1
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Marlet FR, Muñoz SS, Sotiraki N, Eliasen JN, Woessmann J, Weicher J, Dreier JE, Schoof EM, Kohlmeier KA, Maeda K, Galvagnion C. Lipid levels correlate with neuronal and dopaminergic markers during the differentiation of SH-SY5Y cells. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167212. [PMID: 38750771 DOI: 10.1016/j.bbadis.2024.167212] [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: 02/13/2024] [Revised: 04/14/2024] [Accepted: 05/02/2024] [Indexed: 05/24/2024]
Abstract
Parkinson's Disease (PD) is characterised by the loss of dopaminergic neurons and the deposition of protein inclusions called Lewy Bodies (LBs). LBs are heterogeneous structures composed of protein and lipid molecules and their main constituent is the presynaptic protein α-synuclein. SH-SY5Y cells are neuroblastoma cells commonly used to model PD because they express dopaminergic markers and α-synuclein and they can be differentiated into neuronal cells using established protocols. Despite increasing evidence pointing towards a role of lipids in PD, limited knowledge is available on the lipidome of undifferentiated and differentiated SH-SY5Y cells. Using a combination of lipidomics, proteomics, morphological and electrophysiological measurements, we identified specific lipids, including sphingolipids, whose levels are affected by the differentiation of SH-SY5Y neuroblastoma cells and found that the levels of these lipids correlate with those of neuronal and dopaminergic markers. These results provide a quantitative characterisation of the changes in lipidome associated with the differentiation of SH-SY5Y cells into more neuronal and dopaminergic-like phenotype and serve as a basis for further characterisation of lipid disruptions in association with PD and its risk factors in this dopaminergic-like neuronal cell model.
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Affiliation(s)
- Frederik Ravnkilde Marlet
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Sonia Sanz Muñoz
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Nefeli Sotiraki
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jannik Nicklas Eliasen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jakob Woessmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Jan Weicher
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jesper Elmsted Dreier
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Kristi A Kohlmeier
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism group, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen, Denmark
| | - Céline Galvagnion
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark.
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2
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Wang Y, Liu Q, Liu Y, Qiao W, Zhao J, Cao H, Liu Y, Chen L. Advances in the composition, efficacy, and mimicking of human milk phospholipids. Food Funct 2024; 15:6254-6273. [PMID: 38787648 DOI: 10.1039/d4fo00539b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Phospholipids are the essential components of human milk, contributing to the enhancement of cognitive development, regulation of immune functions, and mitigation of elevated cholesterol levels. Infant formulas supplemented with phospholipids can change the composition, content, and globule membrane structure of milk lipids, improving their digestive properties and nutritional value. However, mimicking phospholipids in infant formulas is currently limited, and the supplemented standards of phospholipid species and amounts in infant formulas are unknown. Consequently, there is a significant difference between the phospholipids in infant formulas and those in human milk. This article reviews the recent progress in human milk phospholipid research, aiming to describe the composition, content, and positive effects of human milk phospholipids, as well as summarises the dietary sources of phospholipid supplementation and the current state of human milk phospholipid mimicking in infant formulas. This review provides clear directions for research on mimicking human milk phospholipids and evaluating the nutritional functions of phospholipids in infants.
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Affiliation(s)
- Yuru Wang
- Key Laboratory of Dairy Science, Ministry of Education, Food Science College, Northeast Agricultural University, Harbin, 150030, China.
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
| | - Qian Liu
- Key Laboratory of Dairy Science, Ministry of Education, Food Science College, Northeast Agricultural University, Harbin, 150030, China.
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
| | - Yan Liu
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
| | - Weicang Qiao
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
| | - Junying Zhao
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
| | - Huiru Cao
- Key Laboratory of Dairy Science, Ministry of Education, Food Science College, Northeast Agricultural University, Harbin, 150030, China.
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
| | - Yan Liu
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
| | - Lijun Chen
- Key Laboratory of Dairy Science, Ministry of Education, Food Science College, Northeast Agricultural University, Harbin, 150030, China.
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
- Beijing Sanyuan Foods Co. Ltd., No. 8, Yingchang Street 100076, Yinghai Town, Daxing District, Beijing, China.
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3
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Nielsen IØ, Clemmensen KKB, Fogde DL, Dietrich TN, Giacobini JD, Bilgin M, Jäättelä M, Maeda K. Cationic amphiphilic drugs induce accumulation of cytolytic lysoglycerophospholipids in the lysosomes of cancer cells and block their recycling into common membrane glycerophospholipids. Mol Biol Cell 2024; 35:ar25. [PMID: 38117591 PMCID: PMC10916870 DOI: 10.1091/mbc.e23-06-0263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 12/22/2023] Open
Abstract
Lysosomes are acidic organelles responsible for lipid catabolism, and their functions can be disrupted by cationic amphiphilic drugs that neutralize lumenal pH and thereby inhibit most lysosomal hydrolases. These drugs can also induce lysosomal membrane permeabilization and cancer cell death, but the underlying mechanism remains elusive. Here, we uncover that the cationic amphiphilic drugs induce a substantial accumulation of cytolytic lysoglycerophospholipids within the lysosomes of cancer cells, and thereby prevent the recycling of lysoglycerophospholipids to produce common membrane glycerophospholipids. Using quantitative mass spectrometry-based shotgun lipidomics, we demonstrate that structurally diverse cationic amphiphilic drugs, along with other types of lysosomal pH-neutralizing reagents, elevate the amounts of lysoglycerophospholipids in MCF7 breast carcinoma cells. Lysoglycerophospholipids constitute ∼11 mol% of total glycerophospholipids in lysosomes purified from MCF7 cells, compared with ∼1 mol% in the cell lysates. Treatment with cationic amphiphilic drug siramesine further elevates the lysosomal lysoglycerophospholipid content to ∼24 mol% of total glycerophospholipids. Exogenously added traceable lysophosphatidylcholine is rapidly acylated to form diacylphosphatidylcholine, but siramesine treatment sequesters the lysophosphatidylcholine in the lysosomes and prevents it from undergoing acylation. These findings shed light on the unexplored role of lysosomes in the recycling of lysoglycerophospholipids and uncover the mechanism of action of promising anticancer agents.
