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Makar AN, Boraman A, Mosen P, Simpson JE, Marques J, Michelberger T, Aitken S, Wheeler AP, Winter D, von Kriegsheim A, Gammoh N. The V-ATPase complex component RNAseK is required for lysosomal hydrolase delivery and autophagosome degradation. Nat Commun 2024; 15:7743. [PMID: 39231962 PMCID: PMC11374810 DOI: 10.1038/s41467-024-52049-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/23/2024] [Indexed: 09/06/2024] Open
Abstract
Autophagy is a finely orchestrated process required for the lysosomal degradation of cytosolic components. The final degradation step is essential for clearing autophagic cargo and recycling macromolecules. Using a CRISPR/Cas9-based screen, we identify RNAseK, a highly conserved transmembrane protein, as a regulator of autophagosome degradation. Analyses of RNAseK knockout cells reveal that, while autophagosome maturation is intact, cargo degradation is severely disrupted. Importantly, lysosomal protease activity and acidification remain intact in the absence of RNAseK suggesting a specificity to autolysosome degradation. Analyses of lysosome fractions show reduced levels of a subset of hydrolases in the absence of RNAseK. Of these, the knockdown of PLD3 leads to a defect in autophagosome clearance. Furthermore, the lysosomal fraction of RNAseK-depleted cells exhibits an accumulation of the ESCRT-III complex component, VPS4a, which is required for the lysosomal targeting of PLD3. Altogether, here we identify a lysosomal hydrolase delivery pathway required for efficient autolysosome degradation.
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Affiliation(s)
- Agata N Makar
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, UK
| | - Alina Boraman
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, UK
| | - Peter Mosen
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Joanne E Simpson
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, UK
| | - Jair Marques
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, UK
| | - Tim Michelberger
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, UK
| | - Stuart Aitken
- MRC Human Genetics Unit, Institute of Genetics and Cancer, Crewe Road South, University of Edinburgh, Edinburgh, UK
| | - Ann P Wheeler
- MRC Human Genetics Unit, Institute of Genetics and Cancer, Crewe Road South, University of Edinburgh, Edinburgh, UK
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Alex von Kriegsheim
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, UK
| | - Noor Gammoh
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, UK.
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2
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Singh MK, Shin Y, Ju S, Han S, Kim SS, Kang I. Comprehensive Overview of Alzheimer's Disease: Etiological Insights and Degradation Strategies. Int J Mol Sci 2024; 25:6901. [PMID: 39000011 PMCID: PMC11241648 DOI: 10.3390/ijms25136901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder and affects millions of individuals globally. AD is associated with cognitive decline and memory loss that worsens with aging. A statistical report using U.S. data on AD estimates that approximately 6.9 million individuals suffer from AD, a number projected to surge to 13.8 million by 2060. Thus, there is a critical imperative to pinpoint and address AD and its hallmark tau protein aggregation early to prevent and manage its debilitating effects. Amyloid-β and tau proteins are primarily associated with the formation of plaques and neurofibril tangles in the brain. Current research efforts focus on degrading amyloid-β and tau or inhibiting their synthesis, particularly targeting APP processing and tau hyperphosphorylation, aiming to develop effective clinical interventions. However, navigating this intricate landscape requires ongoing studies and clinical trials to develop treatments that truly make a difference. Genome-wide association studies (GWASs) across various cohorts identified 40 loci and over 300 genes associated with AD. Despite this wealth of genetic data, much remains to be understood about the functions of these genes and their role in the disease process, prompting continued investigation. By delving deeper into these genetic associations, novel targets such as kinases, proteases, cytokines, and degradation pathways, offer new directions for drug discovery and therapeutic intervention in AD. This review delves into the intricate biological pathways disrupted in AD and identifies how genetic variations within these pathways could serve as potential targets for drug discovery and treatment strategies. Through a comprehensive understanding of the molecular underpinnings of AD, researchers aim to pave the way for more effective therapies that can alleviate the burden of this devastating disease.
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Affiliation(s)
- Manish Kumar Singh
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yoonhwa Shin
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Songhyun Ju
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sunhee Han
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sung Soo Kim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Insug Kang
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
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3
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Balusu S, De Strooper B. The necroptosis cell death pathway drives neurodegeneration in Alzheimer's disease. Acta Neuropathol 2024; 147:96. [PMID: 38852117 PMCID: PMC11162975 DOI: 10.1007/s00401-024-02747-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024]
Abstract
Although apoptosis, pyroptosis, and ferroptosis have been implicated in AD, none fully explains the extensive neuronal loss observed in AD brains. Recent evidence shows that necroptosis is abundant in AD, that necroptosis is closely linked to the appearance of Tau pathology, and that necroptosis markers accumulate in granulovacuolar neurodegeneration vesicles (GVD). We review here the neuron-specific activation of the granulovacuolar mediated neuronal-necroptosis pathway, the potential AD-relevant triggers upstream of this pathway, and the interaction of the necrosome with the endo-lysosomal pathway, possibly providing links to Tau pathology. In addition, we underscore the therapeutic potential of inhibiting necroptosis in neurodegenerative diseases such as AD, as this presents a novel avenue for drug development targeting neuronal loss to preserve cognitive abilities. Such an approach seems particularly relevant when combined with amyloid-lowering drugs.
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Affiliation(s)
- Sriram Balusu
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain and Disease Research, 3000, Leuven, Belgium.
- Leuven Brain Institute, KU Leuven, 3000, Leuven, Belgium.
| | - Bart De Strooper
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain and Disease Research, 3000, Leuven, Belgium.
- Leuven Brain Institute, KU Leuven, 3000, Leuven, Belgium.
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK.
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4
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Wang L, Qu F, Yu X, Yang S, Zhao B, Chen Y, Li P, Zhang Z, Zhang J, Han X, Wei D. Cortical lipid metabolic pathway alteration of early Alzheimer's disease and candidate drugs screen. Eur J Med Res 2024; 29:199. [PMID: 38528586 DOI: 10.1186/s40001-024-01730-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 02/12/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Lipid metabolism changes occur in early Alzheimer's disease (AD) patients. Yet little is known about metabolic gene changes in early AD cortex. METHODS The lipid metabolic genes selected from two datasets (GSE39420 and GSE118553) were analyzed with enrichment analysis. Protein-protein interaction network construction and correlation analyses were used to screen core genes. Literature analysis and molecular docking were applied to explore potential therapeutic drugs. RESULTS 60 lipid metabolic genes differentially expressed in early AD patients' cortex were screened. Bioinformatics analyses revealed that up-regulated genes were mainly focused on mitochondrial fatty acid oxidation and mediating the activation of long-chain fatty acids, phosphoproteins, and cholesterol metabolism. Down-regulated genes were mainly focused on lipid transport, carboxylic acid metabolic process, and neuron apoptotic process. Literature reviews and molecular docking results indicated that ACSL1, ACSBG2, ACAA2, FABP3, ALDH5A1, and FFAR4 were core targets for lipid metabolism disorder and had a high binding affinity with compounds including adenosine phosphate, oxidized Photinus luciferin, BMS-488043, and candidate therapeutic drugs especially bisphenol A, benzo(a)pyrene, ethinyl estradiol. CONCLUSIONS AD cortical lipid metabolism disorder was associated with the dysregulation of the PPAR signaling pathway, glycerophospholipid metabolism, adipocytokine signaling pathway, fatty acid biosynthesis, fatty acid degradation, ferroptosis, biosynthesis of unsaturated fatty acids, and fatty acid elongation. Candidate drugs including bisphenol A, benzo(a)pyrene, ethinyl estradiol, and active compounds including adenosine phosphate, oxidized Photinus luciferin, and BMS-488043 have potential therapeutic effects on cortical lipid metabolism disorder of early AD.
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Affiliation(s)
- Linshuang Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Fengxue Qu
- Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Xueyun Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Sixia Yang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Binbin Zhao
- Institute of Gerontology, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Yaojing Chen
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- BABRI Centre, Beijing Normal University, Beijing, 100875, China
| | - Pengbo Li
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- BABRI Centre, Beijing Normal University, Beijing, 100875, China
| | - Zhanjun Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- BABRI Centre, Beijing Normal University, Beijing, 100875, China
| | - Junying Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.
- BABRI Centre, Beijing Normal University, Beijing, 100875, China.
| | - Xuejie Han
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Dongfeng Wei
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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5
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Roske Y, Cappel C, Cremer N, Hoffmann P, Koudelka T, Tholey A, Heinemann U, Daumke O, Damme M. Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation. Nucleic Acids Res 2024; 52:370-384. [PMID: 37994783 PMCID: PMC10783504 DOI: 10.1093/nar/gkad1114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/31/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023] Open
Abstract
The phospholipase D (PLD) family is comprised of enzymes bearing phospholipase activity towards lipids or endo- and exonuclease activity towards nucleic acids. PLD3 is synthesized as a type II transmembrane protein and proteolytically cleaved in lysosomes, yielding a soluble active form. The deficiency of PLD3 leads to the slowed degradation of nucleic acids in lysosomes and chronic activation of nucleic acid-specific intracellular toll-like receptors. While the mechanism of PLD phospholipase activity has been extensively characterized, not much is known about how PLDs bind and hydrolyze nucleic acids. Here, we determined the high-resolution crystal structure of the luminal N-glycosylated domain of human PLD3 in its apo- and single-stranded DNA-bound forms. PLD3 has a typical phospholipase fold and forms homodimers with two independent catalytic centers via a newly identified dimerization interface. The structure of PLD3 in complex with an ssDNA-derived thymidine product in the catalytic center provides insights into the substrate binding mode of nucleic acids in the PLD family. Our structural data suggest a mechanism for substrate binding and nuclease activity in the PLD family and provide the structural basis to design immunomodulatory drugs targeting PLD3.
