bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2020‒06‒07
thirty-two papers selected by
Viktor Korolchuk
Newcastle University


  1. J Cell Biol. 2020 Aug 03. pii: e201903127. [Epub ahead of print]219(8):
    Yamamoto YH, Kasai A, Omori H, Takino T, Sugihara M, Umemoto T, Hamasaki M, Hatta T, Natsume T, Morimoto RI, Arai R, Waguri S, Sato M, Sato K, Bar-Nun S, Yoshimori T, Noda T, Nagata K.
      In macroautophagy, membrane structures called autophagosomes engulf substrates and deliver them for lysosomal degradation. Autophagosomes enwrap a variety of targets with diverse sizes, from portions of cytosol to larger organelles. However, the mechanism by which autophagosome size is controlled remains elusive. We characterized a novel ER membrane protein, ERdj8, in mammalian cells. ERdj8 localizes to a meshwork-like ER subdomain along with phosphatidylinositol synthase (PIS) and autophagy-related (Atg) proteins. ERdj8 overexpression extended the size of the autophagosome through its DnaJ and TRX domains. ERdj8 ablation resulted in a defect in engulfing larger targets. C. elegans, in which the ERdj8 orthologue dnj-8 was knocked down, could perform autophagy on smaller mitochondria derived from the paternal lineage but not the somatic mitochondria. Thus, ERdj8 may play a critical role in autophagosome formation by providing the capacity to target substrates of diverse sizes for degradation.
    DOI:  https://doi.org/10.1083/jcb.201903127
  2. Mol Cell. 2020 May 20. pii: S1097-2765(20)30308-7. [Epub ahead of print]
    He A, Chen X, Tan M, Chen Y, Lu D, Zhang X, Dean JM, Razani B, Lodhi IJ.
      Autophagy is activated by prolonged fasting but cannot overcome the ensuing hepatic lipid overload, resulting in fatty liver. Here, we describe a peroxisome-lysosome metabolic link that restricts autophagic degradation of lipids. Acyl-CoA oxidase 1 (Acox1), the enzyme that catalyzes the first step in peroxisomal β-oxidation, is enriched in liver and further increases with fasting or high-fat diet (HFD). Liver-specific Acox1 knockout (Acox1-LKO) protected mice against hepatic steatosis caused by starvation or HFD due to induction of autophagic degradation of lipid droplets. Hepatic Acox1 deficiency markedly lowered total cytosolic acetyl-CoA levels, which led to decreased Raptor acetylation and reduced lysosomal localization of mTOR, resulting in impaired activation of mTORC1, a central regulator of autophagy. Dichloroacetic acid treatment elevated acetyl-CoA levels, restored mTORC1 activation, inhibited autophagy, and increased hepatic triglycerides in Acox1-LKO mice. These results identify peroxisome-derived acetyl-CoA as a key metabolic regulator of autophagy that controls hepatic lipid homeostasis.
    Keywords:  Acox1; Autophagy; Lipid metabolism; NAFLD; Raptor; fatty acid oxidation; lipophagy; mTOR; peroxisomes
    DOI:  https://doi.org/10.1016/j.molcel.2020.05.007
  3. J Cell Sci. 2020 May 22. pii: jcs228114. [Epub ahead of print]133(10):
    Birgisdottir ÅB, Johansen T.
      Autophagy and endocytosis are membrane-vesicle-based cellular pathways for degradation and recycling of intracellular and extracellular components, respectively. These pathways have a common endpoint at the lysosome, where their cargo is degraded. In addition, the two pathways intersect at different stages during vesicle formation, fusion and trafficking, and share parts of the molecular machinery. Accumulating evidence shows that autophagy is dependent upon endocytosis and vice versa. The emerging joint network of autophagy and endocytosis is of vital importance for cellular metabolism and signaling, and thus also highly relevant in disease settings. In this Review, we will discuss examples of how the autophagy machinery impacts on endocytosis and cell signaling, and highlight how endocytosis regulates the different steps in autophagy in mammalian cells. Finally, we will focus on the interplay of these pathways in the quality control of their common endpoint, the lysosome.
    Keywords:  Autophagy; Endocytosis; LAP; LC3-associated phagocytosis; Lysosome; Phagophore
    DOI:  https://doi.org/10.1242/jcs.228114
  4. Redox Biol. 2020 Apr 20. pii: S2213-2317(20)30022-7. [Epub ahead of print] 101465
    Das A, Bell CM, Berlinicke CA, Marsh-Armstrong N, Zack DJ.
      Retinal ganglion cell (RGC) degeneration is the root cause for vision loss in glaucoma as well as in other forms of optic neuropathy. A variety of studies have implicated abnormal mitochondrial quality control (MQC) as contributing to RGC damage and degeneration in optic neuropathies. The ability to differentiate human pluripotent stem cells (hPSCs) into RGCs provides an opportunity to study RGC MQC in great detail. Degradation of damaged mitochondria is a critical step of MQC, and here we have used hPSC-derived RGCs (hRGCs) to analyze how altered mitochondrial degradation pathways in hRGCs affect their survival. Using pharmacological methods, we have investigated the role of the proteasomal and endo-lysosomal pathways in degrading damaged mitochondria in hRGCs and their precursor stem cells. We found that upon mitochondrial damage induced by the proton uncoupler carbonyl cyanide m-chlorophenyl hydrazone (CCCP), hRGCs more efficiently degraded mitochondria than did their precursor stem cells. We further identified that for degrading damaged mitochondria, stem cells predominantly use the ubiquitine-proteasome system (UPS) while hRGCs use the endo-lysosomal pathway. UPS inhibition causes apoptosis and cell death in stem cells, while hRGC viability is dependent on the endo-lysosomal pathway but not on the UPS pathway. These findings suggest that manipulation of the endo-lysosomal pathway could be therapeutically relevant for RGC protection in treating optic neuropathies associated with mitophagy defects. Endo-lysosome dependent cell survival is also conserved in other human neurons as we found that differentiated human cerebral cortical neurons also degenerated upon endo-lysosomal inhibition but not with proteasome inhibition.