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Affiliation(s)
| | | | | | | | | | - Mesut Bilgin
- Lipidomics Core Facility, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Institute (DCI), DK-2100 Copenhagen, Denmark
| | - Marja Jäättelä
- Cell Death and Metabolism, DK-2100 Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism, DK-2100 Copenhagen, Denmark
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4
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Gerhardtova I, Jankech T, Majerova P, Piestansky J, Olesova D, Kovac A, Jampilek J. Recent Analytical Methodologies in Lipid Analysis. Int J Mol Sci 2024; 25:2249. [PMID: 38396926 PMCID: PMC10889185 DOI: 10.3390/ijms25042249] [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: 01/19/2024] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
Lipids represent a large group of biomolecules that are responsible for various functions in organisms. Diseases such as diabetes, chronic inflammation, neurological disorders, or neurodegenerative and cardiovascular diseases can be caused by lipid imbalance. Due to the different stereochemical properties and composition of fatty acyl groups of molecules in most lipid classes, quantification of lipids and development of lipidomic analytical techniques are problematic. Identification of different lipid species from complex matrices is difficult, and therefore individual analytical steps, which include extraction, separation, and detection of lipids, must be chosen properly. This review critically documents recent strategies for lipid analysis from sample pretreatment to instrumental analysis and data interpretation published in the last five years (2019 to 2023). The advantages and disadvantages of various extraction methods are covered. The instrumental analysis step comprises methods for lipid identification and quantification. Mass spectrometry (MS) is the most used technique in lipid analysis, which can be performed by direct infusion MS approach or in combination with suitable separation techniques such as liquid chromatography or gas chromatography. Special attention is also given to the correct evaluation and interpretation of the data obtained from the lipid analyses. Only accurate, precise, robust and reliable analytical strategies are able to bring complex and useful lipidomic information, which may contribute to clarification of some diseases at the molecular level, and may be used as putative biomarkers and/or therapeutic targets.
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Affiliation(s)
- Ivana Gerhardtova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
| | - Timotej Jankech
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
| | - Juraj Piestansky
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32 Bratislava, Slovakia
- Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32 Bratislava, Slovakia
| | - Dominika Olesova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 05 Bratislava, Slovakia
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Pharmacology and Toxicology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 68/73, SK-041 81 Kosice, Slovakia
| | - Josef Jampilek
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
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5
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Ebstrup ML, Sønder SL, Fogde DL, Heitmann ASB, Dietrich TN, Dias C, Jäättelä M, Maeda K, Nylandsted J. Annexin A7 mediates lysosome repair independently of ESCRT-III. Front Cell Dev Biol 2024; 11:1211498. [PMID: 38348092 PMCID: PMC10860759 DOI: 10.3389/fcell.2023.1211498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 12/21/2023] [Indexed: 02/15/2024] Open
Abstract
Lysosomes are crucial organelles essential for various cellular processes, and any damage to them can severely compromise cell viability. This study uncovers a previously unrecognized function of the calcium- and phospholipid-binding protein Annexin A7 in lysosome repair, which operates independently of the Endosomal Sorting Complex Required for Transport (ESCRT) machinery. Our research reveals that Annexin A7 plays a role in repairing damaged lysosomes, different from its role in repairing the plasma membrane, where it facilitates repair through the recruitment of ESCRT-III components. Notably, our findings strongly suggest that Annexin A7, like the ESCRT machinery, is dispensable for membrane contact site formation within the newly discovered phosphoinositide-initiated membrane tethering and lipid transport (PITT) pathway. Instead, we speculate that Annexin A7 is recruited to damaged lysosomes and promotes repair through its membrane curvature and cross-linking capabilities. Our findings provide new insights into the diverse mechanisms underlying lysosomal membrane repair and highlight the multifunctional role of Annexin A7 in membrane repair.
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Affiliation(s)
| | | | | | | | | | - Catarina Dias
- Membrane Integrity, Danish Cancer Institute, Copenhagen, Denmark
| | - Marja Jäättelä
- Cell Death and Metabolism, Danish Cancer Institute, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism, Danish Cancer Institute, Copenhagen, Denmark
| | - Jesper Nylandsted
- Membrane Integrity, Danish Cancer Institute, Copenhagen, Denmark
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
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6
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Hussain AA, Bilgin M, Carlsson J, Foged MM, Mortensen EL, Bulik CM, Støving RK, Sjögren JM. Elevated lipid class concentrations in females with anorexia nervosa before and after intensive weight restoration treatment-A lipidomics study. Int J Eat Disord 2023; 56:2260-2272. [PMID: 37715358 DOI: 10.1002/eat.24063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
OBJECTIVE To study the plasma lipidome of patients with anorexia nervosa (AN) before and after weight restoration treatment and report associations with AN subtypes and oral contraceptive pill (OCP) usage. METHODS Quantitative shotgun lipidomics analysis was used to study plasma lipids of 50 female patients with AN before and after weight restoration treatment and 50 healthy female controls (HC). The AN group was assessed with blood samples and questionnaires before and after weight restoration. RESULTS In total we quantified 260 lipid species representing 26 lipid classes of which 13 lipid class concentrations were elevated in patients with AN at admission compared with HC. Lipid classes remained elevated after weight restoration treatment of 84 days (median; interquartile range 28), and only the concentration of the ceramide lipid class increased between pre- and post-treatment (p = .03), whereas lysophosphatidylcholine (LPC, p = .02), ether-linked Phosphatidylcholine (LPCO, p = .02), and lysophosphatidylethanolamine (LPE, p = .009) decreased. CONCLUSION In AN, 13 out of 26 lipid class concentrations were elevated at admission and remained elevated post-treatment. Ceramides increased further between pre- and post-weight restoration treatment, which could be related to the rapid weight gain during re-nutrition. Further research is needed to elucidate the effects of weight restoration treatment on short- and long-term lipid profiles in individuals with AN. PUBLIC SIGNIFICANCE STATEMENT Lipidomics research can increase the understanding of AN, a complex and potentially life-threatening eating disorder. By analyzing lipids, or fats, in the body, we can identify biological markers that may inform diagnosis and develop more effective treatments. This research can also shed light on the underlying mechanisms of the disorder, leading to a better understanding of the processes involved in eating behavior.