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Affiliation(s)
- Yvette Roske
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Cedric Cappel
- Biochemical Institute, Kiel University, Kiel, Germany
| | - Nils Cremer
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straβe 10, 13125 Berlin, Germany
| | | | - Tomas Koudelka
- Institute of Experimental Medicine, Kiel University, 24188 Kiel, Germany
| | - Andreas Tholey
- Institute of Experimental Medicine, Kiel University, 24188 Kiel, Germany
| | - Udo Heinemann
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Oliver Daumke
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Markus Damme
- Biochemical Institute, Kiel University, Kiel, Germany
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6
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Lee JC, Shirey RJ, Turner LD, Park H, Lairson LL, Janda KD. Discovery of PLD4 modulators by high-throughput screening and kinetic analysis. RESULTS IN CHEMISTRY 2024; 7:101349. [PMID: 38560090 PMCID: PMC10977906 DOI: 10.1016/j.rechem.2024.101349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Phospholipase D3 (PLD3) and D4 (PLD4) are endolysosomal exonucleases of ssDNA and ssRNA that regulate innate immunity. Polymorphisms of these enzymes are correlated with numerous human diseases, including Alzheimer's, rheumatoid arthritis, and systemic sclerosis. Pharmacological modulation of these immunoregulatory proteins may yield novel immunotherapies and adjuvants. A previous study reported a high-throughput screen (N = 17,952) that discovered a PLD3-selective activator and inhibitor, as well as a nonselective inhibitor, but failed to identify selective modulators of PLD4. However, modulators selective for PLD4 are therapeutically pertinent, since recent reports have shown that regulating this protein has direct implications in cancer and autoimmune diseases. Furthermore, the high expression of PLD4 in dendritic and myeloid cells, in comparison to the broader expression of PLD3, presents the opportunity for a cell-targeted immunotherapy. Here, we describe screening of an expended diversity library (N = 45,760) with an improved platform and report the discovery of one inhibitor and three activators selective for PLD4. Furthermore, kinetic modeling and structural analysis suggest mechanistic differences in the modulation of these hits. These findings further establish the utility of this screening platform and provide a set of chemical scaffolds to guide future small-molecule development for this novel immunoregulator target.
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Affiliation(s)
- Jinny Claire Lee
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ryan J. Shirey
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lewis D. Turner
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyeri Park
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Luke L. Lairson
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kim D. Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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7
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Sudwarts A, Thinakaran G. Alzheimer's genes in microglia: a risk worth investigating. Mol Neurodegener 2023; 18:90. [PMID: 37986179 PMCID: PMC10662636 DOI: 10.1186/s13024-023-00679-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
Despite expressing many key risk genes, the role of microglia in late-onset Alzheimer's disease pathophysiology is somewhat ambiguous, with various phenotypes reported to be either harmful or protective. Herein, we review some key findings from clinical and animal model investigations, discussing the role of microglial genetics in mediating perturbations from homeostasis. We note that impairment to protective phenotypes may include prolonged or insufficient microglial activation, resulting in dysregulated metabolomic (notably lipid-related) processes, compounded by age-related inflexibility in dynamic responses. Insufficiencies of mouse genetics and aggressive transgenic modelling imply severe limitations in applying current methodologies for aetiological investigations. Despite the shortcomings, widely used amyloidosis and tauopathy models of the disease have proven invaluable in dissecting microglial functional responses to AD pathophysiology. Some recent advances have brought modelling tools closer to human genetics, increasing the validity of both aetiological and translational endeavours.
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Affiliation(s)
- Ari Sudwarts
- Byrd Alzheimer's Center and Research Institute, University of South Florida, Tampa, FL, 33613, USA.
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Gopal Thinakaran
- Byrd Alzheimer's Center and Research Institute, University of South Florida, Tampa, FL, 33613, USA.
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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8
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Van Acker ZP, Perdok A, Hellemans R, North K, Vorsters I, Cappel C, Dehairs J, Swinnen JV, Sannerud R, Bretou M, Damme M, Annaert W. Phospholipase D3 degrades mitochondrial DNA to regulate nucleotide signaling and APP metabolism. Nat Commun 2023; 14:2847. [PMID: 37225734 DOI: 10.1038/s41467-023-38501-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 05/04/2023] [Indexed: 05/26/2023] Open
Abstract
Phospholipase D3 (PLD3) polymorphisms are linked to late-onset Alzheimer's disease (LOAD). Being a lysosomal 5'-3' exonuclease, its neuronal substrates remained unknown as well as how a defective lysosomal nucleotide catabolism connects to AD-proteinopathy. We identified mitochondrial DNA (mtDNA) as a major physiological substrate and show its manifest build-up in lysosomes of PLD3-defective cells. mtDNA accretion creates a degradative (proteolytic) bottleneck that presents at the ultrastructural level as a marked abundance of multilamellar bodies, often containing mitochondrial remnants, which correlates with increased PINK1-dependent mitophagy. Lysosomal leakage of mtDNA to the cytosol activates cGAS-STING signaling that upregulates autophagy and induces amyloid precursor C-terminal fragment (APP-CTF) and cholesterol accumulation. STING inhibition largely normalizes APP-CTF levels, whereas an APP knockout in PLD3-deficient backgrounds lowers STING activation and normalizes cholesterol biosynthesis. Collectively, we demonstrate molecular cross-talks through feedforward loops between lysosomal nucleotide turnover, cGAS-STING and APP metabolism that, when dysregulated, result in neuronal endolysosomal demise as observed in LOAD.
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Affiliation(s)
- Zoë P Van Acker
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Anika Perdok
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Ruben Hellemans
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Katherine North
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Inge Vorsters
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Cedric Cappel
- Laboratory for Molecular Cell Biology and Transgenic Research, Institute of Biochemistry, Christian-Albrechts-University Kiel, Otto-Hahn-Platz 9, Kiel, Germany
| | - Jonas Dehairs
- Laboratory of Lipid Metabolism & Cancer, Department of Oncology, KU Leuven, B-3000, Leuven, Belgium
| | - Johannes V Swinnen
- Laboratory of Lipid Metabolism & Cancer, Department of Oncology, KU Leuven, B-3000, Leuven, Belgium
| | - Ragna Sannerud
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Marine Bretou
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Markus Damme
- Laboratory for Molecular Cell Biology and Transgenic Research, Institute of Biochemistry, Christian-Albrechts-University Kiel, Otto-Hahn-Platz 9, Kiel, Germany
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium.
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium.
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9
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Yang H, Oh CK, Amal H, Wishnok JS, Lewis S, Schahrer E, Trudler D, Nakamura T, Tannenbaum SR, Lipton SA. Mechanistic insight into female predominance in Alzheimer's disease based on aberrant protein S-nitrosylation of C3. SCIENCE ADVANCES 2022; 8:eade0764. [PMID: 36516243 PMCID: PMC9750152 DOI: 10.1126/sciadv.ade0764] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protein S-nitros(yl)ation (SNO) is a posttranslational modification involved in diverse processes in health and disease and can contribute to synaptic damage in Alzheimer's disease (AD). To identify SNO proteins in AD brains, we used triaryl phosphine (SNOTRAP) combined with mass spectrometry (MS). We detected 1449 SNO proteins with 2809 SNO sites, representing a wide range of S-nitrosylated proteins in 40 postmortem AD and non-AD human brains from patients of both sexes. Integrative protein ranking revealed the top 10 increased SNO proteins, including complement component 3 (C3), p62 (SQSTM1), and phospholipase D3. Increased levels of S-nitrosylated C3 were present in female over male AD brains. Mechanistically, we show that formation of SNO-C3 is dependent on falling β-estradiol levels, leading to increased synaptic phagocytosis and thus synapse loss and consequent cognitive decline. Collectively, we demonstrate robust alterations in the S-nitrosoproteome that contribute to AD pathogenesis in a sex-dependent manner.
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Affiliation(s)
- Hongmei Yang
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130021, China
| | - Chang-ki Oh
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Haitham Amal
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - John S. Wishnok
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah Lewis
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Emily Schahrer
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dorit Trudler
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tomohiro Nakamura
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven R. Tannenbaum
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Corresponding author. (S.R.T.); (S.A.L.)
| | - Stuart A. Lipton
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Neurosciences, School of Medicine, University of California, San Diego, La Jolla CA 92093, USA
- Corresponding author. (S.R.T.); (S.A.L.)
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10
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Yuan P, Zhang M, Tong L, Morse TM, McDougal RA, Ding H, Chan D, Cai Y, Grutzendler J. PLD3 affects axonal spheroids and network defects in Alzheimer's disease. Nature 2022; 612:328-337. [PMID: 36450991 PMCID: PMC9729106 DOI: 10.1038/s41586-022-05491-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 10/27/2022] [Indexed: 12/03/2022]
Abstract
The precise mechanisms that lead to cognitive decline in Alzheimer's disease are unknown. Here we identify amyloid-plaque-associated axonal spheroids as prominent contributors to neural network dysfunction. Using intravital calcium and voltage imaging, we show that a mouse model of Alzheimer's disease demonstrates severe disruption in long-range axonal connectivity. This disruption is caused by action-potential conduction blockades due to enlarging spheroids acting as electric current sinks in a size-dependent manner. Spheroid growth was associated with an age-dependent accumulation of large endolysosomal vesicles and was mechanistically linked with Pld3-a potential Alzheimer's-disease-associated risk gene1 that encodes a lysosomal protein2,3 that is highly enriched in axonal spheroids. Neuronal overexpression of Pld3 led to endolysosomal vesicle accumulation and spheroid enlargement, which worsened axonal conduction blockades. By contrast, Pld3 deletion reduced endolysosomal vesicle and spheroid size, leading to improved electrical conduction and neural network function. Thus, targeted modulation of endolysosomal biogenesis in neurons could potentially reverse axonal spheroid-induced neural circuit abnormalities in Alzheimer's disease, independent of amyloid removal.
