1
|
Ebner M, Puchkov D, López-Ortega O, Muthukottiappan P, Su Y, Schmied C, Zillmann S, Nikonenko I, Koddebusch J, Dornan GL, Lucht MT, Koka V, Jang W, Koch PA, Wallroth A, Lehmann M, Brügger B, Pende M, Winter D, Haucke V. Nutrient-regulated control of lysosome function by signaling lipid conversion. Cell 2023; 186:5328-5346.e26. [PMID: 37883971 DOI: 10.1016/j.cell.2023.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
Lysosomes serve dual antagonistic functions in cells by mediating anabolic growth signaling and the catabolic turnover of macromolecules. How these janus-faced activities are regulated in response to cellular nutrient status is poorly understood. We show here that lysosome morphology and function are reversibly controlled by a nutrient-regulated signaling lipid switch that triggers the conversion between peripheral motile mTOR complex 1 (mTORC1) signaling-active and static mTORC1-inactive degradative lysosomes clustered at the cell center. Starvation-triggered relocalization of phosphatidylinositol 4-phosphate (PI(4)P)-metabolizing enzymes reshapes the lysosomal surface proteome to facilitate lysosomal proteolysis and to repress mTORC1 signaling. Concomitantly, lysosomal phosphatidylinositol 3-phosphate (PI(3)P), which marks motile signaling-active lysosomes in the cell periphery, is erased. Interference with this PI(3)P/PI(4)P lipid switch module impairs the adaptive response of cells to altering nutrient supply. Our data unravel a key function for lysosomal phosphoinositide metabolism in rewiring organellar membrane dynamics in response to cellular nutrient status.
Collapse
Affiliation(s)
- Michael Ebner
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Dmytro Puchkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Orestes López-Ortega
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
| | - Pathma Muthukottiappan
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, 53115 Bonn, Germany
| | - Yanwei Su
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Christopher Schmied
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Silke Zillmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Iryna Nikonenko
- Department of Basic Neurosciences and the Center for Neuroscience, CMU, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jochen Koddebusch
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Gillian L Dornan
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Max T Lucht
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Vonda Koka
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
| | - Wonyul Jang
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | | | - Alexander Wallroth
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Mario Pende
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, 53115 Bonn, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| |
Collapse
|
2
|
Im E, Jiang Y, Stavrides PH, Darji S, Erdjument-Bromage H, Neubert TA, Choi JY, Wegiel J, Lee JH, Nixon RA. Lysosomal dysfunction in Down syndrome and Alzheimer mouse models is caused by v-ATPase inhibition by Tyr 682-phosphorylated APP βCTF. SCIENCE ADVANCES 2023; 9:eadg1925. [PMID: 37494443 PMCID: PMC10371027 DOI: 10.1126/sciadv.adg1925] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
Lysosome dysfunction arises early and propels Alzheimer's disease (AD). Herein, we show that amyloid precursor protein (APP), linked to early-onset AD in Down syndrome (DS), acts directly via its β-C-terminal fragment (βCTF) to disrupt lysosomal vacuolar (H+)-adenosine triphosphatase (v-ATPase) and acidification. In human DS fibroblasts, the phosphorylated 682YENPTY internalization motif of APP-βCTF binds selectively within a pocket of the v-ATPase V0a1 subunit cytoplasmic domain and competitively inhibits association of the V1 subcomplex of v-ATPase, thereby reducing its activity. Lowering APP-βCTF Tyr682 phosphorylation restores v-ATPase and lysosome function in DS fibroblasts and in vivo in brains of DS model mice. Notably, lowering APP-βCTF Tyr682 phosphorylation below normal constitutive levels boosts v-ATPase assembly and activity, suggesting that v-ATPase may also be modulated tonically by phospho-APP-βCTF. Elevated APP-βCTF Tyr682 phosphorylation in two mouse AD models similarly disrupts v-ATPase function. These findings offer previously unknown insight into the pathogenic mechanism underlying faulty lysosomes in all forms of AD.
Collapse
Affiliation(s)
- Eunju Im
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ying Jiang
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Philip H. Stavrides
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Sandipkumar Darji
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Thomas A. Neubert
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Jun Yong Choi
- Department of Chemistry and Biochemistry, Queens College, Queens, NY 11367, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Jerzy Wegiel
- Department of Developmental Neurobiology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
| | - Ju-Hyun Lee
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ralph A. Nixon
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| |
Collapse
|
3
|
Sugar transporter Slc37a2 regulates bone metabolism in mice via a tubular lysosomal network in osteoclasts. Nat Commun 2023; 14:906. [PMID: 36810735 PMCID: PMC9945426 DOI: 10.1038/s41467-023-36484-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 02/01/2023] [Indexed: 02/23/2023] Open
Abstract
Osteoclasts are giant bone-digesting cells that harbor specialized lysosome-related organelles termed secretory lysosomes (SLs). SLs store cathepsin K and serve as a membrane precursor to the ruffled border, the osteoclast's 'resorptive apparatus'. Yet, the molecular composition and spatiotemporal organization of SLs remains incompletely understood. Here, using organelle-resolution proteomics, we identify member a2 of the solute carrier 37 family (Slc37a2) as a SL sugar transporter. We demonstrate in mice that Slc37a2 localizes to the SL limiting membrane and that these organelles adopt a hitherto unnoticed but dynamic tubular network in living osteoclasts that is required for bone digestion. Accordingly, mice lacking Slc37a2 accrue high bone mass owing to uncoupled bone metabolism and disturbances in SL export of monosaccharide sugars, a prerequisite for SL delivery to the bone-lining osteoclast plasma membrane. Thus, Slc37a2 is a physiological component of the osteoclast's unique secretory organelle and a potential therapeutic target for metabolic bone diseases.
