1
|
Bretou M, Sannerud R, Escamilla-Ayala A, Leroy T, Vrancx C, Van Acker ZP, Perdok A, Vermeire W, Vorsters I, Van Keymolen S, Maxson M, Pavie B, Wierda K, Eskelinen EL, Annaert W. Accumulation of APP C-terminal fragments causes endolysosomal dysfunction through the dysregulation of late endosome to lysosome-ER contact sites. Dev Cell 2024; 59:1571-1592.e9. [PMID: 38626765 DOI: 10.1016/j.devcel.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/02/2023] [Accepted: 03/20/2024] [Indexed: 04/18/2024]
Abstract
Neuronal endosomal and lysosomal abnormalities are among the early changes observed in Alzheimer's disease (AD) before plaques appear. However, it is unclear whether distinct endolysosomal defects are temporally organized and how altered γ-secretase function or amyloid precursor protein (APP) metabolism contribute to these changes. Inhibiting γ-secretase chronically, in mouse embryonic fibroblast and hippocampal neurons, led to a gradual endolysosomal collapse initiated by decreased lysosomal calcium and increased cholesterol, causing downstream defects in endosomal recycling and maturation. This endolysosomal demise is γ-secretase dependent, requires membrane-tethered APP cytoplasmic domains, and is rescued by APP depletion. APP C-terminal fragments (CTFs) localized to late endosome/lysosome-endoplasmic reticulum contacts; an excess of APP-CTFs herein reduced lysosomal Ca2+ refilling from the endoplasmic reticulum, promoting cholesterol accretion. Tonic regulation by APP-CTFs provides a mechanistic explanation for their cellular toxicity: failure to timely degrade APP-CTFs sustains downstream signaling, instigating lysosomal dyshomeostasis, as observed in prodromal AD. This is the opposite of substrates such as Notch, which require intramembrane proteolysis to initiate signaling.
Collapse
Affiliation(s)
- Marine Bretou
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Ragna Sannerud
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | | | - Tom Leroy
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Céline Vrancx
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Zoë P Van Acker
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Anika Perdok
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Wendy Vermeire
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Inge Vorsters
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Sophie Van Keymolen
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Michelle Maxson
- Cell Biology Program, The Hospital for Sick Children, Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Benjamin Pavie
- VIB-BioImaging Core, VIB-Center for Brain and Disease Research, Leuven, Belgium
| | - Keimpe Wierda
- Electrophysiology Expertise Unit, VIB-Center for Brain and Disease Research, Leuven, Belgium
| | | | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium.
| |
Collapse
|
2
|
Fabiano M, Oikawa N, Kerksiek A, Furukawa JI, Yagi H, Kato K, Schweizer U, Annaert W, Kang J, Shen J, Lütjohann D, Walter J. Presenilin Deficiency Results in Cellular Cholesterol Accumulation by Impairment of Protein Glycosylation and NPC1 Function. Int J Mol Sci 2024; 25:5417. [PMID: 38791456 PMCID: PMC11121565 DOI: 10.3390/ijms25105417] [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: 04/11/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Presenilin proteins (PS1 and PS2) represent the catalytic subunit of γ-secretase and play a critical role in the generation of the amyloid β (Aβ) peptide and the pathogenesis of Alzheimer disease (AD). However, PS proteins also exert multiple functions beyond Aβ generation. In this study, we examine the individual roles of PS1 and PS2 in cellular cholesterol metabolism. Deletion of PS1 or PS2 in mouse models led to cholesterol accumulation in cerebral neurons. Cholesterol accumulation was also observed in the lysosomes of embryonic fibroblasts from Psen1-knockout (PS1-KO) and Psen2-KO (PS2-KO) mice and was associated with decreased expression of the Niemann-Pick type C1 (NPC1) protein involved in intracellular cholesterol transport in late endosomal/lysosomal compartments. Mass spectrometry and complementary biochemical analyses also revealed abnormal N-glycosylation of NPC1 and several other membrane proteins in PS1-KO and PS2-KO cells. Interestingly, pharmacological inhibition of N-glycosylation resulted in intracellular cholesterol accumulation prominently in lysosomes and decreased NPC1, thereby resembling the changes in PS1-KO and PS2-KO cells. In turn, treatment of PS1-KO and PS2-KO mouse embryonic fibroblasts (MEFs) with the chaperone inducer arimoclomol partially normalized NPC1 expression and rescued lysosomal cholesterol accumulation. Additionally, the intracellular cholesterol accumulation in PS1-KO and PS2-KO MEFs was prevented by overexpression of NPC1. Collectively, these data indicate that a loss of PS function results in impaired protein N-glycosylation, which eventually causes decreased expression of NPC1 and intracellular cholesterol accumulation. This mechanism could contribute to the neurodegeneration observed in PS KO mice and potentially to the pathogenesis of AD.
Collapse
Affiliation(s)
- Marietta Fabiano
- Department of Neurology, Universitätsklinikum Bonn, 53127 Bonn, Germany
- Institut für Biochemie und Molekularbiologie, Universitätsklinikum Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Naoto Oikawa
- Department of Neurology, Universitätsklinikum Bonn, 53127 Bonn, Germany
| | - Anja Kerksiek
- Institute of Clinical Chemistry and Clinical Pharmacology, Universitätsklinikum Bonn, 53127 Bonn, Germany
| | - Jun-ichi Furukawa
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
- Division of Glyco-Systems Biology, Institute for Glyco-Core Research, Tokai National Higher Education and Research System, Nagoya 466-8550, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
| | - Ulrich Schweizer
- Institut für Biochemie und Molekularbiologie, Universitätsklinikum Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, 3000 Leuven, Belgium
| | - Jongkyun Kang
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jie Shen
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Dieter Lütjohann
- Institute of Clinical Chemistry and Clinical Pharmacology, Universitätsklinikum Bonn, 53127 Bonn, Germany
| | - Jochen Walter
- Department of Neurology, Universitätsklinikum Bonn, 53127 Bonn, Germany
| |
Collapse
|
3
|
Mathekga BSP, Nxumalo Z, Thimiri Govinda Raj DB. Micro and nanofluidics for high throughput drug screening. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 187:93-120. [PMID: 35094783 DOI: 10.1016/bs.pmbts.2021.07.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this book chapter, we elaborate on the state-of-the-art technology developments in high throughput screening, microfluidics and nanofluidics. This book chapter further elaborated on the application of microfluidics and nanofluidics for high throughput drug screening with respect to communicable diseases and non-communicable diseases such as cancer. As a future perspective, there is tremendous potential for microfluidics and nanofluidics to be applied in high throughput drug screening which could be applied for various biotechnology applications such as in cancer precision medicine, point-of-care diagnostics and imaging. With the integration of Fourth industrial revolution (4IR) technologies with micro and nanofluidics technologies, it envisioned that such integration along with digital health would enable next generation technology development in medical field.
