bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2020–02–23
seventeen papers selected by
Viktor Korolchuk, Newcastle University
  1. AMPK activation does not enhance autophagy in neurons in contrast to MTORC1 inhibition: different impact on β-amyloid clearance.
  2. Macroautophagy is repressed during mitosis - seeing is believing.
  3. Autophagy in Parkinson's disease.
  4. Ultrastructural insights into pathogen clearance by autophagy.
  5. The HOPS Complex Subunit VPS39 controls ciliogenesis through autophagy.
  6. LC3C mediates selective autophagy of the MET RTK, inhibiting cancer cell invasion.
  7. Inhibition of USP7 activity selectively eliminates senescent cells in part via restoration of p53 activity.
  8. Beating the ER: novel insights into FAM134B function and regulation.
  9. mTORC1-dependent protein synthesis and autophagy uncouple in the regulation of Apolipoprotein A-I expression.
  10. Autophagic Degradation of NBR1 Restricts Metastatic Outgrowth during Mammary Tumor Progression.
  11. Lipophagy-derived fatty acids undergo extracellular efflux via lysosomal exocytosis.
  12. Autophagic degradation of HAS2 in endothelial cells: A novel mechanism to regulate angiogenesis.
  13. 'High vault-age': non-coding RNA control of autophagy.
  14. Impaired mitophagy links mitochondrial disease to epithelial stress in methylmalonyl-CoA mutase deficiency.
  15. Dimethyloxaloylglycine induces pexophagy in a HIF-2α dependent manner involving autophagy receptor p62.
  16. Microautophagy regulates proteasome homeostasis.
  17. Trehalose limits opportunistic mycobacterial survival during HIV co-infection by reversing HIV-mediated autophagy block.
  1. Autophagy. 2020 Feb 20. 1-16
    AMPK activation does not enhance autophagy in neurons in contrast to MTORC1 inhibition: different impact on β-amyloid clearance.
    Irene Benito-Cuesta, Lara Ordóñez-Gutiérrez, Francisco Wandosell.
      The physiological AKT-MTORC1 and AMPK signaling pathways are considered key nodes in the regulation of anabolism-catabolism, and particularly of macroautophagy/autophagy. Indeed, it is reported that these are altered processes in neurodegenerative proteinopathies such as Alzheimer disease (AD), mainly characterized by deposits of β-amyloid (Aβ) and hyperphosphorylated MAPT. These accumulations disrupt the optimal neuronal proteostasis, and hence, the recovery/enhancement of autophagy has been proposed as a therapeutic approach against these proteinopathies. The purpose of the present study was to characterize the modulation of autophagy by MTORC1 and AMPK signaling pathways in the highly specialized neurons, as well as their repercussions on Aβ production. Using a double transgenic mice model of AD, we demonstrated that MTORC1 inhibition, either in vivo or ex vivo (primary neuronal cultures), was able to reduce amyloid secretion through moderate autophagy induction in neurons. The pharmacological prevention of autophagy in neurons augmented the Aβ secretion and reversed the effect of rapamycin, confirming the anti-amyloidogenic effects of autophagy in neurons. Inhibition of AMPK with compound C generated the expected decrease in autophagy induction, though surprisingly did not increase the Aβ secretion. In contrast, increased activity of AMPK with metformin, AICAR, 2DG, or by gene overexpression did not enhance autophagy but had different effects on Aβ secretion: whereas metformin and 2DG diminished the secreted Aβ levels, AICAR and PRKAA1/AMPK gene overexpression increased them. We conclude that AMPK has a significantly different role in primary neurons than in other reported cells, lacking a direct effect on autophagy-dependent amyloidosis.Abbreviations: 2DG: 2-deoxy-D-glucose; Aβ: β-amyloid; ACACA: acetyl-CoA carboxylase alpha; ACTB: actin beta; AD: Alzheimer disease; AICAR: 5-aminoimidazole-4-carboxamide-1-β-riboside; AKT: AKT kinases group (AKT1 [AKT serine/threonine kinase 1], AKT2 and AKT3); AMPK: adenosine 5'-monophosphate (AMP)-activated protein kinase; APP: amyloid beta precursor protein; APP/PSEN1: B6.Cg-Tg (APPSwe, PSEN1dE9) 85Dbo/J; ATG: autophagy related; ATP: adenosine triphosphate; BafA1: bafilomycin A1; CA: constitutively active; CGN: cerebellar granule neuron; CoC/compound C: dorsommorphin dihydrochloride; ELISA: enzyme-linked immunosorbent assay; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; Gmax: GlutaMAX™; IN1: PIK3C3/VPS34-IN1; KI: kinase-inactive; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3; MAPT/TAU: microtubule associated protein tau; Metf: metformin; MRT: MRT68921; MTORC1: mechanistic target of rapamycin kinase complex 1; NBR1: NBR1 autophagy cargo receptor; PRKAA: 5'-AMP-activated protein kinase catalytic subunit alpha; PtdIns3K: phosphatidylinositol 3-kinase; Rapa: rapamycin; RPS6KB1/S6K: ribosomal protein S6 (RPS6) kinase polypeptide 1; SCR: scramble; SQSTM1/p62: sequestosome 1; ULK1/2: unc-51 like autophagy activating kinase 1/2; WT: wild type.
