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Ai Z, Wang M, Zhou Y, Yuan D, Jian Q, Wu S, Liu B, Yang Y. Deciphering the pharmacological mechanisms of Rostellularia procumbens (L) Nees. Extract alleviates adriamycin-induced nephropathy in vivo and in vitro. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 113:154736. [PMID: 36907143 DOI: 10.1016/j.phymed.2023.154736] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 02/09/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Rostellularia procumbens (L) Nees. is an effective traditional Chinese herbal medicine for the treatment of patients with chronic glomerulonephritis (CGN) in the clinic. However, the underlying molecular mechanisms need further elucidation. PURPOSE This study aims to investigate the renoprotective mechanisms of n-butanol extract from Rostellularia procumbens (L) Nees. (J-NE) in vivo and in vitro. METHODS The components of J-NE were analyzed by UPLC-MS/MS. In vivo, the nephropathy model was induced in mice by tail vein injection with adriamycin (10 mg·kg-1), and mice were treated with vehicle or J-NE or benazepril by daily gavage. In vitro, MPC5 cells exposed to adriamycin (0.3 μg/ml) were treated with J-NE. The effects of J-NE inhibit podocyte apoptosis and protect against adriamycin-induced nephropathy were determined by Network pharmacology, RNA-seq, qPCR, ELISA, immunoblotting, flow cytometry, and TUNEL assay, according to the experimental protocols. RESULT The results showed that treatment significantly improved ADR-induced renal pathological changes, and the therapeutic mechanism of J-NE was related to the inhibition of podocyte apoptosis. Further molecular mechanism studies found that J-NE inhibited inflammation, increase the proteins expression levels of Nephrin and Podocin, reduce TRPC6 and Desmin expression levels and calcium ion levels in podocytes, and decrease the proteins expression levels of PI3K, p-PI3K, Akt and p-Akt to attenuated apoptosis. Furthermore, 38 compounds of J-NE were identified. CONCLUSION J-NE exerted the renoprotective effects by inhibiting podocyte apoptosis, which provides effective evidence for the treatment of J-NE targeting renal injury in CGN.
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Affiliation(s)
- Zhongzhu Ai
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan 430065, China; Modern Engineering Research Center of Traditional Chinese Medicine and Ethnic Medicine of Hubei Province, Wuhan 430065, China
| | - Mengfan Wang
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan 430065, China; Modern Engineering Research Center of Traditional Chinese Medicine and Ethnic Medicine of Hubei Province, Wuhan 430065, China
| | - Yi Zhou
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Dongfeng Yuan
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Qiuyuan Jian
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Songtao Wu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Bo Liu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan 430065, China; Modern Engineering Research Center of Traditional Chinese Medicine and Ethnic Medicine of Hubei Province, Wuhan 430065, China
| | - Yanfang Yang
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan 430065, China; Modern Engineering Research Center of Traditional Chinese Medicine and Ethnic Medicine of Hubei Province, Wuhan 430065, China.
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2
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Gareev I, Gileva Y, Dzidzaria A, Beylerli O, Pavlov V, Agaverdiev M, Mazorov B, Biganyakov I, Vardikyan A, Jin M, Ahmad A. Long non-coding RNAs in oncourology. Noncoding RNA Res 2021; 6:139-145. [PMID: 34504983 PMCID: PMC8405895 DOI: 10.1016/j.ncrna.2021.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 02/06/2023] Open
Abstract
For several decades, research in tumor biology has focused on the involvement of genes encoding a protein. Only recently has it been discovered that a whole class of molecules called non-coding RNAs (ncRNAs) play a key regulatory role in health and disease. Long noncoding RNAs (lncRNAs) are a group of noncoding RNAs longer than 200 nucleotides. It has been found that lncRNAs play a fundamental role in the biology of many types of tumors, including tumors of the genitourinary system. As a result, hundreds of clinical trials dedicated to oncourology have begun, using lncRNA as new biomarkers or treatments. Identifying new specific biomarkers, in the form of lncRNAs, will increase the ability to differentiate the tumor and other processes, determine the localization and extent of the tumor, and the ability to predict the course of the disease, and plan treatment. Therapy of tumors, especially malignant ones, is also a difficult task. When surgery and chemotherapy fail, radiation therapy becomes the treatment choice. Therefore, the possibility that lncRNAs could represent innovative therapeutic agents or targets is an exciting idea. However, the possibility of their use in modern clinical practice is limited, and this is associated with several problems at the pre-, analytical and post-analytical stages. Another problem in the study of lncRNAs is the large number and variety of their functions in tumors. Therefore, solving technological problems in lncRNAs study in oncourology may open up new possibilities for lncRNAs use in modern clinical practice.
