end rule pathway is targeted to and required for the biogenesis of the early endosome. J Cell Sci 2018; 131:jcs.217646. [PMID: 30111582 DOI: 10.1242/jcs.217646] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/30/2018] [Indexed: 12/26/2022] Open
Abstract
The N-end rule pathway is a proteolytic system in which single N-terminal residues of proteins act as N-degrons. These degrons are recognized by N-recognins, facilitating substrate degradation via the ubiquitin (Ub) proteasome system (UPS) or autophagy. We have previously identified a set of N-recognins [UBR1, UBR2, UBR4 (also known as p600) and UBR5 (also known as EDD)] that bind N-degrons through their UBR boxes to promote proteolysis by the proteasome. Here, we show that the 570 kDa N-recognin UBR4 is associated with maturing endosomes through an interaction with Ca2+-bound calmodulin. The endosomal recruitment of UBR4 is essential for the biogenesis of early endosomes (EEs) and endosome-related processes, such as the trafficking of endocytosed protein cargos and degradation of extracellular cargos by endosomal hydrolases. In mouse embryos, UBR4 marks and plays a role in the endosome-lysosome pathway that mediates the heterophagic proteolysis of endocytosed maternal proteins into amino acids. By screening 9591 drugs through the DrugBank database, we identify picolinic acid as a putative ligand for UBR4 that inhibits the biogenesis of EEs. Our results suggest that UBR4 is an essential modulator in the endosome-lysosome system.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sung Tae Kim
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.,Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, United States
| | - Yoon Jee Lee
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Takafumi Tasaki
- Division of Protein Regulation Research, Medical Research Institute, Kanazawa Medical University, Ishikawa, 920-0293, Japan.,Department of Medical Zoology, Kanazawa Medical University, Ishikawa, 920-0293, Japan
| | - Su Ran Mun
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Joonsung Hwang
- World Class Institute, Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongwon, 28116, Republic of Korea
| | - Min Jueng Kang
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, 03080, Republic of Korea
| | - Srinivasrao Ganipisetti
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, 03080, Republic of Korea
| | - Bo Yeon Kim
- World Class Institute, Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongwon, 28116, Republic of Korea
| | - Yong Tae Kwon
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea .,Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
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28
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Slaats GG, Braun F, Hoehne M, Frech LE, Blomberg L, Benzing T, Schermer B, Rinschen MM, Kurschat CE. Urine-derived cells: a promising diagnostic tool in Fabry disease patients. Sci Rep 2018; 8:11042. [PMID: 30038331 PMCID: PMC6056427 DOI: 10.1038/s41598-018-29240-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/04/2018] [Indexed: 12/19/2022] Open
Abstract
Fabry disease is a lysosomal storage disorder resulting from impaired alpha-galactosidase A (α-Gal A) enzyme activity due to mutations in the GLA gene. Currently, powerful diagnostic tools and in vivo research models to study Fabry disease are missing, which is a major obstacle for further improvements in diagnosis and therapy. Here, we explore the utility of urine-derived primary cells of Fabry disease patients. Viable cells were isolated and cultured from fresh urine void. The obtained cell culture, modeling the renal epithelium, is characterized by patient-specific information. We demonstrate that this non-invasive source of patient cells provides an adequate cellular in vivo model as cells exhibit decreased α-Gal A enzyme activity and concomitant globotriaosylceramide accumulation. Subsequent quantitative proteomic analyses revealed dysregulation of endosomal and lysosomal proteins indicating an involvement of the Coordinated Lysosomal Expression and Regulation (CLEAR) network in the disease pathology. This proteomic pattern resembled data from our previously described human podocyte model of Fabry disease. Taken together, the employment of urine-derived primary cells of Fabry disease patients might have diagnostic and prognostic implications in the future. Our findings pave the way towards a more detailed understanding of pathophysiological mechanisms and may allow the development of future tailored therapeutic strategies.