    Keywords:  Autophagy; Glaucoma; Human retinal ganglion cells (hRGCs); Mitophagy; Stem cells; Ubiquitine-proteasome system (UPS)
    DOI:  https://doi.org/10.1016/j.redox.2020.101465
  5. Int Rev Cell Mol Biol. 2020 ;pii: S1937-6448(19)30074-7. [Epub ahead of print]354 63-105
    Gohel R, Kournoutis A, Petridi S, Nezis IP.
      Autophagy is a highly conserved catabolic process in which cytoplasmic material is recycled under various conditions of cellular stress, preventing cell damage and promoting survival in the event of energy or nutrient shortage, or in response to various cytotoxic insults. Autophagy is also responsible for the removal of aggregated proteins and damaged organelles, playing a vital role in the quality control of proteins and organelles. Impairment of autophagy has been linked to various diseases, including cancer and neurodegenerative disorders, making it a very interesting process for further research. Recent research highlighted that autophagy is not random and can be selective, making it even more important to understand the molecular mechanisms of selectivity at the organismal level. Drosophila has been demonstrated to be an excellent animal model for studying selective autophagy, as the autophagic machinery is highly conserved, although much is still left to be explored. In this review, an overview of autophagy and its selectivity in Drosophila will be presented.
    Keywords:  Autophagy; Drosophila; Macroautophagy; Selective autophagy; Selective autophagy receptors
    DOI:  https://doi.org/10.1016/bs.ircmb.2019.08.003
  6. Biochem Biophys Res Commun. 2020 May 30. pii: S0006-291X(20)30872-X. [Epub ahead of print]
    Sato M, Ueda E, Konno A, Hirai H, Kurauchi Y, Hisatsune A, Katsuki H, Seki T.
      Glucocorticoids are released from the adrenal cortex and are important for regulating various physiological functions. However, a persistent increase in glucocorticoids due to chronic stress causes various dysfunctions in the central nervous system which can lead to mental disorders such as depression. Macroautophagy, one of the pathways of the autophagy-lysosome protein degradation system, is dysregulated in psychiatric disorders, implicating a disturbance of protein degradation in the pathogenesis of psychiatric disorders. In the present study, we investigated whether glucocorticoids affect the activity of chaperone-mediated autophagy (CMA) and microautophagy (mA), the other two pathways of the autophagy-lysosome system. Treatment of human-derived AD293 cells and primary cultured rat cortical neurons with dexamethasone, a potent glucocorticoid receptor agonist, and endogenous glucocorticoids decreased both CMA and mA activities. However, this decrease was significantly suppressed by treatment with RU-486, a glucocorticoid receptor antagonist. In addition, dexamethasone significantly decreased lysosomal Hsc70. These findings suggest that glucocorticoids negatively regulate CMA and mA in a glucocorticoid receptor-dependent manner, and provide evidence for CMA and mA as novel therapeutic targets for depression.
    Keywords:  Chaperone-mediated autophagy; Glucocorticoid; Heat shock cognate protein 70; Microautophay
    DOI:  https://doi.org/10.1016/j.bbrc.2020.04.132
  7. Autophagy. 2020 Jun 05.
    Pandey K, Yu XW, Steinmetz A, Alberini CM.
      An increase in protein synthesis following learning is a fundamental and evolutionarily conserved mechanism of long-term memory. To maintain homeostasis, this protein synthesis must be counterbalanced by mechanisms such as protein degradation. Recent studies reported that macroautophagy/autophagy, a major protein degradation mechanism, is required for long-term memory formation. However, how learning regulates autophagy and recruits it into long-term memory formation remains to be established. Here, we show that inhibitory avoidance in rats significantly increases the levels of autophagy and lysosomal degradation proteins, including BECN1/beclin 1, LC3-II, SQSTM1/p62 and LAMP1, as well as autophagic flux in the hippocampus. Moreover, pharmacological inhibition or targeted molecular disruption of the learning-induced autophagy impairs long-term memory, leaving short-term memory intact. The increase in autophagy proteins results from active translation of their mRNA and not from changes in their total mRNA levels. Additionally, the induction of autophagy requires the immediate early gene Arc/Arg3.1. Finally, in contrast to classical regulation of autophagy in other systems, we found that the increase in autophagy upon learning is dispensable for the increase in protein synthesis. We conclude that coupling between learning-induced translation and autophagy, rather than translation per se, is an essential mechanism of long-term memory.
    Keywords:  Arc/Arg3.1; autophagic flux; autophagy; learning; memory; translating ribosome affinity purification; translation
    DOI:  https://doi.org/10.1080/15548627.2020.1775393
  8. Front Cell Dev Biol. 2020 ;8 299
    Wang L, Lu G, Shen HM.
      Mitophagy is a key mitochondrial quality control mechanism for effective and selective elimination of damaged mitochondria through the autophagy-lysosome machinery. Defective mitophagy is associated with pathogenesis of important human diseases including neurodegenerative diseases, heart failure, innate immunity, and cancer. In the past two decades, the mechanistic studies of mitophagy have made many breakthroughs with the discoveries of phosphatase and tensin homolog (PTEN)-induced kinase protein 1 (PINK1)-parkin-mediated ubiquitin (Ub)-driven pathway and BCL2/adenovirus E1B 19 kDa protein-interacting proteins 3 (BNIP3)/NIX or FUN14 domain containing 1 (FUNDC1) mitochondrial receptor-mediated pathways. Recently, several isoforms of dual phosphatase PTEN, such as PTEN-long (PTEN-L), have been identified, and some of them are implicated in the mitophagy process via their protein phosphatase activity. In this review, we aim to discuss the regulatory roles of PTEN isoforms in mitophagy. These discoveries may provide new opportunities for development of novel therapeutic strategies for mitophagy-related diseases such as neurodegenerative disorders via targeting PTEN isoforms and mitophagy.
