DGAT1 activity synchronises with mitophagy to protect cells from metabolic rewiring by iron  depletion

Mitophagy removes defective mitochondria via lysosomal elimination. Increased mitophagy coincides with metabolic reprogramming, yet it remains unknown whether mitophagy is a cause or consequence of such state changes. The signalling pathways that integrate with mitophagy to sustain cell and tissue integrity also remain poorly defined. We performed temporal metabolomics on mammalian cells treated with deferiprone, a therapeutic iron chelator that stimulates PINK1/PARKIN‐independent mitophagy. Iron depletion profoundly rewired the metabolome, hallmarked by remodelling of lipid metabolism within minutes of treatment. DGAT1‐dependent lipid droplet biosynthesis occurred several hours before mitochondrial clearance, with lipid droplets bordering mitochondria upon iron chelation. We demonstrate that DGAT1 inhibition restricts mitophagy in vitro, with impaired lysosomal homeostasis and cell viability. Importantly, genetic depletion of DGAT1 in vivo significantly impaired neuronal mitophagy and locomotor function in Drosophila. Our data define iron depletion as a potent signal that rapidly reshapes metabolism and establishes an unexpected synergy between lipid homeostasis and mitophagy that safeguards cell and tissue integrity.

[1]  Valentina Scandella,et al.  Lipid droplet availability affects neural stem/progenitor cell metabolism and proliferation , 2021, Nature Communications.

[2]  J. Lippincott-Schwartz,et al.  Lipid droplets in the nervous system , 2021, The Journal of cell biology.

[3]  N. Chandel Glycolysis. , 2021, Cold Spring Harbor perspectives in biology.

[4]  L. Collinson,et al.  Adipose triglyceride lipase protects renal cell endocytosis in a Drosophila dietary model of chronic kidney disease , 2021, PLoS biology.

[5]  L. Kirshenbaum,et al.  Oxidized phosphatidylcholines trigger ferroptosis in cardiomyocytes during ischemia/reperfusion injury. , 2021, American journal of physiology. Heart and circulatory physiology.

[6]  A. Reith,et al.  Pharmacological rescue of impaired mitophagy in Parkinson’s disease-related LRRK2 G2019S knock-in mice , 2020, bioRxiv.

[7]  E. Ikonen,et al.  Lipid Droplet Nucleation. , 2020, Trends in cell biology.

[8]  Michael J. Munson,et al.  GAK and PRKCD are positive regulators of PRKN-independent mitophagy , 2020, Nature Communications.

[9]  N. Leitinger,et al.  Innate immune signaling in Drosophila shifts anabolic lipid metabolism from triglyceride storage to phospholipid synthesis to support immune function , 2020, PLoS genetics.

[10]  T. G. McWilliams,et al.  Monitoring autophagy in cancer: from bench to bedside. , 2020, Seminars in cancer biology.

[11]  I. Yanatori,et al.  Iron loss triggers mitophagy through induction of mitochondrial ferritin , 2020, EMBO reports.

[12]  D. Philpott,et al.  Mitophagy pathways in health and disease , 2020, The Journal of cell biology.

[13]  Zheng-tan Zhang,et al.  Excess diacylglycerol at the endoplasmic reticulum disrupts endomembrane homeostasis and autophagy , 2020, BMC biology.

[14]  T. Castro-Gomes,et al.  Measuring Intracellular Vesicle Density and Dispersion Using Fluorescence Microscopy and ImageJ/FIJI. , 2020, Bio-protocol.

[15]  Robert W. Taylor,et al.  FBXL4 deficiency increases mitochondrial removal by autophagy , 2020, EMBO molecular medicine.

[16]  T. Walther,et al.  Lipid Droplets in Brown Adipose Tissue Are Dispensable for Cold-Induced Thermogenesis , 2020, bioRxiv.

[17]  T. Fujimoto,et al.  Multifarious roles of lipid droplets in autophagy - Target, product, and what else? , 2020, Seminars in cell & developmental biology.

[18]  S. Weidlich,et al.  HIF1α-dependent mitophagy facilitates cardiomyoblast differentiation , 2020, Cell stress.

[19]  P. Boya,et al.  The mito-QC Reporter for Quantitative Mitophagy Assessment in Primary Retinal Ganglion Cells and Experimental Glaucoma Models , 2020, International journal of molecular sciences.