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Affiliation(s)
- Gisela G Slaats
- Department II of Internal Medicine Medicine and Center for Rare Diseases Cologne, University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Fabian Braun
- Department II of Internal Medicine Medicine and Center for Rare Diseases Cologne, University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Hoehne
- Department II of Internal Medicine Medicine and Center for Rare Diseases Cologne, University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Systems Biology of Aging, University of Cologne, Cologne, Germany
| | - Laura E Frech
- Department II of Internal Medicine Medicine and Center for Rare Diseases Cologne, University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Linda Blomberg
- Department II of Internal Medicine Medicine and Center for Rare Diseases Cologne, University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine Medicine and Center for Rare Diseases Cologne, University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Systems Biology of Aging, University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine Medicine and Center for Rare Diseases Cologne, University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Systems Biology of Aging, University of Cologne, Cologne, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine Medicine and Center for Rare Diseases Cologne, University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Christine E Kurschat
- Department II of Internal Medicine Medicine and Center for Rare Diseases Cologne, University Hospital of Cologne, Cologne, Germany. .,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
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29
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Hagmann H, Brinkkoetter PT. Experimental Models to Study Podocyte Biology: Stock-Taking the Toolbox of Glomerular Research. Front Pediatr 2018; 6:193. [PMID: 30057894 PMCID: PMC6053518 DOI: 10.3389/fped.2018.00193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/11/2018] [Indexed: 01/17/2023] Open
Abstract
Diseases affecting the glomeruli of the kidney, the renal filtration units, are a leading cause of chronic kidney disease and end-stage renal failure. Despite recent advances in the understanding of glomerular biology, treatment of these disorders has remained extraordinarily challenging in many cases. The use of experimental models has proven invaluable to study renal, and in particular, glomerular biology and disease. Over the past 15 years, studies identified different and very distinct pathogenic mechanisms that result in damage, loss of glomerular visceral epithelial cells (podocytes) and progressive renal disease. However, animal studies and, in particular, mouse studies are often protracted and cumbersome due to the long reproductive cycle and high keeping costs. Transgenic and heterologous expression models have been speeded-up by novel gene editing techniques, yet they still take months. In addition, given the complex cellular biology of the filtration barrier, certain questions may not be directly addressed using mouse models due to the limited accessibility of podocytes for analysis and imaging. In this review, we will describe alternative models to study podocyte biology experimentally. We specifically discuss current podocyte cell culture models, their role in experimental strategies to analyze pathophysiologic mechanisms as well as limitations with regard to transferability of results. We introduce current models in Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio that allow for analysis of protein interactions, and principle signaling pathways in functional biological structures, and enable high-throughput transgenic expression or compound screens in multicellular organisms.
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Affiliation(s)
| | - Paul T. Brinkkoetter
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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30
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Targeted deletion of the AAA-ATPase Ruvbl1 in mice disrupts ciliary integrity and causes renal disease and hydrocephalus. Exp Mol Med 2018; 50:1-17. [PMID: 29959317 PMCID: PMC6026120 DOI: 10.1038/s12276-018-0108-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 02/06/2023] Open
Abstract
Ciliopathies comprise a large number of hereditary human diseases and syndromes caused by mutations resulting in dysfunction of either primary or motile cilia. Both types of cilia share a similar architecture. While primary cilia are present on most cell types, expression of motile cilia is limited to specialized tissues utilizing ciliary motility. We characterized protein complexes of ciliopathy proteins and identified the conserved AAA-ATPase Ruvbl1 as a common novel component. Here, we demonstrate that Ruvbl1 is crucial for the development and maintenance of renal tubular epithelium in mice: both constitutive and inducible deletion in tubular epithelial cells result in renal failure with tubular dilatations and fewer ciliated cells. Moreover, inducible deletion of Ruvbl1 in cells carrying motile cilia results in hydrocephalus, suggesting functional relevance in both primary and motile cilia. Cilia of Ruvbl1-negative cells lack crucial proteins, consistent with the concept of Ruvbl1-dependent cytoplasmic pre-assembly of ciliary protein complexes. A protein involved in building and maintaining thin protrusions from cell surfaces called cilia is implicated in “ciliopathies”, diseases in which ciliary function is disrupted. These include polycystic kidney disease and disorders collectively known as ciliary dyskinesias. “Primary cilia” perform sensory functions, detecting external chemical and physical signals and initiating responses within cells. In addition, “motile cilia” beat rhythmically to move fluids surrounding cells. Researchers in Germany and the Netherlands, led by Bernhard Schermer and Max C. Liebau at the University of Cologne, studied a protein called Ruvbl1, known to interact with DNA and other proteins. The researchers found it is crucial for the functioning of both types of cilia. Deleting the gene for Ruvbl1 in mice caused kidney failure and a build-up of fluid in the brain known as hydrocephalus. The research could help understand and ultimately treat ciliopathies.