Collapse
|
4
|
Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo. Nat Commun 2022; 13:6212. [PMID: 36266287 PMCID: PMC9584938 DOI: 10.1038/s41467-022-33951-0] [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: 02/11/2022] [Accepted: 10/06/2022] [Indexed: 12/24/2022] Open
Abstract
Lysosomes are well-established as the main cellular organelles for the degradation of macromolecules and emerging as regulatory centers of metabolism. They are of crucial importance for cellular homeostasis, which is exemplified by a plethora of disorders related to alterations in lysosomal function. In this context, protein complexes play a decisive role, regulating not only metabolic lysosomal processes but also lysosome biogenesis, transport, and interaction with other organelles. Using cross-linking mass spectrometry, we analyze lysosomes and early endosomes. Based on the identification of 5376 cross-links, we investigate protein-protein interactions and structures of lysosome- and endosome-related proteins. In particular, we present evidence for a tetrameric assembly of the lysosomal hydrolase PPT1 and a heterodimeric structure of FLOT1/FLOT2 at lysosomes and early endosomes. For FLOT1-/FLOT2-positive early endosomes, we identify >300 putative cargo proteins and confirm eleven substrates for flotillin-dependent endocytosis, including the latrophilin family of adhesion G protein-coupled receptors.
Collapse
|
5
|
Lie PPY, Yoo L, Goulbourne CN, Berg MJ, Stavrides P, Huo C, Lee JH, Nixon RA. Axonal transport of late endosomes and amphisomes is selectively modulated by local Ca 2+ efflux and disrupted by PSEN1 loss of function. SCIENCE ADVANCES 2022; 8:eabj5716. [PMID: 35486730 PMCID: PMC9054012 DOI: 10.1126/sciadv.abj5716] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Dysfunction and mistrafficking of organelles in autophagy- and endosomal-lysosomal pathways are implicated in neurodegenerative diseases. Here, we reveal selective vulnerability of maturing degradative organelles (late endosomes/amphisomes) to disease-relevant local calcium dysregulation. These organelles undergo exclusive retrograde transport in axons, with occasional pauses triggered by regulated calcium efflux from agonist-evoked transient receptor potential cation channel mucolipin subfamily member 1 (TRPML1) channels-an effect greatly exaggerated by exogenous agonist mucolipin synthetic agonist 1 (ML-SA1). Deacidification of degradative organelles, as seen after Presenilin 1 (PSEN1) loss of function, induced pathological constitutive "inside-out" TRPML1 hyperactivation, slowing their transport comparably to ML-SA1 and causing accumulation in dystrophic axons. The mechanism involved calcium-mediated c-Jun N-terminal kinase (JNK) activation, which hyperphosphorylated dynein intermediate chain (DIC), reducing dynein activity. Blocking TRPML1 activation, JNK activity, or DIC1B serine-80 phosphorylation reversed transport deficits in PSEN1 knockout neurons. Our results, including features demonstrated in Alzheimer-mutant PSEN1 knockin mice, define a mechanism linking dysfunction and mistrafficking in lysosomal pathways to neuritic dystrophy under neurodegenerative conditions.
Collapse
Affiliation(s)
- Pearl P. Y. Lie
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Langone Medical Center, New York, NY 10016, USA
| | - Lang Yoo
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Langone Medical Center, New York, NY 10016, USA
| | - Chris N. Goulbourne
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Martin J. Berg
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Philip Stavrides
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Chunfeng Huo
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Ju-Hyun Lee
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Langone Medical Center, New York, NY 10016, USA
| | - Ralph A. Nixon
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Langone Medical Center, New York, NY 10016, USA
- Department of Cell Biology, New York University Langone Medical Center, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA
- Corresponding author.
| |
Collapse
|
6
|
Le TS, Takahashi M, Isozumi N, Miyazato A, Hiratsuka Y, Matsumura K, Taguchi T, Maenosono S. Quick and Mild Isolation of Intact Lysosomes Using Magnetic-Plasmonic Hybrid Nanoparticles. ACS NANO 2022; 16:885-896. [PMID: 34978188 DOI: 10.1021/acsnano.1c08474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rapid and efficient isolation of intact lysosomes is necessary to study their functions and metabolites by proteomic analysis. We developed a swift and robust nanoparticle-based magnetic separation method in which magnetic-plasmonic hybrid nanoparticles (MPNPs) conjugated with amino dextran (aDxt) were targeted to the lumen of lysosomes via the endocytosis pathway. For well-directed magnetic separation of the lysosomes, it is important to trace the intracellular trafficking of the aDxt-conjugated MPNPs (aDxt-MPNPs) in the endocytosis pathway. Therefore, we analyzed the intracellular transport process of the aDxt-MPNPs by investigating the time-dependent colocalization of plasmonic scattering of aDxt-MPNPs and immunostained marker proteins of organelles using the threshold Manders' colocalization coefficient (Rt). Detailed analysis of time variations of Rt for early and late endosomes and lysosomes allowed us to derive the transport kinetics of aDxt-MPNPs in a cell. After confirming the incubation time required for sufficient accumulation of aDxt-MPNPs in lysosomes, the lysosomes were magnetically isolated as intact as possible. By varying the elapsed time from homogenization to complete isolation of lysosomes (tdelay) and temperature (T), the influences of tdelay and T on the protein composition of the lysosomes were investigated by polyacrylamide gel electrophoresis and amino acid analysis. We found that the intactness of lysosomes could become impaired quite quickly, and to isolate lysosomes as intact as possible with high purity, tdelay = 30 min and T = 4 °C were optimal settings.
Collapse
Affiliation(s)
- The Son Le
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Mari Takahashi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Noriyoshi Isozumi
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Akio Miyazato
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Yuichi Hiratsuka
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Kazuaki Matsumura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Tomohiko Taguchi
- Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki Aoba, Sendai Aoba-ku, Miyagi 980-8578, Japan
| | - Shinya Maenosono
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| |
Collapse
|
7
|
Ayagama T, Bose SJ, Capel RA, Priestman DA, Berridge G, Fischer R, Galione A, Platt FM, Kramer H, Burton RA. A modified density gradient proteomic-based method to analyze endolysosomal proteins in cardiac tissue. iScience 2021; 24:102949. [PMID: 34466782 PMCID: PMC8384914 DOI: 10.1016/j.isci.2021.102949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/04/2021] [Accepted: 08/02/2021] [Indexed: 11/22/2022] Open
Abstract
The importance of lysosomes in cardiac physiology and pathology is well established, and evidence for roles in calcium signaling is emerging. We describe a label-free proteomics method suitable for small cardiac tissue biopsies based on density-separated fractionation, which allows study of endolysosomal (EL) proteins. Density gradient fractions corresponding to tissue lysate; sarcoplasmic reticulum (SR), mitochondria (Mito) (1.3 g/mL); and EL with negligible contamination from SR or Mito (1.04 g/mL) were analyzed using Western blot, enzyme activity assay, and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis (adapted discontinuous Percoll and sucrose differential density gradient). Kyoto Encyclopedia of Genes and Genomes, Reactome, Panther, and Gene Ontology pathway analysis showed good coverage of RAB proteins and lysosomal cathepsins (including cardiac-specific cathepsin D) in the purified EL fraction. Significant EL proteins recovered included catalytic activity proteins. We thus present a comprehensive protocol and data set of guinea pig atrial EL organelle proteomics using techniques also applicable for non-cardiac tissue.