Collapse
Affiliation(s)
| | - Zandile Nxumalo
- Synthetic Nanobiotechnology and Biomachines Group, Synthetic Biology and Precision Medicine Centre, CSIR, Pretoria, South Africa
| | - Deepak B Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines Group, Synthetic Biology and Precision Medicine Centre, CSIR, Pretoria, South Africa.
| |
Collapse
|
4
|
Lipids in Pathophysiology and Development of the Membrane Lipid Therapy: New Bioactive Lipids. MEMBRANES 2021; 11:membranes11120919. [PMID: 34940418 PMCID: PMC8708953 DOI: 10.3390/membranes11120919] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/19/2022]
Abstract
Membranes are mainly composed of a lipid bilayer and proteins, constituting a checkpoint for the entry and passage of signals and other molecules. Their composition can be modulated by diet, pathophysiological processes, and nutritional/pharmaceutical interventions. In addition to their use as an energy source, lipids have important structural and functional roles, e.g., fatty acyl moieties in phospholipids have distinct impacts on human health depending on their saturation, carbon length, and isometry. These and other membrane lipids have quite specific effects on the lipid bilayer structure, which regulates the interaction with signaling proteins. Alterations to lipids have been associated with important diseases, and, consequently, normalization of these alterations or regulatory interventions that control membrane lipid composition have therapeutic potential. This approach, termed membrane lipid therapy or membrane lipid replacement, has emerged as a novel technology platform for nutraceutical interventions and drug discovery. Several clinical trials and therapeutic products have validated this technology based on the understanding of membrane structure and function. The present review analyzes the molecular basis of this innovative approach, describing how membrane lipid composition and structure affects protein-lipid interactions, cell signaling, disease, and therapy (e.g., fatigue and cardiovascular, neurodegenerative, tumor, infectious diseases).
Collapse
|
5
|
Wouters R, Michiels C, Sannerud R, Kleizen B, Dillen K, Vermeire W, Ayala AE, Demedts D, Schekman R, Annaert W. Assembly of γ-secretase occurs through stable dimers after exit from the endoplasmic reticulum. J Cell Biol 2021; 220:212501. [PMID: 34292306 PMCID: PMC8302450 DOI: 10.1083/jcb.201911104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/29/2020] [Accepted: 06/07/2021] [Indexed: 01/22/2023] Open
Abstract
γ-Secretase affects many physiological processes through targeting >100 substrates; malfunctioning links γ-secretase to cancer and Alzheimer’s disease. The spatiotemporal regulation of its stoichiometric assembly remains unresolved. Fractionation, biochemical assays, and imaging support prior formation of stable dimers in the ER, which, after ER exit, assemble into full complexes. In vitro ER budding shows that none of the subunits is required for the exit of others. However, knockout of any subunit leads to the accumulation of incomplete subcomplexes in COPII vesicles. Mutating a DPE motif in presenilin 1 (PSEN1) abrogates ER exit of PSEN1 and PEN-2 but not nicastrin. We explain this by the preferential sorting of PSEN1 and nicastrin through Sec24A and Sec24C/D, respectively, arguing against full assembly before ER exit. Thus, dimeric subcomplexes aided by Sec24 paralog selectivity support a stepwise assembly of γ-secretase, controlling final levels in post-Golgi compartments.
Collapse
Affiliation(s)
- Rosanne Wouters
- Laboratory for Membrane Trafficking, Vlaams Instituut voor Biotechnologie Center for Brain and Disease Research, Katholieke Universiteit Leuven, Leuven, Belgium.,Department of Neurosciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Christine Michiels
- Laboratory for Membrane Trafficking, Vlaams Instituut voor Biotechnologie Center for Brain and Disease Research, Katholieke Universiteit Leuven, Leuven, Belgium.,Department of Neurosciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Ragna Sannerud
- Laboratory for Membrane Trafficking, Vlaams Instituut voor Biotechnologie Center for Brain and Disease Research, Katholieke Universiteit Leuven, Leuven, Belgium.,Department of Neurosciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Bertrand Kleizen
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Katleen Dillen
- Laboratory for Membrane Trafficking, Vlaams Instituut voor Biotechnologie Center for Brain and Disease Research, Katholieke Universiteit Leuven, Leuven, Belgium.,Department of Neurosciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Wendy Vermeire
- Laboratory for Membrane Trafficking, Vlaams Instituut voor Biotechnologie Center for Brain and Disease Research, Katholieke Universiteit Leuven, Leuven, Belgium.,Department of Neurosciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Abril Escamilla Ayala
- Vlaams Instituut voor Biotechnologie BioImaging Core, Vlaams Instituut voor Biotechnologie Center for Brain and Disease Research, Leuven, Belgium
| | - David Demedts
- Laboratory for Membrane Trafficking, Vlaams Instituut voor Biotechnologie Center for Brain and Disease Research, Katholieke Universiteit Leuven, Leuven, Belgium.,Department of Neurosciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Randy Schekman
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA
| | - Wim Annaert
- Laboratory for Membrane Trafficking, Vlaams Instituut voor Biotechnologie Center for Brain and Disease Research, Katholieke Universiteit Leuven, Leuven, Belgium.,Department of Neurosciences, Katholieke Universiteit Leuven, Leuven, Belgium
| |
Collapse
|
6
|
Grobler L, Suleman E, Thimiri Govinda Raj DB. Patents and technology transfer in CRISPR technology. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:153-182. [PMID: 33934836 DOI: 10.1016/bs.pmbts.2021.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CRISPR technology has revolutionized biological research in the last decade and many academic institutions and companies have patented CRISPR systems and applications. Several patents have been filed for various applications of CRISPR in different industries such as agriculture, synthetic biology, bio-nanotechnology and precision medicine. Despite tremendous pressure on the technology transfer teams, several startups and spin-out companies are already using CRISPR technologies for commercial applications. In this chapter, we discuss the different CRISPR nucleases and their applications. Secondly, we detail our current opinion and perspective on the CRISPR patent and technology landscape for non-mammalian systems. We present two case-studies on CRISPR diagnostics companies, SHERLOCK and Mammoth Biosciences, who are currently at the forefront of establishing diagnostics platforms for coronavirus (SARS-CoV-2) detection. Finally, our chapter identifies future advancements and possible challenges that CRISPR technology might face in non-mammalian systems.