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31
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Höhne M, Frese CK, Grahammer F, Dafinger C, Ciarimboli G, Butt L, Binz J, Hackl MJ, Rahmatollahi M, Kann M, Schneider S, Altintas MM, Schermer B, Reinheckel T, Göbel H, Reiser J, Huber TB, Kramann R, Seeger-Nukpezah T, Liebau MC, Beck BB, Benzing T, Beyer A, Rinschen MM. Single-nephron proteomes connect morphology and function in proteinuric kidney disease. Kidney Int 2018; 93:1308-1319. [PMID: 29530281 DOI: 10.1016/j.kint.2017.12.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/01/2017] [Accepted: 12/14/2017] [Indexed: 12/25/2022]
Abstract
In diseases of many parenchymatous organs, heterogeneous deterioration of individual functional units determines the clinical prognosis. However, the molecular characterization at the level of such individual subunits remains a technological challenge that needs to be addressed in order to better understand pathological mechanisms. Proteinuric glomerular kidney diseases are frequent and assorted diseases affecting a fraction of glomeruli and their draining tubules to variable extents, and for which no specific treatment exists. Here, we developed and applied a mass spectrometry-based methodology to investigate heterogeneity of proteomes from individually isolated nephron segments from mice with proteinuric kidney disease. In single glomeruli from two different mouse models of sclerotic glomerular disease, we identified a coherent protein expression module consisting of extracellular matrix protein deposition (reflecting glomerular sclerosis), glomerular albumin (reflecting proteinuria) and LAMP1, a lysosomal protein. This module was associated with a loss of podocyte marker proteins while genetic ablation of LAMP1-correlated lysosomal proteases could ameliorate glomerular damage in vivo. Furthermore, proteomic analyses of individual glomeruli from patients with genetic sclerotic and non-sclerotic proteinuric diseases revealed increased abundance of lysosomal proteins, in combination with a decreased abundance of mutated gene products. Thus, altered protein homeostasis (proteostasis) is a conserved key mechanism in proteinuric kidney diseases. Moreover, our technology can capture intra-individual variability in diseases of the kidney and other tissues at a sub-biopsy scale.
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Affiliation(s)
- Martin Höhne
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Christian K Frese
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Florian Grahammer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claudia Dafinger
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Department of Pediatrics, Division of Pediatric Nephrology, University Hospital of Cologne, Cologne, Germany
| | | | - Linus Butt
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Julia Binz
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Matthias J Hackl
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Mahdieh Rahmatollahi
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Martin Kann
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Simon Schneider
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Bernhard Schermer
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Thomas Reinheckel
- Institut of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies and Center for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University, Freiburg, Germany
| | - Heike Göbel
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Jochen Reiser
- Rush University Medical Center, Chicago, Illinois, USA
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies and Center for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University, Freiburg, Germany
| | - Rafael Kramann
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
| | | | - Max C Liebau
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany; Department of Pediatrics, Division of Pediatric Nephrology, University Hospital of Cologne, Cologne, Germany
| | - Bodo B Beck
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Department of Human Genetics, University Hospital Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Andreas Beyer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany.
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32
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Schroeter CB, Koehler S, Kann M, Schermer B, Benzing T, Brinkkoetter PT, Rinschen MM. Protein half-life determines expression of proteostatic networks in podocyte differentiation. FASEB J 2018; 32:4696-4713. [PMID: 29694247 DOI: 10.1096/fj.201701307r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Podocytes are highly specialized, epithelial, postmitotic cells, which maintain the renal filtration barrier. When adapting to considerable metabolic and mechanical stress, podocytes need to accurately maintain their proteome. Immortalized podocyte cell lines are a widely used model for studying podocyte biology in health and disease in vitro. In this study, we performed a comprehensive proteomic analysis of the cultured human podocyte proteome in both proliferative and differentiated conditions at a depth of >7000 proteins. Similar to mouse podocytes, human podocyte differentiation involved a shift in proteostasis: undifferentiated podocytes have high expression of proteasomal proteins, whereas differentiated podocytes have high expression of lysosomal proteins. Additional analyses with pulsed stable-isotope labeling by amino acids in cell culture and protein degradation assays determined protein dynamics and half-lives. These studies unraveled a globally increased stability of proteins in differentiated podocytes. Mitochondrial, cytoskeletal, and membrane proteins were stabilized, particularly in differentiated podocytes. Importantly, protein half-lives strongly contributed to protein abundance in each state. These data suggest that regulation of protein turnover of particular cellular functions determines podocyte differentiation, a paradigm involving mitophagy and, potentially, of importance in conditions of increased podocyte stress and damage.-Schroeter, C. B., Koehler, S., Kann, M., Schermer, B., Benzing, T., Brinkkoetter, P. T., Rinschen, M. M. Protein half-life determines expression of proteostatic networks in podocyte differentiation.