[20]  Konnor C. La,et al.  Maintaining Iron Homeostasis Is the Key Role of Lysosomal Acidity for Cell Proliferation. , 2020, Molecular cell.

[21]  D. Selkoe,et al.  Parkinson’s disease: proteinopathy or lipidopathy? , 2020, npj Parkinson's Disease.

[22]  I. Ganley,et al.  Outstanding Questions in Mitophagy: What we Do and Do Not Know. , 2020, Journal of molecular biology.

[23]  J. Goodman,et al.  Spatial compartmentalization of lipid droplet biogenesis. , 2020, Biochimica et biophysica acta. Molecular and cell biology of lipids.

[24]  P. Giavalisco,et al.  Local Fatty Acid Channeling into Phospholipid Synthesis Drives Phagophore Expansion during Autophagy , 2019, Cell.

[25]  G. Ball,et al.  Semi-automated quantitation of mitophagy in cells and tissues , 2019, Mechanisms of Ageing and Development.

[26]  A. Schulze,et al.  Greasing the Wheels of the Cancer Machine: The Role of Lipid Metabolism in Cancer. , 2019, Cell metabolism.

[27]  J. Frahm,et al.  Impaired lysosomal acidification triggers iron deficiency and inflammation in vivo , 2019, eLife.

[28]  T. Moritz,et al.  Lipidomics in Ulcerative Colitis Reveal Alteration in Mucosal Lipid Composition Associated With the Disease State. , 2019, Inflammatory bowel diseases.

[29]  M. Leach,et al.  De novo phosphatidylcholine synthesis is required for autophagosome membrane formation and maintenance during autophagy , 2019, Autophagy.

[30]  James H. Stronge,et al.  Selective Autophagy of Mitochondria on a Ubiquitin-Endoplasmic-Reticulum Platform , 2019, Developmental cell.

[31]  T. G. McWilliams,et al.  Autophagy in the mammalian nervous system: a primer for neuroscientists , 2019, Health psychology and behavioral medicine.

[32]  E. Ikonen,et al.  Seipin Facilitates Triglyceride Flow to Lipid Droplet and Counteracts Droplet Ripening via Endoplasmic Reticulum Contact. , 2019, Developmental cell.

[33]  T. Wyss-Coray,et al.  Lipid droplet accumulating microglia represent a dysfunctional and pro-inflammatory state in the aging brain , 2019, bioRxiv.

[34]  Ana S. H. Costa,et al.  Acute Iron Deprivation Reprograms Human Macrophage Metabolism and Reduces Inflammation In Vivo , 2019, Cell reports.

[35]  M. Grabherr,et al.  Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes , 2018, Scientific Reports.

[36]  K. Buhman,et al.  DGAT1 deficiency disrupts lysosome function in enterocytes during dietary fat absorption. , 2019, Biochimica et biophysica acta. Molecular and cell biology of lipids.

[37]  E. Ikonen,et al.  Moving out but keeping in touch: contacts between endoplasmic reticulum and lipid droplets. , 2019, Current opinion in cell biology.

[38]  O. Shirihai,et al.  Mitochondria Bound to Lipid Droplets: Where Mitochondrial Dynamics Regulate Lipid Storage and Utilization. , 2019, Cell metabolism.

[39]  F. Parveen,et al.  An Updated Review of Lysophosphatidylcholine Metabolism in Human Diseases , 2019, International journal of molecular sciences.

[40]  S. Girardin,et al.  Listeria hijacks host mitophagy through a novel mitophagy receptor to evade killing , 2019, Nature Immunology.

[41]  P. Boya,et al.  A comparative map of macroautophagy and mitophagy in the vertebrate eye , 2019, Autophagy.

[42]  S. Cloonan,et al.  Mitochondrial Iron in Human Health and Disease. , 2019, Annual review of physiology.

[43]  S. Ichinose,et al.  An alternative mitophagy pathway mediated by Rab9 protects the heart against ischemia , 2019, The Journal of clinical investigation.

[44]  I. Ganley,et al.  Investigating Mitophagy and Mitochondrial Morphology In Vivo Using mito-QC: A Comprehensive Guide. , 2019, Methods in molecular biology.

[45]  J. Olzmann,et al.  Dynamics and functions of lipid droplets , 2018, Nature Reviews Molecular Cell Biology.