Collapse
Affiliation(s)
- Lichelle Grobler
- Synthetic Nanobiotechnology and Biomachines Group, ERA Synthetic Biology, Centre for Synthetic Biology and Precision Medicine, CSIR, Pretoria, South Africa
| | - Essa Suleman
- Veterinary Molecular Diagnostics and Vaccines, Medical Devices and Diagnostics Impact Area, CSIR, Pretoria, South Africa
| | - Deepak B Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines Group, ERA Synthetic Biology, Centre for Synthetic Biology and Precision Medicine, CSIR, Pretoria, South Africa.
| |
Collapse
|
7
|
Nweke EE, Thimiri Govinda Raj DB. Development of insect cell line using CRISPR technology. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:1-20. [PMID: 33934833 DOI: 10.1016/bs.pmbts.2021.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this chapter, we delineated the methods of CRISPR technology that has been used for the development of engineered insect cell line. We elaborated on how CRISPR/Cas9 genome editing in Drosophila melanogaster, Bombyx mori, Spodoptera frugiperda (Sf9 and Sf21), and Mosquitoes enabled the use of model or non-model insect system in various biological and medical applications. Also, the application of synthetic baculovirus genome along with CRISPR/Cas9 vector system to enable genome editing of insect cell systems for treatment of communicable and non-communicable diseases.
Collapse
Affiliation(s)
| | - Deepak B Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines Group, ERA Synthetic Biology, Centre for Synthetic Biology and Precision Medicine, CSIR, Pretoria, South Africa.
| |
Collapse
|
8
|
Nxumalo Z, Takundwa MM, Thimiri Govinda Raj DB. Patents, ethics, biosafety and regulation using CRISPR technology. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:345-365. [PMID: 34127200 DOI: 10.1016/bs.pmbts.2021.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this review chapter, we provide full comprehensive analysis on the patent, ethics and biosafety regulation with respect to the application of CRISPR technology in mammalian systems. We focused on recent development in CRISPR technology and its patent landscape between countries such as US, European Union, China and Australia. Further, we emphasized on the current scenarios on the ethics regulations with respect to CRISPR research, its applicability in patent and technology transfer. Finally, we elaborated on the biosafety regulation on CRISPR/Cas9 technology application in both mammalian and non-mammalian host system.
Collapse
Affiliation(s)
- Zandile Nxumalo
- Synthetic Nanobiotechnology and Biomachines Group, Centre for Synthetic Biology and Precision Medicine, CSIR, Pretoria, South Africa
| | - Mutsa M Takundwa
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Deepak B Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines Group, Centre for Synthetic Biology and Precision Medicine, CSIR, Pretoria, South Africa.
| |
Collapse
|
9
|
Yagi R, Masuda T, Ogata S, Mori A, Ito S, Ohtsuki S. Proteomic Evaluation of Plasma Membrane Fraction Prepared from a Mouse Liver and Kidney Using a Bead Homogenizer: Enrichment of Drug-Related Transporter Proteins. Mol Pharm 2020; 17:4101-4113. [PMID: 32902293 DOI: 10.1021/acs.molpharmaceut.0c00547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Quantifying the protein levels of drug transporters in plasma membrane fraction helps elucidate the function of these transporters. In this study, we conducted a proteomic evaluation of enriched drug-related transporter proteins in plasma membrane fraction prepared from mouse liver and kidney tissues using the membrane protein extraction kit and a bead homogenizer. Crude and plasma membrane fractions were prepared using either the Dounce or bead homogenizer, and protein levels were determined using quantitative proteomics. In liver tissues, the plasma membrane fractions were more enriched in transporter proteins than the crude membrane fractions; the average enrichment ratios of plasma-to-crude membrane fractions were 3.31 and 6.93 using the Dounce and bead homogenizers, respectively. The concentrations of transporter proteins in plasma membrane fractions determined using the bead homogenizer were higher than those determined using the Dounce homogenizer. Meanwhile, in kidney tissues, the plasma membrane fractions were enriched in transporters localized in the brush-border membrane to the same degree for both the homogenizers; however, the membrane fractions obtained using either homogenizer were not enriched in Na+/K+-ATPase and transporters localized in the basolateral membrane. These results indicate that fractionation, using the bead homogenizer, yielded transporter-enriched plasma membrane fractions from mouse liver and kidney tissues; however, no enrichment of basolateral transporters was observed in plasma membrane fractions prepared from kidney tissues.