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Affiliation(s)
- Peng Yuan
- Department of Neurology, Yale University, New Haven, CT, USA.,Department of Rehabilitation Medicine, Huashan Hospital, State Key Laboratory of Medical Neurobiology, Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Mengyang Zhang
- Department of Neurology, Yale University, New Haven, CT, USA.,Department of Neuroscience, Yale University, New Haven, CT, USA.,Interdepartmental Neuroscience Program, Yale University, New Haven, CT, USA.,Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Lei Tong
- Department of Neurology, Yale University, New Haven, CT, USA
| | - Thomas M Morse
- Department of Neuroscience, Yale University, New Haven, CT, USA
| | - Robert A McDougal
- Department of Neuroscience, Yale University, New Haven, CT, USA.,Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Hui Ding
- Department of Neurology, Yale University, New Haven, CT, USA.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Diane Chan
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Yifei Cai
- Department of Neurology, Yale University, New Haven, CT, USA
| | - Jaime Grutzendler
- Department of Neurology, Yale University, New Haven, CT, USA. .,Department of Neuroscience, Yale University, New Haven, CT, USA. .,Wu Tsai Institute, Yale University, New Haven, CT, USA.
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11
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Umachandran S, Mohamed W, Jayaraman M, Hyde G, Brazill D, Baskar R. A PKC that controls polyphosphate levels, pinocytosis and exocytosis, regulates stationary phase onset in Dictyostelium. J Cell Sci 2022; 135:274945. [PMID: 35362518 DOI: 10.1242/jcs.259289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 03/25/2022] [Indexed: 11/20/2022] Open
Abstract
Many cells can pause their growth cycle, a topic much enriched by studies of the stationary phase (SP) of model microorganisms. While several kinases are implicated in SP onset, a possible role for protein kinase C remains unknown. We show that Dictyostelium discoideum cells lacking pkcA entered SP at a reduced cell density, but only in shaking conditions. Precocious SP entry occurs because extracellular polyphosphate (polyP) levels reach a threshold at the lower cell density; adding exopolyphosphatase to pkcA- cells reverses the effect and mimics wild type growth. PkcA's regulation of polyP depended on inositol hexakisphosphate kinase and phospholipase D. PkcA- mutants also had higher actin levels, higher rates of exocytosis and lower pinocytosis rates. Postlysosomes were smaller and present in fewer pkcA- cells, compared to the wildtype. Overall, the results suggest that a reduced PkcA level triggers SP primarily because cells do not acquire or retain nutrients as efficiently, thus mimicking, or amplifying, the conditions of actual starvation.
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Affiliation(s)
- Shalini Umachandran
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology-Madras, Chennai-600036, India
| | - Wasima Mohamed
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology-Madras, Chennai-600036, India
| | - Meenakshi Jayaraman
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology-Madras, Chennai-600036, India
| | - Geoff Hyde
- Independent Researcher, Randwick, New South Wales, Australia
| | - Derrick Brazill
- Department of Biological Sciences, Hunter College, New York, NY 10065, USA
| | - Ramamurthy Baskar
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology-Madras, Chennai-600036, India
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12
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Goodman LD, Bellen HJ. Recent insights into the role of glia and oxidative stress in Alzheimer's disease gained from Drosophila. Curr Opin Neurobiol 2022; 72:32-38. [PMID: 34418791 PMCID: PMC8854453 DOI: 10.1016/j.conb.2021.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 02/03/2023]
Abstract
Here, we discuss findings made using Drosophila on Alzheimer's disease (AD) risk and progression. Recent studies have investigated the mechanisms underlying glia-mediated neuroprotection in AD. First, we discuss a novel mechanism of glial lipid droplet formation that occurs in response to elevated reactive oxygen species in neurons. The data suggest that disruptions to this process contribute to AD risk. We further discuss novel mechanistic insights into glia-mediated Aβ42-clearance made using the fly. Finally, we highlight work that provides evidence that the aberrant accumulation of reactive oxygen species in AD may not just be a consequence of disease but contribute to disease progression as well. Cumulatively, the discussed studies highlight recent, relevant discoveries in AD made using Drosophila.
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Affiliation(s)
- Lindsey D. Goodman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA,CORRESPONDANCE
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
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13
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Becker T, Cappel C, Di Matteo F, Sonsalla G, Kaminska E, Spada F, Cappello S, Damme M, Kielkowski P. AMPylation profiling during neuronal differentiation reveals extensive variation on lysosomal proteins. iScience 2021; 24:103521. [PMID: 34917898 PMCID: PMC8668991 DOI: 10.1016/j.isci.2021.103521] [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: 03/10/2021] [Revised: 07/20/2021] [Accepted: 11/23/2021] [Indexed: 12/02/2022] Open
Abstract
Protein AMPylation is a posttranslational modification with an emerging role in neurodevelopment. In metazoans two highly conserved protein AMP-transferases together with a diverse group of AMPylated proteins have been identified using chemical proteomics and biochemical techniques. However, the function of AMPylation remains largely unknown. Particularly problematic is the localization of thus far identified AMPylated proteins and putative AMP-transferases. We show that protein AMPylation is likely a posttranslational modification of luminal lysosomal proteins characteristic in differentiating neurons. Through a combination of chemical proteomics, gel-based separation of modified and unmodified proteins, and an activity assay, we determine that the modified, lysosomal soluble form of exonuclease PLD3 increases dramatically during neuronal maturation and that AMPylation correlates with its catalytic activity. Together, our findings indicate that AMPylation is a so far unknown lysosomal posttranslational modification connected to neuronal differentiation and it may provide a molecular rationale behind lysosomal storage diseases and neurodegeneration. Profiling of AMPylation during neuronal differentiation AMPylation is a potential PTM of luminal lysosomal proteins Phos-tag gel enables the separation of non-AMPylated and AMPylated proteins The modified lysosomal soluble form of PLD3 increases during neuronal maturation
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Affiliation(s)
- Tobias Becker
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Cedric Cappel
- University of Kiel, Institute of Biochemistry, Olshausenstr. 40, 24098 Kiel, Germany
| | - Francesco Di Matteo
- Max Planck Institute of Psychiatry, Kraepelinstraße 2, 80804 Munich, Germany.,International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Kraepelinstraße 2-10, 80804 Munich, Germany
| | - Giovanna Sonsalla
- LMU Munich, Department of Physiological Genomics, Biomedical Center (BMC), Großhadernerstr. 9, 82152 Planegg, Germany.,Helmholtz Zentrum München, Institute for Stem Cell Research, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.,Graduate School of Systemic Neurosciences (GSN), Großhadernerstr. 2, 82152 Planegg, Germany
| | - Ewelina Kaminska
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Fabio Spada
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Silvia Cappello
- Max Planck Institute of Psychiatry, Kraepelinstraße 2, 80804 Munich, Germany
| | - Markus Damme
- University of Kiel, Institute of Biochemistry, Olshausenstr. 40, 24098 Kiel, Germany
| | - Pavel Kielkowski
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
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14
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Cleavage of DNA and RNA by PLD3 and PLD4 limits autoinflammatory triggering by multiple sensors. Nat Commun 2021; 12:5874. [PMID: 34620855 PMCID: PMC8497607 DOI: 10.1038/s41467-021-26150-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 09/15/2021] [Indexed: 11/26/2022] Open
Abstract
Phospholipase D3 (PLD3) and PLD4 polymorphisms have been associated with several important inflammatory diseases. Here, we show that PLD3 and PLD4 digest ssRNA in addition to ssDNA as reported previously. Moreover, Pld3−/−Pld4−/− mice accumulate small ssRNAs and develop spontaneous fatal hemophagocytic lymphohistiocytosis (HLH) characterized by inflammatory liver damage and overproduction of Interferon (IFN)-γ. Pathology is rescued in Unc93b13d/3dPld3−/−Pld4−/− mice, which lack all endosomal TLR signaling; genetic codeficiency or antibody blockade of TLR9 or TLR7 ameliorates disease less effectively, suggesting that both RNA and DNA sensing by TLRs contributes to inflammation. IFN-γ made a minor contribution to pathology. Elevated type I IFN and some other remaining perturbations in Unc93b13d/3dPld3−/−Pld4−/− mice requires STING (Tmem173). Our results show that PLD3 and PLD4 regulate both endosomal TLR and cytoplasmic/STING nucleic acid sensing pathways and have implications for the treatment of nucleic acid-driven inflammatory disease. Loss of function polymorphisms of phospholipase D3 and D4 are associated with inflammatory diseases and their function is unclear. Here the authors show that PLD3/4 function as RNAses and deletion of these proteins in mice leads to accumulation of ssRNA which exacerbates inflammation through TLR signalling.