    Keywords:  2-deoxy-D-glucose; aicar; alzheimer; amyloid accumulation; bafilomycin A1; cultured cerebellar granule neuron; dorsomorphin; metformin; rapamycin; sh-SY5Y
    DOI:  https://doi.org/10.1080/15548627.2020.1728095
  2. Autophagy. 2020 Feb 20. 1-2
    Macroautophagy is repressed during mitosis - seeing is believing.
    Richard I Odle, Simon J Cook.
      For the last two decades there has been wide ranging debate about the status of macroautophagy during mitosis. Because metazoan cells undergo an "open" mitosis in which the nuclear envelope breaks down, it has been proposed that macroautophagy must be inhibited to maintain genome integrity. While many studies have agreed that the number of autophagosomes is greatly reduced in cells undergoing mitosis, there has been no consensus on whether this reflects decreased autophagosome synthesis or increased autophagosome degradation. Reviewing the literature we were concerned that many studies relied too heavily on autophagy assays that were simply not appropriate for a relatively brief event such as mitosis. Using highly dynamic omegasome markers we have recently shown unequivocally that autophagosome synthesis is repressed at the onset of mitosis and is restored once cell division is complete. This is accomplished by CDK1, the master regulator of mitosis, taking over the function of MTORC1, to ensure autophagy is repressed during mitosis.
    Keywords:  ATG13 (autophagy related 13); Autophagy; CDK1 (cyclin dependent kinase 1); MTOR (mechanistic target of rapamycin kinase); MTORC1 (MTOR complex 1); RPTOR/RAPTOR (regulatory associated protein of MTOR complex 1); ULK1 (unc-51 like autophagy activating kinase 1); mitosis; omegasome
    DOI:  https://doi.org/10.1080/15548627.2020.1725405
  3. J Mol Biol. 2020 Feb 13. pii: S0022-2836(20)30103-0. [Epub ahead of print]
    Autophagy in Parkinson's disease.
    Xu Hou, Jens O Watzlawik, Fabienne C Fiesel, Wolfdieter Springer.
      Impaired protein homeostasis and accumulation of damaged or abnormally modified protein are common disease mechanisms in many neurodegenerative disorders including Parkinson's disease (PD). As one of the major degradation pathways, autophagy plays a pivotal role in maintaining effective turnover of proteins and damaged organelles in cells. Several decades of research efforts led to insights into the potential contribution of impaired autophagy machinery to α-synuclein accumulation and degeneration of dopaminergic neurons, two major features of PD pathology. In this review, we summarize recent pathological, genetic, and mechanistic findings that link defective autophagy with PD pathogenesis in human patients, animal and cellular models and discuss current challenges in the field.
    Keywords:  Parkinson’s disease; chaperone-mediated autophagy; macroautophagy; mitophagy; α-synuclein
    DOI:  https://doi.org/10.1016/j.jmb.2020.01.037
  4. Traffic. 2020 Feb 21.
    Ultrastructural insights into pathogen clearance by autophagy.
    Chieko Kishi-Itakura, Nicholas T Ktistakis, Folma Buss.