Collapse
Affiliation(s)
- Ryotaro Yagi
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Seiryo Ogata
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Ayano Mori
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Shingo Ito
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| |
Collapse
|
10
|
Thimiri Govinda Raj DB, Khan NA, Venkatachalam S, Arumugam S. Efficient Nanobiotechnology Method for Magnetic Lysosome Enrichment Using DMSA-SPMNP 2.0. BIONANOSCIENCE 2020. [DOI: 10.1007/s12668-020-00736-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
11
|
Thimiri Govinda Raj DB, Khan NA, Venkatachalam S, Chu DT, Arumugam S. Step-by-Step Protocol for Superparamagnetic Nanoparticle-Based Endosome and Lysosome Isolation from Eukaryotic Cell. Methods Mol Biol 2020; 2125:167-172. [PMID: 30771190 DOI: 10.1007/7651_2019_212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Here, we report our step-by-step protocol for superparamagnetic nanoparticle (SPMNP)-based endosome and lysosome isolation from HeLa. Briefly, we synthesized SPMNP 1.0 with iron oxide (Fe3O4) core using thermal decomposition method. Further, we performed ligand-exchange strategy for surface functionalization of SPMNP 1.0 with dimercaptosuccinic acid (DMSA). Thus, we generated DMSA-SPMNP 2.0 and used DMSA-SPMNP 2.0 to isolate endosomes and lysosome from HeLa cells. Using our SPMNP subcellular fractionation protocol, we are able to isolate high-pure-high-yield lysosomes using DMSA-SPMNP 2.0 for lysosome proteomics and lipidomics in order to better understand subcellular compartments.
Collapse
Affiliation(s)
- Deepak B Thimiri Govinda Raj
- Envirotransgene® Bio-solutions Global Chennai India and Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.
| | | | | | - Dinh Toi Chu
- Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam
- Institute for Research and Development, Duy Tan University, Danang, Vietnam
- School of Odonto Stomatology, Hanoi Medical University, Hanoi, Vietnam
| | - Sivakumar Arumugam
- School of Bio Sciences and Technology (SBST), VIT University, Vellore, TN, India
| |
Collapse
|
12
|
Thimiri Govinda Raj DB, Khan NA, Venkatachalam S, Arumugam S, Palaniswamy S. Synthesis of Hybrid Gold Nanoparticle (AuNP) Functionalized Superparamagnetic Nanoparticles (SPMNPs) for Efficient Coupling of Biomolecules. Methods Mol Biol 2020; 2125:73-75. [PMID: 31463891 DOI: 10.1007/7651_2019_254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recently, we reported our methodology for isolating plasma membrane and lysosome from eukaryotic cell using superparamagnetic nanoparticles (SPMNPs). Here in this article, we report a step-by-step protocol for synthesis of hybrid gold nanoparticle (AuNP), surface functionalization of AuNPs on superparamagnetic nanoparticles (SPMNPs), and potential use of hybrid AuNP-SPMNP for efficient coupling of biomolecules.
Collapse
Affiliation(s)
| | - Niamat Ali Khan
- Envirotransgene® Bio-solutions Global, Chennai, India
- DTCG®, Chennai, India
| | | | - Sivakumar Arumugam
- School of Bio Sciences and Technology (SBST), VIT University, Vellore, Tamil Nadu, India
| | - Selvamani Palaniswamy
- Department of Pharmaceutical Technology, Anna University, Tiruchirappalli, Tamil Nadu, India
| |
Collapse
|
13
|
Thimiri Govinda Raj DB, Khan NA, Venkatachalam S, Chu DT. Step-by-Step Protocol for Superparamagnetic Nanoparticle-Based Plasma Membrane Isolation from Eukaryotic Cell. Methods Mol Biol 2020; 2125:173-179. [PMID: 30771189 DOI: 10.1007/7651_2019_211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Here, we elaborate our detailed protocol for synthesis, functionalization, and application of superparamagnetic nanoparticle (SPMNP) for plasma membrane and lysosome isolation. We used standard thermal decomposition-based synthesis of iron oxide (Fe3O4) core SPMNP 1.0. Using ligand addition methodology, we surface functionalized SPMNP 1.0 with phospholipids and generated phospholipid-SPMNP 2.0. Further we used NH2-phospholipid-SPMNP 2.0 to isolate plasma membrane. Using our SPMNP subcellular fractionation protocol, we are able to isolate high-pure-high-yield plasma membrane using NH2-phospholipid-SPMNP 2.0. As a future perspective, we propose to use SPMNP on clinical patient samples and perform mass spectrometry-based proteomics, lipidomics, and glycomics for early cancer diagnosis.
Collapse
Affiliation(s)
- Deepak B Thimiri Govinda Raj
- Envirotransgene® Bio-solutions Global Chennai India and Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.
| | | | | | - Dinh Toi Chu
- Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam
- Institute for Research and Development, Duy Tan University, Danang, Vietnam
- School of Odonto Stomatology, Hanoi Medical University, Hanoi, Vietnam
| |
Collapse
|
14
|
Li Y, Qin H, Ye M. An overview on enrichment methods for cell surface proteome profiling. J Sep Sci 2019; 43:292-312. [PMID: 31521063 DOI: 10.1002/jssc.201900700] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022]
Abstract
Cell surface proteins are essential for many important biological processes, including cell-cell interactions, signal transduction, and molecular transportation. With the characteristics of low abundance, high hydrophobicity, and high heterogeneity, it is difficult to get a comprehensive view of cell surface proteome by direct analysis. Thus, it is important to selectively enrich the cell surface proteins before liquid chromatography with mass spectrometry analysis. In recent years, a variety of enrichment methods have been developed. Based on the separation mechanism, these methods could be mainly classified into three types. The first type is based on their difference in the physicochemical property, such as size, density, charge, and hydrophobicity. The second one is based on the bimolecular affinity interaction with lectin or antibody. And the third type is based on the chemical covalent coupling to free side groups of surface-exposed proteins or carbohydrate chains, such as primary amines, carboxyl groups, glycan side chains. In addition, metabolic labeling and enzymatic reaction-based methods have also been employed to selectively isolate cell surface proteins. In this review, we will provide a comprehensive overview of the enrichment methods for cell surface proteome profiling.