    Keywords:  BNIP3; PINK1; PTEN; PTEN-L; Parkin; mitophagy
    DOI:  https://doi.org/10.3389/fcell.2020.00299
  9. EMBO Rep. 2020 Jun 02. e48686
    Han H, Tan J, Wang R, Wan H, He Y, Yan X, Guo J, Gao Q, Li J, Shang S, Chen F, Tian R, Liu W, Liao L, Tang B, Zhang Z.
      Impairment of PINK1/parkin-mediated mitophagy is currently proposed to be the molecular basis of mitochondrial abnormality in Parkinson's disease (PD). We here demonstrate that PINK1 directly phosphorylates Drp1 on S616. Drp1S616 phosphorylation is significantly reduced in cells and mouse tissues deficient for PINK1, but unaffected by parkin inactivation. PINK1-mediated mitochondrial fission is Drp1S616 phosphorylation dependent. Overexpression of either wild-type Drp1 or of the phosphomimetic mutant Drp1S616D , but not a dephosphorylation-mimic mutant Drp1S616A , rescues PINK1 deficiency-associated phenotypes in Drosophila. Moreover, Drp1 restores PINK1-dependent mitochondrial fission in ATG5-null cells and ATG7-null Drosophila. Reduced Drp1S616 phosphorylation is detected in fibroblasts derived from 4 PD patients harboring PINK1 mutations and in 4 out of 7 sporadic PD cases. Taken together, we have identified Drp1 as a substrate of PINK1 and a novel mechanism how PINK1 regulates mitochondrial fission independent of parkin and autophagy. Our results further link impaired PINK1-mediated Drp1S616 phosphorylation with the pathogenesis of both familial and sporadic PD.
    Keywords:  Parkinson’s disease; autophagy; human dermal fibroblasts; mitochondrial dynamics; parkin
    DOI:  https://doi.org/10.15252/embr.201948686
  10. J Cell Biol. 2020 Aug 03. pii: e202003063. [Epub ahead of print]219(8):
    Pedersen NM, Wenzel EM, Wang L, Antoine S, Chavrier P, Stenmark H, Raiborg C.
      Cancer cells break tissue barriers by use of small actin-rich membrane protrusions called invadopodia. Complete invadopodia maturation depends on protrusion outgrowth and the targeted delivery of the matrix metalloproteinase MT1-MMP via endosomal transport by mechanisms that are not known. Here, we show that the ER protein Protrudin orchestrates invadopodia maturation and function. Protrudin formed contact sites with MT1-MMP-positive endosomes that contained the RAB7-binding Kinesin-1 adaptor FYCO1, and depletion of RAB7, FYCO1, or Protrudin inhibited MT1-MMP-dependent extracellular matrix degradation and cancer cell invasion by preventing anterograde translocation and exocytosis of MT1-MMP. Moreover, when endosome translocation or exocytosis was inhibited by depletion of Protrudin or Synaptotagmin VII, respectively, invadopodia were unable to expand and elongate. Conversely, when Protrudin was overexpressed, noncancerous cells developed prominent invadopodia-like protrusions and showed increased matrix degradation and invasion. Thus, Protrudin-mediated ER-endosome contact sites promote cell invasion by facilitating translocation of MT1-MMP-laden endosomes to the plasma membrane, enabling both invadopodia outgrowth and MT1-MMP exocytosis.
    DOI:  https://doi.org/10.1083/jcb.202003063
  11. Acta Naturae. 2020 Jan-Mar;12(1):12(1): 18-32
    Kudriaeva AA, Sokolov AV, Belogurov AAJ.
      Autophagy is a conservative and evolutionarily ancient process that enables the transfer of various cellular compounds, organelles, and potentially dangerous cellular components to the lysosome for their degradation. This process is crucial for the recycling of energy and substrates, which are required for cellular biosynthesis. Autophagy not only plays a major role in the survival of cells under stress conditions, but is also actively involved in maintaining cellular homeostasis. It has multiple effects on the immune system and cellular remodeling during organism development. The effectiveness of autophagy is ensured by a controlled interaction between two organelles - the autophagosome and the lysosome. Despite significant progress in the description of the molecular mechanisms underlying autophagic-lysosomal system (ALS) functioning, many fundamental questions remain. Namely, the specialized functions of lysosomes and the role of ALS in the pathogenesis of human diseases are still enigmatic. Understanding of the mechanisms that are triggered at all stages of autophagic- lysosomal degradation, from the initiation of autophagy to the terminal stage of substrate destruction in the lysosome, may result in new approaches that could help better uderstand ALS and, therefore, selectively control cellular proteostasis.
    Keywords:  autolysosomal degradation; autophagy; lysosome
    DOI:  https://doi.org/10.32607/actanaturae.10936
  12. Autophagy. 2020 Jun 02. 1-12
    Varusai TM, Jupe S, Sevilla C, Matthews L, Gillespie M, Stein L, Wu G, D'Eustachio P, Metzakopian E, Hermjakob H.
      The 21st century has revealed much about the fundamental cellular process of autophagy. Autophagy controls the catabolism and recycling of various cellular components both as a constitutive process and as a response to stress and foreign material invasion. There is considerable knowledge of the molecular mechanisms of autophagy, and this is still growing as new modalities emerge. There is a need to investigate autophagy mechanisms reliably, comprehensively and conveniently. Reactome is a freely available knowledgebase that consists of manually curated molecular events (reactions) organized into cellular pathways (https://reactome.org/). Pathways/reactions in Reactome are hierarchically structured, graphically presented and extensively annotated. Data analysis tools, such as pathway enrichment, expression data overlay and species comparison, are also available. For customized analysis, information can also be programmatically queried. Here, we discuss the curation and annotation of the molecular mechanisms of autophagy in Reactome. We also demonstrate the value that Reactome adds to research by reanalyzing a previously published work on genome-wide CRISPR screening of autophagy components.ABBREVIATIONS: CMA: chaperone-mediated autophagy; GO: Gene Ontology; MA: macroautophagy; MI: microautophagy; MTOR: mechanistic target of rapamycin kinase; SQSTM1: sequestosome 1.