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Affiliation(s)
- Alia Arif Hussain
- Eating Disorder Research Unit, Mental Health Center, Ballerup, Copenhagen University Hospital-Mental Health Services CPH, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mesut Bilgin
- Lipidomics Core Facility, Danish Cancer Institute, Copenhagen, Denmark
| | - Jessica Carlsson
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Competence Centre for Transcultural Psychiatry, Mental Health Centre Ballerup, Mental Health Services of the Capital Region of Denmark, Copenhagen, Denmark
| | - Mads Møller Foged
- Lipidomics Core Facility, Danish Cancer Institute, Copenhagen, Denmark
| | - Erik Lykke Mortensen
- Unit of Medical Psychology, Section of Environmental Health, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | - Cynthia M Bulik
- Department of Psychiatry, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - René Klinkby Støving
- Center for Eating Disorders, Odense University Hospital, Odense, Denmark
- Research Unit for Medical Endocrinology, Odense University Hospital, Odense, Denmark
- Research Unit, Child and Adolescent Psychiatry, Mental Health Services in the Region of Southern Denmark, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jan Magnus Sjögren
- Eating Disorder Research Unit, Mental Health Center, Ballerup, Copenhagen University Hospital-Mental Health Services CPH, Copenhagen, Denmark
- Institute of Clinical Science, Department of Psychiatry, Umeå University, Umeå, Sweden
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7
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Shields PG. Role of untargeted omics biomarkers of exposure and effect for tobacco research. ADDICTION NEUROSCIENCE 2023; 7:100098. [PMID: 37396411 PMCID: PMC10310069 DOI: 10.1016/j.addicn.2023.100098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Tobacco research remains a clear priority to improve individual and population health, and has recently become more complex with emerging combustible and noncombustible tobacco products. The use of omics methods in prevention and cessation studies are intended to identify new biomarkers for risk, compared risks related to other products and never use, and compliance for cessation and reinitation. to assess the relative effects of tobacco products to each other. They are important for the prediction of reinitiation of tobacco use and relapse prevention. In the research setting, both technical and clinical validation is required, which presents a number of complexities in the omics methodologies from biospecimen collection and sample preparation to data collection and analysis. When the results identify differences in omics features, networks or pathways, it is unclear if the results are toxic effects, a healthy response to a toxic exposure or neither. The use of surrogate biospecimens (e.g., urine, blood, sputum or nasal) may or may not reflect target organs such as the lung or bladder. This review describes the approaches for the use of omics in tobacco research and provides examples of prior studies, along with the strengths and limitations of the various methods. To date, there is little consistency in results, likely due to small number of studies, limitations in study size, the variability in the analytic platforms and bioinformatic pipelines, differences in biospecimen collection and/or human subject study design. Given the demonstrated value for the use of omics in clinical medicine, it is anticipated that the use in tobacco research will be similarly productive.
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Affiliation(s)
- Peter G. Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH
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8
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Skorda A, Lauridsen AR, Wu C, Huang J, Mrackova M, Winther NI, Jank V, Sztupinszki Z, Strauss R, Bilgin M, Maeda K, Liu B, Luo Y, Jäättelä M, Kallunki T. Activation of invasion by oncogenic reprogramming of cholesterol metabolism via increased NPC1 expression and macropinocytosis. Oncogene 2023; 42:2495-2506. [PMID: 37420029 PMCID: PMC10421736 DOI: 10.1038/s41388-023-02771-x] [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: 11/22/2022] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/09/2023]
Abstract
Cancer cells are dependent on cholesterol, and they possess strictly controlled cholesterol homeostasis mechanisms. These allow them to smoothly switch between cholesterol synthesis and uptake to fulfill their needs and to adapt environmental changes. Here we describe a mechanism of how cancer cells employ oncogenic growth factor signaling to promote uptake and utilization of extracellular cholesterol via Myeloid Zinc Finger 1 (MZF1)-mediated Niemann Pick C1 (NPC1) expression and upregulated macropinocytosis. Expression of p95ErbB2, highly oncogenic, standard-treatment resistant form of ErbB2 mobilizes lysosomes and activates EGFR, invasion and macropinocytosis. This is connected to a metabolic shift from cholesterol synthesis to uptake due to macropinocytosis-enabled flow of extracellular cholesterol. NPC1 increase facilitates extracellular cholesterol uptake and is necessary for the invasion of ErbB2 expressing breast cancer spheroids and ovarian cancer organoids, indicating a regulatory role for NPC1 in the process. The ability to obtain cholesterol as a byproduct of increased macropinocytosis allows cancer cells to direct the resources needed for the energy-consuming cholesterol synthesis towards other activities such as invasion. These results demonstrate that macropinocytosis is not only an alternative energy source for cancer cells but also an efficient way to provide building material, such as cholesterol, for its macromolecules and membranes.