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15
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Wang W, Wu J, Liu P, Tang X, Pang H, Xie T, Xu F, Shao J, Chen Y, Liu B, Zheng Y. Urinary Proteomics Identifying Novel Biomarkers for the Diagnosis and Phenotyping of Carotid Artery Stenosis. Front Mol Biosci 2021; 8:714706. [PMID: 34447787 PMCID: PMC8383446 DOI: 10.3389/fmolb.2021.714706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/26/2021] [Indexed: 01/12/2023] Open
Abstract
Background: Carotid artery stenosis (CAS) is caused by the formation of atherosclerotic plaques inside the arterial wall and accounts for 20–30% of all strokes. The development of an early, noninvasive diagnostic method and the identification of high-risk patients for ischemic stroke is essential to the management of CAS in clinical practice. Methods: We used the data-independent acquisition (DIA) technique to conduct a urinary proteomic study in patients with CAS and healthy controls. We identified the potential diagnosis and risk stratification biomarkers of CAS. And Ingenuity pathway analysis was used for functional annotation of differentially expressed proteins (DEPs). Furthermore, receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic values of DEPs. Results: A total of 194 DEPs were identified between CAS patients and healthy controls by DIA quantification. The bioinformatics analysis showed that these DEPs were correlated with the pathogenesis of CAS. We further identified 32 DEPs in symptomatic CAS compared to asymptomatic CAS, and biological function analysis revealed that these proteins are mainly related to immune/inflammatory pathways. Finally, a biomarker panel of six proteins (ACP2, PLD3, HLA-C, GGH, CALML3, and IL2RB) exhibited potential diagnostic value in CAS and good discriminative power for differentiating symptomatic and asymptomatic CAS with high sensitivity and specificity. Conclusions: Our study identified novel potential urinary biomarkers for noninvasive early screening and risk stratification of CAS.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianqiang Wu
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Liu
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyue Tang
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haiyu Pang
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Xie
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fang Xu
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiang Shao
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuexin Chen
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bao Liu
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuehong Zheng
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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16
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Shirey RJ, Turner LD, Lairson LL, Janda KD. Modulators of immunoregulatory exonucleases PLD3 and PLD4 identified by high-throughput screen. Bioorg Med Chem Lett 2021; 49:128293. [PMID: 34332037 DOI: 10.1016/j.bmcl.2021.128293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 10/20/2022]
Abstract
PLD3 and PLD4 have recently been revealed to be endosomal exonucleases that regulate the innate immune response by digesting the ligands of nucleic acid sensors. These enzymes can suppress RNA and DNA innate immune sensors like toll-like receptor 9, and PLD4-deficent mice exhibit inflammatory disease. Targeting these immunoregulatory enzymes presents an opportunity to indirectly regulate innate immune nucleic acid sensors that could yield immunotherapies, adjuvants, and nucleic acid drug stabilizers. To aid in delineating the therapeutic potential of these targets, we have developed a high-throughput fluorescence enzymatic assay to identify modulators of PLD3 and PLD4. Screening of a diversity library (N = 17952) yielded preferential inhibitors of PLD3 and PLD4 in addition to a PLD3 selective activator. The modulation models of these compounds were delineated by kinetic analysis. This work presents an inexpensive and simple method to identify modulators of these immunoregulatory exonucleases.
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Affiliation(s)
- Ryan J Shirey
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Lewis D Turner
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Luke L Lairson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Kim D Janda
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States.
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17
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Liu YH, Zhang HF, Jin JY, Wei YQ, Wang CY, Fan LL, Liu L. Case Report: A Homozygous Mutation (p.Y62X) of Phospholipase D3 May Lead to a New Leukoencephalopathy Syndrome. Front Aging Neurosci 2021; 13:671296. [PMID: 34267643 PMCID: PMC8276716 DOI: 10.3389/fnagi.2021.671296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Leukodystrophies are a heterogeneous group of inherited disorders with highly variable clinical manifestations and pathogenetic backgrounds. At present, variants in more than 20 genes have been described and may be responsible for different types of leukodystrophies. Members of the phospholipase D family of enzymes catalyze the hydrolysis of membrane phospholipids. Meanwhile, phospholipase D3 (PLD3) has also been found to exhibit single stranded DNA (ssDNA) acid 5' exonuclease activity. Variants in phospholipase D3 (PLD3) may increase the risk of Alzheimer's disease and spinocerebellar ataxia, but this hypothesis has not been fully confirmed. In this study, we identified a novel homozygous mutation (NM_012268.3: c.186C>G/ p.Y62X) of PLD3 in a consanguineous family with white matter lesions, hearing and vision loss, and kidney disease by whole exome sequencing. Real-time PCR revealed that the novel mutation may lead to non-sense-mediated messenger RNA (mRNA) decay. This may be the first case report on the homozygous mutation of PLD3 in patients worldwide. Our studies indicated that homozygous mutation of PLD3 may result in a novel leukoencephalopathy syndrome with white matter lesions, hearing and vision loss, and kidney disease.
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Affiliation(s)
- Yi-Hui Liu
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China.,Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Hai-Feng Zhang
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Jie-Yuan Jin
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yan-Qiu Wei
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Chen-Yu Wang
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Liang-Liang Fan
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China.,Department of Cell Biology, The School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Disease, School of Life Sciences, Central South University, Changsha, China
| | - Lv Liu
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China.,Department of Cell Biology, The School of Life Sciences, Central South University, Changsha, China
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18
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Santa-Marinha L, Castanho I, Silva RR, Bravo FV, Miranda AM, Meira T, Morais-Ribeiro R, Marques F, Xu Y, Point du Jour K, Wenk M, Chan RB, Di Paolo G, Pinto V, Oliveira TG. Phospholipase D1 Ablation Disrupts Mouse Longitudinal Hippocampal Axis Organization and Functioning. Cell Rep 2021; 30:4197-4208.e6. [PMID: 32209478 DOI: 10.1016/j.celrep.2020.02.102] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/29/2020] [Accepted: 02/27/2020] [Indexed: 01/01/2023] Open
Abstract
Phosphatidic acid (PA) is a signaling lipid involved in the modulation of synaptic structure and functioning. Based on previous work showing a decreasing PA gradient along the longitudinal axis of the rodent hippocampus, we asked whether the dorsal hippocampus (DH) and the ventral hippocampus (VH) are differentially affected by PA modulation. Here, we show that phospholipase D1 (PLD1) is a major hippocampal PA source, compared to PLD2, and that PLD1 ablation affects predominantly the lipidome of the DH. Moreover, Pld1 knockout (KO) mice show specific deficits in novel object recognition and social interaction and disruption in the DH-VH dendritic arborization differentiation in CA1/CA3 pyramidal neurons. Also, Pld1 KO animals present reduced long-term depression (LTD) induction and reduced GluN2A and SNAP-25 protein levels in the DH. Overall, we observe that PLD1-derived PA reduction leads to differential lipid signatures along the longitudinal hippocampal axis, predominantly affecting DH organization and functioning.
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Affiliation(s)
- Luísa Santa-Marinha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Isabel Castanho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Rita Ribeiro Silva
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Francisca Vaz Bravo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - André Miguel Miranda
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Torcato Meira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Rafaela Morais-Ribeiro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Fernanda Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Yimeng Xu
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Kimberly Point du Jour
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Markus Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Robin Barry Chan
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Gilbert Di Paolo
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Vítor Pinto
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Tiago Gil Oliveira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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19
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Nackenoff AG, Hohman TJ, Neuner SM, Akers CS, Weitzel NC, Shostak A, Ferguson SM, Mobley B, Bennett DA, Schneider JA, Jefferson AL, Kaczorowski CC, Schrag MS. PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer's disease. PLoS Genet 2021; 17:e1009406. [PMID: 33830999 PMCID: PMC8031396 DOI: 10.1371/journal.pgen.1009406] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/09/2021] [Indexed: 11/19/2022] Open
Abstract
Phospholipase D3 (PLD3) is a protein of unclear function that structurally resembles other members of the phospholipase D superfamily. A coding variant in this gene confers increased risk for the development of Alzheimer's disease (AD), although the magnitude of this effect has been controversial. Because of the potential significance of this obscure protein, we undertook a study to observe its distribution in normal human brain and AD-affected brain, determine whether PLD3 is relevant to memory and cognition in sporadic AD, and to evaluate its molecular function. In human neuropathological samples, PLD3 was primarily found within neurons and colocalized with lysosome markers (LAMP2, progranulin, and cathepsins D and B). This colocalization was also present in AD brain with prominent enrichment on lysosomal accumulations within dystrophic neurites surrounding β-amyloid plaques. This pattern of protein distribution was conserved in mouse brain in wild type and the 5xFAD mouse model of cerebral β-amyloidosis. We discovered PLD3 has phospholipase D activity in lysosomes. A coding variant in PLD3 reported to confer AD risk significantly reduced enzymatic activity compared to wild-type PLD3. PLD3 mRNA levels in the human pre-frontal cortex inversely correlated with β-amyloid pathology severity and rate of cognitive decline in 531 participants enrolled in the Religious Orders Study and Rush Memory and Aging Project. PLD3 levels across genetically diverse BXD mouse strains and strains crossed with 5xFAD mice correlated strongly with learning and memory performance in a fear conditioning task. In summary, this study identified a new functional mammalian phospholipase D isoform which is lysosomal and closely associated with both β-amyloid pathology and cognition.