Collapse
Affiliation(s)
- Thamali Ayagama
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Samuel J. Bose
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Rebecca A. Capel
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | | | - Georgina Berridge
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Antony Galione
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Frances M. Platt
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, W12 0NN UK
| | | |
Collapse
|
8
|
Abstract
Lysosomes are the main degradative organelles of almost all eukaryotic cells. They fulfil a crucial function in cellular homeostasis, and impairments in lysosomal function are connected to a continuously increasing number of pathological conditions. In recent years, lysosomes are furthermore emerging as control centers of cellular metabolism, and major regulators of cellular signaling were shown to be activated at the lysosomal surface. To date, >300 proteins were demonstrated to be located in/at the lysosome, and the lysosomal proteome and interactome is constantly growing. For the identification of these proteins, and their involvement in cellular mechanisms or disease progression, mass spectrometry (MS)-based proteomics has proven its worth in a large number of studies. In this review, we are recapitulating the application of MS-based approaches for the investigation of the lysosomal proteome, and their application to a diverse set of research questions. Numerous strategies were applied for the enrichment of lysosomes or lysosomal proteins and their identification by MS-based methods. This allowed for the characterization of the lysosomal proteome, the investigation of lysosome-related disorders, the utilization of lysosomal proteins as biomarkers for diseases, and the characterization of lysosome-related cellular mechanisms. While these >60 studies provide a comprehensive picture of the lysosomal proteome across several model organisms and pathological conditions, various proteomics approaches have not been applied to lysosomes yet, and a large number of questions are still left unanswered.
Collapse
Affiliation(s)
- Pathma Muthukottiappan
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Nussallee 11, 53115 Bonn, Germany.
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Nussallee 11, 53115 Bonn, Germany.
| |
Collapse
|
9
|
van Leeuwen T, Araman C, Pieper Pournara L, Kampstra ASB, Bakkum T, Marqvorsen MHS, Nascimento CR, Groenewold GJM, van der Wulp W, Camps MGM, Janssen GMC, van Veelen PA, van Westen GJP, Janssen APA, Florea BI, Overkleeft HS, Ossendorp FA, Toes REM, van Kasteren SI. Bioorthogonal protein labelling enables the study of antigen processing of citrullinated and carbamylated auto-antigens. RSC Chem Biol 2021; 2:855-862. [PMID: 34212151 PMCID: PMC8190914 DOI: 10.1039/d1cb00009h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/22/2021] [Indexed: 11/21/2022] Open
Abstract
Proteolysis is fundamental to many biological processes. In the immune system, it underpins the activation of the adaptive immune response: degradation of antigenic material into short peptides and presentation thereof on major histocompatibility complexes, leads to activation of T-cells. This initiates the adaptive immune response against many pathogens. Studying proteolysis is difficult, as the oft-used polypeptide reporters are susceptible to proteolytic sequestration themselves. Here we present a new approach that allows the imaging of antigen proteolysis throughout the processing pathway in an unbiased manner. By incorporating bioorthogonal functionalities into the protein in place of methionines, antigens can be followed during degradation, whilst leaving reactive sidechains open to templated and non-templated post-translational modifications, such as citrullination and carbamylation. Using this approach, we followed and imaged the post-uptake fate of the commonly used antigen ovalbumin, as well as the post-translationally citrullinated and/or carbamylated auto-antigen vinculin in rheumatoid arthritis, revealing differences in antigen processing and presentation.
Collapse
Affiliation(s)
- Tyrza van Leeuwen
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Can Araman
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Linda Pieper Pournara
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Arieke S B Kampstra
- Department of Rheumatology, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - Thomas Bakkum
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Mikkel H S Marqvorsen
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Clarissa R Nascimento
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - G J Mirjam Groenewold
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Willemijn van der Wulp
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Marcel G M Camps
- Department of Immunology, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - Gerard J P van Westen
- Computational Drug Discovery, Drug Discovery and Safety, LACDR, Leiden University Leiden The Netherlands
| | - Antonius P A Janssen
- Department of Molecular Physiology, Leiden Institute of Chemistry and the Oncode Institute, Leiden University Leiden The Netherlands
| | - Bogdan I Florea
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Herman S Overkleeft
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Ferry A Ossendorp
- Department of Immunology, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - Sander I van Kasteren
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| |
Collapse
|
10
|
Parenti G, Medina DL, Ballabio A. The rapidly evolving view of lysosomal storage diseases. EMBO Mol Med 2021; 13:e12836. [PMID: 33459519 PMCID: PMC7863408 DOI: 10.15252/emmm.202012836] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022] Open
Abstract
Lysosomal storage diseases are a group of metabolic disorders caused by deficiencies of several components of lysosomal function. Most commonly affected are lysosomal hydrolases, which are involved in the breakdown and recycling of a variety of complex molecules and cellular structures. The understanding of lysosomal biology has progressively improved over time. Lysosomes are no longer viewed as organelles exclusively involved in catabolic pathways, but rather as highly dynamic elements of the autophagic-lysosomal pathway, involved in multiple cellular functions, including signaling, and able to adapt to environmental stimuli. This refined vision of lysosomes has substantially impacted on our understanding of the pathophysiology of lysosomal disorders. It is now clear that substrate accumulation triggers complex pathogenetic cascades that are responsible for disease pathology, such as aberrant vesicle trafficking, impairment of autophagy, dysregulation of signaling pathways, abnormalities of calcium homeostasis, and mitochondrial dysfunction. Novel technologies, in most cases based on high-throughput approaches, have significantly contributed to the characterization of lysosomal biology or lysosomal dysfunction and have the potential to facilitate diagnostic processes, and to enable the identification of new therapeutic targets.