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Affiliation(s)
- Aikaterini Skorda
- Cancer Invasion and Resistance, Danish Cancer Institute, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Anna Røssberg Lauridsen
- Cancer Invasion and Resistance, Danish Cancer Institute, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Chengnan Wu
- Cancer Invasion and Resistance, Danish Cancer Institute, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Jinrong Huang
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Monika Mrackova
- Cancer Invasion and Resistance, Danish Cancer Institute, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Nuggi Ingholt Winther
- Cancer Invasion and Resistance, Danish Cancer Institute, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Vanessa Jank
- Cancer Invasion and Resistance, Danish Cancer Institute, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Zsofia Sztupinszki
- Translational Cancer Genomics, Danish Cancer Institute, Copenhagen, Denmark
| | - Robert Strauss
- Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark
| | - Mesut Bilgin
- Lipidomics Core Facility, Danish Cancer Institute, Copenhagen, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen, Denmark
| | - Bin Liu
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Marja Jäättelä
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tuula Kallunki
- Cancer Invasion and Resistance, Danish Cancer Institute, Strandboulevarden 49, 2100, Copenhagen, Denmark.
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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9
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Rolver MG, Holland LKK, Ponniah M, Prasad NS, Yao J, Schnipper J, Kramer S, Elingaard-Larsen L, Pedraz-Cuesta E, Liu B, Pardo LA, Maeda K, Sandelin A, Pedersen SF. Chronic acidosis rewires cancer cell metabolism through PPARα signaling. Int J Cancer 2023; 152:1668-1684. [PMID: 36533672 PMCID: PMC10108231 DOI: 10.1002/ijc.34404] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
The mechanisms linking tumor microenvironment acidosis to disease progression are not understood. Here, we used mammary, pancreatic, and colon cancer cells to show that adaptation to growth at an extracellular pH (pHe ) mimicking acidic tumor niches is associated with upregulated net acid extrusion capacity and elevated intracellular pH at physiological pHe , but not at acidic pHe . Using metabolic profiling, shotgun lipidomics, imaging and biochemical analyses, we show that the acid adaptation-induced phenotype is characterized by a shift toward oxidative metabolism, increased lipid droplet-, triacylglycerol-, peroxisome content and mitochondrial hyperfusion. Peroxisome proliferator-activated receptor-α (PPARA, PPARα) expression and activity are upregulated, at least in part by increased fatty acid uptake. PPARα upregulates genes driving increased mitochondrial and peroxisomal mass and β-oxidation capacity, including mitochondrial lipid import proteins CPT1A, CPT2 and SLC25A20, electron transport chain components, peroxisomal proteins PEX11A and ACOX1, and thioredoxin-interacting protein (TXNIP), a negative regulator of glycolysis. This endows acid-adapted cancer cells with increased capacity for utilizing fatty acids for metabolic needs, while limiting glycolysis. As a consequence, the acid-adapted cells exhibit increased sensitivity to PPARα inhibition. We conclude that PPARα is a key upstream regulator of metabolic changes favoring cancer cell survival in acidic tumor niches.
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Affiliation(s)
- Michala G Rolver
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lya K K Holland
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Muthulakshmi Ponniah
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nanditha S Prasad
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jiayi Yao
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Julie Schnipper
- Laboratory of Cellular and Molecular Physiology, University of Picardie Jules Verne, Amiens, France
| | - Signe Kramer
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Elena Pedraz-Cuesta
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bin Liu
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Luis A Pardo
- Oncophysiology Group, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Kenji Maeda
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Albin Sandelin
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Stine Falsig Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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10
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Mønsted MØ, Bilgin M, Kuzma M, Pelantová H, Pedersen K, Tomášová P, Nazmutdinova A, Šedivá B, Funda D, Castro-Mejía JL, Holm LJ, Nielsen DS, Haupt-Jorgensen M. Reduced phosphatidylcholine level in the intestinal mucus layer of prediabetic NOD mice. APMIS 2023; 131:237-248. [PMID: 36811202 DOI: 10.1111/apm.13302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease with rising incidence. Pre- and manifest T1D is associated with intestinal barrier dysfunction, skewed microbiota composition, and serum dyslipidemia. The intestinal mucus layer protects against pathogens and its structure and phosphatidylcholine (PC) lipid composition may be compromised in T1D, potentially contributing to barrier dysfunction. This study compared prediabetic Non-Obese Diabetic (NOD) mice to healthy C57BL/6 mice by analyzing the intestinal mucus PC profile by shotgun lipidomics, plasma metabolomics by mass spectrometry and nuclear magnetic resonance, intestinal mucus production by histology, and cecal microbiota composition by 16 S rRNA sequencing. Jejunal mucus PC class levels were decreased in early prediabetic NOD vs C57BL/6 mice. In colonic mucus of NOD mice, the level of several PC species was reduced throughout prediabetes. In plasma, similar reductions of PC species were observed in early prediabetic NOD mice, where also increased beta-oxidation was prominent. No histological alterations were found in jejunal nor colonic mucus between the mouse strains. However, the β-diversity of the cecal microbiota composition differed between prediabetic NOD and C57BL/6 mice, and the bacterial species driving this difference were related to decreased short-chain fatty acid (SCFA)-production in the NOD mice. This study reports reduced levels of PCs in the intestinal mucus layer and plasma of prediabetic NOD mice as well as reduced proportions of SCFA-producing bacteria in cecal content at early prediabetes, possibly contributing to intestinal barrier dysfunction and T1D.