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Affiliation(s)
- Christina B Schroeter
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Sybille Koehler
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Martin Kann
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (SybaCol), Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (SybaCol), Cologne, Germany
| | - Paul T Brinkkoetter
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (SybaCol), Cologne, Germany
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33
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Serrano-Perez MC, Tilley FC, Nevo F, Arrondel C, Sbissa S, Martin G, Tory K, Antignac C, Mollet G. Endoplasmic reticulum-retained podocin mutants are massively degraded by the proteasome. J Biol Chem 2018; 293:4122-4133. [PMID: 29382718 DOI: 10.1074/jbc.ra117.001159] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/23/2018] [Indexed: 12/13/2022] Open
Abstract
Podocin is a key component of the slit diaphragm in the glomerular filtration barrier, and mutations in the podocin-encoding gene NPHS2 are a common cause of hereditary steroid-resistant nephrotic syndrome. A mutant allele encoding podocin with a p.R138Q amino acid substitution is the most frequent pathogenic variant in European and North American children, and the corresponding mutant protein is poorly expressed and retained in the endoplasmic reticulum both in vitro and in vivo To better understand the defective trafficking and degradation of this mutant, we generated human podocyte cell lines stably expressing podocinwt or podocinR138Q Although it has been proposed that podocin has a hairpin topology, we present evidence for podocinR138QN-glycosylation, suggesting that most of the protein has a transmembrane topology. We find that N-glycosylated podocinR138Q has a longer half-life than non-glycosylated podocinR138Q and that the latter is far more rapidly degraded than podocinwt Consistent with its rapid degradation, podocinR138Q is exclusively degraded by the proteasome, whereas podocinwt is degraded by both the proteasomal and the lysosomal proteolytic machineries. In addition, we demonstrate an enhanced interaction of podocinR138Q with calnexin as the mechanism of endoplasmic reticulum retention. Calnexin knockdown enriches the podocinR138Q non-glycosylated fraction, whereas preventing exit from the calnexin cycle increases the glycosylated fraction. Altogether, we propose a model in which hairpin podocinR138Q is rapidly degraded by the proteasome, whereas transmembrane podocinR138Q degradation is delayed due to entry into the calnexin cycle.
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Affiliation(s)
- Maria-Carmen Serrano-Perez
- From the Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris 75015, France.,the Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris 75015, France
| | - Frances C Tilley
- From the Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris 75015, France.,the Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris 75015, France
| | - Fabien Nevo
- From the Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris 75015, France.,the Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris 75015, France
| | - Christelle Arrondel
- From the Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris 75015, France.,the Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris 75015, France
| | - Selim Sbissa
- From the Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris 75015, France.,the Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris 75015, France
| | - Gaëlle Martin
- From the Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris 75015, France.,the Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris 75015, France
| | - Kalman Tory
- the MTA-SE Lendület Nephrogenetic Laboratory, Hungarian Academy of Sciences and First Department of Pediatrics, Semmelweis University, Budapest 1083, Hungary, and
| | - Corinne Antignac
- From the Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris 75015, France.,the Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris 75015, France.,the Département de Génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Paris 75015, France
| | - Géraldine Mollet
- From the Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris 75015, France, .,the Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris 75015, France
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34
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Hagmann H, Mangold N, Rinschen MM, Koenig T, Kunzelmann K, Schermer B, Benzing T, Brinkkoetter PT. Proline-dependent and basophilic kinases phosphorylate human TRPC6 at serine 14 to control channel activity through increased membrane expression. FASEB J 2017; 32:208-219. [PMID: 28877958 DOI: 10.1096/fj.201700309r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/21/2017] [Indexed: 01/01/2023]
Abstract
Signaling via the transient receptor potential (TRP) ion channel C6 plays a pivotal role in hereditary and sporadic glomerular kidney disease. Several studies have identified gain-of-function mutations of TRPC6 and report induced expression and enhanced channel activity of TRPC6 in association with glomerular diseases. Interfering with TRPC6 activity may open novel therapeutic pathways. TRPC6 channel activity is controlled by protein expression and stability as well as intracellular trafficking. Identification of regulatory phosphorylation sites in TRPC6 and corresponding protein kinases is essential to understand the regulation of TRPC6 activity and may result in future therapeutic strategies. In this study, an unbiased phosphoproteomic screen of human TRPC6 identified several novel serine phosphorylation sites. The phosphorylation site at serine 14 of TRPC6 is embedded in a basophilic kinase motif that is highly conserved across species. We confirmed serine 14 as a target of MAPKs and proline-directed kinases like cyclin-dependent kinase 5 (Cdk5) in cell-based as well as in vitro kinase assays and quantitative phosphoproteomic analysis of TRPC6. Phosphorylation of TRPC6 at serine 14 enhances channel conductance by boosting membrane expression of TRPC6, whereas protein stability and multimerization of TRPC6 are not altered, making serine 14 phosphorylation a potential drug target to interfere with TRPC6 channel activity.-Hagmann, H., Mangold, N., Rinschen, M. M., Koenig, T., Kunzelmann, K., Schermer, B., Benzing, T., Brinkkoetter, P. T. Proline-dependent and basophilic kinases phosphorylate human TRPC6 at serine 14 to control channel activity through increased membrane expression.