    Keywords:  Annotation; Reactome; autophagy; biocuration; curation; enrichment analysis; knowledgebase; mechanistic analysis; molecular reactions; pathways
    DOI:  https://doi.org/10.1080/15548627.2020.1761659
  13. Front Endocrinol (Lausanne). 2020 ;11 266
    Gonzalez CD, Resnik R, Vaccaro MI.
      Proteins to be secreted through so-called "conventional mechanisms" are characterized by the presence of an N-terminal peptide that is a leader or signal peptide, needed for access to the endoplasmic reticulum and the Golgi apparatus for further secretion. However, some relevant cytosolic proteins lack of this signal peptides and should be secreted by different unconventional or "non-canonical" processes. One form of this unconventional secretion was named secretory autophagy (SA) because it is specifically associated with the autophagy pathway. It is defined by ATG proteins that regulate the biogenesis of the autophagosome, its representative organelle. The canonical macroautophagy involves the fusion of the autophagosomes with lysosomes for content degradation, whereas the SA pathway bypasses this degradative process to allow the secretion. ATG5, as well as other factors involved in autophagy such as BCN1, are also activated as part of the secretory pathway. SA has been recognized as a new mechanism that is becoming of increasing relevance to explain the unconventional secretion of a series of cytosolic proteins that have critical biological importance. Also, SA may play a role in the release of aggregation-prone protein since it has been related to the autophagosome biogenesis machinery. SA requires the autophagic pathway and both, secretory autophagy and canonical degradative autophagy are at the same time, integrated and highly regulated processes that interact in ultimate cross-talking molecular mechanisms. The potential implications of alterations in SA, its cargos, pathways, and regulation in human diseases such as metabolic/aging pathological processes are predictable. Further research of SA as potential target of therapeutic intervention is deserved.
    Keywords:  ATG (autophagy-related) proteins; IL-1β; aggregate-prone proteins; macroautophagy; unconventional protein secretion
    DOI:  https://doi.org/10.3389/fendo.2020.00266
  14. Antioxid Redox Signal. 2020 Jun 04.
    Fão L, Rego AC.
      Significance: The molecular processes that determine Huntington's disease (HD) pathogenesis are not yet fully understood, and until now no effective neuroprotective therapeutic strategies have been developed. Mitochondria are one of most important organelles required for neuronal homeostasis, by providing metabolic pathways relevant for energy production, regulating calcium homeostasis, or controlling free radical generation and cell death. Because augmented reactive oxygen species (ROS) accompanied by mitochondrial dysfunction are relevant early HD mechanisms, targeting these cellular mechanisms may constitute relevant therapeutic approaches. Recent Advances: Previous findings point toward a close relationship between mitochondrial dysfunction and redox changes in HD. Mutant huntingtin (mHTT) can directly interact with mitochondrial proteins, as translocase of the inner membrane 23 (TIM23), disrupting mitochondrial proteostasis and favoring ROS production and HD progression. Furthermore, abnormal brain and muscle redox signaling contributes to altered proteostasis and motor impairment in HD, which can be improved with the mitochondria-targeted antioxidant mitoquinone or resveratrol, an SIRT1 activator that ameliorates mitochondrial biogenesis and function. Critical Issues: Various antioxidants and metabolic enhancers have been studied in HD; however, the real outcome of these molecules is still debatable. New compounds have proven to ameliorate mitochondrial and redox-based signaling pathways in early stages of HD, potentially precluding selective neurodegeneration. Future Directions: Unraveling the molecular etiology of deregulated mitochondrial function and dynamics, and oxidative stress opens new prospects for HD therapeutics. In this review, we explore the role of redox unbalance and mitochondrial dysfunction in HD progression, and further describe advances on clinical trials in HD based on mitochondrial and redox-based therapeutic strategies.
    Keywords:  Huntington's disease; mitochondrial dysfunction; mutant huntingtin; oxidative stress; therapies
    DOI:  https://doi.org/10.1089/ars.2019.8004
  15. J Cell Sci. 2020 Jun 01. pii: jcs.240622. [Epub ahead of print]
    Ranjitha HB, Ammanathan V, Guleria N, Hosamani M, Sreenivasa BP, Dhanesh VV, Santhoshkumar R, Sagar BKC, Mishra BP, Singh RK, Sanyal A, Manjithaya R, Basagoudanavar SH.
      Foot-and-mouth disease virus (FMDV) is a picornavirus that causes contagious acute infection in cloven-hoofed animals. FMDV replication associated viral protein expression induces endoplasmic reticulum (ER) stress and unfolded protein response (UPR), in turn inducing autophagy to restore cellular homeostasis. We observed that inhibition of BiP, a master regulator of ER stress and UPR, decreased FMDV infection confirming their involvement. Further, we show that the FMDV infection induces UPR mainly through PKR-like ER kinase (PERK)-mediated pathway. Knockdown of PERK and chemical inhibition of PERK activation resulted in decreased expression of FMDV proteins along with the reduction of autophagy marker protein LC3B-II. There are conflicting reports on the role of autophagy in FMDV multiplication. Our study systematically demonstrates that during FMDV infection, PERK mediated UPR stimulated an increased level of endogenous LC3B-II and turnover of SQSTM1, thus confirming the activation of functional autophagy. Modulation of UPR and autophagy by pharmacological and genetic approaches resulted in reduced viral progeny, by enhancing antiviral interferon response. Taken together, this study underscores the prospect of exploring the PERK mediated autophagy as an antiviral target.
    Keywords:  Autophagy; Foot-and-mouth disease virus; Interferon; LC3; P-eIF2α; PERK; Unfolded protein response
    DOI:  https://doi.org/10.1242/jcs.240622
  16. Elife. 2020 Jun 02. pii: e55745. [Epub ahead of print]9
    Sun Y, Li M, Zhao D, Li X, Yang C, Wang X.