Collapse
Affiliation(s)
- Giancarlo Parenti
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Diego L Medina
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,SSM School for Advanced Studies, Federico II University, Naples, Italy
| |
Collapse
|
11
|
Tharkeshwar AK, Demedts D, Annaert W. Superparamagnetic Nanoparticles for Lysosome Isolation to Identify Spatial Alterations in Lysosomal Protein and Lipid Composition. STAR Protoc 2020; 1:100122. [PMID: 33377016 PMCID: PMC7756972 DOI: 10.1016/j.xpro.2020.100122] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Lysosomes are dynamic organelles that serve as regulatory hubs in cellular homeostasis. Changes in lysosome morphology, composition, and turnover are typically linked to disease. These characteristics make enrichment protocols based on biophysical parameters challenging. However, organelle enrichment methods are essential to facilitate their biomolecular analysis. We describe the synthesis and use of superparamagnetic iron oxide nanoparticles (SPIONs) for high-yield purification of lysosomes compatible with “omics” analysis. NANOLYSE (Nanoparticles for Lysosome Isolation) provides a reliable strategy in fingerprinting the biomolecular composition of lysosomes. For complete details on the use and execution of this protocol, please refer to Tharkeshwar et al. (2017). Lysosome isolation from adherent cells using superparamagnetic iron oxide nanoparticles Enriched lysosomes with high intactness, compatible for functional, biochemical studies NANOLYSE is highly reproducible and compatible for proteome and lipidome profiling NANOLYSE is an unbiased method to identify lysosomal dyshomeostasis in a disease context
Collapse
Affiliation(s)
- Arun Kumar Tharkeshwar
- Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - David Demedts
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| |
Collapse
|
12
|
Francis L, Harrell A, Hallifax D, Galetin A. Utilising Magnetically Isolated Lysosomes for Direct Quantification of Intralysosomal Drug Concentrations by LC-MS/MS Analysis: An Investigatory Study With Imipramine. J Pharm Sci 2020; 109:2891-2901. [PMID: 32504630 DOI: 10.1016/j.xphs.2020.05.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/23/2020] [Accepted: 05/26/2020] [Indexed: 11/28/2022]
Abstract
Lysosomes are acidic intracellular organelles that can extensively sequester basic lipophilic drugs due to pH and membrane partitioning, and therefore may significantly influence subcellular drug concentrations. Current in vitro methods for lysosomal drug sequestration evaluation typically lack the ability to accurately and sensitively quantify drug concentrations directly within the lysosome. In the current study, magnetic lysosomal isolation was used in the lysosome rich rat NR8383 cell line and combined with LC-MS/MS analysis to quantify intralysosomal concentrations and lysosomal partitioning (KpLysosome) values of imipramine. The purity of the isolated lysosomes was validated by enzymatic and electron microscopy analysis. Lysosomal imipramine accumulation was explored using 2 methods: addition of imipramine to cells followed by lysosomal isolation (Method 1), and direct addition of imipramine to isolated lysosomes (Method 2). This work highlighted that both experimental buffers and ATP influence intralysosomal drug concentrations, and non-specific drug binding and re-distribution limits the use of Method 1. Method 2 may benefit future lysosomal drug accumulation studies, as imipramine demonstrated high KpLysosome values (3500), comparable to in silico predictions. This study reports a novel method for the direct quantification of intralysosomal drug concentrations that has the ability to be adapted to other cell types.
Collapse
Affiliation(s)
- Laura Francis
- Centre for Applied Pharmacokinetic Research, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | | | - David Hallifax
- Centre for Applied Pharmacokinetic Research, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Aleksandra Galetin
- Centre for Applied Pharmacokinetic Research, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
13
|
Cook SR, Badell-Grau RA, Kirkham ED, Jones KM, Kelly BP, Winston J, Waller-Evans H, Allen ND, Lloyd-Evans E. Detrimental effect of zwitterionic buffers on lysosomal homeostasis in cell lines and iPSC-derived neurons. AMRC OPEN RESEARCH 2020; 2:21. [PMID: 32490352 PMCID: PMC7266671 DOI: 10.12688/amrcopenres.12903.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Good's buffers are commonly used for cell culture and, although developed to have minimal to no biological impact, they cause alterations in cellular processes such as autophagy and lysosomal enzyme activity. Using Chinese hamster ovary cells and induced pluripotent stem cell-derived neurons, this study explores the effect of zwitterionic buffers, specifically HEPES, on lysosomal volume and Ca2+ levels. Certain zwitterionic buffers lead to lysosomal expansion and reduced lysosomal Ca2+. Care should be taken when selecting buffers for growth media to avoid detrimental impacts on lysosomal function.