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Affiliation(s)
- Henning Hagmann
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Nicole Mangold
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Tim Koenig
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; and
| | - Karl Kunzelmann
- Department of Physiology, University Regensburg, Regensburg, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Paul T Brinkkoetter
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany;
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35
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Rinschen MM, Hoppe AK, Grahammer F, Kann M, Völker LA, Schurek EM, Binz J, Höhne M, Demir F, Malisic M, Huber TB, Kurschat C, Kizhakkedathu JN, Schermer B, Huesgen PF, Benzing T. N-Degradomic Analysis Reveals a Proteolytic Network Processing the Podocyte Cytoskeleton. J Am Soc Nephrol 2017; 28:2867-2878. [PMID: 28724775 DOI: 10.1681/asn.2016101119] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 05/08/2017] [Indexed: 11/03/2022] Open
Abstract
Regulated intracellular proteostasis, controlled in part by proteolysis, is essential in maintaining the integrity of podocytes and the glomerular filtration barrier of the kidney. We applied a novel proteomics technology that enables proteome-wide identification, mapping, and quantification of protein N-termini to comprehensively characterize cleaved podocyte proteins in the glomerulus in vivo We found evidence that defined proteolytic cleavage results in various proteoforms of important podocyte proteins, including those of podocin, nephrin, neph1, α-actinin-4, and vimentin. Quantitative mapping of N-termini demonstrated perturbation of protease action during podocyte injury in vitro, including diminished proteolysis of α-actinin-4. Differentially regulated protease substrates comprised cytoskeletal proteins as well as intermediate filaments. Determination of preferential protease motifs during podocyte damage indicated activation of caspase proteases and inhibition of arginine-specific proteases. Several proteolytic processes were clearly site-specific, were conserved across species, and could be confirmed by differential migration behavior of protein fragments in gel electrophoresis. Some of the proteolytic changes discovered in vitro also occurred in two in vivo models of podocyte damage (WT1 heterozygous knockout mice and puromycin aminonucleoside-treated rats). Thus, we provide direct and systems-level evidence that the slit diaphragm and podocyte cytoskeleton are regulated targets of proteolytic modification, which is altered upon podocyte damage.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Ann-Kathrin Hoppe
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Florian Grahammer
- Department of Medicine III, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Medicine IV, Medical Center and Faculty of Medicine - University of Freiburg, Freiburg, Germany
| | - Martin Kann
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Linus A Völker
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Eva-Maria Schurek
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Julie Binz
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Martin Höhne
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Milena Malisic
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Tobias B Huber
- Department of Medicine III, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Medicine IV, Medical Center and Faculty of Medicine - University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies and Center for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University, Freiburg, Germany; and
| | - Christine Kurschat
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Department of Pathology and Laboratory Medicine, Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Bernhard Schermer
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany;
| | - Thomas Benzing
- Department II of Internal Medicine, .,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
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36
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Kohli P, Höhne M, Jüngst C, Bertsch S, Ebert LK, Schauss AC, Benzing T, Rinschen MM, Schermer B. The ciliary membrane-associated proteome reveals actin-binding proteins as key components of cilia. EMBO Rep 2017; 18:1521-1535. [PMID: 28710093 DOI: 10.15252/embr.201643846] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 06/06/2017] [Accepted: 06/13/2017] [Indexed: 01/01/2023] Open
Abstract
Primary cilia are sensory, antennae-like organelles present on the surface of many cell types. They have been involved in a variety of diseases collectively termed ciliopathies. As cilia are essential regulators of cell signaling, the composition of the ciliary membrane needs to be strictly regulated. To understand regulatory processes at the ciliary membrane, we report the targeting of a genetically engineered enzyme specifically to the ciliary membrane to allow biotinylation and identification of the membrane-associated proteome. Bioinformatic analysis of the comprehensive dataset reveals high-stoichiometric presence of actin-binding proteins inside the cilium. Immunofluorescence stainings and complementary interaction proteomic analyses confirm these findings. Depolymerization of branched F-actin causes further enrichment of the actin-binding and actin-related proteins in cilia, including Myosin 5a (Myo5a). Interestingly, Myo5a knockout decreases ciliation while enhanced levels of Myo5a are observed in cilia upon induction of ciliary disassembly. In summary, we present a novel approach to investigate dynamics of the ciliary membrane proteome in mammalian cells and identify actin-binding proteins as mechanosensitive components of cilia that might have important functions in cilia membrane dynamics.