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Affiliation(s)
- Ilgiz Gareev
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Yulia Gileva
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Aleksandr Dzidzaria
- Urology Department, Russian Scientific Center of Radiology of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Ozal Beylerli
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Valentin Pavlov
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Murad Agaverdiev
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Bakhodur Mazorov
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Ilfat Biganyakov
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Andranik Vardikyan
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Mei Jin
- The First Affiliated Hospital of Harbin Medical University, 23 Youzheng St, Harbin, 150001, Heilongjiang Province, China
| | - Aamir Ahmad
- Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
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3
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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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4
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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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Hoyer KJR, Dittrich S, Bartram MP, Rinschen MM. Quantification of molecular heterogeneity in kidney tissue by targeted proteomics. J Proteomics 2019. [DOI: 10.1016/j.jprot.2018.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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6
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Rinschen MM, Limbutara K, Knepper MA, Payne DM, Pisitkun T. From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology. Physiol Rev 2019; 98:2571-2606. [PMID: 30182799 DOI: 10.1152/physrev.00057.2017] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Classical physiological studies using electrophysiological, biophysical, biochemical, and molecular techniques have created a detailed picture of molecular transport, bioenergetics, contractility and movement, and growth, as well as the regulation of these processes by external stimuli in cells and organisms. Newer systems biology approaches are beginning to provide deeper and broader understanding of these complex biological processes and their dynamic responses to a variety of environmental cues. In the past decade, advances in mass spectrometry-based proteomic technologies have provided invaluable tools to further elucidate these complex cellular processes, thereby confirming, complementing, and advancing common views of physiology. As one notable example, the application of proteomics to study the regulation of kidney function has yielded novel insights into the chemical and physical processes that tightly control body fluids, electrolytes, and metabolites to provide optimal microenvironments for various cellular and organ functions. Here, we systematically review, summarize, and discuss the most significant key findings from functional proteomic studies in renal epithelial physiology. We also identify further improvements in technological and bioinformatics methods that will be essential to advance precision medicine in nephrology.
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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 ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Kavee Limbutara
- 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 ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Mark A Knepper
- 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 ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - D Michael Payne
- 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 ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Trairak Pisitkun
- 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 ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
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7
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Stella M, Chinello C, Cazzaniga A, Smith A, Galli M, Piga I, Grasso A, Grasso M, Del Puppo M, Varallo M, Bovo G, Magni F. Histology-guided proteomic analysis to investigate the molecular profiles of clear cell Renal Cell Carcinoma grades. J Proteomics 2019; 191:38-47. [DOI: 10.1016/j.jprot.2018.04.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/10/2018] [Accepted: 04/14/2018] [Indexed: 11/24/2022]
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8
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Rinschen MM. Single glomerular proteomics: A novel tool for translational glomerular cell biology. Methods Cell Biol 2019; 154:1-14. [DOI: 10.1016/bs.mcb.2019.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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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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10
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Staubach S, Wenzel A, Beck BB, Rinschen MM, Müller S, Hanisch FG. Autosomal Tubulointerstitial Kidney Disease-MUC1 Type: Differential Proteomics Suggests that Mutated MUC1 (insC) Affects Vesicular Transport in Renal Epithelial Cells. Proteomics 2018; 18:e1700456. [DOI: 10.1002/pmic.201700456] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/15/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Simon Staubach
- Institute of Biochemistry II; Medical Faculty; University of Cologne; Cologne Germany
| | - Andrea Wenzel
- Institute for Human Genetics; University of Cologne; Cologne Germany
| | - Bodo B. Beck
- Institute for Human Genetics; University of Cologne; Cologne Germany
| | - Markus M. Rinschen
- Department II of Internal Medicine; University of Cologne; Cologne Germany
- Center for Molecular Medicine Cologne; University of Cologne; Cologne Germany
| | - Stefan Müller
- Center for Molecular Medicine Cologne; University of Cologne; Cologne Germany
| | - Franz-Georg Hanisch
- Institute of Biochemistry II; Medical Faculty; University of Cologne; Cologne Germany