Collapse
Affiliation(s)
- Sophie R. Cook
- School of Biosciences, Sir Martin Evans Building, Cardiff
University, Cardiff, CF10 3AX, UK
| | - Rafael A. Badell-Grau
- School of Biosciences, Sir Martin Evans Building, Cardiff
University, Cardiff, CF10 3AX, UK
| | - Emily D. Kirkham
- School of Biosciences, Sir Martin Evans Building, Cardiff
University, Cardiff, CF10 3AX, UK
| | - Kimberley M. Jones
- School of Biosciences, Sir Martin Evans Building, Cardiff
University, Cardiff, CF10 3AX, UK
| | - Brendan P. Kelly
- School of Biosciences, Sir Martin Evans Building, Cardiff
University, Cardiff, CF10 3AX, UK
| | - Jincy Winston
- School of Biosciences, Sir Martin Evans Building, Cardiff
University, Cardiff, CF10 3AX, UK
| | - Helen Waller-Evans
- Medicines Discovery Institute, Main Building, Cardiff
University, Cardiff, CF10 3AT, UK
| | - Nicholas D. Allen
- School of Biosciences, Sir Martin Evans Building, Cardiff
University, Cardiff, CF10 3AX, UK
| | - Emyr Lloyd-Evans
- School of Biosciences, Sir Martin Evans Building, Cardiff
University, Cardiff, CF10 3AX, UK
| |
Collapse
|
14
|
Thimiri Govinda Raj DB, Khan NA, Venkatachalam S, Arumugam S. Efficient Nanobiotechnology Method for Magnetic Lysosome Enrichment Using DMSA-SPMNP 2.0. BIONANOSCIENCE 2020. [DOI: 10.1007/s12668-020-00736-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
15
|
Sarkar C, Jones JW, Hegdekar N, Thayer JA, Kumar A, Faden AI, Kane MA, Lipinski MM. PLA2G4A/cPLA2-mediated lysosomal membrane damage leads to inhibition of autophagy and neurodegeneration after brain trauma. Autophagy 2020; 16:466-485. [PMID: 31238788 PMCID: PMC6999646 DOI: 10.1080/15548627.2019.1628538] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 05/16/2019] [Accepted: 05/28/2019] [Indexed: 12/18/2022] Open
Abstract
Lysosomal membrane permeabilization (LMP) is observed under many pathological conditions, leading to cellular dysfunction and death. However, the mechanisms by which lysosomal membranes become leaky in vivo are not clear. Our data demonstrate that LMP occurs in neurons following controlled cortical impact induced (CCI) traumatic brain injury (TBI) in mice, leading to impaired macroautophagy (autophagy) and neuronal cell death. Comparison of LC-MS/MS lysosomal membrane lipid profiles from TBI and sham animals suggested a role for PLA2G4A/cPLA2 (phospholipase A2, group IVA [cytosolic, calcium-dependent]) in TBI-induced LMP. Activation of PLA2G4A caused LMP and inhibition of autophagy flux in cell lines and primary neurons. In vivo pharmacological inhibition of PLA2G4A attenuated TBI-induced LMP, as well as subsequent impairment of autophagy and neuronal loss, and was associated with improved neurological outcomes. Inhibition of PLA2G4A in vitro limited amyloid-β-induced LMP and inhibition of autophagy. Together, our data indicate that PLA2G4A -mediated lysosomal membrane damage is involved in neuronal cell death following CCI-induced TBI and potentially in other neurodegenerative disorders.Abbreviations: AACOCF3, arachidonyl trifluoromethyl ketone; ACTB/β-actin, actin, beta; AD, Alzheimer disease; ATG5, autophagy related 5; ATG7, autophagy related 7; ATG12, autophagy related 12; BECN1, beclin 1, autophagy related; C1P, ceramide-1-phosphate; CCI, controlled cortical impact; CTSD, cathepsin D; CTSL, cathepsin L; GFP, green fluorescent protein; IF, immunofluorescence; LAMP1, lysosomal-associated membrane protein 1; LAMP2, lysosomal-associated membrane protein 2; LC-MS/MS, liquid chromatography-tandem mass spectrometry; LMP, Lysosomal membrane permeabilization; LPC, lysophosphatidylcholine; LPE, lysophosphatidylethanolamine; MAP1LC3/LC3, microtuble-associated protein 1 light chain 3; NAGLU, alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB); PC, diacyl glycerophosphatidylcholine; PE, diacyl glycerophosphatidylethanolamine; PE-O, plasmanyl glycerophosphatidylethanolamine; PE-P, plasmenyl glycerophosphatidylethanolamine; PLA2G4A/cPLA2, phospholipase A2, group IVA (cytosolic, calcium-dependent); RBFOX3, RNA binding protein, fox-1 homolog (C. elegans) 3; RFP, red fluorescent protein; ROS, reactive oxygen species; SQSTM1, sequestosome 1; TUBA1/α-tubulin, tubulin, alpha; TBI, traumatic brain injury; TFEB, transcription factor EB; ULK1, unc-51 like kinase 1.
Collapse
Affiliation(s)
- Chinmoy Sarkar
- Department of Anesthesiology, Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jace W. Jones
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Nivedita Hegdekar
- Department of Anesthesiology, Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Julia A. Thayer
- Department of Anesthesiology, Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alok Kumar
- Department of Anesthesiology, Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Molecular Medicine and Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow-U.P., India
| | - Alan I. Faden
- Department of Anesthesiology, Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Marta M. Lipinski
- Department of Anesthesiology, Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| |
Collapse
|
16
|
Ponnaiyan S, Akter F, Singh J, Winter D. Comprehensive draft of the mouse embryonic fibroblast lysosomal proteome by mass spectrometry based proteomics. Sci Data 2020; 7:68. [PMID: 32103020 PMCID: PMC7044164 DOI: 10.1038/s41597-020-0399-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/23/2020] [Indexed: 11/09/2022] Open
Abstract
Lysosomes are the main degradative organelles of cells and involved in a variety of processes including the recycling of macromolecules, storage of compounds, and metabolic signaling. Despite an increasing interest in the proteomic analysis of lysosomes, no systematic study of sample preparation protocols for lysosome enriched fractions has been performed to date. In the current study, we used samples enriched for lysosomes by paramagnetic nanoparticles and systematically evaluated experimental parameters for the analysis of the lysosomal proteome. This includes different approaches for the concentration of lysosome-containing fractions; desalting of samples by solid phase extraction; fractionation of peptide samples; and different gradient lengths for LC-MS/MS analyses of unfractionated samples by data dependent and data independent acquisition. Furthermore, we evaluated four different digestion methods including filter aided sample preparation (FASP), in-gel digestion, and in-solution digestion using either RapiGest or urea. Using the combined data, we generated a benchmark lysosomal proteome data set for mouse embryonic fibroblasts as well as a spectral library for the analysis of lysosomes by data independent acquisition.