      Lysosomes play important roles in cellular degradation to maintain cell homeostasis. In order to understand whether and how lysosomes alter with age and contribute to lifespan regulation, we characterized multiple properties of lysosomes during the aging process in C. elegans. We uncovered age-dependent alterations in lysosomal morphology, motility, acidity and degradation activity, all of which indicate a decline in lysosome function with age. The age-associated lysosomal changes are suppressed in the long-lived mutants daf-2, eat-2 and isp-1, which extend lifespan by inhibiting insulin/IGF-1 signaling, reducing food intake and impairing mitochondrial function, respectively. We found that 43 lysosome genes exhibit reduced expression with age, including genes encoding subunits of the proton pump V-ATPase and cathepsin proteases. The expression of lysosome genes is upregulated in the long-lived mutants, and this upregulation requires the functions of DAF-16/FOXO and SKN-1/NRF2 transcription factors. Impairing lysosome function affects clearance of aggregate-prone proteins and disrupts lifespan extension in daf-2, eat-2 and isp-1 worms. Our data indicate that lysosome function is modulated by multiple longevity pathways and is important for lifespan extension.
    Keywords:  C. elegans; DAF-16/FOXO; SKN-1/NRF2; aging; cell biology; insuin/igf-1 signaling; longevity pathways; lysosome
    DOI:  https://doi.org/10.7554/eLife.55745
  17. Nat Commun. 2020 Jun 01. 11(1): 2714
    Balsa E, Perry EA, Bennett CF, Jedrychowski M, Gygi SP, Doench JG, Puigserver P.
      Electron transport chain (ETC) defects occurring from mitochondrial disease mutations compromise ATP synthesis and render cells vulnerable to nutrient and oxidative stress conditions. This bioenergetic failure is thought to underlie pathologies associated with mitochondrial diseases. However, the precise metabolic processes resulting from a defective mitochondrial ETC that compromise cell viability under stress conditions are not entirely understood. We design a whole genome gain-of-function CRISPR activation screen using human mitochondrial disease complex I (CI) mutant cells to identify genes whose increased function rescue glucose restriction-induced cell death. The top hit of the screen is the cytosolic Malic Enzyme (ME1), that is sufficient to enable survival and proliferation of CI mutant cells under nutrient stress conditions. Unexpectedly, this metabolic rescue is independent of increased ATP synthesis through glycolysis or oxidative phosphorylation, but dependent on ME1-produced NADPH and glutathione (GSH). Survival upon nutrient stress or pentose phosphate pathway (PPP) inhibition depends on compensatory NADPH production through the mitochondrial one-carbon metabolism that is severely compromised in CI mutant cells. Importantly, this defective CI-dependent decrease in mitochondrial NADPH production pathway or genetic ablation of SHMT2 causes strong increases in inflammatory cytokine signatures associated with redox dependent induction of ASK1 and activation of stress kinases p38 and JNK. These studies find that a major defect of CI deficiencies is decreased mitochondrial one-carbon NADPH production that is associated with increased inflammation and cell death.
    DOI:  https://doi.org/10.1038/s41467-020-16423-1
  18. Aging Cell. 2020 May 31. e13163
    Mao K, Chen J, Yu H, Li H, Ren Y, Wu X, Wen Y, Zou F, Li W.
      Poly (ADP-ribose) polymerase 1 (PARP1) is a master regulator of diverse biological processes such as DNA repair, oxidative stress, and apoptosis. PARP1 can be activated by aggregated α-synuclein, and this process in turn exacerbates toxicity of α-synuclein. This circle is closely linked to the evolution of Parkinson's disease (PD) that characterized by progressive neurodegeneration and motor deficits. Here, we reported the PARP1, as a novel upstream molecular of transcription factor EB (TFEB), participates in regulation of autophagy in α-synuclein aggregated cells and mice. PARP1 inhibition not only enhances the nuclear transcription of TFEB via SIRT1 mediated down-regulation of mTOR signaling but also reduces nuclear export of TFEB by attenuating the TFEB-CRM1 interaction. Our results revealed that PARP1 inhibition lessened the accumulation of α-synuclein in PD models. Also, oral administration of PARP1 inhibitor Veliparib prevented neurodegeneration and improved motor ability in α-synucleinA53T transgenic mice. These findings identify that PARP1 signaling pathway regulates TFEB-mediated autophagy, pointing to potential therapeutic strategy of PD via enhancing protein degradation systems.
    Keywords:  PARP1; Parkinson's disease; SIRT1; TFEB; autophagy
    DOI:  https://doi.org/10.1111/acel.13163
  19. Exp Cell Res. 2020 May 27. pii: S0014-4827(20)30358-X. [Epub ahead of print] 112112
    Zhang J, Zhang S, Shi Q, Allen TD, You F, Yang D.
      Inhibition of Aurora-B kinase is a synthetic lethal therapy for tumors that overexpress the MYC oncoprotein. It is currently unclear whether co-occurring oncogenic alterations might influence this synthetic lethality by conferring more or less potency in the killing of tumor cells. To identify such modifiers, isogenic cell lines were utilized to test a variety of cancer genes that have been previously demonstrated to promote survival under conditions of cellular stress, contribute to chemoresistance and/or suppress MYC-primed apoptosis. It was found that Bcl-2 and Bcl-xL, two antiapoptotic members of the Bcl-2 family, can partially suppress the synthetic lethality, but not multinucleation, elicited by a pan-aurora kinase inhibitor, VX-680. Suppression was show to stem from the inhibition of autophagy, specifically in multinucleated cells, rather than a general inhibition of apoptosis. The anti-autophagic activity of Bcl-2 also impacted polyploid cell recovery in colony-forming assays, suggesting a route of escape from MYC-VX-680 synthetic lethality that may have clinical consequences. These findings expand on previous conclusions that autophagic death of VX-680-induced polyploid cells is mediated by Atg6. Bcl-2 and Bcl-xL negatively modulate MYC-VX-680 synthetic lethality and it is the anti-autophagic activity of these two Bcl-2 family proteins, specifically in multinucleate cells, that contributes to resistance to Aurora kinase-targeting drugs.