      Autophagy defends cells against proliferation of bacteria such as Salmonella in the cytosol. After escape from a damaged Salmonella-containing vacuole (SCV) exposing luminal glycans that bind to Galectin-8, the host cell ubiquitination machinery deposits a dense layer of ubiquitin around the cytosolic bacteria. The nature and spatial distribution of this ubiquitin coat in relation to other autophagy-related membranes are unknown. Using Transmission Electron Microscopy we determined the exact localisation of ubiquitin, the ruptured SCV membrane and phagophores around cytosolic Salmonella. Ubiquitin was not predominantly present on the Salmonella surface, but enriched on the fragmented SCV. Cytosolic bacteria without SCVs were less efficiently targeted by phagophores. Single bacteria were contained in single phagophores but multiple bacteria could be within large autophagic vacuoles reaching 30 μm in circumference. These large phagophores followed the contour of the engulfed bacteria, they were frequently in close association with endoplasmic reticulum membranes and, within them, remnants of the SCV were seen associated with each engulfed particle. Our data suggest that the Salmonella SCV has a major role in the formation of autophagic phagophores and highlight evolutionary conserved parallel mechanisms between xenophagy and mitophagy with the fragmented SCV and the damaged outer mitochondrial membrane serving similar functions. This article is protected by copyright. All rights reserved.
    Keywords:  Salmonella; autophagy; electron microscopy; phagophore; xenophagy
    DOI:  https://doi.org/10.1111/tra.12723
  5. Hum Mol Genet. 2020 Feb 20. pii: ddaa029. [Epub ahead of print]
    The HOPS Complex Subunit VPS39 controls ciliogenesis through autophagy.
    Daniela Iaconis, Claudia Crina, Simona Brillante, Alessia Indrieri, Manuela Morleo, Brunella Franco.
      Primary cilia are microtubule-based organelles that assemble and protrude from the surface of most mammalian cells during quiescence. The biomedical relevance of cilia is indicated by disorders ascribed to cilia dysfunction, known as ciliopathies, that display distinctive features including renal cystic disease. In this report, we demonstrate that VPS39, a component of the homotypic fusion and vacuole protein sorting (HOPS) complex, acts as a negative regulator of ciliogenesis in human renal cells, by controlling the localization of the intraflagellar transport 20 (IFT20) protein at the base of cilia through autophagy. Moreover, we show that VPS39 controls ciliogenesis through autophagy also in vivo in renal tubules of Medaka fish. These observations suggest a direct involvement of the HOPS complex in the regulation of autophagy-mediated ciliogenesis and eventually in target selection. Interestingly, we show that the impact of autophagy modulation on ciliogenesis is cell-type dependent and strictly related to environmental stimuli. This report adds a further tile to the cilia-autophagy connection and suggests that VPS39 could represent a new biological target for the recovery of the cilia-related phenotypes observed in the kidneys of patients affected by ciliopathies.
    DOI:  https://doi.org/10.1093/hmg/ddaa029
  6. Autophagy. 2020 Feb 16. 1-3
    LC3C mediates selective autophagy of the MET RTK, inhibiting cancer cell invasion.
    Emily S Bell, Paula Pinto Coelho, Morag Park.
      Macroautophagy/autophagy is an evolutionarily conserved degradative process with a central role in maintaining cellular homeostasis under conditions of stress, and recent evidence suggests this may occur in part through direct modification of cell signaling. The MET/HGF receptor tyrosine kinase (RTK) signaling axis is an important mediator of cell motility and invasion in normal cell functions and in cancer. We discovered a role for autophagy in regulating ligand-activated MET signaling and cellular responses. When autophagy is induced by starvation, the HGF-activated and internalized MET RTK is selectively recruited for autophagic degradation through complex formation with the MAP1LC3C autophagy protein. Decreased LC3C expression in cancer results in loss of autophagic degradation of MET and enhanced HGF-stimulated cell invasion implicated in metastatic progression. This emerging role for autophagy in selectively regulating signaling proteins has implications for understanding cellular adaptations to stress and the functions of autophagy at different stages of cancer progression.
    Keywords:  Autophagy; HGF; invasion; LC3C; MET RTK; cancer; cell migration; signaling; signalophagy
    DOI:  https://doi.org/10.1080/15548627.2020.1728099
  7. Aging Cell. 2020 Feb 16. e13117
    Inhibition of USP7 activity selectively eliminates senescent cells in part via restoration of p53 activity.