[46]  S. Dunnett,et al.  Phosphorylation of Parkin at serine 65 is essential for its activation in vivo , 2018, Royal Society Open Biology.

[47]  J. Ricci,et al.  No Parkin Zone: Mitophagy without Parkin. , 2018, Trends in cell biology.

[48]  R. Huganir,et al.  Mitochondrial Stasis Reveals p62-Mediated Ubiquitination in Parkin-Independent Mitophagy and Mitigates Nonalcoholic Fatty Liver Disease. , 2018, Cell metabolism.

[49]  M. Grabherr,et al.  Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes , 2018, Scientific Reports.

[50]  N. Davoust,et al.  Physiological and pathological roles of FATP-mediated lipid droplets in Drosophila and mice retina , 2018, PLoS genetics.

[51]  Nektarios Tavernarakis,et al.  Mechanisms of mitophagy in cellular homeostasis, physiology and pathology , 2018, Nature Cell Biology.

[52]  Nektarios Tavernarakis,et al.  The Role of Mitophagy in Innate Immunity , 2018, Front. Immunol..

[53]  H. McBride Mitochondria and endomembrane origins , 2018, Current Biology.

[54]  A. Petcherski,et al.  Mitochondria Bound to Lipid Droplets Have Unique Bioenergetics, Composition, and Dynamics that Support Lipid Droplet Expansion. , 2018, Cell metabolism.

[55]  A. Giovane,et al.  Ophthalmic acid is a marker of oxidative stress in plants as in animals. , 2018, Biochimica et biophysica acta. General subjects.

[56]  A. Lane,et al.  Acute loss of iron–sulfur clusters results in metabolic reprogramming and generation of lipid droplets in mammalian cells , 2018, The Journal of Biological Chemistry.

[57]  A. Prescott,et al.  Basal Mitophagy Occurs Independently of PINK1 in Mouse Tissues of High Metabolic Demand , 2018, Cell metabolism.

[58]  A. Whitworth,et al.  Basal mitophagy is widespread in Drosophila but minimally affected by loss of Pink1 or parkin , 2018, bioRxiv.

[59]  I. Ganley,et al.  The mammalian ULK1 complex and autophagy initiation , 2017, Essays in biochemistry.

[60]  I. Ganley,et al.  Mammalian mitophagy – from in vitro molecules to in vivo models , 2017, The FEBS journal.

[61]  S. Tait,et al.  Parkin-Independent Mitophagy Controls Chemotherapeutic Response in Cancer Cells. , 2017, Cell reports.

[62]  R. Zechner,et al.  Cytosolic lipolysis and lipophagy: two sides of the same coin , 2017, Nature Reviews Molecular Cell Biology.

[63]  Robert V Farese,et al.  Lipid Droplet Biogenesis. , 2017, Annual review of cell and developmental biology.

[64]  Robert V Farese,et al.  Triglyceride Synthesis by DGAT1 Protects Adipocytes from Lipid-Induced ER Stress during Lipolysis. , 2017, Cell Metabolism.

[65]  J. Olzmann,et al.  DGAT1-Dependent Lipid Droplet Biogenesis Protects Mitochondrial Function during Starvation-Induced Autophagy. , 2017, Developmental cell.

[66]  Pingsheng Liu,et al.  Lipid droplet proteins and metabolic diseases. , 2017, Biochimica et biophysica acta. Molecular basis of disease.

[67]  M. Malumbres,et al.  Programmed mitophagy is essential for the glycolytic switch during cell differentiation , 2017, The EMBO journal.

[68]  M. Muqit,et al.  PINK1 and Parkin: emerging themes in mitochondrial homeostasis. , 2017, Current opinion in cell biology.

[69]  Joo Young Lee,et al.  Oxidized phosphatidylcholine induces the activation of NLRP3 inflammasome in macrophages , 2017, Journal of leukocyte biology.

[70]  J. Luzio,et al.  Endolysosomes Are the Principal Intracellular Sites of Acid Hydrolase Activity , 2016, Current Biology.

[71]  E. Abel,et al.  Lipids, lysosomes, and autophagy , 2016, Journal of Lipid Research.

[72]  Michael J. Munson,et al.  mito-QC illuminates mitophagy and mitochondrial architecture in vivo , 2016, The Journal of cell biology.

[73]  M. Mattson,et al.  Lipid-laden cells differentially distributed in the aging brain are functionally active and correspond to distinct phenotypes , 2016, Scientific Reports.