    Keywords:  AURKB; Apoptosis; Autophagy; Bcl-2; Bcl-xL; MYC; VX-680
    DOI:  https://doi.org/10.1016/j.yexcr.2020.112112
  20. AMRC Open Res. 2020 May 18. 2 21
    Cook SR, Badell-Grau RA, Kirkham ED, Jones KM, Kelly BP, Winston J, Waller-Evans H, Allen ND, Lloyd-Evans E.
      Good's buffers are commonly used for cell culture and, although developed to have minimal to no biological impact, they cause alterations in cellular processes such as autophagy and lysosomal enzyme activity. Using Chinese hamster ovary cells and induced pluripotent stem cell-derived neurons, this study explores the effect of zwitterionic buffers, specifically HEPES, on lysosomal volume and Ca2+ levels. Certain zwitterionic buffers lead to lysosomal expansion and reduced lysosomal Ca2+. Care should be taken when selecting buffers for growth media to avoid detrimental impacts on lysosomal function.
    Keywords:  Ca2+; HEPES; iPSC; lysosomal disease; lysosome; neuron; zwitterionic buffer
    DOI:  https://doi.org/10.12688/amrcopenres.12903.1
  21. Mol Cell. 2020 Jun 04. pii: S1097-2765(20)30303-8. [Epub ahead of print]78(5): 811-813
    Molinari M.
      Liang et al. (2020) reports on a genome-wide screen that reveals new aspects of starvation-induced degradation of the endoplasmic reticulum.
    DOI:  https://doi.org/10.1016/j.molcel.2020.05.002
  22. FASEB J. 2020 Jun 05.
    Wang Y, Nakajima T, Diao P, Yamada Y, Nakamura K, Nakayama J, Tanaka N, Aoyama T, Kamijo Y.
      Metabolic changes in sulfatides and other sulfated glycans have been related to various diseases, including Alzheimer's disease (AD). However, the importance of polyunsaturated fatty acids (PUFA) in sulfated lysosomal substrate metabolism and its related disorders is currently unknown. We investigated the effects of deficiency or supplementation of PUFA on the metabolism of sulfatides and sulfated glycosaminoglycans (sGAGs) in sulfatide-rich organs (brain and kidney) of mice. A PUFA-deficient diet for over 5 weeks significantly reduced the sulfatide expression by increasing the sulfatide degradative enzymes arylsulfatase A and galactosylceramidase in brain and kidney. This sulfatide degradation was clearly associated with the activation of autophagy and lysosomal hyperfunction, the former of which was induced by suppression of the Erk/mTOR pathway. A PUFA-deficient diet also activated the degradation of sGAGs in the brain and kidney and that of amyloid precursor proteins in the brain, indicating an involvement in general lysosomal function and the early developmental process of AD. PUFA supplementation prevented all of the above abnormalities. Taken together, a PUFA deficiency might lead to sulfatide and sGAG degradation associated with autophagy activation and general lysosomal hyperfunction and play a role in many types of disease development, suggesting a possible benefit of prophylactic PUFA supplementation.
    Keywords:  Erk1/2; amyloid precursor protein; glycosaminoglycans; lysosome enzyme; mTOR; nutritional deprivation
    DOI:  https://doi.org/10.1096/fj.202000030RR
  23. Mol Brain. 2020 Jun 02. 13(1): 86
    Choi H, Kim IS, Mun JY.
      Propionic acid (PPA) is a short-chain fatty acid that is an important mediator of cellular metabolism. It is also a by-product of human gut enterobacteria and a common food preservative. A recent study found that rats administered with PPA showed autistic-like behaviors like restricted interest, impaired social behavior, and impaired reversal in a T-maze task. This study aimed to identify a link between PPA and autism phenotypes facilitated by signaling mechanisms in hippocampal neurons. Findings indicated autism-like pathogenesis associated with reduced dendritic spines in PPA-treated hippocampal neurons. To uncover the mechanisms underlying this loss, we evaluated autophagic flux, a functional readout of autophagy, using relevant biomedical markers. Results indicated that autophagic flux is impaired in PPA-treated hippocampal neurons. At a molecular level, the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) pathway was activated and autophagic activity was impaired. We also observed that a MAPK inhibitor rescued dendritic spine loss in PPA-treated hippocampal neurons. Taken together, these results suggest a previously unknown link between PPA and autophagy in spine formation regulation in hippocampal neurons via MAPK/ERK signaling. Our results indicate that MAPK/ERK signaling participates in autism pathogenesis by autophagy disruption affecting dendritic spine density. This study may help to elucidate other mechanisms underlying autism and provide a potential strategy for treating ASD-associated pathology.
    Keywords:  Autophagy; MAPK/ERK signaling; Propionic acid; Short-chain fatty acid; Spine density
    DOI:  https://doi.org/10.1186/s13041-020-00626-0
  24. Drug Des Devel Ther. 2020 ;14 1813-1823
    Liu J, Liu P, Xu T, Chen Z, Kong H, Chu W, Wang Y, Liu Y.
      Introduction: Berberine has been reported to inhibit cancer cell growth by apoptosis induction and exhibits a protective role against cancer progression. The current study aims to investigate the effects of berberine on acute lymphoblastic leukemia (ALL) and the mechanism beyond apoptosis.Methods: Cell viability was determined in ALL cell lines EU-6 and SKW-3 using trypan blue staining. Cell autophagy was determined by immunofluorescence and Western blot. ALL xenograft mice were established to investigate the anti-tumor effects of BBR. The molecular mechanism was explored in ALL cell lines using siRNA and signaling inhibitors.
    Results: Herein, we show that berberine treatment significantly inhibits ALL cell viability and promotes cell death by inducing autophagy in a dose-dependent manner. Moreover, berberine significantly alleviates the aggressive pathological condition in ALL xenograft mice. Mechanistic studies exhibit that berberine induces autophagic death in ALL cells by inactivating AKT/mTORC1 signaling. Chemically targeting AKT/mTORC1 signaling controls berberine-induced cell autophagy in vitro, and blockade of autophagic process blunts berberine-alleviated pathological condition in vivo.