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Affiliation(s)
- Priyanka Kohli
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Christian Jüngst
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sabine Bertsch
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Lena K Ebert
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Astrid C Schauss
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany .,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
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37
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Koehler S, Brähler S, Braun F, Hagmann H, Rinschen MM, Späth MR, Höhne M, Wunderlich FT, Schermer B, Benzing T, Brinkkoetter PT. Construction of a viral T2A-peptide based knock-in mouse model for enhanced Cre recombinase activity and fluorescent labeling of podocytes. Kidney Int 2017; 91:1510-1517. [PMID: 28187984 DOI: 10.1016/j.kint.2016.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 11/23/2016] [Accepted: 12/01/2016] [Indexed: 12/16/2022]
Abstract
Podocyte injury is a key event in glomerular disease leading to proteinuria and opening the path toward glomerular scarring. As a consequence, glomerular research strives to discover molecular mechanisms and signaling pathways affecting podocyte health. The hNphs2.Cre mouse model has been a valuable tool to manipulate podocyte-specific genes and to label podocytes for lineage tracing and purification. Here we designed a novel podocyte-specific tricistronic Cre mouse model combining codon improved Cre expression and fluorescent cell labeling with mTomato under the control of the endogenous Nphs2 promoter using viral T2A-peptides. Independent expression of endogenous podocin, codon improved Cre, and mTomato was confirmed by immunofluorescence, fluorescent activated cell sorting and protein analyses. Nphs2pod.T2A.ciCre.T2A.mTomato/wild-type mice developed normally and did not show any signs of glomerular disease or off-target effects under basal conditions and in states of disease. Nphs2pod.T2A.ciCre.T2A.mTomato/wild-type-mediated gene recombination was superior to conventional hNphs2.Cre mice-mediated gene recombination. Last, we compared Cre efficiency in a disease model by mating Nphs2pod.T2A.ciCre.T2A.mTomato/wild-type and hNphs2.Cre mice to Phb2fl/fl mice. The podocyte-specific Phb2 knockout by Nphs2pod.T2A.ciCre.T2A.mTomato/wild-type mice resulted in an aggravated glomerular injury as compared to a podocyte-specific Phb2 gene deletion triggered by hNphs2.Cre. Thus, we generated the first tricistronic podocyte mouse model combining enhanced Cre recombinase efficiency and fluorescent labeling in podocytes without the need for additional matings with conventional reporter mouse lines.
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Affiliation(s)
- Sybille Koehler
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Sebastian Brähler
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Fabian Braun
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Henning Hagmann
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Martin R Späth
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | | | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Paul T Brinkkoetter
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
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38
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Ganner A, Neumann-Haefelin E. Genetic kidney diseases: Caenorhabditis elegans as model system. Cell Tissue Res 2017; 369:105-118. [PMID: 28484847 DOI: 10.1007/s00441-017-2622-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/31/2017] [Indexed: 12/18/2022]
Abstract
Despite its apparent simplicity, the nematode Caenorhabditis elegans has a high rating as a model in molecular and developmental biology and biomedical research. C. elegans has no excretory system comparable with the mammalian kidney but many of the genes and molecular pathways involved in human kidney diseases are conserved in C. elegans. The plethora of genetic, molecular and imaging tools available in C. elegans has enabled major discoveries in renal research and advanced our understanding of the pathogenesis of genetic kidney diseases. In particular, studies in C. elegans have pioneered the fundamental role of cilia for cystic kidney diseases. In addition, proteins of the glomerular filtration barrier and podocytes are critical for cell recognition, assembly of functional neuronal circuits, mechanosensation and signal transduction in C. elegans. C. elegans has also proved tremendously valuable for aging research and the Von Hippel-Lindau tumor suppressor gene has been shown to modulate lifespan in the nematode. Further, studies of the excretory canal, membrane transport and ion channel function in C. elegans have provided insights into mechanisms of tubulogenesis and cellular homeostasis. This review recounts the way that C. elegans can be used to investigate various aspects of genetic and molecular nephrology. This model system opens up an exciting and new area of study of renal development and diseases.