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Affiliation(s)
- Mia Øgaard Mønsted
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
| | - Mesut Bilgin
- Lipidomics Core Facility, Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Marek Kuzma
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | - Helena Pelantová
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | - Kristina Pedersen
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
| | - Petra Tomášová
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | | | - Blanka Šedivá
- Faculty of Applied Sciences, University of West Bohemia, Plzeň, The Czech Republic
| | - David Funda
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | | | - Laurits Juulskov Holm
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
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11
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Foged MM, Maeda K, Bilgin M. Profiling the Mammalian Lipidome by Quantitative Shotgun Lipidomics. Methods Mol Biol 2023; 2625:89-102. [PMID: 36653635 DOI: 10.1007/978-1-0716-2966-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The emerging field of lipidomics presents the systems biology approach to identify and quantify the full lipid repertoire of cells, tissues, and organisms. The importance of the lipidome is demonstrated by a number of biological studies on dysregulation of lipid metabolism in human diseases such as cancer, diabetes, and neurodegenerative diseases. Exploring changes and regulations in the huge networks of lipids and their metabolic pathways requires a lipidomics methodology: advanced mass spectrometry that resolves the complexity of the lipidome. Here, we report a comprehensive protocol of quantitative shotgun lipidomics that enables identification and quantification of hundreds of molecular lipid species, covering a wide range of lipid classes, extracted from cultured mammalian cells.
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Affiliation(s)
- Mads Møller Foged
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mesut Bilgin
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark. .,Lipidomics Core Facility, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center , Copenhagen, Denmark.
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12
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Pärn A, Olsen D, Tuvikene J, Kaas M, Borisova E, Bilgin M, Elhauge M, Vilstrup J, Madsen P, Ambrozkiewicz MC, Goz RU, Timmusk T, Tarabykin V, Gustafsen C, Glerup S. PCSK9 deficiency alters brain lipid composition without affecting brain development and function. Front Mol Neurosci 2023; 15:1084633. [PMID: 36733269 PMCID: PMC9887304 DOI: 10.3389/fnmol.2022.1084633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/16/2022] [Indexed: 01/18/2023] Open
Abstract
PCSK9 induces lysosomal degradation of the low-density lipoprotein (LDL) receptor (LDLR) in the liver, hereby preventing removal of LDL cholesterol from the circulation. Accordingly, PCSK9 inhibitory antibodies and siRNA potently reduce LDL cholesterol to unprecedented low levels and are approved for treatment of hypercholesterolemia. In addition, PCSK9 inactivation alters the levels of several other circulating lipid classes and species. Brain function is critically influenced by cholesterol and lipid composition. However, it remains unclear how the brain is affected long-term by the reduction in circulating lipids as achieved with potent lipid lowering therapeutics such as PCSK9 inhibitors. Furthermore, it is unknown if locally expressed PCSK9 affects neuronal circuits through regulation of receptor levels. We have studied the effect of lifelong low peripheral cholesterol levels on brain lipid composition and behavior in adult PCSK9 KO mice. In addition, we studied the effect of PCSK9 on neurons in culture and in vivo in the developing cerebral cortex. We found that PCSK9 reduced LDLR and neurite complexity in cultured neurons, but neither PCSK9 KO nor overexpression affected cortical development in vivo. Interestingly, PCSK9 deficiency resulted in changes of several lipid classes in the adult cortex and cerebellum. Despite the observed changes, PCSK9 KO mice had unchanged behavior compared to WT controls. In conclusion, our findings demonstrate that altered PCSK9 levels do not compromise brain development or function in mice, and are in line with clinical trials showing that PCSK9 inhibitors have no adverse effects on cognitive function.
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Affiliation(s)
- Angela Pärn
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,*Correspondence: Angela Pärn, ✉
| | - Ditte Olsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jürgen Tuvikene
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia,Protobios LLC, Tallinn, Estonia
| | - Mathias Kaas
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Ekaterina Borisova
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, Berlin, Germany,Tomsk National Research Medical Center of the Russian Academy of Sciences, Research Institute of Medical Genetics, Tomsk, Russia
| | - Mesut Bilgin
- Danish Cancer Society Research Center, Lipidomics Core Facility, Copenhagen, Denmark
| | - Mie Elhauge
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Joachim Vilstrup
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,Draupnir Bio ApS, INCUBA Skejby, Aarhus, Denmark
| | - Peder Madsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,Draupnir Bio ApS, INCUBA Skejby, Aarhus, Denmark
| | - Mateusz C. Ambrozkiewicz
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Roman U. Goz
- Department of Neurobiology, University of Pittsburgh Medical School, Pittsburgh, PA, United States
| | - Tõnis Timmusk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia,Protobios LLC, Tallinn, Estonia
| | - Victor Tarabykin
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, Berlin, Germany,Tomsk National Research Medical Center of the Russian Academy of Sciences, Research Institute of Medical Genetics, Tomsk, Russia
| | - Camilla Gustafsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,Draupnir Bio ApS, INCUBA Skejby, Aarhus, Denmark,Camilla Gustafsen, ✉
| | - Simon Glerup
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,Draupnir Bio ApS, INCUBA Skejby, Aarhus, Denmark,Simon Glerup, ✉
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13
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Ursolic Acid Impairs Cellular Lipid Homeostasis and Lysosomal Membrane Integrity in Breast Carcinoma Cells. Cells 2022; 11:cells11244079. [PMID: 36552844 PMCID: PMC9776894 DOI: 10.3390/cells11244079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer is one of the leading causes of death worldwide, thus the search for new cancer therapies is of utmost importance. Ursolic acid is a naturally occurring pentacyclic triterpene with a wide range of pharmacological activities including anti-inflammatory and anti-neoplastic effects. The latter has been assigned to its ability to promote apoptosis and inhibit cancer cell proliferation by poorly defined mechanisms. In this report, we identify lysosomes as the essential targets of the anti-cancer activity of ursolic acid. The treatment of MCF7 breast cancer cells with ursolic acid elevates lysosomal pH, alters the cellular lipid profile, and causes lysosomal membrane permeabilization and leakage of lysosomal enzymes into the cytosol. Lysosomal membrane permeabilization precedes the essential hallmarks of apoptosis placing it as an initial event in the cascade of effects induced by ursolic acid. The disruption of the lysosomal function impairs the autophagic pathway and likely partakes in the mechanism by which ursolic acid kills cancer cells. Furthermore, we find that combining treatment with ursolic acid and cationic amphiphilic drugs can significantly enhance the degree of lysosomal membrane permeabilization and cell death in breast cancer cells.