Collapse
Affiliation(s)
- Srigayatri Ponnaiyan
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany
| | - Fatema Akter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany
- Department of Pharmacology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Jasjot Singh
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, 53115, Germany.
| |
Collapse
|
17
|
Lee JH, Wolfe DM, Darji S, McBrayer MK, Colacurcio DJ, Kumar A, Stavrides P, Mohan PS, Nixon RA. β2-adrenergic Agonists Rescue Lysosome Acidification and Function in PSEN1 Deficiency by Reversing Defective ER-to-lysosome Delivery of ClC-7. J Mol Biol 2020; 432:2633-2650. [PMID: 32105735 DOI: 10.1016/j.jmb.2020.02.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023]
Abstract
Lysosomal dysfunction is considered pathogenic in Alzheimer disease (AD). Loss of presenilin-1 (PSEN1) function causing AD impedes acidification via defective vacuolar ATPase (vATPase) V0a1 subunit delivery to lysosomes. We report that isoproterenol (ISO) and related β2-adrenergic agonists reacidify lysosomes in PSEN1 Knock out (KO) cells and fibroblasts from PSEN1 familial AD patients, which restores lysosomal proteolysis, calcium homeostasis, and normal autophagy flux. We identify a novel rescue mechanism involving Portein Kinase A (PKA)-mediated facilitation of chloride channel-7 (ClC-7) delivery to lysosomes which reverses markedly lowered chloride (Cl-) content in PSEN1 KO lysosomes. Notably, PSEN1 loss of function impedes Endoplasmic Reticulum (ER)-to-lysosome delivery of ClC-7. Transcriptomics of PSEN1-deficient cells reveals strongly downregulated ER-to-lysosome transport pathways and reversibility by ISO, thus accounting for lysosomal Cl- deficits that compound pH elevation due to deficient vATPase and its rescue by β2-adrenergic agonists. Our findings uncover a broadened PSEN1 role in lysosomal ion homeostasis and novel pH modulation of lysosomes through β2-adrenergic regulation of ClC-7, which can potentially be modulated therapeutically.
Collapse
Affiliation(s)
- Ju-Hyun Lee
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA; Department of Psychiatry, Langone Medical Center, New York, NY, 10016, USA.
| | - Devin M Wolfe
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Sandipkumar Darji
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Mary Kate McBrayer
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Daniel J Colacurcio
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Asok Kumar
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Philip Stavrides
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Panaiyur S Mohan
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA; Department of Psychiatry, Langone Medical Center, New York, NY, 10016, USA
| | - Ralph A Nixon
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA; Department of Psychiatry, Langone Medical Center, New York, NY, 10016, USA; Department of Cell Biology, Langone Medical Center, New York, NY, 10016, USA; Neuroscience Institute, New York University, New York, NY 10016, USA.
| |
Collapse
|
18
|
Singh J, Kaade E, Muntel J, Bruderer R, Reiter L, Thelen M, Winter D. Systematic Comparison of Strategies for the Enrichment of Lysosomes by Data Independent Acquisition. J Proteome Res 2020; 19:371-381. [PMID: 31738065 DOI: 10.1021/acs.jproteome.9b00580] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In mammalian cells, the lysosome is the main organelle for the degradation of macromolecules and the recycling of their building blocks. Correct lysosomal function is essential, and mutations in every known lysosomal hydrolase result in so-called lysosomal storage disorders, a group of rare and often fatal inherited diseases. Furthermore, it is becoming more and more apparent that lysosomes play also decisive roles in other diseases, such as cancer and common neurodegenerative disorders. This leads to an increasing interest in the proteomic analysis of lysosomes for which enrichment is a prerequisite. In this study, we compared the four most common strategies for the enrichment of lysosomes using data-independent acquisition. We performed centrifugation at 20,000 × g to generate an organelle-enriched pellet, two-step sucrose density gradient centrifugation, enrichment by superparamagnetic iron oxide nanoparticles (SPIONs), and immunoprecipitation using a 3xHA tagged version of the lysosomal membrane protein TMEM192. Our results show that SPIONs and TMEM192 immunoprecipitation outperform the other approaches with enrichment factors of up to 118-fold for certain proteins relative to whole cell lysates. Furthermore, we achieved an increase in identified lysosomal proteins and a higher reproducibility in protein intensities for label-free quantification in comparison to the other strategies.
Collapse
Affiliation(s)
- Jasjot Singh
- Institute for Biochemistry and Molecular Biology , University of Bonn , 53115 Bonn , Germany
| | - Edgar Kaade
- Institute for Biochemistry and Molecular Biology , University of Bonn , 53115 Bonn , Germany
| | - Jan Muntel
- Biognosys , 8952 Schlieren , Switzerland
| | | | | | - Melanie Thelen
- Institute for Biochemistry and Molecular Biology , University of Bonn , 53115 Bonn , Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology , University of Bonn , 53115 Bonn , Germany
| |
Collapse
|
19
|
Woods AG, Sokolowska I, Ngounou Wetie AG, Channaveerappa D, Dupree EJ, Jayathirtha M, Aslebagh R, Wormwood KL, Darie CC. Mass Spectrometry for Proteomics-Based Investigation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:1-26. [DOI: 10.1007/978-3-030-15950-4_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
20
|
Amick J, Tharkeshwar AK, Amaya C, Ferguson SM. WDR41 supports lysosomal response to changes in amino acid availability. Mol Biol Cell 2018; 29:2213-2227. [PMID: 29995611 PMCID: PMC6249801 DOI: 10.1091/mbc.e17-12-0703] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
C9orf72 mutations are a major cause of amyotrophic lateral sclerosis and frontotemporal dementia. The C9orf72 protein undergoes regulated recruitment to lysosomes and has been broadly implicated in control of lysosome homeostasis. However, although evidence strongly supports an important function for C9orf72 at lysosomes, little is known about the lysosome recruitment mechanism. In this study, we identify an essential role for WDR41, a prominent C9orf72 interacting protein, in C9orf72 lysosome recruitment. Analysis of human WDR41 knockout cells revealed that WDR41 is required for localization of the protein complex containing C9orf72 and SMCR8 to lysosomes. Such lysosome localization increases in response to amino acid starvation but is not dependent on either mTORC1 inhibition or autophagy induction. Furthermore, WDR41 itself exhibits a parallel pattern of regulated association with lysosomes. This WDR41-dependent recruitment of C9orf72 to lysosomes is critical for the ability of lysosomes to support mTORC1 signaling as constitutive targeting of C9orf72 to lysosomes relieves the requirement for WDR41 in mTORC1 activation. Collectively, this study reveals an essential role for WDR41 in supporting the regulated binding of C9orf72 to lysosomes and solidifies the requirement for a larger C9orf72 containing protein complex in coordinating lysosomal responses to changes in amino acid availability.