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Affiliation(s)
- Alex G. Nackenoff
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Memory and Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Timothy J. Hohman
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Memory and Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Sarah M. Neuner
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Carolyn S. Akers
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Memory and Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Nicole C. Weitzel
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Memory and Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Alena Shostak
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Memory and Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Shawn M. Ferguson
- Department of Cell Biology, Yale University, New Haven, Connecticut, United States of America
| | - Bret Mobley
- Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Julie A. Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Angela L. Jefferson
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Memory and Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | | | - Matthew S. Schrag
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Memory and Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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20
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Ando K, Houben S, Homa M, de Fisenne MA, Potier MC, Erneux C, Brion JP, Leroy K. Alzheimer's Disease: Tau Pathology and Dysfunction of Endocytosis. Front Mol Neurosci 2021; 13:583755. [PMID: 33551742 PMCID: PMC7862548 DOI: 10.3389/fnmol.2020.583755] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/22/2020] [Indexed: 11/21/2022] Open
Affiliation(s)
- Kunie Ando
- Laboratory of Histology, Neuroanatomy and Neuropathology, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, Brussels, Belgium
| | - Sarah Houben
- Laboratory of Histology, Neuroanatomy and Neuropathology, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, Brussels, Belgium
| | - Mégane Homa
- Laboratory of Histology, Neuroanatomy and Neuropathology, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, Brussels, Belgium
| | - Marie-Ange de Fisenne
- Laboratory of Histology, Neuroanatomy and Neuropathology, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, Brussels, Belgium
| | - Marie-Claude Potier
- ICM Institut du Cerveau et de la Moelle épinière, CNRS UMR7225, INSERM U1127, UPMC, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Christophe Erneux
- Institut de Recherche Interdisciplinaire en Biologie Humaine et moléculaire (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Pierre Brion
- Laboratory of Histology, Neuroanatomy and Neuropathology, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, Brussels, Belgium
| | - Karelle Leroy
- Laboratory of Histology, Neuroanatomy and Neuropathology, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, Brussels, Belgium
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21
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Cappel C, Gonzalez AC, Damme M. Quantification and characterization of the 5' exonuclease activity of the lysosomal nuclease PLD3 by a novel cell-based assay. J Biol Chem 2020; 296:100152. [PMID: 33288674 PMCID: PMC7857491 DOI: 10.1074/jbc.ra120.015867] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/01/2020] [Accepted: 12/06/2020] [Indexed: 01/09/2023] Open
Abstract
Phospholipase D3 (PLD3) and phospholipase D4 (PLD4), the most recently described lysosomal nucleases, are associated with Alzheimer’s disease, spinocerebellar ataxia, and systemic lupus erythematosus. They exhibit 5′ exonuclease activity on single-stranded DNA, hydrolyzing it at the acidic pH associated with the lysosome. However, their full cellular function is inadequately understood. To examine these enzymes, we developed a robust and automatable cell-based assay based on fluorophore- and fluorescence-quencher-coupled oligonucleotides for the quantitative determination of acidic 5′ exonuclease activity. We validated the assay under knockout and PLD-overexpression conditions and then applied it to characterize PLD3 and PLD4 biochemically. Our experiments revealed PLD3 as the principal acid 5′ exonuclease in HeLa cells, where it showed a markedly higher specific activity compared with PLD4. We further used our newly developed assay to determine the substrate specificity and inhibitory profile of PLD3 and found that proteolytic processing of PLD3 is dispensable for its hydrolytic activity. We followed the expression, proteolytic processing, and intracellular distribution of genetic PLD3 variants previously associated with Alzheimer’s disease and investigated each variant's effect on the 5′ nuclease activity of PLD3, finding that some variants lead to reduced activity, but others not. The development of a PLD3/4-specific biochemical assay will be instrumental in understanding better both nucleases and their incompletely understood roles in vitro and in vivo.
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Affiliation(s)
- Cedric Cappel
- Biochemical Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Markus Damme
- Biochemical Institute, Christian-Albrechts-University of Kiel, Kiel, Germany.
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22
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Marshall KE, Vadukul DM, Staras K, Serpell LC. Misfolded amyloid-β-42 impairs the endosomal-lysosomal pathway. Cell Mol Life Sci 2020; 77:5031-5043. [PMID: 32025743 PMCID: PMC7658065 DOI: 10.1007/s00018-020-03464-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/29/2022]
Abstract
Misfolding and aggregation of proteins is strongly linked to several neurodegenerative diseases, but how such species bring about their cytotoxic actions remains poorly understood. Here we used specifically-designed optical reporter probes and live fluorescence imaging in primary hippocampal neurons to characterise the mechanism by which prefibrillar, oligomeric forms of the Alzheimer's-associated peptide, Aβ42, exert their detrimental effects. We used a pH-sensitive reporter, Aβ42-CypHer, to track Aβ internalisation in real-time, demonstrating that oligomers are rapidly taken up into cells in a dynamin-dependent manner, and trafficked via the endo-lysosomal pathway resulting in accumulation in lysosomes. In contrast, a non-assembling variant of Aβ42 (vAβ42) assayed in the same way is not internalised. Tracking ovalbumin uptake into cells using CypHer or Alexa Fluor tags shows that preincubation with Aβ42 disrupts protein uptake. Our results identify a potential mechanism by which amyloidogenic aggregates impair cellular function through disruption of the endosomal-lysosomal pathway.
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Affiliation(s)
- Karen E Marshall
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, BN1 9QG, UK
| | - Devkee M Vadukul
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, BN1 9QG, UK
| | - Kevin Staras
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, BN1 9QG, UK.
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, BN1 9QG, UK.
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23
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Cataloguing and Selection of mRNAs Localized to Dendrites in Neurons and Regulated by RNA-Binding Proteins in RNA Granules. Biomolecules 2020; 10:biom10020167. [PMID: 31978946 PMCID: PMC7072219 DOI: 10.3390/biom10020167] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
Spatiotemporal translational regulation plays a key role in determining cell fate and function. Specifically, in neurons, local translation in dendrites is essential for synaptic plasticity and long-term memory formation. To achieve local translation, RNA-binding proteins in RNA granules regulate target mRNA stability, localization, and translation. To date, mRNAs localized to dendrites have been identified by comprehensive analyses. In addition, mRNAs associated with and regulated by RNA-binding proteins have been identified using various methods in many studies. However, the results obtained from these numerous studies have not been compiled together. In this review, we have catalogued mRNAs that are localized to dendrites and are associated with and regulated by the RNA-binding proteins fragile X mental retardation protein (FMRP), RNA granule protein 105 (RNG105, also known as Caprin1), Ras-GAP SH3 domain binding protein (G3BP), cytoplasmic polyadenylation element binding protein 1 (CPEB1), and staufen double-stranded RNA binding proteins 1 and 2 (Stau1 and Stau2) in RNA granules. This review provides comprehensive information on dendritic mRNAs, the neuronal functions of mRNA-encoded proteins, the association of dendritic mRNAs with RNA-binding proteins in RNA granules, and the effects of RNA-binding proteins on mRNA regulation. These findings provide insights into the mechanistic basis of protein-synthesis-dependent synaptic plasticity and memory formation and contribute to future efforts to understand the physiological implications of local regulation of dendritic mRNAs in neurons.
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24
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Guix FX. The interplay between aging‐associated loss of protein homeostasis and extracellular vesicles in neurodegeneration. J Neurosci Res 2019; 98:262-283. [DOI: 10.1002/jnr.24526] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 08/29/2019] [Accepted: 08/31/2019] [Indexed: 12/11/2022]
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25
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Thakur R, Naik A, Panda A, Raghu P. Regulation of Membrane Turnover by Phosphatidic Acid: Cellular Functions and Disease Implications. Front Cell Dev Biol 2019; 7:83. [PMID: 31231646 PMCID: PMC6559011 DOI: 10.3389/fcell.2019.00083] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/03/2019] [Indexed: 01/23/2023] Open
Abstract
Phosphatidic acid (PA) is a simple glycerophospholipid with a well-established role as an intermediate in phospholipid biosynthesis. In addition to its role in lipid biosynthesis, PA has been proposed to act as a signaling molecule that modulates several aspects of cell biology including membrane transport. PA can be generated in eukaryotic cells by several enzymes whose activity is regulated in the context of signal transduction and enzymes that can metabolize PA thus terminating its signaling activity have also been described. Further, several studies have identified PA binding proteins and changes in their activity are proposed to be mediators of the signaling activity of this lipid. Together these enzymes and proteins constitute a PA signaling toolkit that mediates the signaling functions of PA in cells. Recently, a number of novel genetic models for the analysis of PA function in vivo and analytical methods to quantify PA levels in cells have been developed and promise to enhance our understanding of PA functions. Studies of several elements of the PA signaling toolkit in a single cell type have been performed and are presented to provide a perspective on our understanding of the biochemical and functional organization of pools of PA in a eukaryotic cell. Finally, we also provide a perspective on the potential role of PA in human disease, synthesizing studies from model organisms, human disease genetics and analysis using recently developed PLD inhibitors.
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Affiliation(s)
- Rajan Thakur
- National Centre for Biological Sciences-TIFR, Bengaluru, India
| | - Amruta Naik
- National Centre for Biological Sciences-TIFR, Bengaluru, India
| | - Aniruddha Panda
- National Centre for Biological Sciences-TIFR, Bengaluru, India
| | - Padinjat Raghu
- National Centre for Biological Sciences-TIFR, Bengaluru, India
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26
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Van Acker ZP, Bretou M, Annaert W. Endo-lysosomal dysregulations and late-onset Alzheimer's disease: impact of genetic risk factors. Mol Neurodegener 2019; 14:20. [PMID: 31159836 PMCID: PMC6547588 DOI: 10.1186/s13024-019-0323-7] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/10/2019] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence supports that cellular dysregulations in the degradative routes contribute to the initiation and progression of neurodegenerative diseases, including Alzheimer's disease. Autophagy and endolysosomal homeostasis need to be maintained throughout life as they are major cellular mechanisms involved in both the production of toxic amyloid peptides and the clearance of misfolded or aggregated proteins. As such, alterations in endolysosomal and autophagic flux, as a measure of degradation activity in these routes or compartments, may directly impact as well on disease-related mechanisms such as amyloid-β clearance through the blood-brain-barrier and the interneuronal spreading of amyloid-β and/or Tau seeds, affecting synaptic function, plasticity and metabolism. The emerging of several genetic risk factors for late-onset Alzheimer's disease that are functionally related to endocytic transport regulation, including cholesterol metabolism and clearance, supports the notion that in particular the autophagy/lysosomal flux might become more vulnerable during ageing thereby contributing to disease onset. In this review we discuss our current knowledge of the risk genes APOE4, BIN1, CD2AP, PICALM, PLD3 and TREM2 and their impact on endolysosomal (dys)regulations in the light of late-onset Alzheimer's disease pathology.