    Yonghan He, Wen Li, Dongwen Lv, Xin Zhang, Xuan Zhang, Yuma T Ortiz, Vivekananda Budamagunta, Judith Campisi, Guangrong Zheng, Daohong Zhou.
      The accumulation of senescent cells (SnCs) is a causal factor of various age-related diseases as well as some of the side effects of chemotherapy. Pharmacological elimination of SnCs (senolysis) has the potential to be developed into novel therapeutic strategies to treat these diseases and pathological conditions. Here we show that ubiquitin-specific peptidase 7 (USP7) is a novel target for senolysis because inhibition of USP7 with an inhibitor or genetic depletion of USP7 by RNA interference induces apoptosis selectively in SnCs. The senolytic activity of USP7 inhibitors is likely attributable in part to the promotion of the human homolog of mouse double minute 2 (MDM2) ubiquitination and degradation by the ubiquitin-proteasome system. This degradation increases the levels of p53, which in turn induces the pro-apoptotic proteins PUMA, NOXA, and FAS and inhibits the interaction of BCL-XL and BAK to selectively induce apoptosis in SnCs. Further, we show that treatment with a USP7 inhibitor can effectively eliminate SnCs and suppress the senescence-associated secretory phenotype (SASP) induced by doxorubicin in mice. These findings suggest that small molecule USP7 inhibitors are novel senolytics that can be exploited to reduce chemotherapy-induced toxicities and treat age-related diseases.
    Keywords:  MDM2; Senescence; USP7; apoptosis; p53; senolytics
    DOI:  https://doi.org/10.1111/acel.13117
  8. EMBO J. 2020 Feb 19. e104546
    Beating the ER: novel insights into FAM134B function and regulation.
    Chiara De Leonibus, Laura Cinque, Carmine Settembre.
      To maintain cellular homeostasis, the endoplasmic reticulum (ER) necessitates a continuous removal of ER fragments via a selective, receptor-mediated, form of autophagy known as ER-phagy. In this issue of The EMBO Journal, Jiang et al (2020) shed light on how the best characterized autophagy receptor FAM134B mediates ER membrane fragmentation, the earliest event during ER-phagy. They propose a dynamic model for FAM134B protein oligomerization and ER membrane scission, which are driven by CAMK2B-mediated phosphorylation of the receptor and are altered in sensory neuropathy.
    DOI:  https://doi.org/10.15252/embj.2020104546
  9. Metabolism. 2020 Feb 18. pii: S0026-0495(20)30050-0. [Epub ahead of print] 154186
    mTORC1-dependent protein synthesis and autophagy uncouple in the regulation of Apolipoprotein A-I expression.
    Konstantina Georgila, Michalis Gounis, Sophia Havaki, Vassilis G Gorgoulis, Aristides G Eliopoulos.
       BACKGROUND: Apolipoprotein A-I (ApoA-I) is involved in reverse cholesterol transport as a major component of HDL, but also conveys anti-thrombotic, anti-oxidative, anti-inflammatory and immune-regulatory properties that are pertinent to its protective roles in cardiovascular, inflammatory and malignant pathologies. Despite the pleiotropy in ApoA-I functions, the regulation of intracellular ApoA-I levels remains poorly explored.
    METHODS: HepG2 hepatoma cells and primary mouse hepatocytes were used as in vitro models to study the impact of genetic and chemical inhibitors of autophagy and the proteasome on ApoA-I by immunoblot, immunofluorescence and electron microscopy. Different growth conditions were implemented in conjunction with mTORC inhibitors to model the influence of nutrient scarcity versus sufficiency on ApoA-I regulation. Hepatic ApoA-I expression was also evaluated in high fat diet-fed mice displaying blockade in autophagy.
    RESULTS: Under nutrient-rich conditions, basal ApoA-I levels in liver cells are sustained by the balancing act of autophagy and of mTORC1-dependent de novo protein synthesis. ApoA-I proteolysis occurs through a canonical autophagic pathway involving Beclin1 and ULK1 and the receptor protein p62/SQSTM1 that targets ApoA-I to autophagosomes. However, upon aminoacid insufficiency, suppression of ApoA-I synthesis prevails, rendering mTORC1 inactivation dispensable for autophagy-mediated ApoA-I proteolysis.