Collapse
Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
| |
Collapse
|
15
|
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: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
Collapse
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.
| |
Collapse
|
16
|
Wu Y, Wu S, Ma S, Yan F, Weng Z. Cytocompatible Modification of Thermoresponsive Polymers on Living Cells for Membrane Proteomic Isolation and Analysis. Anal Chem 2019; 91:3187-3194. [DOI: 10.1021/acs.analchem.8b04201] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yuanzi Wu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350002, China
| | - Shuigen Wu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350002, China
| | - Shanyun Ma
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350002, China
| | - Fen Yan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350002, China
| | - Zuquan Weng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350002, China
| |
Collapse
|
17
|
Magnetic capture of polydopamine-encapsulated Hela cells for the analysis of cell surface proteins. J Proteomics 2018; 172:76-81. [DOI: 10.1016/j.jprot.2017.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/25/2017] [Accepted: 10/12/2017] [Indexed: 12/16/2022]
|
18
|
Wang C, Shou Y, Pan J, Du Y, Liu C, Wang H. The relationship between cholesterol level and Alzheimer’s disease-associated APP proteolysis/Aβ metabolism. Nutr Neurosci 2018; 22:453-463. [DOI: 10.1080/1028415x.2017.1416942] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Chaoqun Wang
- School of Medicine, Hangzhou Normal University, Hangzhou, People’s Republic of China
| | - Yikai Shou
- School of Medicine, Hangzhou Normal University, Hangzhou, People’s Republic of China
| | - Jie Pan
- Department of Endocrinology and Metabolism, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
- Institute of Gastroenterology, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yue Du
- School of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Cuiqing Liu
- College of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Huanhuan Wang
- School of Medicine, Hangzhou Normal University, Hangzhou, People’s Republic of China
| |
Collapse
|
19
|
Thimiri Govinda Raj DB, Khan NA. Surface functionalization dependent subcellular localization of Superparamagnetic nanoparticle in plasma membrane and endosome. NANO CONVERGENCE 2018; 5:4. [PMID: 29492374 PMCID: PMC5813047 DOI: 10.1186/s40580-018-0136-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/31/2018] [Indexed: 05/22/2023]
Abstract
In this article, we elaborate the application of thermal decomposition based synthesis of Fe3O4 superparamagnetic nanoparticle (SPMNP) in subcellular fractionation context. Here, we performed surface functionalization of SPMNP with phospholipids and dimercaptosuccinic acid. Surprisingly, we observed surface functionalization dependent SPMNP localization in subcellular compartments such as plasma membrane, endosomes and lysosomes. By using SPMNP based subcellular localization with pulse-chase methodology, we could use SPMNP for high pure-high yield organelle (plasma membrane, endosomes and lysosome) fractionation. Further, SPMNP that are distinctly localized in subcellular compartments can be used as technology for subcellular fractionation that can complement existing tools for cell biology research. As a future perspective, isolated magnetic organelles can be extended to protein/protein complex purification for biochemical and structural biology studies.
Collapse
Affiliation(s)
- Deepak B. Thimiri Govinda Raj
- Envirotransgene® Bio-solutions Global Chennai, Tamil Nadu, India
- Biotechnology Centre for Oslo, Centre for Molecular Medicine Norway (NCMM), Blindern, P.O. Box 1137, 0318 Oslo, Norway
| | - Niamat Ali Khan
- Laboratory of Lipid Metabolism and Cancer, O&N I, Herestraat 49, Box 902, 3000 Louvain, Belgium
| |
Collapse
|
20
|
Tharkeshwar AK, Gevaert K, Annaert W. Organellar Omics-A Reviving Strategy to Untangle the Biomolecular Complexity of the Cell. Proteomics 2017; 18:e1700113. [PMID: 29125683 DOI: 10.1002/pmic.201700113] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022]
Abstract
A eukaryotic cell encompasses many membrane-enclosed organelles, each of these holding several types of biomolecules that exhibit tremendous diversity in terms of their localization and expression. Despite the development of increasingly sensitive analytical tools, the enormous biomolecular complexity that exists within a cell cannot yet be fully resolved as low abundant molecules often remain unrecognized. Moreover, a drawback of whole cell analysis is that it does not provide spatial information and therefore it is not capable of assigning distinct biomolecules to specific compartments or analyzing changes in the composition of these compartments. Reduction of the biomolecular complexity of a sample helps to identify low abundant molecules, but such a reductionist approach requires methods that enable proper isolation and purification of individual cellular organelles. Decades of research have led to the development of a plethora of isolation methods for a broad range of subcellular organelles; yet, in particular, intrinsically dynamic compartments belonging to the endocytic machinery, including the plasma membrane, remain difficult to isolate in a sufficiently pure fraction. In this review, we discuss various methods that are commonly used to isolate subcellular organelles from cells and evaluate their advantages and disadvantages.
Collapse
Affiliation(s)
- Arun Kumar Tharkeshwar
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Laboratory for Membrane Trafficking, Department of Neurosciences, KU Leuven, Leuven, Belgium.,Department of Cell Biology, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry, Ghent University, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Laboratory for Membrane Trafficking, Department of Neurosciences, KU Leuven, Leuven, Belgium
| |
Collapse
|
21
|
Escribá PV. Membrane-lipid therapy: A historical perspective of membrane-targeted therapies - From lipid bilayer structure to the pathophysiological regulation of cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1493-1506. [PMID: 28577973 DOI: 10.1016/j.bbamem.2017.05.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Our current understanding of membrane lipid composition, structure and functions has led to the investigation of their role in cell signaling, both in healthy and pathological cells. As a consequence, therapies based on the regulation of membrane lipid composition and structure have been recently developed. This novel field, known as Membrane Lipid Therapy, is growing and evolving rapidly, providing treatments that are now in use or that are being studied for their application to oncological disorders, Alzheimer's disease, spinal cord injury, stroke, diabetes, obesity, and neuropathic pain. This field has arisen from relevant discoveries on the behavior of membranes in recent decades, and it paves the way to adopt new approaches in modern pharmacology and nutrition. This innovative area will promote further investigation into membranes and the development of new therapies with molecules that target the cell membrane. Due to the prominent roles of membranes in the cells' physiology and the paucity of therapeutic approaches based on the regulation of the lipids they contain, it is expected that membrane lipid therapy will provide new treatments for numerous pathologies. The first on-purpose rationally designed molecule in this field, minerval, is currently being tested in clinical trials and it is expected to enter the market around 2020. However, it seems feasible that during the next few decades other membrane regulators will also be marketed for the treatment of human pathologies. This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá.