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Affiliation(s)
- Athina Ganner
- Department of Nephrology, Medical Center, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Elke Neumann-Haefelin
- Department of Nephrology, Medical Center, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany.
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39
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Rinschen MM, Grahammer F, Hoppe AK, Kohli P, Hagmann H, Kretz O, Bertsch S, Höhne M, Göbel H, Bartram MP, Gandhirajan RK, Krüger M, Brinkkoetter PT, Huber TB, Kann M, Wickström SA, Benzing T, Schermer B. YAP-mediated mechanotransduction determines the podocyte's response to damage. Sci Signal 2017; 10:10/474/eaaf8165. [PMID: 28400537 DOI: 10.1126/scisignal.aaf8165] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Podocytes are terminally differentiated cells of the kidney filtration barrier. They are subjected to physiological filtration pressure and considerable mechanical strain, which can be further increased in various kidney diseases. When injury causes cytoskeletal reorganization and morphological alterations of these cells, the filtration barrier may become compromised and allow proteins to leak into the urine (a condition called proteinuria). Using time-resolved proteomics, we showed that podocyte injury stimulated the activity of the transcriptional coactivator YAP and the expression of YAP target genes in a rat model of glomerular disease before the development of proteinuria. Although the activities of YAP and its ortholog TAZ are activated by mechanical stress in most cell types, injury reduced YAP and TAZ activity in cultured human and mouse podocyte cell lines grown on stiff substrates. Culturing these cells on soft matrix or inhibiting stress fiber formation recapitulated the damage-induced YAP up-regulation observed in vivo, indicating a mechanotransduction-dependent mechanism of YAP activation in podocytes. YAP overexpression in cultured podocytes increased the abundance of extracellular matrix-related proteins that can contribute to fibrosis. YAP activity was increased in mouse models of diabetic nephropathy, and the YAP target CTGF was highly expressed in renal biopsies from glomerular disease patients. Although overexpression of human YAP in mice induced mild proteinuria, pharmacological inhibition of the interaction between YAP and its partner TEAD in rats ameliorated glomerular disease and reduced damage-induced mechanosignaling in the glomeruli. Thus, perturbation of YAP-dependent mechanosignaling is a potential therapeutic target for treating some glomerular diseases.
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Affiliation(s)
- Markus M Rinschen
- Department of Internal Medicine II, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Florian Grahammer
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany.,III. Medical Clinic and Polyclinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ann-Kathrin Hoppe
- Department of Internal Medicine II, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Priyanka Kohli
- Department of Internal Medicine II, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany
| | - Henning Hagmann
- Department of Internal Medicine II, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Oliver Kretz
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany.,III. Medical Clinic and Polyclinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Neuroanatomy, Institute of Anatomy, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sabine Bertsch
- Department of Internal Medicine II, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department of Internal Medicine II, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Heike Göbel
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Malte P Bartram
- Department of Internal Medicine II, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | | | - Marcus Krüger
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany
| | - Paul-Thomas Brinkkoetter
- Department of Internal Medicine II, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Tobias B Huber
- Department of Medicine IV, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany.,III. Medical Clinic and Polyclinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,Center for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Martin Kann
- Department of Internal Medicine II, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Sara A Wickström
- Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany.,Skin Homeostasis and Ageing, Paul Gerson Unna Research Group, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Thomas Benzing
- Department of Internal Medicine II, University of Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department of Internal Medicine II, University of Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
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40
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Roshanravan H, Kim EY, Dryer SE. 20-Hydroxyeicosatetraenoic Acid (20-HETE) Modulates Canonical Transient Receptor Potential-6 (TRPC6) Channels in Podocytes. Front Physiol 2016; 7:351. [PMID: 27630573 PMCID: PMC5005377 DOI: 10.3389/fphys.2016.00351] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/02/2016] [Indexed: 01/08/2023] Open