    CONCLUSION: These data underscore the major contribution of post-transcriptional mechanisms to ApoA-I levels which differentially involve mTORC1-dependent signaling to protein synthesis and autophagy, depending on nutrient availability. Given the established role of ApoA-I in HDL-mediated reverse cholesterol transport, this mode of ApoA-I regulation may reflect a hepatocellular response to the organismal requirement for maintenance of cholesterol and lipid reserves under conditions of nutrient scarcity.
    Keywords:  ApoA-I; Autophagy; mTORC1
    DOI:  https://doi.org/10.1016/j.metabol.2020.154186
  10. Dev Cell. 2020 Feb 12. pii: S1534-5807(20)30057-5. [Epub ahead of print]
    Autophagic Degradation of NBR1 Restricts Metastatic Outgrowth during Mammary Tumor Progression.
    Timothy Marsh, Candia M Kenific, Deepthisri Suresh, Hugo Gonzalez, Eliah R Shamir, Wenbin Mei, Alexandra Tankka, Andrew M Leidal, Sandhya Kalavacherla, Kimberly Woo, Zena Werb, Jayanta Debnath.
      Although autophagy is being pursued as a therapeutic target in clinical oncology trials, its effects on metastasis, the principal cause of cancer mortality, remain unclear. Here, we utilize mammary cancer models to temporally delete essential autophagy regulators during carcinoma progression. Though genetic ablation of autophagy strongly attenuates primary mammary tumor growth, impaired autophagy promotes spontaneous metastasis and enables the outgrowth of disseminated tumor cells into overt macro-metastases. Transcriptomic analysis reveals that autophagy deficiency elicits a subpopulation of otherwise luminal tumor cells exhibiting basal differentiation traits, which is reversed upon preventing accumulation of the autophagy cargo receptor, Neighbor to BRCA1 (NBR1). Furthermore, pharmacological and genetic induction of autophagy suppresses pro-metastatic differentiation and metastatic outgrowth. Analysis of human breast cancer data reveal that autophagy gene expression inversely correlates with pro-metastatic differentiation signatures and predicts overall and distant metastasis-free survival. Overall, these findings highlight autophagy-dependent control of NBR1 as a key determinant of metastatic progression.
    Keywords:  Keratin14; NBR1; Rubicon; TP63; autophagy; breast cancer; chloroquine; metastasis
    DOI:  https://doi.org/10.1016/j.devcel.2020.01.025
  11. Autophagy. 2020 Feb 19. 1-16
    Lipophagy-derived fatty acids undergo extracellular efflux via lysosomal exocytosis.
    Wenqi Cui, Aishwarya Sathyanarayan, Michael Lopresti, Mariam Aghajan, Chi Chen, Douglas G Mashek.
      The autophagic degradation of lipid droplets (LDs), termed lipophagy, is a major mechanism that contributes to lipid turnover in numerous cell types. While numerous factors, including nutrient deprivation or overexpression of PNPLA2/ATGL (patatin-like phospholipase domain containing 2) drive lipophagy, the trafficking of fatty acids (FAs) produced from this pathway is largely unknown. Herein, we show that PNPLA2 and nutrient deprivation promoted the extracellular efflux of FAs. Inhibition of autophagy or lysosomal lipid degradation attenuated FA efflux highlighting a critical role for lipophagy in this process. Rather than direct transport of FAs across the lysosomal membrane, lipophagy-derived FA efflux requires lysosomal fusion to the plasma membrane. The lysosomal Ca2+ channel protein MCOLN1/TRPML1 (mucolipin 1) regulates lysosomal-plasma membrane fusion and its overexpression increased, while inhibition blocked FA efflux. In addition, inhibition of autophagy/lipophagy or MCOLN1, or sequestration of extracellular FAs with BSA attenuated the oxidation and re-esterification of lipophagy-derived FAs. Overall, these studies show that the well-established pathway of lysosomal fusion to the plasma membrane is the primary route for the disposal of FAs derived from lipophagy. Moreover, the efflux of FAs and their reuptake or subsequent extracellular trafficking to adjacent cells may play an important role in cell-to-cell lipid exchange and signaling.Abbreviations: ACTB: beta actin; ADRA1A: adrenergic receptor alpha, 1a; ALB: albumin; ATG5: autophagy related 5; ATG7: autophagy related 7; BafA1: bafilomycin A1; BECN1: beclin 1; BHBA: beta-hydroxybutyrate; BSA: bovine serum albumin; CDH1: e-cadherin; CQ: chloroquine; CTSB: cathepsin B; DGAT: diacylglycerol O-acyltransferase; FA: fatty acid; HFD: high-fat diet; LAMP1: lysosomal-associated membrane protein 1; LD: lipid droplet; LIPA/LAL: lysosomal acid lipase A; LLME: Leu-Leu methyl ester hydrobromide; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MCOLN1/TRPML1: mucolipin 1; MEF: mouse embryo fibroblast; PBS: phosphate-buffered saline; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PLIN: perilipin; PNPLA2/ATGL patatin-like phospholipase domain containing 2; RUBCN (rubicon autophagy regulator); SM: sphingomyelin; TAG: triacylglycerol; TMEM192: transmembrane protein 192; VLDL: very low density lipoprotein.