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Affiliation(s)
- Zoë P. Van Acker
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, Gasthuisberg, O&N4, Rm. 7.159, Herestraat 49, B-3000 Leuven, Belgium
| | - Marine Bretou
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, Gasthuisberg, O&N4, Rm. 7.159, Herestraat 49, B-3000 Leuven, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, Gasthuisberg, O&N4, Rm. 7.159, Herestraat 49, B-3000 Leuven, Belgium
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27
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Demirev AV, Song HL, Cho MH, Cho K, Peak JJ, Yoo HJ, Kim DH, Yoon SY. V232M substitution restricts a distinct O-glycosylation of PLD3 and its neuroprotective function. Neurobiol Dis 2019; 129:182-194. [PMID: 31121321 DOI: 10.1016/j.nbd.2019.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 04/15/2019] [Accepted: 05/17/2019] [Indexed: 01/10/2023] Open
Abstract
The link between Val232Met variant of phospholipase D3 (PLD3) and late-onset Alzheimer's disease (AD) is still obscure. While it may not affect directly the amyloid precursor protein function, PLD3 could be regulating multiple cellular compartments. Here, we investigated the function of wild-type human PLD3 (PLD3WT) and the Val232Met variant (PLD3VM) in the presence of β-amyloid (Aβ) in a Drosophila melanogaster model of AD. We expressed PLD3WT in CNS of the Aβ-model flies and monitored its effect on the ER stress, cell apoptosis and recovery the Aβ-induced cognitive impairment. The expression reduced ER stress and neuronal apoptosis, which resulted in normalized antioxidative phospholipids levels and brain protection. A specific O-glycosylation at pT271 in PLD3 is essential for its normal trafficking and cellular localization. The V232 M substitution impairs this O-glycosylation, leading to enlarged lysosomes and plausibly aberrant protein recycling. PLD3VM was less neuroprotective, and while, PLD3WT expression enhances the lysosomal functions, V232 M attenuated PLD3's trafficking to the lysosomes. Thus, the V232 M mutation may affect AD pathogenesis. Further understanding of the mechanistic role of PLD3 in AD could lead to developing novel therapeutic agents.
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Affiliation(s)
| | - Ha-Lim Song
- Department of Brain Science, Asan Medical Center, Bio-Medical Institute of Technology (BMIT), University of Ulsan College of Medicine, Seoul, Republic of Korea; ADEL Institute of Science and Technology (AIST), ADEL, Inc., Seoul, Republic of Korea
| | - Mi-Hyang Cho
- Department of Brain Science, Asan Medical Center, Bio-Medical Institute of Technology (BMIT), University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kwangmin Cho
- ADEL Institute of Science and Technology (AIST), ADEL, Inc., Seoul, Republic of Korea
| | - Jong-Jin Peak
- Department of Brain Science, Asan Medical Center, Bio-Medical Institute of Technology (BMIT), University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hyun Ju Yoo
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Dong-Hou Kim
- Department of Brain Science, Asan Medical Center, Bio-Medical Institute of Technology (BMIT), University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Seung-Yong Yoon
- Department of Brain Science, Asan Medical Center, Bio-Medical Institute of Technology (BMIT), University of Ulsan College of Medicine, Seoul, Republic of Korea; ADEL Institute of Science and Technology (AIST), ADEL, Inc., Seoul, Republic of Korea.
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28
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Guix FX, Sartório CL, Ill-Raga G. BACE1 Translation: At the Crossroads Between Alzheimer's Disease Neurodegeneration and Memory Consolidation. J Alzheimers Dis Rep 2019; 3:113-148. [PMID: 31259308 PMCID: PMC6597968 DOI: 10.3233/adr-180089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human life unfolds not only in time and space, but also in the recollection and interweaving of memories. Therefore, individual human identity depends fully on a proper access to the autobiographical memory. Such access is hindered under pathological conditions such as Alzheimer’s disease, which affects millions of people worldwide. Unfortunately, no effective cure exists to prevent this disorder, the impact of which will rise alarmingly within the next decades. While Alzheimer’s disease is largely considered to be the outcome of amyloid-β (Aβ) peptide accumulation in the brain, conceiving this complex disorder strictly as the result of Aβ-neurotoxicity is perhaps a too straight-line simplification. Instead, complementary to this view, the tableau of molecular disarrangements in the Alzheimer’s disease brain may be reflecting, at least in part, a loss of function phenotype in memory processing. Here we take BACE1 translation and degradation as a gateway to study molecular mechanisms putatively involved in the transition between memory and neurodegeneration. BACE1 participates in the excision of Aβ-peptide from its precursor holoprotein, but plays a role in synaptic plasticity too. Its translation is governed by eIF2α phosphorylation: a hub integrating cellular responses to stress, but also a critical switch in memory consolidation. Paralleling these dualities, the eIF2α-kinase HRI has been shown to be a nitric oxide-dependent physiological activator of hippocampal BACE1 translation. Finally, beholding BACE1 as a representative protease active in the CNS, we venture a new perspective on the cellular basis of memory, which may incorporate neurodegeneration in itself as a drift in memory consolidating systems.
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Affiliation(s)
- Francesc X Guix
- Department of Molecular Neuropathology, Centro de Biología Molecular Severo Ochoa-CSIC, Madrid, Spain
| | - Carmem L Sartório
- Division of Physiological Sciences, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Gerard Ill-Raga
- Division of Physiological Sciences, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
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29
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Sala Frigerio C, Wolfs L, Fattorelli N, Thrupp N, Voytyuk I, Schmidt I, Mancuso R, Chen WT, Woodbury ME, Srivastava G, Möller T, Hudry E, Das S, Saido T, Karran E, Hyman B, Perry VH, Fiers M, De Strooper B. The Major Risk Factors for Alzheimer's Disease: Age, Sex, and Genes Modulate the Microglia Response to Aβ Plaques. Cell Rep 2019; 27:1293-1306.e6. [PMID: 31018141 PMCID: PMC7340153 DOI: 10.1016/j.celrep.2019.03.099] [Citation(s) in RCA: 469] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/05/2019] [Accepted: 03/26/2019] [Indexed: 12/21/2022] Open
Abstract
Gene expression profiles of more than 10,000 individual microglial cells isolated from cortex and hippocampus of male and female AppNL-G-F mice over time demonstrate that progressive amyloid-β accumulation accelerates two main activated microglia states that are also present during normal aging. Activated response microglia (ARMs) are composed of specialized subgroups overexpressing MHC type II and putative tissue repair genes (Dkk2, Gpnmb, and Spp1) and are strongly enriched with Alzheimer's disease (AD) risk genes. Microglia from female mice progress faster in this activation trajectory. Similar activated states are also found in a second AD model and in human brain. Apoe, the major genetic risk factor for AD, regulates the ARMs but not the interferon response microglia (IRMs). Thus, the ARMs response is the converging point for aging, sex, and genetic AD risk factors.
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Affiliation(s)
- Carlo Sala Frigerio
- VIB Centre for Brain Disease Research, Leuven, Belgium; University of Leuven, Department of Neurosciences and Leuven Brain Institute, Leuven, Belgium; UK Dementia Research Institute, University College London, London, UK.
| | - Leen Wolfs
- VIB Centre for Brain Disease Research, Leuven, Belgium; University of Leuven, Department of Neurosciences and Leuven Brain Institute, Leuven, Belgium
| | - Nicola Fattorelli
- VIB Centre for Brain Disease Research, Leuven, Belgium; University of Leuven, Department of Neurosciences and Leuven Brain Institute, Leuven, Belgium
| | - Nicola Thrupp
- VIB Centre for Brain Disease Research, Leuven, Belgium; University of Leuven, Department of Neurosciences and Leuven Brain Institute, Leuven, Belgium
| | - Iryna Voytyuk
- VIB Centre for Brain Disease Research, Leuven, Belgium; University of Leuven, Department of Neurosciences and Leuven Brain Institute, Leuven, Belgium
| | - Inga Schmidt
- VIB Centre for Brain Disease Research, Leuven, Belgium; University of Leuven, Department of Neurosciences and Leuven Brain Institute, Leuven, Belgium
| | - Renzo Mancuso
- VIB Centre for Brain Disease Research, Leuven, Belgium; University of Leuven, Department of Neurosciences and Leuven Brain Institute, Leuven, Belgium
| | - Wei-Ting Chen
- VIB Centre for Brain Disease Research, Leuven, Belgium; University of Leuven, Department of Neurosciences and Leuven Brain Institute, Leuven, Belgium
| | - Maya E Woodbury
- Foundational Neuroscience Center, AbbVie, Inc., Cambridge, MA, USA
| | - Gyan Srivastava
- Foundational Neuroscience Center, AbbVie, Inc., Cambridge, MA, USA
| | - Thomas Möller
- Foundational Neuroscience Center, AbbVie, Inc., Cambridge, MA, USA
| | - Eloise Hudry
- Department of Neurology, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Sudeshna Das
- Department of Neurology, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Takaomi Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako-shi, Saitama, Japan
| | - Eric Karran
- Foundational Neuroscience Center, AbbVie, Inc., Cambridge, MA, USA
| | - Bradley Hyman
- Department of Neurology, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - V Hugh Perry
- UK Dementia Research Institute, University College London, London, UK; Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Mark Fiers
- VIB Centre for Brain Disease Research, Leuven, Belgium; University of Leuven, Department of Neurosciences and Leuven Brain Institute, Leuven, Belgium
| | - Bart De Strooper
- VIB Centre for Brain Disease Research, Leuven, Belgium; University of Leuven, Department of Neurosciences and Leuven Brain Institute, Leuven, Belgium; UK Dementia Research Institute, University College London, London, UK.