- Center for Molecular Medicine Cologne; University of Cologne; Cologne Germany
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11
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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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12
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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: 55] [Impact Index Per Article: 7.9] [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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13
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Pereira EM, Labilloy A, Eshbach ML, Roy A, Subramanya AR, Monte S, Labilloy G, Weisz OA. Characterization and phosphoproteomic analysis of a human immortalized podocyte model of Fabry disease generated using CRISPR/Cas9 technology. Am J Physiol Renal Physiol 2016; 311:F1015-F1024. [PMID: 27681560 DOI: 10.1152/ajprenal.00283.2016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/20/2016] [Indexed: 01/22/2023] Open
Abstract
Fabry nephropathy is a major cause of morbidity and premature death in patients with Fabry disease (FD), a rare X-linked lysosomal storage disorder. Gb3, the main substrate of α-galactosidase A (α-Gal A), progressively accumulates within cells in a variety of tissues. Establishment of cell models has been useful as a tool for testing hypotheses of disease pathogenesis. We applied CRISPR/Cas9 genome editing technology to the GLA gene to develop human kidney cell models of FD in human immortalized podocytes, which are the main affected renal cell type. Our podocytes lack detectable α-Gal A activity and have increased levels of Gb3. To explore different pathways that could have distinct patterns of activation under conditions of α-gal A deficiency, we used a high-throughput antibody array to perform phosphorylation profiling of CRISPR/Cas9-edited and control podocytes. Changes in both total protein levels and in phosphorylation status per site were observed. Analysis of our candidate proteins suggests that multiple signaling pathways are impaired in FD.
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Affiliation(s)
- Ester M Pereira
- Laboratory of Immunogenetics and Molecular Biology, Federal University of Piaui, Teresina, Brazil
| | - Anatália Labilloy
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and
| | - Megan L Eshbach
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and
| | - Ankita Roy
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and
| | - Arohan R Subramanya
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and
| | - Semiramis Monte
- Laboratory of Immunogenetics and Molecular Biology, Federal University of Piaui, Teresina, Brazil;
| | - Guillaume Labilloy
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Ora A Weisz
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and
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14
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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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15
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Rinschen MM, Bharill P, Wu X, Kohli P, Reinert MJ, Kretz O, Saez I, Schermer B, Höhne M, Bartram MP, Aravamudhan S, Brooks BR, Vilchez D, Huber TB, Müller RU, Krüger M, Benzing T. The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes. Hum Mol Genet 2016; 25:1328-44. [PMID: 26792178 DOI: 10.1093/hmg/ddw016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/16/2016] [Indexed: 11/13/2022] Open
Abstract
The PHB-domain protein podocin maintains the renal filtration barrier and its mutation is an important cause of hereditary nephrotic syndrome. Podocin and its Caenorhabditis elegans orthologue MEC-2 have emerged as key components of mechanosensitive membrane protein signalling complexes. Whereas podocin resides at a specialized cell junction at the podocyte slit diaphragm, MEC-2 is found in neurons required for touch sensitivity. Here, we show that the ubiquitin ligase Ubr4 is a key component of the podocin interactome purified both from cultured podocytes and native glomeruli. It colocalizes with podocin and regulates its stability. In C. elegans, this process is conserved. Here, Ubr4 is responsible for the degradation of mislocalized MEC-2 multimers. Ubiquitylomic analysis of mouse glomeruli revealed that podocin is ubiquitylated at two lysine residues. These sites were Ubr4-dependent and were conserved across species. Molecular dynamics simulations revealed that ubiquitylation of one site, K301, do not only target podocin/MEC-2 for proteasomal degradation, but may also affect stability and disassembly of the multimeric complex. We suggest that Ubr4 is a key regulator of podocyte foot process proteostasis.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany,
| | - Puneet Bharill
- Department II of Internal Medicine, Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Blood, and Lung Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Priyanka Kohli
- Department II of Internal Medicine, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | | | - Oliver Kretz
- Renal Division, University Hospital Freiburg, Freiburg, Germany, Neuroanatomy, University of Freiburg, Freiburg, Germany
| | - Isabel Saez
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | - Bernhard Schermer
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | | | - Sriram Aravamudhan
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany and
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Blood, and Lung Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Vilchez
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | - Tobias B Huber
- Renal Division, University Hospital Freiburg, Freiburg, Germany, BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Marcus Krüger
- Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | - Thomas Benzing
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, 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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