    Keywords:  Fatty acid; MCOLN1/TRPML1; PNPLA2/ATGL; lipid droplets; lipid metabolism; lipophagy
    DOI:  https://doi.org/10.1080/15548627.2020.1728097
  12. Matrix Biol. 2020 Feb 18. pii: S0945-053X(20)30011-1. [Epub ahead of print]
    Autophagic degradation of HAS2 in endothelial cells: A novel mechanism to regulate angiogenesis.
    Carolyn G Chen, Maria A Gubbiotti, Aastha Kapoor, Xiaorui Han, Yanglei Yu, Robert J Linhardt, Renato V Iozzo.
      Hyaluronan plays a key role in regulating inflammation and tumor angiogenesis. Of the three transmembrane hyaluronan synthases, HAS2 is the main pro-angiogenic enzyme responsible for excessive hyaluronan production. We discovered that HAS2 was degraded in vascular endothelial cells via autophagy evoked by nutrient deprivation, mTOR inhibition, or pro-autophagic proteoglycan fragments endorepellin and endostatin. Using live-cell and super-resolution confocal microscopy, we found that protracted autophagy evoked a dynamic interaction between HAS2 and ATG9A, a key transmembrane autophagic protein. This regulatory axis of HAS2 degradation occurred in various cell types and species and in vivo upon nutrient deprivation. Inhibiting in vivo autophagic flux via chloroquine showed increased levels of HAS2 in the heart and aorta. Functionally, autophagic induction via endorepellin or mTOR inhibition markedly suppressed extracellular hyaluronan production in vascular endothelial cells and inhibited ex vivo angiogenic sprouting. Thus, we propose autophagy as a novel catabolic mechanism regulating hyaluronan production in endothelial cells and demonstrate a new link between autophagy and angiogenesis that could lead to potential therapeutic modalities for angiogenesis.
    Keywords:  ATG9A; endorepellin; extracellular matrix; hyaluronan; mTOR
    DOI:  https://doi.org/10.1016/j.matbio.2020.02.001
  13. Open Biol. 2020 Feb;10(2): 190307
    'High vault-age': non-coding RNA control of autophagy.
    Magdalena Büscher, Rastislav Horos, Matthias W Hentze.
      RNA-binding proteins typically change the fate of RNA, such as stability, translation or processing. Conversely, we recently uncovered that the small non-coding vault RNA 1-1 (vtRNA1-1) directly binds to the autophagic receptor p62/SQSTM1 and changes the protein's function. We refer to this process as 'riboregulation'. Here, we discuss this newly uncovered vault RNA function against the background of three decades of vault RNA research. We highlight the vtRNA1-1-p62 interaction as an example of riboregulation of a key cellular process.
    Keywords:  p62; riboregulation; vault RNA 1-1
    DOI:  https://doi.org/10.1098/rsob.190307
  14. Nat Commun. 2020 Feb 20. 11(1): 970
    Impaired mitophagy links mitochondrial disease to epithelial stress in methylmalonyl-CoA mutase deficiency.
    Alessandro Luciani, Anke Schumann, Marine Berquez, Zhiyong Chen, Daniela Nieri, Mario Failli, Huguette Debaix, Beatrice Paola Festa, Natsuko Tokonami, Andrea Raimondi, Alessio Cremonesi, Diego Carrella, Patrick Forny, Stefan Kölker, Francesca Diomedi Camassei, Francisca Diaz, Carlos T Moraes, Diego Di Bernardo, Matthias R Baumgartner, Olivier Devuyst.