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30
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Tan M, Li J, Ma F, Zhang X, Zhao Q, Cao X. PLD3 Rare Variants Identified in Late-Onset Alzheimer's Disease Affect Amyloid-β Levels in Cellular Model. Front Neurosci 2019; 13:116. [PMID: 30837833 PMCID: PMC6382672 DOI: 10.3389/fnins.2019.00116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/30/2019] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing studies have reported that rare variants in PLD3 were associated with increased risk of late-onset Alzheimer’s disease (LOAD) in European cohorts. The association has been replicated in a Han Chinese cohort, two rare variants p.I163M in exon7 and p.R356H in exon11 of PLD3 were found to be associated with LOAD risk. Whether these variants have deleterious effects on protein function, and the underlying mechanisms by which they influence LOAD pathogenesis are unknown. Our results are the first to validate the hypothesis that these variants could lead to reduced PLD3 activity and affect amyloid-β levels in cellular model of AD, possibly via autophagy-dependent mTOR signaling pathway, indicating that PLD3 may represent a new therapeutic target for AD.
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Affiliation(s)
- Mengshan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Jieqiong Li
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Fangchen Ma
- Department of Neurology, Qingdao Municipal Hospital, Weifang Medical University, Qingdao, China
| | - Xing Zhang
- Department of Neurology, Qingdao Municipal Hospital, Dalian Medical University, Dalian, China
| | - Qingfei Zhao
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Xipeng Cao
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
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31
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Takatori S, Wang W, Iguchi A, Tomita T. Genetic Risk Factors for Alzheimer Disease: Emerging Roles of Microglia in Disease Pathomechanisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:83-116. [PMID: 30747419 DOI: 10.1007/978-3-030-05542-4_5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The accumulation of aggregated amyloid β (Aβ) peptides in the brain is deeply involved in Alzheimer disease (AD) pathogenesis. Mutations in APP and presenilins play major roles in Aβ pathology in rare autosomal-dominant forms of AD, whereas pathomechanisms of sporadic AD, accounting for the majority of cases, remain unknown. In this chapter, we review current knowledge on genetic risk factors of AD, clarified by recent advances in genome analysis technology. Interestingly, TREM2 and many genes associated with disease risk are predominantly expressed in microglia, suggesting that these risk factors are involved in pathogenicity through common mechanisms involving microglia. Therefore, we focus on factors closely associated with microglia and discuss their possible roles in pathomechanisms of AD. Furthermore, we review current views on the pathological roles of microglia and emphasize the importance of microglial changes in response to Aβ deposition and mechanisms underlying the phenotypic changes. Importantly, functional outcomes of microglial activation can be both protective and deleterious to neurons. We further describe the involvement of microglia in tau pathology and the activation of other glial cells. Through these topics, we shed light on microglia as a promising target for drug development for AD and other neurological disorders.
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Affiliation(s)
- Sho Takatori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Wenbo Wang
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Akihiro Iguchi
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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Blanco-Luquin I, Altuna M, Sánchez-Ruiz de Gordoa J, Urdánoz-Casado A, Roldán M, Cámara M, Zelaya V, Erro ME, Echavarri C, Mendioroz M. PLD3 epigenetic changes in the hippocampus of Alzheimer's disease. Clin Epigenetics 2018; 10:116. [PMID: 30208929 PMCID: PMC6134774 DOI: 10.1186/s13148-018-0547-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 08/27/2018] [Indexed: 12/18/2022] Open
Abstract
Background Whole-exome sequencing has revealed a rare missense variant in PLD3 gene (rs145999145) to be associated with late onset Alzheimer’s disease (AD). Nevertheless, the association remains controversial and little is known about the role of PLD3 in AD. Interestingly, PLD3 encodes a phospholipase that may be involved in amyloid precursor protein (APP) processing. Our aim was to gain insight into the epigenetic mechanisms regulating PLD3 gene expression in the human hippocampus affected by AD. Results We assessed PLD3 mRNA expression by qPCR and protein levels by Western blot in frozen hippocampal samples from a cohort of neuropathologically confirmed pure AD cases and controls. Next, we profiled DNA methylation at cytosine-phosphate-guanine dinucleotide (CpG) site resolution by pyrosequencing and further validated results by bisulfite cloning sequencing in two promoter regions of the PLD3 gene. A 1.67-fold decrease in PLD3 mRNA levels (p value < 0.001) was observed in the hippocampus of AD cases compared to controls, and a slight decrease was also found by Western blot at protein level. Moreover, PLD3 mRNA levels inversely correlated with the average area of β-amyloid burden (tau-b = − 0,331; p value < 0.01) in the hippocampus. A differentially methylated region was identified within the alternative promoter of PLD3 gene showing higher DNA methylation levels in the AD hippocampus compared to controls (21.7 ± 4.7% vs. 18.3 ± 4.8%; p value < 0.05). Conclusions PLD3 gene is downregulated in the human hippocampus in AD cases compared to controls. Altered epigenetic mechanisms, such as differential DNA methylation within an alternative promoter of PLD3 gene, may be involved in the pathological processes of AD. Moreover, PLD3 mRNA expression inversely correlates with hippocampal β-amyloid burden, which adds evidence to the hypothesis that PLD3 protein may contribute to AD development by modifying APP processing. Electronic supplementary material The online version of this article (10.1186/s13148-018-0547-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Idoia Blanco-Luquin
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain
| | - Miren Altuna
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain.,Department of Neurology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain
| | - Javier Sánchez-Ruiz de Gordoa
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain.,Department of Neurology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain
| | - Amaya Urdánoz-Casado
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain
| | - Miren Roldán
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain
| | - María Cámara
- Department of Neurology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain
| | - Victoria Zelaya
- Department of Pathology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), 31008, Pamplona, Navarra, Spain
| | - María Elena Erro
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain.,Department of Neurology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain
| | - Carmen Echavarri
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain.,Hospital Psicogeriátrico Josefina Arregui, 31800, Alsasua, Navarra, Spain
| | - Maite Mendioroz
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain. .,Department of Neurology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), C/ Irunlarrea, 3, 31008, Pamplona, Navarra, Spain.
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33
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Gavin AL, Huang D, Huber C, Mårtensson A, Tardif V, Skog PD, Blane TR, Thinnes TC, Osborn K, Chong HS, Kargaran F, Kimm P, Zeitjian A, Sielski RL, Briggs M, Schulz SR, Zarpellon A, Cravatt B, Pang ES, Teijaro J, de la Torre JC, O'Keeffe M, Hochrein H, Damme M, Teyton L, Lawson BR, Nemazee D. PLD3 and PLD4 are single-stranded acid exonucleases that regulate endosomal nucleic-acid sensing. Nat Immunol 2018; 19:942-953. [PMID: 30111894 PMCID: PMC6105523 DOI: 10.1038/s41590-018-0179-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/28/2018] [Indexed: 01/06/2023]
Abstract
The sensing of microbial genetic material by leukocytes often elicits beneficial pro-inflammatory cytokines, but dysregulated responses can cause severe pathogenesis. Genome-wide association studies have linked the gene encoding phospholipase D3 (PLD3) to Alzheimer's disease and have linked PLD4 to rheumatoid arthritis and systemic sclerosis. PLD3 and PLD4 are endolysosomal proteins whose functions are obscure. Here, PLD4-deficient mice were found to have an inflammatory disease, marked by elevated levels of interferon-γ (IFN-γ) and splenomegaly. These phenotypes were traced to altered responsiveness of PLD4-deficient dendritic cells to ligands of the single-stranded DNA sensor TLR9. Macrophages from PLD3-deficient mice also had exaggerated TLR9 responses. Although PLD4 and PLD3 were presumed to be phospholipases, we found that they are 5' exonucleases, probably identical to spleen phosphodiesterase, that break down TLR9 ligands. Mice deficient in both PLD3 and PLD4 developed lethal liver inflammation in early life, which indicates that both enzymes are needed to regulate inflammatory cytokine responses via the degradation of nucleic acids.
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Affiliation(s)
- Amanda L Gavin
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Deli Huang
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christoph Huber
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- , Bottmingen, Switzerland
| | - Annica Mårtensson
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Sophiris Bio, La Jolla, CA, USA
| | - Virginie Tardif
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University, Philadelphia, PA, USA
| | - Patrick D Skog
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tanya R Blane
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Therese C Thinnes
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kent Osborn
- The University of California, San Diego, La Jolla, CA, USA
| | - Hayley S Chong
- The University of California, San Diego, La Jolla, CA, USA
| | | | - Phoebe Kimm
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Armen Zeitjian
- The University of California, San Diego, La Jolla, CA, USA
| | | | - Megan Briggs
- The University of California, San Diego, La Jolla, CA, USA
| | - Sebastian R Schulz
- Division of Molecular Immunology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Alessandro Zarpellon
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin Cravatt
- The Department of Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ee Shan Pang
- Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - John Teijaro
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Juan Carlos de la Torre
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Meredith O'Keeffe
- Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | | | - Markus Damme
- Biochemisches Institut, Christian-Albrechts-Universität, Kiel, Germany
| | - Luc Teyton
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Brian R Lawson
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David Nemazee
- The Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
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34
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Mukadam AS, Breusegem SY, Seaman MNJ. Analysis of novel endosome-to-Golgi retrieval genes reveals a role for PLD3 in regulating endosomal protein sorting and amyloid precursor protein processing. Cell Mol Life Sci 2018; 75:2613-2625. [PMID: 29368044 PMCID: PMC6003983 DOI: 10.1007/s00018-018-2752-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/15/2017] [Accepted: 01/15/2018] [Indexed: 11/25/2022]
Abstract
The processing of amyloid precursor protein (APP) to the neurotoxic pro-aggregatory Aβ peptide is controlled by the mechanisms that govern the trafficking and localisation of APP. We hypothesised that genes involved in endosomal protein sorting could play an important role in regulating APP processing and, therefore, analysed ~ 40 novel endosome-to-Golgi retrieval genes previously identified in a genome-wide siRNA screen. We report that phospholipase D3 (PLD3), a type II membrane protein, functions in endosomal protein sorting and plays an important role in regulating APP processing. PLD3 co-localises with APP in endosomes and loss of PLD3 function results in reduced endosomal tubules, impaired trafficking of several membrane proteins and reduced association of sortilin-like 1 with APP.