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14
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Stahl-Meyer K, Bilgin M, Holland LKK, Stahl-Meyer J, Kirkegaard T, Petersen NHT, Maeda K, Jäättelä M. Galactosyl- and glucosylsphingosine induce lysosomal membrane permeabilization and cell death in cancer cells. PLoS One 2022; 17:e0277058. [PMID: 36409725 PMCID: PMC9678304 DOI: 10.1371/journal.pone.0277058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/18/2022] [Indexed: 11/22/2022] Open
Abstract
Isomeric lysosphingolipids, galactosylsphingosine (GalSph) and glucosylsphingosine (GlcSph), are present in only minute levels in healthy cells. Due to defects in their lysosomal hydrolysis, they accumulate at high levels and cause cytotoxicity in patients with Krabbe and Gaucher diseases, respectively. Here, we show that GalSph and GlcSph induce lysosomal membrane permeabilization, a hallmark of lysosome-dependent cell death, in human breast cancer cells (MCF7) and primary fibroblasts. Supporting lysosomal leakage as a causative event in lysosphingolipid-induced cytotoxicity, treatment of MCF7 cells with lysosome-stabilizing cholesterol prevented GalSph- and GlcSph-induced cell death almost completely. In line with this, fibroblasts from a patient with Niemann-Pick type C disease, which is caused by defective lysosomal cholesterol efflux, were significantly less sensitive to lysosphingolipid-induced lysosomal leakage and cell death. Prompted by the data showing that MCF7 cells with acquired resistance to lysosome-destabilizing cationic amphiphilic drugs (CADs) were partially resistant to the cell death induced by GalSph and GlcSph, we compared these cell death pathways with each other. Like CADs, GalSph and GlcSph activated the cyclic AMP (cAMP) signalling pathway, and cAMP-inducing forskolin sensitized cells to cell death induced by low concentrations of lysosphingolipids. Contrary to CADs, lysosphingolipid-induced cell death was independent of lysosomal Ca2+ efflux through P2X purinerigic receptor 4. These data reveal GalSph and GlcSph as lysosome-destabilizing lipids, whose putative use in cancer therapy should be further investigated. Furthermore, the data supports the development of lysosome stabilizing drugs for the treatment of Krabbe and Gaucher diseases and possibly other sphingolipidoses.
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Affiliation(s)
- Kamilla Stahl-Meyer
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
- Orphazyme A/S, Copenhagen, Denmark
| | - Mesut Bilgin
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Lya K. K. Holland
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jonathan Stahl-Meyer
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | | | - Kenji Maeda
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
- * E-mail: (MJ); (KM)
| | - Marja Jäättelä
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Cellular and molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (MJ); (KM)
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15
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Scrima S, Tiberti M, Campo A, Corcelle-Termeau E, Judith D, Foged MM, Clemmensen KKB, Tooze SA, Jäättelä M, Maeda K, Lambrughi M, Papaleo E. Unraveling membrane properties at the organelle-level with LipidDyn. Comput Struct Biotechnol J 2022; 20:3604-3614. [PMID: 35860415 PMCID: PMC9283888 DOI: 10.1016/j.csbj.2022.06.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 12/22/2022] Open
Abstract
Lipidomics of organelles could be used to design models for molecular simulations. The bottleneck is the analysis and rationalization of the data from simulations. LipidDyn is an automated pipeline to streamline the analyses of lipid bilayers. LipidDyn allows to collect analysis in a non-time-consuming and reproducible manner. We applied LipidDyn to different case studies to illustrate its potential.
Cellular membranes are formed from different lipids in various amounts and proportions depending on the subcellular localization. The lipid composition of membranes is sensitive to changes in the cellular environment, and its alterations are linked to several diseases. Lipids not only form lipid-lipid interactions but also interact with other biomolecules, including proteins. Molecular dynamics (MD) simulations are a powerful tool to study the properties of cellular membranes and membrane-protein interactions on different timescales and resolutions. Over the last few years, software and hardware for biomolecular simulations have been optimized to routinely run long simulations of large and complex biological systems. On the other hand, high-throughput techniques based on lipidomics provide accurate estimates of the composition of cellular membranes at the level of subcellular compartments. Lipidomic data can be analyzed to design biologically relevant models of membranes for MD simulations. Similar applications easily result in a massive amount of simulation data where the bottleneck becomes the analysis of the data. In this context, we developed LipidDyn, a Python-based pipeline to streamline the analyses of MD simulations of membranes of different compositions. Once the simulations are collected, LipidDyn provides average properties and time series for several membrane properties such as area per lipid, thickness, order parameters, diffusion motions, lipid density, and lipid enrichment/depletion. The calculations exploit parallelization, and the pipeline includes graphical outputs in a publication-ready form. We applied LipidDyn to different case studies to illustrate its potential, including membranes from cellular compartments and transmembrane protein domains. LipidDyn is available free of charge under the GNU General Public License from https://github.com/ELELAB/LipidDyn.