    Discussion: In conclusion, our study reveals that berberine could induce ALL cell autophagic death by inactivating AKT/mTORC1 signaling that could be used to develop small molecule drug for ALL treatment.
    Keywords:  AKT/mTORC1; acute lymphoblastic leukemia; autophagy; berberine
    DOI:  https://doi.org/10.2147/DDDT.S239247
  25. Life Sci Alliance. 2020 Jul;pii: e201800253. [Epub ahead of print]3(7):
    Colaco A, Fernández-Suárez ME, Shepherd D, Gal L, Bibi C, Chuartzman S, Diot A, Morten K, Eden E, Porter FD, Poulton J, Platt N, Schuldiner M, Platt FM.
      Niemann-Pick disease type C (NPC) is a rare lysosomal storage disease caused by mutations in either the NPC1 or NPC2 genes. Mutations in the NPC1 gene lead to the majority of clinical cases (95%); however, the function of NPC1 remains unknown. To gain further insights into the biology of NPC1, we took advantage of the homology between the human NPC1 protein and its yeast orthologue, Niemann-Pick C-related protein 1 (Ncr1). We recreated the NCR1 mutant in yeast and performed screens to identify compensatory or redundant pathways that may be involved in NPC pathology, as well as proteins that were mislocalized in NCR1-deficient yeast. We also identified binding partners of the yeast Ncr1 orthologue. These screens identified several processes and pathways that may contribute to NPC pathogenesis. These included alterations in mitochondrial function, cytoskeleton organization, metal ion homeostasis, lipid trafficking, calcium signalling, and nutrient sensing. The mitochondrial and cytoskeletal abnormalities were validated in patient cells carrying mutations in NPC1, confirming their dysfunction in NPC disease.
    DOI:  https://doi.org/10.26508/lsa.201800253
  26. Mol Nutr Food Res. 2020 Jun 01. e1901231
    Zheng K, Ma J, Wang Y, He Z, Deng K.
      SCOPE: The development of novel compounds that trigger non-apoptotic cell death may represent alternative therapeutic strategies for esophageal squamous cell carcinoma (ESCC) treatment. Cellular senescence suppresses tumorigenesis by halting the proliferation of tumor cells, implying the induction of senescence as a promising anticancer strategy, especially when combined with senolytic agents that specially kill senescent cells. This study is designed to screen novel anti-ESCC compounds from natural product resource and identify its mechanism-of-action.METHODS AND RESULTS: We identify the significant anti-cancer effect and the underlying mechanism of SFN, an isothiocyanate derived from cruciferous vegetables, through RNA-seq, western blot and immunofluorescent assays. We find that SFN inhibits proliferation of ESCC cells through inducing senescence. Mechanistically, SFN induces reactive oxygen species (ROS) via disrupting the balance between glutathione (GSH) and oxidized glutathione (GSSG), leading to DNA damage. In addition, ROS deregulates autophagy and promotes lysosome abnormal biogenesis through regulating mTOR/TFE3 axis. Finally, the inhibited autophagic flux facilitates exosome production, resulting in exosome-mediated paracrine senescence.
    CONCLUSIONS: This study suggests the important roles of autophagy and exosome-mediated paracrine senescence in cancer therapy and highlights SFN as a potent anti-ESCC drug candidate. This article is protected by copyright. All rights reserved.
    Keywords:  ROS; autophagy; exosome; senescence; sulforaphane
    DOI:  https://doi.org/10.1002/mnfr.201901231
  27. Cell Mol Gastroenterol Hepatol. 2020 Jun 02. pii: S2352-345X(20)30089-8. [Epub ahead of print]
    Bohin N, McGowan KP, Keeley TM, Carlson EA, Yan KS, Samuelson LC.
      BACKGROUND & AIMS: Intestinal crypts have a remarkable capacity to regenerate after injury from loss of crypt base columnar (CBC) stem cells. Following injury, facultative stem cells (FSCs) are activated to replenish the epithelium and replace lost CBCs. Our aim was to assess the role of insulin-like growth factor-1 (IGF-1) to activate FSCs for crypt repair.METHODS: The intestinal regenerative response was measured after whole-body 12 Gy γ-irradiation of adult mice. IGF-1 signaling or its downstream effector mTORC1 were inhibited by administering BMS-754807 or rapamycin, respectively. Mice with inducible Rptor gene deletion were studied to test the role of mTORC1 signaling in the intestinal epithelium. FSC activation post-irradiation was measured by lineage tracing.
    RESULTS: We observed a coordinate increase in growth factor expression, including IGF-1, at 2 days post-irradiation, followed by a surge in mTORC1 activity during the regenerative phase of crypt repair at day 4. IGF-1 was localized to pericryptal mesenchymal cells, and IGF-1 receptor was broadly expressed in crypt progenitor cells. Inhibition of IGF-1 signaling via BMS-754807 treatment impaired crypt regeneration after 12 Gy irradiation, with no effect on homeostasis. Similarly, rapamycin inhibition of mTORC1 during the growth factor surge blunted the regenerative response. Analysis of Villin-CreERT2;Rptorfl/fl mice showed that epithelial mTORC1 signaling was essential for crypt regeneration. Lineage tracing from Bmi1-marked cells showed that rapamycin blocked FSC activation post-irradiation.
    CONCLUSIONS: Our study shows that IGF-1 signaling through mTORC1 drives crypt regeneration. We propose that IGF1 release from pericryptal cells stimulates mTORC1 in FSCs to regenerate lost CBCs.
    Keywords:  IGF-1; Raptor; crypt regeneration; intestinal repair; intestinal stem cells; rapamycin
    DOI:  https://doi.org/10.1016/j.jcmgh.2020.05.013
  28. Steroids. 2020 May 30. pii: S0039-128X(20)30097-0. [Epub ahead of print] 108672
    Xu J, Zhang M, Lin X, Wang Y, He X.