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Affiliation(s)
- Aamir S Mukadam
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Sophia Y Breusegem
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Matthew N J Seaman
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
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35
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Guimas Almeida C, Sadat Mirfakhar F, Perdigão C, Burrinha T. Impact of late-onset Alzheimer's genetic risk factors on beta-amyloid endocytic production. Cell Mol Life Sci 2018; 75:2577-2589. [PMID: 29704008 PMCID: PMC11105284 DOI: 10.1007/s00018-018-2825-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/04/2018] [Accepted: 04/23/2018] [Indexed: 12/21/2022]
Abstract
The increased production of the 42 aminoacids long beta-amyloid (Aβ42) peptide has been established as a causal mechanism of the familial early onset Alzheimer's disease (AD). In contrast, the causal mechanisms of the late-onset AD (LOAD), that affects most AD patients, remain to be established. Indeed, Aβ42 accumulation has been detected more than 30 years before diagnosis. Thus, the mechanisms that control Aβ accumulation in LOAD likely go awry long before pathogenesis becomes detectable. Early on, APOE4 was identified as the biggest genetic risk factor for LOAD. However, since APOE4 is not present in all LOAD patients, genome-wide association studies of thousands of LOAD patients were undertaken to identify other genetic variants that could explain the development of LOAD. PICALM, BIN1, CD2AP, SORL1, and PLD3 are now with APOE4 among the identified genes at highest risk in LOAD that have been implicated in Aβ42 production. Recent evidence indicates that the regulation of the endocytic trafficking of the amyloid precursor protein (APP) and/or its secretases to and from sorting endosomes is determinant for Aβ42 production. Thus, here, we will review the described mechanisms, whereby these genetic risk factors can contribute to the enhanced endocytic production of Aβ42. Dissecting causal LOAD mechanisms of Aβ42 accumulation, underlying the contribution of each genetic risk factor, will be required to identify therapeutic targets for novel personalized preventive strategies.
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Affiliation(s)
- Cláudia Guimas Almeida
- Neuronal Trafficking in Aging Lab, CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo Mártires da Pátria, 130, 1169-056, Lisbon, Portugal.
| | - Farzaneh Sadat Mirfakhar
- Neuronal Trafficking in Aging Lab, CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo Mártires da Pátria, 130, 1169-056, Lisbon, Portugal
| | - Catarina Perdigão
- Neuronal Trafficking in Aging Lab, CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo Mártires da Pátria, 130, 1169-056, Lisbon, Portugal
| | - Tatiana Burrinha
- Neuronal Trafficking in Aging Lab, CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo Mártires da Pátria, 130, 1169-056, Lisbon, Portugal
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36
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Herber J, Njavro J, Feederle R, Schepers U, Müller UC, Bräse S, Müller SA, Lichtenthaler SF. Click Chemistry-mediated Biotinylation Reveals a Function for the Protease BACE1 in Modulating the Neuronal Surface Glycoproteome. Mol Cell Proteomics 2018; 17:1487-1501. [PMID: 29716987 DOI: 10.1074/mcp.ra118.000608] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/16/2018] [Indexed: 01/09/2023] Open
Abstract
The cell surface proteome is dynamic and has fundamental roles in cell signaling. Many surface membrane proteins are proteolytically released into a cell's secretome, where they can have additional functions in cell-cell-communication. Yet, it remains challenging to determine the surface proteome and to compare it to the cell secretome, under serum-containing cell culture conditions. Here, we set up and evaluated the 'surface-spanning protein enrichment with click sugars' (SUSPECS) method for cell surface membrane glycoprotein biotinylation, enrichment and label-free quantitative mass spectrometry. SUSPECS is based on click chemistry-mediated labeling of glycoproteins, is compatible with labeling of living cells and can be combined with secretome analyses in the same experiment. Immunofluorescence-based confocal microscopy demonstrated that SUSPECS selectively labeled cell surface proteins. Nearly 700 transmembrane glycoproteins were consistently identified at the surface of primary neurons. To demonstrate the utility of SUSPECS, we applied it to the protease BACE1, which is a key drug target in Alzheimer's disease. Pharmacological BACE1-inhibition selectively remodeled the neuronal surface glycoproteome, resulting in up to 7-fold increased abundance of the BACE1 substrates APP, APLP1, SEZ6, SEZ6L, CNTN2, and CHL1, whereas other substrates were not or only mildly affected. Interestingly, protein changes at the cell surface only partly correlated with changes in the secretome. Several altered proteins were validated by immunoblots in neurons and mouse brains. Apparent nonsubstrates, such as TSPAN6, were also increased, indicating that BACE1-inhibition may lead to unexpected secondary effects. In summary, SUSPECS is broadly useful for determination of the surface glycoproteome and its correlation with the secretome.
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Affiliation(s)
- Julia Herber
- From the ‡German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,§Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Jasenka Njavro
- From the ‡German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,§Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Regina Feederle
- From the ‡German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,¶Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,‖Institute for Diabetes and Obesity, Monoclonal Antibody Research Group, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Munich, Germany
| | - Ute Schepers
- **Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics (ITG), Karlsruhe, Germany
| | - Ulrike C Müller
- ‡‡Department of Functional Genomics, Institute for Pharmacy and Molecular Biotechnology, Heidelberg University Heidelberg, Germany
| | - Stefan Bräse
- **Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics (ITG), Karlsruhe, Germany
| | - Stephan A Müller
- From the ‡German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,§Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Stefan F Lichtenthaler
- From the ‡German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; .,§Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,¶Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,§§Institute for Advanced Study, Technische Universität München, Munich, Germany
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37
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Gonzalez AC, Schweizer M, Jagdmann S, Bernreuther C, Reinheckel T, Saftig P, Damme M. Unconventional Trafficking of Mammalian Phospholipase D3 to Lysosomes. Cell Rep 2018; 22:1040-1053. [PMID: 29386126 DOI: 10.1016/j.celrep.2017.12.100] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/10/2017] [Accepted: 12/26/2017] [Indexed: 01/08/2023] Open
Abstract
Variants in the phospholipase D3 (PLD3) gene have genetically been linked to late-onset Alzheimer's disease. We present a detailed biochemical analysis of PLD3 and reveal its endogenous localization in endosomes and lysosomes. PLD3 reaches lysosomes as a type II transmembrane protein via a (for mammalian cells) uncommon intracellular biosynthetic route that depends on the ESCRT (endosomal sorting complex required for transport) machinery. PLD3 is sorted into intraluminal vesicles of multivesicular endosomes, and ESCRT-dependent sorting correlates with ubiquitination. In multivesicular endosomes, PLD3 is subjected to proteolytic cleavage, yielding a stable glycosylated luminal polypeptide and a rapidly degraded N-terminal membrane-bound fragment. This pathway closely resembles the delivery route of carboxypeptidase S to the yeast vacuole. Our experiments reveal a biosynthetic route of PLD3 involving proteolytic processing and ESCRT-dependent sorting for its delivery to lysosomes in mammalian cells.
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Affiliation(s)
| | - Michaela Schweizer
- Center of Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Sebastian Jagdmann
- Biochemical Institute, Christian-Albrechts-University of Kiel, Kiel 24118, Germany
| | - Christian Bernreuther
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Medical Faculty, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Paul Saftig
- Biochemical Institute, Christian-Albrechts-University of Kiel, Kiel 24118, Germany
| | - Markus Damme
- Biochemical Institute, Christian-Albrechts-University of Kiel, Kiel 24118, Germany.
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38
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Sasaguri H, Nilsson P, Hashimoto S, Nagata K, Saito T, De Strooper B, Hardy J, Vassar R, Winblad B, Saido TC. APP mouse models for Alzheimer's disease preclinical studies. EMBO J 2017; 36:2473-2487. [PMID: 28768718 PMCID: PMC5579350 DOI: 10.15252/embj.201797397] [Citation(s) in RCA: 454] [Impact Index Per Article: 64.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/09/2017] [Accepted: 07/07/2017] [Indexed: 12/11/2022] Open
Abstract
Animal models of human diseases that accurately recapitulate clinical pathology are indispensable for understanding molecular mechanisms and advancing preclinical studies. The Alzheimer's disease (AD) research community has historically used first‐generation transgenic (Tg) mouse models that overexpress proteins linked to familial AD (FAD), mutant amyloid precursor protein (APP), or APP and presenilin (PS). These mice exhibit AD pathology, but the overexpression paradigm may cause additional phenotypes unrelated to AD. Second‐generation mouse models contain humanized sequences and clinical mutations in the endogenous mouse App gene. These mice show Aβ accumulation without phenotypes related to overexpression but are not yet a clinical recapitulation of human AD. In this review, we evaluate different APP mouse models of AD, and review recent studies using the second‐generation mice. We advise AD researchers to consider the comparative strengths and limitations of each model against the scientific and therapeutic goal of a prospective preclinical study.
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Affiliation(s)
- Hiroki Sasaguri
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan .,Department of Neurology and Neurological Science, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Per Nilsson
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan.,Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden
| | - Shoko Hashimoto
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan
| | - Kenichi Nagata
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan.,Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Bart De Strooper
- Dementia Research Institute, University College London, London, UK.,Department for Neurosciences, KU Leuven, Leuven, Belgium.,VIB Center for Brain and Disease Research, Leuven, Belgium
| | - John Hardy
- Reta Lila Research Laboratories and the Department of Molecular Neuroscience, University College London Institute of Neurology, London, UK
| | - Robert Vassar
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bengt Winblad
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan
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