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Affiliation(s)
- Simone Scrima
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Alessia Campo
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elisabeth Corcelle-Termeau
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Delphine Judith
- Institut Cochin, Inserm U1016-CNRS, UMR8104, Université de Paris, Paris, France
| | - Mads Møller Foged
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | | | - Sharon A Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Marja Jäättelä
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Matteo Lambrughi
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
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16
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Vit G, Duro J, Rajendraprasad G, Hertz EPT, Holland LKK, Weisser MB, McEwan BC, Lopez‐Mendez B, Sotelo‐Parrilla P, Jeyaprakash AA, Montoya G, Mailand N, Maeda K, Kettenbach A, Barisic M, Nilsson J. Chemogenetic profiling reveals PP2A-independent cytotoxicity of proposed PP2A activators iHAP1 and DT-061. EMBO J 2022; 41:e110611. [PMID: 35695070 PMCID: PMC9289710 DOI: 10.15252/embj.2022110611] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 01/01/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is an abundant phosphoprotein phosphatase that acts as a tumor suppressor. For this reason, compounds able to activate PP2A are attractive anticancer agents. The compounds iHAP1 and DT-061 have recently been reported to selectively stabilize specific PP2A-B56 complexes to mediate cell killing. We were unable to detect direct effects of iHAP1 and DT-061 on PP2A-B56 activity in biochemical assays and composition of holoenzymes. Therefore, we undertook genome-wide CRISPR-Cas9 synthetic lethality screens to uncover biological pathways affected by these compounds. We found that knockout of mitotic regulators is synthetic lethal with iHAP1 while knockout of endoplasmic reticulum (ER) and Golgi components is synthetic lethal with DT-061. Indeed we showed that iHAP1 directly blocks microtubule assembly both in vitro and in vivo and thus acts as a microtubule poison. In contrast, DT-061 disrupts both the Golgi apparatus and the ER and lipid synthesis associated with these structures. Our work provides insight into the biological pathways perturbed by iHAP1 and DT-061 causing cellular toxicity and argues that these compounds cannot be used for dissecting PP2A-B56 biology.
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Affiliation(s)
- Gianmatteo Vit
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Joana Duro
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Girish Rajendraprasad
- Cell Division and CytoskeletonDanish Cancer Society Research CenterCopenhagenDenmark
| | - Emil P T Hertz
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Lya Katrine Kauffeldt Holland
- Cell Death and Metabolism UnitCenter for Autophagy, Recycling and Disease (CARD)Danish Cancer Society Research Center (DCRC)CopenhagenDenmark
| | - Melanie Bianca Weisser
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Brennan C McEwan
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA,Norris Cotton Cancer CenterLebanonNHUSA
| | - Blanca Lopez‐Mendez
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | | | | | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Kenji Maeda
- Cell Death and Metabolism UnitCenter for Autophagy, Recycling and Disease (CARD)Danish Cancer Society Research Center (DCRC)CopenhagenDenmark
| | - Arminja Kettenbach
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Marin Barisic
- Cell Division and CytoskeletonDanish Cancer Society Research CenterCopenhagenDenmark,Department of Cellular and Molecular MedicineFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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17
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Stahl-Meyer J, Holland LKK, Liu B, Maeda K, Jäättelä M. Lysosomal Changes in Mitosis. Cells 2022; 11:cells11050875. [PMID: 35269496 PMCID: PMC8909281 DOI: 10.3390/cells11050875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 01/27/2023] Open
Abstract
The recent discovery demonstrating that the leakage of cathepsin B from mitotic lysosomes assists mitotic chromosome segregation indicates that lysosomal membrane integrity can be spatiotemporally regulated. Unlike many other organelles, structural and functional alterations of lysosomes during mitosis remain, however, largely uncharted. Here, we demonstrate substantial differences in lysosomal proteome, lipidome, size, and pH between lysosomes that were isolated from human U2OS osteosarcoma cells either in mitosis or in interphase. The combination of pharmacological synchronization and mitotic shake-off yielded ~68% of cells in mitosis allowing us to investigate mitosis-specific lysosomal changes by comparing cell populations that were highly enriched in mitotic cells to those mainly in the G1 or G2 phases of the cell cycle. Mitotic cells had significantly reduced levels of lysosomal-associated membrane protein (LAMP) 1 and the active forms of lysosomal cathepsin B protease. Similar trends were observed in levels of acid sphingomyelinase and most other lysosomal proteins that were studied. The altered protein content was accompanied by increases in the size and pH of LAMP2-positive vesicles. Moreover, mass spectrometry-based shotgun lipidomics of purified lysosomes revealed elevated levels of sphingolipids, especially sphingomyelin and hexocylceramide, and lysoglyserophospholipids in mitotic lysosomes. Interestingly, LAMPs and acid sphingomyelinase have been reported to stabilize lysosomal membranes, whereas sphingomyelin and lysoglyserophospholipids have an opposite effect. Thus, the observed lysosomal changes during the cell cycle may partially explain the reduced lysosomal membrane integrity in mitotic cells.
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Affiliation(s)
- Jonathan Stahl-Meyer
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; (L.K.K.H.); (B.L.); (K.M.)
- Correspondence: (J.S.-M.); (M.J.)
| | - Lya Katrine Kauffeldt Holland
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; (L.K.K.H.); (B.L.); (K.M.)
| | - Bin Liu
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; (L.K.K.H.); (B.L.); (K.M.)
| | - Kenji Maeda
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; (L.K.K.H.); (B.L.); (K.M.)
| | - Marja Jäättelä
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; (L.K.K.H.); (B.L.); (K.M.)
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Correspondence: (J.S.-M.); (M.J.)