Abstract
The arachidonic acid metabolite 20-hydroxyeicosatetraenoic acid (20-HETE) regulates renal function, including changes in glomerular function evoked during tubuloglomerular feedback (TGF). This study describes the cellular actions of 20-HETE on cultured podocytes, assessed by whole-cell recordings from cultured podocytes combined with pharmacological and cell-biological manipulations of cells. Bath superfusion of 20-HETE activates cationic currents that are blocked by the pan-TRP blocker SKF-96365 and by 50 μM La3+, and which are attenuated after siRNA knockdown of TRPC6 subunits. Similar currents are evoked by a membrane-permeable analog of diacylgycerol (OAG), but OAG does not occlude responses to maximally-activating concentrations of 20-HETE (20 μM). Exposure to 20-HETE also increased steady-state surface abundance of TRPC6 subunits in podocytes as assessed by cell-surface biotinylation assays, and increased cytosolic concentrations of reactive oxygen species (ROS). TRPC6 activation by 20-HETE was eliminated in cells pretreated with TEMPOL, a membrane-permeable superoxide dismutase mimic. Activation of TRPC6 by 20-HETE was also blocked when whole-cell recording pipettes contained GDP-βS, indicating a role for either small or heterotrimeric G proteins in the transduction cascade. Responses to 20-HETE were eliminated by siRNA knockdown of podocin, a protein that organizes NADPH oxidase complexes with TRPC6 subunits in this cell type. In summary, modulation of ionic channels in podocytes may contribute to glomerular actions of 20-HETE.
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Affiliation(s)
- Hila Roshanravan
- Department of Biology and Biochemistry, University of Houston Houston, TX, USA
| | - Eun Y Kim
- Department of Biology and Biochemistry, University of Houston Houston, TX, USA
| | - Stuart E Dryer
- Department of Biology and Biochemistry, University of HoustonHouston, TX, USA; Division of Nephrology, Baylor College of MedicineHouston, TX, USA
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41
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Rinschen MM, Schroeter CB, Koehler S, Ising C, Schermer B, Kann M, Benzing T, Brinkkoetter PT. Quantitative deep mapping of the cultured podocyte proteome uncovers shifts in proteostatic mechanisms during differentiation. Am J Physiol Cell Physiol 2016; 311:C404-17. [PMID: 27357545 DOI: 10.1152/ajpcell.00121.2016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/27/2016] [Indexed: 11/22/2022]
Abstract
The renal filtration barrier is maintained by the renal podocyte, an epithelial postmitotic cell. Immortalized mouse podocyte cell lines-both in the differentiated and undifferentiated state-are widely utilized tools to estimate podocyte injury and cytoskeletal rearrangement processes in vitro. Here, we mapped the cultured podocyte proteome at a depth of more than 8,800 proteins and quantified 7,240 proteins. Copy numbers of proteins mutated in forms of hereditary nephrotic syndrome or focal segmental glomerulosclerosis (FSGS) were assessed. We found that cultured podocytes express abundant copy numbers of endogenous receptors, such as tyrosine kinase membrane receptors, the G protein-coupled receptor (GPCR), NPR3 (ANP receptor), and several poorly characterized GPCRs. The data set was correlated with deep mapping mRNA sequencing ("mRNAseq") data from the native mouse podocyte, the native mouse podocyte proteome and staining intensities from the human protein atlas. The generated data set was similar to these previously published resources, but several native and high-abundant podocyte-specific proteins were not identified in the data set. Notably, this data set detected general perturbations in proteostatic mechanisms as a dominant alteration during podocyte differentiation, with high proteasome activity in the undifferentiated state and markedly increased expression of lysosomal proteins in the differentiated state. Phosphoproteomics analysis of mouse podocytes at a resolution of more than 3,000 sites suggested a preference of phosphorylation of actin filament-associated proteins in the differentiated state. The data set obtained here provides a resource and provides the means for deep mapping of the native podocyte proteome and phosphoproteome in a similar manner.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; and Systems Biology of Ageing Cologne, SybaCol, Cologne, Germany
| | - Christina B Schroeter
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Sybille Koehler
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Christina Ising
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; and Systems Biology of Ageing Cologne, SybaCol, Cologne, Germany
| | - Martin Kann
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; and Systems Biology of Ageing Cologne, SybaCol, Cologne, Germany
| | - Paul T Brinkkoetter
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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