Collapse
Affiliation(s)
- Pablo V Escribá
- Department of Biology, University of the Balearic Islands, E-07122 Palma de Mallorca, Spain.
| |
Collapse
|
22
|
Abstract
The organization of eukaryotic cells into distinct subcompartments is vital for all functional processes, and aberrant protein localization is a hallmark of many diseases. Microscopy methods, although powerful, are usually low-throughput and dependent on the availability of fluorescent fusion proteins or highly specific and sensitive antibodies. One method that provides a global picture of the cell is localization of organelle proteins by isotope tagging (LOPIT), which combines biochemical cell fractionation using density gradient ultracentrifugation with multiplexed quantitative proteomics mass spectrometry, allowing simultaneous determination of the steady-state distribution of hundreds of proteins within organelles. Proteins are assigned to organelles based on the similarity of their gradient distribution to those of well-annotated organelle marker proteins. We have substantially re-developed our original LOPIT protocol (published by Nature Protocols in 2006) to enable the subcellular localization of thousands of proteins per experiment (hyperLOPIT), including spatial resolution at the suborganelle and large protein complex level. This Protocol Extension article integrates all elements of the hyperLOPIT pipeline, including an additional enrichment strategy for chromatin, extended multiplexing capacity of isobaric mass tags, state-of-the-art mass spectrometry methods and multivariate machine-learning approaches for analysis of spatial proteomics data. We have also created an open-source infrastructure to support analysis of quantitative mass-spectrometry-based spatial proteomics data (http://bioconductor.org/packages/pRoloc) and an accompanying interactive visualization framework (http://www. bioconductor.org/packages/pRolocGUI). The procedure we outline here is applicable to any cell culture system and requires ∼1 week to complete sample preparation steps, ∼2 d for mass spectrometry data acquisition and 1-2 d for data analysis and downstream informatics.
Collapse
|
23
|
Escribá PV. WITHDRAWN: Membrane-lipid therapy: A historical perspective of membrane-targeted therapies-From lipid bilayer structure to the pathophysiological regulation of cells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2017:S0005-2736(17)30139-6. [PMID: 28476630 DOI: 10.1016/j.bbamem.2017.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/23/2017] [Accepted: 04/25/2017] [Indexed: 11/19/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.bbamem.2017.05.017. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
Collapse
Affiliation(s)
- Pablo V Escribá
- Department of Biology, University of the Balearic Islands, E-07122 Palma de Mallorca, Spain.
| |
Collapse
|
24
|
A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics: the case of NPC1 deficiency. Sci Rep 2017; 7:41408. [PMID: 28134274 PMCID: PMC5278418 DOI: 10.1038/srep41408] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023] Open
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) have mainly been used as cellular carriers for genes and therapeutic products, while their use in subcellular organelle isolation remains underexploited. We engineered SPIONs targeting distinct subcellular compartments. Dimercaptosuccinic acid-coated SPIONs are internalized and accumulate in late endosomes/lysosomes, while aminolipid-SPIONs reside at the plasma membrane. These features allowed us to establish standardized magnetic isolation procedures for these membrane compartments with a yield and purity permitting proteomic and lipidomic profiling. We validated our approach by comparing the biomolecular compositions of lysosomes and plasma membranes isolated from wild-type and Niemann-Pick disease type C1 (NPC1) deficient cells. While the accumulation of cholesterol and glycosphingolipids is seen as a primary hallmark of NPC1 deficiency, our lipidomics analysis revealed the buildup of several species of glycerophospholipids and other storage lipids in selectively late endosomes/lysosomes of NPC1-KO cells. While the plasma membrane proteome remained largely invariable, we observed pronounced alterations in several proteins linked to autophagy and lysosomal catabolism reflecting vesicular transport obstruction and defective lysosomal turnover resulting from NPC1 deficiency. Thus the use of SPIONs provides a major advancement in fingerprinting subcellular compartments, with an increased potential to identify disease-related alterations in their biomolecular compositions.
Collapse
|
25
|
Lloyd-Evans E, Haslett LJ. The lysosomal storage disease continuum with ageing-related neurodegenerative disease. Ageing Res Rev 2016; 32:104-121. [PMID: 27516378 DOI: 10.1016/j.arr.2016.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 07/19/2016] [Accepted: 07/29/2016] [Indexed: 12/11/2022]
Abstract
Lysosomal storage diseases and diseases of ageing share many features both at the physiological level and with respect to the mechanisms that underlie disease pathogenesis. Although the exact pathophysiology is not exactly the same, it is astounding how many similar pathways are altered in all of these diseases. The aim of this review is to provide a summary of the shared disease mechanisms, outlining the similarities and differences and how genetics, insight into rare diseases and functional research has changed our perspective on the causes underlying common diseases of ageing. The lysosome should no longer be considered as just the stomach of the cell or as a suicide bag, it has an emerging role in cellular signalling, nutrient sensing and recycling. The lysosome is of fundamental importance in the pathophysiology of diseases of ageing and by comparing against the LSDs we not only identify common pathways but also therapeutic targets so that ultimately more effective treatments can be developed for all neurodegenerative diseases.