Collapse
Affiliation(s)
- Joseph Amick
- Department of Cell Biology and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Arun Kumar Tharkeshwar
- Department of Cell Biology and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Catherine Amaya
- Department of Cell Biology and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Shawn M Ferguson
- Department of Cell Biology and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| |
Collapse
|
21
|
Lloyd-Lewis B, Krueger CC, Sargeant TJ, D'Angelo ME, Deery MJ, Feret R, Howard JA, Lilley KS, Watson CJ. Stat3-mediated alterations in lysosomal membrane protein composition. J Biol Chem 2018; 293:4244-4261. [PMID: 29343516 PMCID: PMC5868265 DOI: 10.1074/jbc.ra118.001777] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Indexed: 12/19/2022] Open
Abstract
Lysosome function is essential in cellular homeostasis. In addition to its recycling role, the lysosome has recently been recognized as a cellular signaling hub. We have shown in mammary epithelial cells, both in vivo and in vitro, that signal transducer and activator of transcription 3 (Stat3) modulates lysosome biogenesis and can promote the release of lysosomal proteases that culminates in cell death. To further investigate the impact of Stat3 on lysosomal function, we conducted a proteomic screen of changes in lysosomal membrane protein components induced by Stat3 using an iron nanoparticle enrichment strategy. Our results show that Stat3 activation not only elevates the levels of known membrane proteins but results in the appearance of unexpected factors, including cell surface proteins such as annexins and flotillins. These data suggest that Stat3 may coordinately regulate endocytosis, intracellular trafficking, and lysosome biogenesis to drive lysosome-mediated cell death in mammary epithelial cells. The methodologies described in this study also provide significant improvements to current techniques used for the purification and analysis of the lysosomal proteome.
Collapse
Affiliation(s)
- Bethan Lloyd-Lewis
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom,
| | - Caroline C Krueger
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Timothy J Sargeant
- the Lysosomal Diseases Research Unit, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia, and
| | - Michael E D'Angelo
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Michael J Deery
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Renata Feret
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Julie A Howard
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Kathryn S Lilley
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Christine J Watson
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom,
| |
Collapse
|
22
|
Kosicek M, Gudelj I, Horvatic A, Jovic T, Vuckovic F, Lauc G, Hecimovic S. N-glycome of the Lysosomal Glycocalyx is Altered in Niemann-Pick Type C Disease (NPC) Model Cells. Mol Cell Proteomics 2018; 17:631-642. [PMID: 29367433 DOI: 10.1074/mcp.ra117.000129] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 12/18/2017] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence implicates lysosomal dysfunction in the pathogenesis of neurodegenerative diseases, including the rare inherited lysosomal storage disorders (LSDs) and the most common neurodegenerative diseases, such as Alzheimer's and Parkinson's disease (AD and PD). Although the triggers of the lysosomal impairment may involve the accumulated macromolecules or dysfunction of the lysosomal enzymes, the role of the lysosomal glycocalyx in the lysosomal (dys)function has not been studied. The goal of this work was to analyze whether there are changes in the lysosomal glycocalyx in a cellular model of a LSD Niemann-Pick type C disease (NPC). Using the ferrofluid nanoparticles we isolated lysosomal organelles from NPC1-null and CHOwt cells. The magnetically isolated lysosomal fractions were enriched with the lysosomal marker protein LAMP1 and showed the key features of NPC disease: 3-fold higher cholesterol content and 4-5 fold enlarged size of the particles compared with the lysosomal fractions of wt cells. These lysosomal fractions were further processed to isolate lysosomal membrane proteins using Triton X-114 and their N-glycome was analyzed by HILIC-UPLC. N-glycans presented in each chromatographic peak were elucidated using MALDI-TOF/TOF-MS. We detected changes in the N-glycosylation pattern of the lysosomal glycocalyx of NPC1-null versus wt cells which involved high-mannose and sialylated N-glycans. To the best of our knowledge this study is the first to report N-glycome profiling of the lysosomal glycocalyx in NPC disease cellular model and the first to report the specific changes in the lysosomal glycocalyx in NPC1-null cells. We speculate that changes in the lysosomal glycocalyx may contribute to lysosomal (dys)function. Further glycome profiling of the lysosomal glycocalyx in other LSDs as well as the most common neurodegenerative diseases, such as AD and PD, is necessary to better understand the role of the lysosomal glycocalyx and to reveal its potential contribution in lysosomal dysfunction leading to neurodegeneration.
Collapse
Affiliation(s)
- Marko Kosicek
- From the ‡Laboratory for Neurodegenerative Disease Research, Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivan Gudelj
- §Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Anita Horvatic
- ¶ERA Chair team, Internal Diseases Clinic, University of Zagreb, Faculty of Veterinary Medicine, Heinzelova 55, 10000 Zagreb, Croatia
| | - Tanja Jovic
- From the ‡Laboratory for Neurodegenerative Disease Research, Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia.,‖University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Frano Vuckovic
- §Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Gordan Lauc
- §Genos Glycoscience Research Laboratory, Zagreb, Croatia.,‖University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Silva Hecimovic
- From the ‡Laboratory for Neurodegenerative Disease Research, Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia;
| |
Collapse
|
23
|
Wang A, Carraro-Lacroix LR, Owen C, Gao B, Corey PN, Tyrrell P, Brumell JH, Voronov I. Activity-independent targeting of mTOR to lysosomes in primary osteoclasts. Sci Rep 2017; 7:3005. [PMID: 28592812 PMCID: PMC5462732 DOI: 10.1038/s41598-017-03494-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/28/2017] [Indexed: 12/14/2022] Open
Abstract
Mammalian target of rapamycin (mTOR) is activated by numerous stimuli, including amino acids and growth factors. This kinase is part of the mTOR complex 1 (mTORC1) which regulates cell proliferation, differentiation, and autophagy. Active mTORC1 is located on lysosomes and has been reported to disassociate from the lysosomal surface in the absence of amino acids. Furthermore, mTORC1 activity has been linked to the vacuolar H+-ATPases (V-ATPases), the proton pumps responsible for lysosomal acidification; however, the exact role of the V-ATPases in mTORC1 signaling is not known. To elucidate the mechanisms involved in mTORC1 regulation by the V-ATPases, we used primary osteoclasts derived from mice carrying a point (R740S) mutation in the a3 subunit of the V-ATPase. In these cells, the mutant protein is expressed but the pump is not functional, resulting in higher lysosomal pH. By analyzing mTOR activation, mTOR/lysosome co-localization, and lysosomal positioning using confocal microscopy, fractionation, and ultrapure lysosomal purification methods, we demonstrate that in primary osteoclasts, mTOR is localized on the lysosomal surface even when mTOR activity is inhibited. Our findings reveal that mTOR targeting to the lysosome in osteoclasts is activity-independent, and that its disassociation from the lysosome during starvation is not universal.