[74]  T. Tatsuta,et al.  Lipid droplet–mediated ER homeostasis regulates autophagy and cell survival during starvation , 2016, The Journal of cell biology.

[75]  Valentin Jaumouillé,et al.  The position of lysosomes within the cell determines their luminal pH , 2016, The Journal of cell biology.

[76]  A. Postle,et al.  Antioxidant Role for Lipid Droplets in a Stem Cell Niche of Drosophila , 2015, Cell.

[77]  Nels C. Elde,et al.  Buried Treasure: Evolutionary Perspectives on Microbial Iron Piracy , 2015, Trends in Genetics.

[78]  M. Malumbres,et al.  AMPK and PFKFB3 mediate glycolysis and survival in response to mitophagy during mitotic arrest , 2015, Nature Cell Biology.

[79]  M. Mari,et al.  Lipid droplets and their component triglycerides and steryl esters regulate autophagosome biogenesis , 2015, The EMBO journal.

[80]  Joerg M. Buescher,et al.  A roadmap for interpreting (13)C metabolite labeling patterns from cells. , 2015, Current opinion in biotechnology.

[81]  Wenxian Wu,et al.  Phosphorylation of ULK1 by AMPK regulates translocation of ULK1 to mitochondria and mitophagy , 2015, FEBS letters.

[82]  S. Gross,et al.  AMPK activation promotes lipid droplet dispersion on detyrosinated microtubules to increase mitochondrial fatty acid oxidation , 2015, Nature Communications.

[83]  J. Lippincott-Schwartz,et al.  Fatty acid trafficking in starved cells: regulation by lipid droplet lipolysis, autophagy, and mitochondrial fusion dynamics. , 2015, Developmental cell.

[84]  J. V. Van Eyk,et al.  Lipid-induced NOX2 activation inhibits autophagic flux by impairing lysosomal enzyme activity[S] , 2015, Journal of Lipid Research.

[85]  Zhiping Xie,et al.  Storage lipid synthesis is necessary for autophagy induced by nitrogen starvation , 2015, FEBS letters.

[86]  M. AndresAllen,et al.  Mitophagy is required for acute cardioprotection by simvastatin. , 2014 .

[87]  Robert V Farese,et al.  Cardiomyocyte-specific Loss of Diacylglycerol Acyltransferase 1 (DGAT1) Reproduces the Abnormalities in Lipids Found in Severe Heart Failure* , 2014, The Journal of Biological Chemistry.

[88]  T. Proikas-Cezanne,et al.  Neutral Lipid Stores and Lipase PNPLA5 Contribute to Autophagosome Biogenesis , 2014, Current Biology.

[89]  Jamey D. Young Metabolic flux rewiring in mammalian cell cultures. , 2013, Current opinion in biotechnology.

[90]  J. James,et al.  Loss of iron triggers PINK1/Parkin-independent mitophagy , 2013, EMBO reports.

[91]  Robert V Farese,et al.  Balancing the fat: lipid droplets and human disease , 2013, EMBO molecular medicine.

[92]  B. Miller,et al.  Lipidomic analysis of human plasma reveals ether-linked lipids that are elevated in morbidly obese humans compared to lean , 2013, Diabetology & Metabolic Syndrome.

[93]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[94]  R. Milo,et al.  Rethinking glycolysis: on the biochemical logic of metabolic pathways. , 2012, Nature chemical biology.

[95]  P. Xue,et al.  Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells , 2012, Nature Cell Biology.

[96]  Paul Thompson,et al.  Phospholipids and insulin resistance in psychosis: a lipidomics study of twin pairs discordant for schizophrenia , 2012, Genome Medicine.

[97]  Hong Wang,et al.  Perilipin 5, a lipid droplet-associated protein, provides physical and metabolic linkage to mitochondria[S] , 2011, Journal of Lipid Research.

[98]  M. V. Vander Heiden,et al.  Aerobic glycolysis: meeting the metabolic requirements of cell proliferation. , 2011, Annual review of cell and developmental biology.

[99]  O. Shirihai,et al.  Fatty Acids Suppress Autophagic Turnover in β-Cells* , 2011, The Journal of Biological Chemistry.

[100]  Jianguo Xia,et al.  Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst , 2011, Nature Protocols.