      Deregulation of mitochondrial network in terminally differentiated cells contributes to a broad spectrum of disorders. Methylmalonic acidemia (MMA) is one of the most common inherited metabolic disorders, due to deficiency of the mitochondrial methylmalonyl-coenzyme A mutase (MMUT). How MMUT deficiency triggers cell damage remains unknown, preventing the development of disease-modifying therapies. Here we combine genetic and pharmacological approaches to demonstrate that MMUT deficiency induces metabolic and mitochondrial alterations that are exacerbated by anomalies in PINK1/Parkin-mediated mitophagy, causing the accumulation of dysfunctional mitochondria that trigger epithelial stress and ultimately cell damage. Using drug-disease network perturbation modelling, we predict targetable pathways, whose modulation repairs mitochondrial dysfunctions in patient-derived cells and alleviate phenotype changes in mmut-deficient zebrafish. These results suggest a link between primary MMUT deficiency, diseased mitochondria, mitophagy dysfunction and epithelial stress, and provide potential therapeutic perspectives for MMA.
    DOI:  https://doi.org/10.1038/s41467-020-14729-8
  15. Biochem Biophys Res Commun. 2020 Feb 16. pii: S0006-291X(20)30319-3. [Epub ahead of print]
    Dimethyloxaloylglycine induces pexophagy in a HIF-2α dependent manner involving autophagy receptor p62.
    Yizhu Mu, Yunash Maharjan, Raghbendra Kumar Dutta, Hyunsoo Kim, Xiaofan Wei, Jin Hwi Kim, Donghyun Kim, Channy Park, Raekil Park.
      Peroxisomes are metabolically active oxygen demanding organelles with a high abundance of oxidases making it vulnerable to low oxygen levels such as hypoxic conditions. However, the exact mechanism of peroxisome degradation in hypoxic condition remains elusive. In order to study the mechanism of peroxisome degradation in hypoxic condition, we use Dimethyloxaloylglycine (DMOG), a cell-permeable prolyl-4-hydroxylase inhibitor, which mimics hypoxic condition by stabilizing hypoxia-inducible factors. Here we report that DMOG degraded peroxisomes by selectively activating pexophagy in a HIF-2α dependent manner involving autophagy receptor p62. Furthermore, DMOG not only increased peroxisome turnover by pexophagy but also reduced HIF-2α dependent peroxisome proliferation at the transcriptional level. Taken together, our data suggest that hypoxic condition is a negative regulator for peroxisome abundance through increasing pexophagy and decreasing peroxisome proliferation in HIF-2α dependent manner.
    Keywords:  Dimethyloxaloylglycine (DMOG); HIF-2α; Peroxisome biogenesis; Pexophagy; p62
    DOI:  https://doi.org/10.1016/j.bbrc.2020.02.051
  16. Curr Genet. 2020 Feb 20.
    Microautophagy regulates proteasome homeostasis.
    Jianhui Li, Mark Hochstrasser.
      Proteasomes are highly abundant protein complexes that are responsible for most regulated protein degradation in cells under favorable growth conditions. When yeast cells are under nutritional stress, most proteasomes exit the nucleus and either accumulate in cytoplasmic condensates called proteasome storage granules (PSGs) or are directed to the vacuole by autophagy. Nitrogen starvation does not cause PSG formation but leads to degradation of proteasomes through the classical macroautophagy pathway. By contrast, carbon starvation or extended incubation in stationary phase results in both PSG formation and macroautophagy of proteasomes. Unexpectedly, we found that glucose limitation also causes proteasomes to be taken up directly into vacuoles by a microautophagy mechanism. Macro- and micro-autophagy occur in parallel in glucose-starved cells, and microautophagy appears biased toward aberrant or inactive proteasomes, leaving functional proteasomes to accumulate in PSGs. PSGs dissolve and proteasomes remobilize to the nucleus within minutes after glucose refeeding. We showed that AMP-activated protein kinase (AMPK) and endosomal-sorting-complex-required-for-transport (ESCRT) factors are required for proteasome microautophagy and also impact PSG dissipation and nuclear reimport of proteasomes after glucose refeeding. The insoluble protein deposit (IPOD) compartment provides an alternative means of proteasome homeostasis, including when microautophagy is impaired. Our findings reveal a surprising diversity of mechanisms for proteasome quality and quantity control during starvation. A mechanistic understanding of the AMPK-regulated ESCRT-mediated microautophagy pathway could provide new avenues for manipulating proteasome homeostasis and treating human disease.