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18
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Chao HC, McLuckey SA. In-Depth Structural Characterization and Quantification of Cerebrosides and Glycosphingosines with Gas-Phase Ion Chemistry. Anal Chem 2021; 93:7332-7340. [PMID: 33957046 DOI: 10.1021/acs.analchem.1c01021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cerebrosides (n-HexCer) and glycosphingosines (n-HexSph) constitute two sphingolipid subclasses. Both are comprised of a monosaccharide headgroup (glucose or galactose in mammalian cells) linked via either an α- or β-glycosidic linkage to the sphingoid backbone (n = α or β, depending upon the nature of the linkage to the anomeric carbon of the sugar). Cerebrosides have an additional amide-bonded fatty acyl chain linked to the sphingoid backbone. While differentiating the multiple isomers (i.e. glucose vs galactose, α- vs β-linkage) is difficult, it is crucial for understanding their specific biological roles in health and disease states. Shotgun tandem mass spectrometry has been a powerful tool in both lipidomics and glycomics analysis but is often limited in its ability to distinguish isomeric species. This work describes a new strategy combining shotgun tandem mass spectrometry with gas-phase ion chemistry to achieve both differentiation and quantification of isomeric cerebrosides and glycosphingosines. Briefly, deprotonated cerebrosides, [n-HexCer-H]-, or glycosphingosines, [n-HexSph-H]-, are reacted with terpyridine (Terpy) magnesium complex dications, [Mg(Terpy)2]2+, in the gas phase to produce a charge-inverted complex cation, [n-HexCer-H+MgTerpy]+ or [n-HexSph-H+MgTerpy]+. The collision-induced dissociation (CID) of the charge-inverted complex cations leads to significant spectral differences between the two groups of isomers, α-GalCer, β-GlcCer, and β-GalCer for cerebrosides and α-GlcSph, α-GalSph, β-GlcSph, and β-GalSph for glycosphingosines, which allows for isomer distinction. Moreover, we describe a quantification strategy with the normalized percent area extracted from selected diagnostic ions that quantify either three isomeric cerebroside or four isomeric glycosphingosine mixtures. The analytical performance was also evaluated in terms of accuracy, repeatability, and interday precision. Furthermore, CID of the product ions resulting from 443 Da loss from the charge-inverted complex cations ([n-HexCer-H+MgTerpy]+) has been performed and demonstrated for localization of the double-bond position on the amide-bonded monounsaturated fatty acyl chain in the cerebroside structure. The proposed strategy was successfully applied to the analysis of total cerebroside extracts from the porcine brain, providing in-depth structural information on cerebrosides from a biological mixture.
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Affiliation(s)
- Hsi-Chun Chao
- Department of Chemistry Purdue University 560 Oval Drive West Lafayette, Indiana 47907, United States
| | - Scott A McLuckey
- Department of Chemistry Purdue University 560 Oval Drive West Lafayette, Indiana 47907, United States
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19
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Nielsen IØ, Groth-Pedersen L, Dicroce-Giacobini J, Jonassen ASH, Mortensen M, Bilgin M, Schmiegelow K, Jäättelä M, Maeda K. Cationic amphiphilic drugs induce elevation in lysoglycerophospholipid levels and cell death in leukemia cells. Metabolomics 2020; 16:91. [PMID: 32851548 DOI: 10.1007/s11306-020-01710-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Repurposing of cationic amphiphilic drugs (CADs) emerges as an attractive therapeutic solution against various cancers, including leukemia. CADs target lysosomal lipid metabolism and preferentially kill cancer cells via induction of lysosomal membrane permeabilization, but the exact effects of CADs on the lysosomal lipid metabolism remain poorly illuminated. OBJECTIVES We aimed to systematically monitor CAD-induced alterations in the quantitative lipid profiles of leukemia cell lines in order to chart effects of CADs on the metabolism of various lipid classes present in these cells. METHODS We conducted this study on eight cultured cell lines representing two leukemia types, acute lymphoblastic leukemia and acute myeloid leukemia. Mass spectrometry-based quantitative shotgun lipidomics was employed to quantify the levels of around 400 lipid species of 26 lipid classes in the leukemia cell lines treated or untreated with a CAD, siramesine. RESULTS The two leukemia types displayed high, but variable sensitivities to CADs and distinct profiles of cellular lipids. Treatment with siramesine rapidly altered the levels of diverse lipid classes in both leukemia types. These included sphingolipid classes previously reported to play key roles in CAD-induced cell death, but also lipids of other categories. We demonstrated that the treatment with siramesine additionally elevated the levels of numerous cytolytic lysoglycerophospholipids in positive correlation with the sensitivity of individual leukemia cell lines to siramesine. CONCLUSIONS Our study shows that CAD treatment alters balance in the metabolism of glycerophospholipids, and proposes elevation in the levels of lysoglycerophospholipids as part of the mechanism leading to CAD-induced cell death of leukemia cells.
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Affiliation(s)
- Inger Ødum Nielsen
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center (DCRC), 2100, Copenhagen, Denmark
| | - Line Groth-Pedersen
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center (DCRC), 2100, Copenhagen, Denmark
| | - Jano Dicroce-Giacobini
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center (DCRC), 2100, Copenhagen, Denmark
| | - Anna Sofie Holm Jonassen
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center (DCRC), 2100, Copenhagen, Denmark
| | - Monika Mortensen
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center (DCRC), 2100, Copenhagen, Denmark
| | - Mesut Bilgin
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center (DCRC), 2100, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Juliane Marie Centre, Rigshospitalet University Hospital, 2100, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Marja Jäättelä
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center (DCRC), 2100, Copenhagen, Denmark.
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark.
| | - Kenji Maeda
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center (DCRC), 2100, Copenhagen, Denmark.
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