Collapse
|
26
|
Dooley J, Tian L, Schonefeldt S, Delghingaro-Augusto V, Garcia-Perez JE, Pasciuto E, Di Marino D, Carr EJ, Oskolkov N, Lyssenko V, Franckaert D, Lagou V, Overbergh L, Vandenbussche J, Allemeersch J, Chabot-Roy G, Dahlstrom JE, Laybutt DR, Petrovsky N, Socha L, Gevaert K, Jetten AM, Lambrechts D, Linterman MA, Goodnow CC, Nolan CJ, Lesage S, Schlenner SM, Liston A. Genetic predisposition for beta cell fragility underlies type 1 and type 2 diabetes. Nat Genet 2016; 48:519-27. [PMID: 26998692 DOI: 10.1038/ng.3531] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/26/2016] [Indexed: 12/12/2022]
Abstract
Type 1 (T1D) and type 2 (T2D) diabetes share pathophysiological characteristics, yet mechanistic links have remained elusive. T1D results from autoimmune destruction of pancreatic beta cells, whereas beta cell failure in T2D is delayed and progressive. Here we find a new genetic component of diabetes susceptibility in T1D non-obese diabetic (NOD) mice, identifying immune-independent beta cell fragility. Genetic variation in Xrcc4 and Glis3 alters the response of NOD beta cells to unfolded protein stress, enhancing the apoptotic and senescent fates. The same transcriptional relationships were observed in human islets, demonstrating the role of beta cell fragility in genetic predisposition to diabetes.
Collapse
Affiliation(s)
- James Dooley
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Lei Tian
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Susann Schonefeldt
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | | | - Josselyn E Garcia-Perez
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Emanuela Pasciuto
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Daniele Di Marino
- Department of Informatics, Università della Svizzera Italiana, Lugano, Switzerland
| | - Edward J Carr
- Lymphocyte Signaling and Development Institute Strategic Programme, Babraham Institute, Cambridge, UK
| | - Nikolay Oskolkov
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden.,Department of Translational Pathophysiology, Steno Diabetes Center, Gentofte, Denmark
| | - Dean Franckaert
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Vasiliki Lagou
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium.,Department of Neurosciences, University of Leuven, Leuven, Belgium
| | - Lut Overbergh
- Department of Clinical and Experimental Medicine, University of Leuven, Leuven, Belgium
| | - Jonathan Vandenbussche
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | | | - Genevieve Chabot-Roy
- Immunology-Oncology Section, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Jane E Dahlstrom
- Australian National University Medical School, Canberra, Australian Capital Territory, Australia.,Department of Anatomical Pathology, Canberra Hospital, Garran, Australian Capital Territory, Australia
| | - D Ross Laybutt
- Garvan Institute of Medical Research, University of New South Wales, Sydney, New South Wales, Australia
| | - Nikolai Petrovsky
- Department of Endocrinology, Flinders University, Adelaide, South Australia, Australia
| | - Luis Socha
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Anton M Jetten
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium.,Department of Oncology, University of Leuven, Leuven, Belgium
| | - Michelle A Linterman
- Lymphocyte Signaling and Development Institute Strategic Programme, Babraham Institute, Cambridge, UK
| | - Chris C Goodnow
- Garvan Institute of Medical Research, University of New South Wales, Sydney, New South Wales, Australia
| | - Christopher J Nolan
- Australian National University Medical School, Canberra, Australian Capital Territory, Australia.,Department of Endocrinology, Canberra Hospital, Garran, Australian Capital Territory, Australia
| | - Sylvie Lesage
- Immunology-Oncology Section, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Susan M Schlenner
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Adrian Liston
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| |
Collapse
|
27
|
Laudanski P, Charkiewicz K, Kisielewski R, Kuc P, Koc-Zorawska E, Raba G, Kraczkowski J, Dymicka-Piekarska V, Chabowski A, Kacerovsky M, Jacobsson B, Zabielski P, Blachnio-Zabielska A. Plasma C16-Cer levels are increased in patients with preterm labor. Prostaglandins Other Lipid Mediat 2016; 123:40-5. [DOI: 10.1016/j.prostaglandins.2016.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/21/2016] [Accepted: 04/28/2016] [Indexed: 01/14/2023]
|
28
|
Thimiri Govinda Raj DB, Khan NA. Designer nanoparticle: nanobiotechnology tool for cell biology. NANO CONVERGENCE 2016; 3:22. [PMID: 28191432 PMCID: PMC5271163 DOI: 10.1186/s40580-016-0082-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/29/2016] [Indexed: 05/17/2023]
Abstract
This article discusses the use of nanotechnology for subcellular compartment isolation and its application towards subcellular omics. This technology review significantly contributes to our understanding on use of nanotechnology for subcellular systems biology. Here we elaborate nanobiotechnology approach of using superparamagnetic nanoparticles (SPMNPs) optimized with different surface coatings for subcellular organelle isolation. Using pulse-chase approach, we review that SPMNPs interacted differently with the cell depending on its surface functionalization. The article focuses on the use of functionalized-SPMNPs as a nanobiotechnology tool to isolate high quality (both purity and yield) plasma membranes and endosomes or lysosomes. Such nanobiotechnology tool can be applied in generating subcellular compartment inventories. As a future perspective, this strategy could be applied in areas such as immunology, cancer and stem cell research.