Collapse
Affiliation(s)
- Andrew Wang
- Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
| | | | - Celeste Owen
- Centre for Modeling Human Disease, Samuel Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Bowen Gao
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Paul N Corey
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Pascal Tyrrell
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada.,Department of Medical Imaging, University of Toronto, Toronto, ON, Canada
| | - John H Brumell
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Irina Voronov
- Faculty of Dentistry, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
24
|
Thelen M, Winter D, Braulke T, Gieselmann V. SILAC-Based Comparative Proteomic Analysis of Lysosomes from Mammalian Cells Using LC-MS/MS. Methods Mol Biol 2017; 1594:1-18. [PMID: 28456973 DOI: 10.1007/978-1-4939-6934-0_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mass spectrometry-based proteomics of lysosomal proteins has led to significant advances in understanding lysosomal function and pathology. The ever-increasing sensitivity and resolution of mass spectrometry in combination with labeling procedures which allow comparative quantitative proteomics can be applied to shed more light on the steadily increasing range of lysosomal functions. In addition, investigation of alterations in lysosomal protein composition in the many lysosomal storage diseases may yield further insights into the molecular pathology of these disorders. Here, we describe a protocol which allows to determine quantitative differences in the lysosomal proteome of cells which are genetically and/or biochemically different or have been exposed to certain stimuli. The method is based on stable isotope labeling of amino acids in cell culture (SILAC). Cells are exposed to superparamagnetic iron oxide particles which are endocytosed and delivered to lysosomes. After homogenization of cells, intact lysosomes are rapidly enriched by passing the cell homogenates over a magnetic column. Lysosomes are eluted after withdrawal of the magnetic field and subjected to mass spectrometry.
Collapse
Affiliation(s)
- Melanie Thelen
- Institute for Biochemistry and Molecular Biology, Rheinische-Friedrich-Wilhelms-University, Bonn, Germany.
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Rheinische-Friedrich-Wilhelms-University, Bonn, Germany
| | - Thomas Braulke
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Volkmar Gieselmann
- Institute for Biochemistry and Molecular Biology, Rheinische-Friedrich-Wilhelms-University, Bonn, Germany
| |
Collapse
|
25
|
Lee JH, McBrayer MK, Wolfe DM, Haslett LJ, Kumar A, Sato Y, Lie PPY, Mohan P, Coffey EE, Kompella U, Mitchell CH, Lloyd-Evans E, Nixon RA. Presenilin 1 Maintains Lysosomal Ca(2+) Homeostasis via TRPML1 by Regulating vATPase-Mediated Lysosome Acidification. Cell Rep 2015; 12:1430-44. [PMID: 26299959 DOI: 10.1016/j.celrep.2015.07.050] [Citation(s) in RCA: 236] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 04/22/2015] [Accepted: 07/24/2015] [Indexed: 12/28/2022] Open
Abstract
Presenilin 1 (PS1) deletion or Alzheimer's disease (AD)-linked mutations disrupt lysosomal acidification and proteolysis, which inhibits autophagy. Here, we establish that this phenotype stems from impaired glycosylation and instability of vATPase V0a1 subunit, causing deficient lysosomal vATPase assembly and function. We further demonstrate that elevated lysosomal pH in Presenilin 1 knockout (PS1KO) cells induces abnormal Ca(2+) efflux from lysosomes mediated by TRPML1 and elevates cytosolic Ca(2+). In WT cells, blocking vATPase activity or knockdown of either PS1 or the V0a1 subunit of vATPase reproduces all of these abnormalities. Normalizing lysosomal pH in PS1KO cells using acidic nanoparticles restores normal lysosomal proteolysis, autophagy, and Ca(2+) homeostasis, but correcting lysosomal Ca(2+) deficits alone neither re-acidifies lysosomes nor reverses proteolytic and autophagic deficits. Our results indicate that vATPase deficiency in PS1 loss-of-function states causes lysosomal/autophagy deficits and contributes to abnormal cellular Ca(2+) homeostasis, thus linking two AD-related pathogenic processes through a common molecular mechanism.
Collapse
Affiliation(s)
- Ju-Hyun Lee
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA; Department of Psychiatry, New York University, New York, NY 10016, USA
| | - Mary Kate McBrayer
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Devin M Wolfe
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Luke J Haslett
- Division of Pathophysiology and Repair, Cardiff University, Cardiff CF10 3XQ, UK
| | - Asok Kumar
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA; Department of Pathology, New York University, New York, NY 10016, USA
| | - Yutaka Sato
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Pearl P Y Lie
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Panaiyur Mohan
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA; Department of Psychiatry, New York University, New York, NY 10016, USA
| | - Erin E Coffey
- Department of Anatomy and Cell Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Uday Kompella
- Pharmaceutical Science and Ophthalmology, University of Colorado, Aurora, CO 80045, USA
| | - Claire H Mitchell
- Department of Anatomy and Cell Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emyr Lloyd-Evans
- Division of Pathophysiology and Repair, Cardiff University, Cardiff CF10 3XQ, UK
| | - Ralph A Nixon
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA; Department of Psychiatry, New York University, New York, NY 10016, USA; Department of Cell Biology, New York University, New York, NY 10016, USA.
| |
Collapse
|