[101]  Y. Rao,et al.  Genome-wide screen for modifiers of Parkinson's disease genes in Drosophila , 2011, Molecular Brain.

[102]  Robert V Farese,et al.  DGAT enzymes are required for triacylglycerol synthesis and lipid droplets in adipocytes[S] , 2011, Journal of Lipid Research.

[103]  B. Viollet,et al.  Phosphorylation of ULK1 (hATG1) by AMP-Activated Protein Kinase Connects Energy Sensing to Mitophagy , 2011, Science.

[104]  Cahir J. O'Kane,et al.  Lysosomal positioning coordinates cellular nutrient responses , 2011, Nature Cell Biology.

[105]  D. Richardson,et al.  Mitochondrial iron trafficking and the integration of iron metabolism between the mitochondrion and cytosol , 2010, Proceedings of the National Academy of Sciences.

[106]  L. Cantley,et al.  Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation , 2009, Science.

[107]  David S. Wishart,et al.  MetaboAnalyst: a web server for metabolomic data analysis and interpretation , 2009, Nucleic Acids Res..

[108]  P. Storz,et al.  Mitochondrial diacylglycerol initiates protein-kinase-D1-mediated ROS signaling , 2009, Journal of Cell Science.

[109]  V. Beneš,et al.  The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. , 2009, Clinical chemistry.

[110]  Robert V Farese,et al.  The Endoplasmic Reticulum Enzyme DGAT2 Is Found in Mitochondria-associated Membranes and Has a Mitochondrial Targeting Signal That Promotes Its Association with Mitochondria* , 2009, Journal of Biological Chemistry.

[111]  G. Gores,et al.  The lysosomal‐mitochondrial axis in free fatty acid–induced hepatic lipotoxicity , 2008, Hepatology.

[112]  A. Munnich,et al.  Redistribution of accumulated cell iron: a modality of chelation with therapeutic implications. , 2008, Blood.

[113]  B. Dickson,et al.  A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila , 2007, Nature.

[114]  Y. Ohsaki,et al.  Cholesterol depletion induces autophagy. , 2006, Biochemical and biophysical research communications.

[115]  Anne E Carpenter,et al.  CellProfiler: image analysis software for identifying and quantifying cell phenotypes , 2006, Genome Biology.

[116]  M. Tomita,et al.  Differential Metabolomics Reveals Ophthalmic Acid as an Oxidative Stress Biomarker Indicating Hepatic Glutathione Consumption* , 2006, Journal of Biological Chemistry.

[117]  K. North,et al.  Quantitation of long-chain acylcarnitines by HPLC/fluorescence detection: application to plasma and tissue specimens from patients with carnitine palmitoyltransferase-II deficiency. , 2005, Clinica chimica acta; international journal of clinical chemistry.

[118]  A. Hunter,et al.  Lathosterolosis: an inborn error of human and murine cholesterol synthesis due to lathosterol 5-desaturase deficiency. , 2003, Human molecular genetics.

[119]  J. C. Greene,et al.  Mitochondrial pathology and apoptotic muscle degeneration in Drosophila parkin mutants , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[120]  Robert V Farese,et al.  Triglyceride accumulation protects against fatty acid-induced lipotoxicity , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[121]  P. Bernardi,et al.  Effects of fatty acids on mitochondria: implications for cell death. , 2002, Biochimica et biophysica acta.

[122]  G. Weiss,et al.  Iron-dependent changes in cellular energy metabolism: influence on citric acid cycle and oxidative phosphorylation. , 1999, Biochimica et biophysica acta.

[123]  R. Zidovetzki,et al.  Ceramides modulate protein kinase C activity and perturb the structure of Phosphatidylcholine/Phosphatidylserine bilayers. , 1999, Biophysical journal.

[124]  Xiaodong Wang,et al.  Induction of Apoptotic Program in Cell-Free Extracts: Requirement for dATP and Cytochrome c , 1996, Cell.

[125]  O. Saugstad Hypoxanthine as an Indicator of Hypoxia: Its Role in Health and Disease through Free Radical Production , 1988, Pediatric Research.

[126]  S. Dimauro,et al.  Mitochondrial diseases , 2016, Nature Reviews Disease Primers.

[127]  Sandra Castillo,et al.  Liquid chromatography-mass spectrometry (LC-MS)-based lipidomics for studies of body fluids and tissues. , 2011, Methods in molecular biology.