Collapse
Affiliation(s)
- Deepak B. Thimiri Govinda Raj
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation and Unit of Virus Host-Cell Interactions (UVHCI), UJF-EMBL-CNRS, UMR 5233 Grenoble, France
- Envirotransgene Bio-solutions Global, Chennai, India
- Biotechnology Centre for Oslo, Centre for Molecular Medicine Norway (NCMM), P.O. Box 1137, Blindern, 0318 Oslo, Norway
| | - Niamat Ali Khan
- Laboratory of Lipid Metabolism and Cancer, O&N I, Herestraat 49, Box 902, 3000 Louvain, Belgium
| |
Collapse
|
29
|
Early etiology of Alzheimer's disease: tipping the balance toward autophagy or endosomal dysfunction? Acta Neuropathol 2015; 129:363-81. [PMID: 25556159 PMCID: PMC4331606 DOI: 10.1007/s00401-014-1379-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/18/2014] [Accepted: 12/20/2014] [Indexed: 12/11/2022]
Abstract
Alzheimer’s disease (AD) is the most common form of dementia in the elderly. This brain neuropathology is characterized by a progressive synaptic dysfunction and neuronal loss, which lead to decline in memory and other cognitive functions. Histopathologically, AD manifests via synaptic abnormalities, neuronal degeneration as well as the deposition of extracellular amyloid plaques and intraneuronal neurofibrillary tangles. While the exact pathogenic contribution of these two AD hallmarks and their abundant constituents [aggregation-prone amyloid β (Aβ) peptide species and hyperphosphorylated tau protein, respectively] remain debated, a growing body of evidence suggests that their development may be paralleled or even preceded by the alterations/dysfunctions in the endolysosomal and the autophagic system. In AD-affected neurons, abnormalities in these cellular pathways are readily observed already at early stages of disease development, and even though many studies agree that defective lysosomal degradation may relate to or even underlie some of these deficits, specific upstream molecular defects are still deliberated. In this review we summarize various pathogenic events that may lead to these cellular abnormalities, in light of our current understanding of molecular mechanisms that govern AD progression. In addition, we also highlight the increasing evidence supporting mutual functional dependence of the endolysosomal trafficking and autophagy, in particular focusing on those molecules and processes which may be of significance to AD.
Collapse
|
30
|
Han D, Moon S, Kim Y, Min H, Kim Y. Characterization of the membrane proteome and N-glycoproteome in BV-2 mouse microglia by liquid chromatography-tandem mass spectrometry. BMC Genomics 2014; 15:95. [PMID: 24495382 PMCID: PMC3938046 DOI: 10.1186/1471-2164-15-95] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 02/03/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Microglial cells are resident macrophages of the central nervous system and important cellular mediators of the immune response and neuroinflammatory processes. In particular, microglial activation and communication between microglia, astrocytes, and neurons are hallmarks of the pathogenesis of several neurodegenerative diseases. Membrane proteins and their N-linked glycosylation mediate this microglial activation and regulate many biological process including signal transduction, cell-cell communication, and the immune response. Although membrane proteins and N-glycosylation represent a valuable source of drug target and biomarker discovery, the knowledge of their expressed proteome in microglia is very limited. RESULTS To generate a large-scale repository, we constructed a membrane proteome and N-glycoproteome from BV-2 mouse microglia using a novel integrated approach, comprising of crude membrane fractionation, multienzyme-digestion FASP, N-glyco-FASP, and various mass spectrometry. We identified 6928 proteins including 2850 membrane proteins and 1450 distinct N-glycosylation sites on 760 N-glycoproteins, of which 556 were considered novel N-glycosylation sites. Especially, a total of 114 CD antigens are identified via MS-based analysis in normal conditions of microglia for the first time. Our bioinformatics analysis provides a rich proteomic resource for examining microglial function in, for example, cell-to-cell communication and immune responses. CONCLUSIONS Herein, we introduce a novel integrated proteomic approach for improved identification of membrane protein and N-glycosylation sites. To our knowledge, this workflow helped us to obtain the first and the largest membrane proteomic and N-glycoproteomic datesets for mouse microglia. Collectively, our proteomics and bioinformatics analysis significantly expands the knowledge of the membrane proteome and N-glycoproteome expressed in microglia within the brain and constitutes a foundation for ongoing proteomic studies and drug development for various neurological diseases.
Collapse
Affiliation(s)
| | | | | | | | - Youngsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, 28 Yongon-Dong, Seoul 110-799, Korea.
| |
Collapse
|
31
|
Klose C, Surma MA, Simons K. Organellar lipidomics—background and perspectives. Curr Opin Cell Biol 2013; 25:406-13. [DOI: 10.1016/j.ceb.2013.03.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/21/2013] [Indexed: 11/27/2022]
|
32
|
Coen K, Flannagan RS, Baron S, Carraro-Lacroix LR, Wang D, Vermeire W, Michiels C, Munck S, Baert V, Sugita S, Wuytack F, Hiesinger PR, Grinstein S, Annaert W. Lysosomal calcium homeostasis defects, not proton pump defects, cause endo-lysosomal dysfunction in PSEN-deficient cells. ACTA ACUST UNITED AC 2012; 198:23-35. [PMID: 22753898 PMCID: PMC3392942 DOI: 10.1083/jcb.201201076] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Presenilin (PSEN) deficiency is accompanied by accumulation of endosomes and autophagosomes, likely caused by impaired endo-lysosomal fusion. Recently, Lee et al. (2010. Cell. doi: http://dx.doi.org/10.1016/j.cell.2010.05.008) attributed this phenomenon to PSEN1 enabling the transport of mature V0a1 subunits of the vacuolar ATPase (V-ATPase) to lysosomes. In their view, PSEN1 mediates the N-glycosylation of V0a1 in the endoplasmic reticulum (ER); consequently, PSEN deficiency prevents V0a1 glycosylation, compromising the delivery of unglycosylated V0a1 to lysosomes, ultimately impairing V-ATPase function and lysosomal acidification. We show here that N-glycosylation is not a prerequisite for proper targeting and function of this V-ATPase subunit both in vitro and in vivo in Drosophila melanogaster. We conclude that endo-lysosomal dysfunction in PSEN(-/-) cells is not a consequence of failed N-glycosylation of V0a1, or compromised lysosomal acidification. Instead, lysosomal calcium storage/release is significantly altered in PSEN(-/-) cells and neurons, thus providing an alternative hypothesis that accounts for the impaired lysosomal fusion capacity and accumulation of endomembranes that accompanies PSEN deficiency.
Collapse
Affiliation(s)
- Katrijn Coen
- Department of Human Genetics, VIB Center for the Biology of Disease, Leuven, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|