    Keywords:  AMPK; ESCRT; Microautophagy; Proteasome; Proteasome storage granule (PSG)
    DOI:  https://doi.org/10.1007/s00294-020-01059-x
  17. Autophagy. 2020 Feb 20. 1-20
    Trehalose limits opportunistic mycobacterial survival during HIV co-infection by reversing HIV-mediated autophagy block.
    Vartika Sharma, Muzamil Makhdoomi, Lakshyaveer Singh, Purnima Kumar, Nabab Khan, Sarman Singh, H N Verma, Kalpana Luthra, Sovan Sarkar, Dhiraj Kumar.
      Opportunistic bacterial infections amongst HIV-infected individuals contribute significantly to HIV-associated mortality. The role of HIV-mediated modulation of innate mechanisms like autophagy in promoting opportunistic infections, however, remains obscure. Here we show, HIV reactivation in or infection of macrophages inhibits autophagy and helps the survival of pathogenic Mycobacterium tuberculosis (Mtb) and nonpathogenic non-tuberculous mycobacterial strains (NTMs). The HIV-mediated impairment of xenophagy flux facilitated bacterial survival. Activation of autophagy by trehalose could induce xenophagy flux and kill intracellular Mtb or NTMs either during single or co-infections. Trehalose, we delineate, activates PIKFYVE leading to TFEB nuclear translocation in MCOLN1-dependent manner to induce autophagy. Remarkably, trehalose significantly reduced HIV-p24 levels in ex-vivo-infected PBMCs or PBMCs from treatment-naive HIV patients and also controlled mycobacterial survival within Mtb-infected animals. To conclude, we report leveraging of HIV-mediated perturbed host innate-immunity by opportunistic bacterial pathogens and show an attractive therapeutic strategy for HIV and associated co-morbidities.Abbreviations: AIDS: acquired immune deficiency syndrome; AMPK: AMP-activated protein kinase; ATG5: autophagy related 5; BafA1: bafilomycin A1; CFU: colony forming unit; CTSD: cathepsin D; CD63: CD63 molecule; EGFP: enhanced green fluorescent protein; FRET: Förster resonance energy transfer; GABARAP: gamma-aminobutyric acid receptor-associated protein; GAPDH: glyceraldehyde 3-phosphate dehydrogenase; GLUT: glucose transporter; HIV: human immunodeficiency virus; hMDMs: human monocyte derived macrophages; IL2: interleukin 2; LAMP1: lysosomal-associated membrane protein 1; LC3B-II: lipidated microtubule-associated proteins 1A/1B light chain 3B; Mtb: Mycobacterium tuberculosis; MTOR: mechanistic target of rapamycin; mRFP: monomeric red fluorescent protein; M6PR: mannose-6-phosphate receptor; NAC: N- acetyl- L -cysteine; NTM's: non-tuberculous mycobacteria; PBMC: Peripheral Blood Mononuclear cells; PIKFYVE: phosphoinositide kinase; FYVE-Type Zinc Finger; PHA: phytohemagglutinin; PMA: phorbol 12-myristate 13-acetate; PtdIns(3,5)P2: Phosphatidylinositol 3,5-bisphosphate; ptfLC3: pEGFP-mRFP-LC3; ROS: reactive oxygen species; SQSTM1: sequestosome1; TFEB: transcription factor EB; MCOLN1/TRPML1: mucolipin 1; PIP4P1/TMEM55B: Human trans-membrane Protein 55B; UVRAG: UV Radiation Resistance Associate; VPS35: vacuolar protein sorting associated protein 35; WDR45: WD repeat domain 45; YCAM: Yellow Chameleon.
    Keywords:  HIV-TB co-infection; mcoln1/TRPML1; non-tuberculous mycobacteria; opportunistic infection; pikfyve; trehalose; xenophagy
    DOI:  https://doi.org/10.1080/15548627.2020.1725374
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