      Allium chinense, as a side dish on Asian table, is often used in folk medicine for its health benefits. (25R)-5α-spirostan-3β-yl-3-O-acetyl-O-β-D-glucopyranosyl-(1→2)-O-[β-D-glucopyranosyl-(1→3)]-O-β-D-glucopyranosyl-(1→4)-β-D-galactopyranoside (A-24) is a bioactive steroidal saponin isolated from Allium chinense. Previously, we have shown that A-24 has cytotoxic effects on cancer cells, but not on normal cells. To further explore the underlying mechanisms, in this study, we investigated the anticancer activity of A-24 in human gastric cancer cell lines in terms of cell proliferation, colony formation, cell cycle, induction of apoptosis/autophagy, and PI3K/Akt/mTOR pathway. A-24 showed dose-dependent cytotoxicity in SGC-7901 and AGS cell lines, it induced intrinsic mitochondrial pathway of apoptosis as well as autophagy, G2/M phase arrest and modulation of cyclinB1, p-cdc2, p-wee1 and p-Histone H3 expression. Furthermore, A-24 downregulated the phosphorylation of Akt at Ser473 and mTOR at Ser2448 in PI3K/Akt/mTOR pathway, and its downstream substrates p-p70S6K and p-4EBP1 in a dose-dependent manner. In addition, the pre-treatment of tumor cells with 3-methyladenine (3-MA) and LY294002 increased A-24-induced apoptosis. Collectively, these findings highlight the significance of downregulation of PI3K/Akt/mTOR pathway in A-24-induced apoptosis and autophagy, and the potential application of A-24 as a novel candidate in the treatment of human gastric adenocarcinoma.
    Keywords:  Allium chinense; apoptosis; autophagy; gastric cancer; steroidal saponin
    DOI:  https://doi.org/10.1016/j.steroids.2020.108672
  29. Hypertension. 2020 Jun 01. HYPERTENSIONAHA12015058
    Kumar V, Kurth T, Zheleznova NN, Yang C, Cowley AW.
      We have reported that a high-salt (4.0% NaCl) dietary intake activates mTORC1 and inhibition of this pathway with rapamycin blunts the chronic phase of salt-induced hypertension and renal injury in Dahl salt-sensitive (SS) rats. In SS rats, high-salt intake is known to increase the renal production of H2O2 by NOX4, the most abundant NOX isoform in the kidney, and the global knockout of NOX4 blunts salt-sensitivity in these rats. Here, we explored the hypothesis that elevations of H2O2 by NOX4 in high-salt fed SS rat stimulate mTORC1 for the full development of salt-induced hypertension and renal injury. Our in vitro studies found that H2O2 activates mTORC1 independent of PI3K/AKT and AMPK pathways. To determine the in vivo relevance of NOX4/H2O2/mTORC1 in the salt-induced hypertension, SS-Nox4 knockout (SSNox4-/-) rats were daily administrated with vehicle/rapamycin fed a high-salt diet for 21 days. Rapamycin treatment of SSNox4-/- rats had shown no augmented effect on the salt-induced hypertension nor upon indices of renal injury. Significant reductions of renal T lymphocyte and macrophage together with inhibition of cell proliferation were observed in rapamycin treated rats suggesting a role of mTORC1 independent of NOX4 in the proliferation of immune cell. Given the direct activation of mTORC1 by H2O2 and absence of any further protection from salt-induced hypertension in rapamycin-treated SSNox4-/- rats, we conclude that NOX4-H2O2 is a major upstream activator of mTORC1 that contributes importantly to salt-induced hypertension and renal injury in the SS rat model.
    Keywords:  amino acid; glucose; insulin; rapamycin; reactive oxygen species
    DOI:  https://doi.org/10.1161/HYPERTENSIONAHA.120.15058
  30. Neuron. 2020 Jun 03. pii: S0896-6273(20)30352-4. [Epub ahead of print]106(5): 705-707
    Mayl K, Sreedharan J.
      Mutations in TANK-binding kinase 1 (TBK1) are linked to ALS-FTD. In this issue of Neuron, Gerbino et al. (2020) show how missense mutations in the kinase domain of TBK1 differentially affect disease onset and progression in an ALS mouse model.
    DOI:  https://doi.org/10.1016/j.neuron.2020.05.006
  31. Biomolecules. 2020 May 30. pii: E837. [Epub ahead of print]10(6):
    Ivanova MM, Dao J, Kasaci N, Adewale B, Fikry J, Goker-Alpan O.
      Enzyme replacement therapy (ERT) with recombinant alpha-galactosidase A (rh-α-Gal A) is the standard treatment for Fabry disease (FD). ERT has shown a significant impact on patients; however, there is still morbidity and mortality in FD, resulting in progressive cardiac, renal, and cerebrovascular pathology. The main pathway for delivery of rh-α-Gal A to lysosome is cation-independent mannose-6-phosphate receptor (CI-M6PR) endocytosis, also known as insulin-like growth factor 2 receptor (IGF2R) endocytosis. This study aims to investigate the mechanisms of uptake of rh-α-Gal-A in different cell types, with the exploration of clathrin-dependent and caveolin assisted receptor-mediated endocytosis and the dynamics of autophagy-lysosomal functions. rh-α-Gal-A uptake was evaluated in primary fibroblasts, urine originated kidney epithelial cells, and peripheral blood mononuclear cells derived from Fabry patients and healthy controls, and in cell lines HEK293, HTP1, and HUVEC. Uptake of rh-α-Gal-A was more efficient in the cells with the lowest endogenous enzyme activity. Chloroquine and monensin significantly blocked the uptake of rh-α-Gal-A, indicating that the clathrin-mediated endocytosis is involved in recombinant enzyme delivery. Alternative caveolae-mediated endocytosis coexists with clathrin-mediated endocytosis. However, clathrin-dependent endocytosis is a dominant mechanism for enzyme uptake in all cell lines. These results show that the uptake of rh-α-Gal-A occurs rapidly and activates the autophagy-lysosomal pathway.
    Keywords:  Fabry disease; IGF2R/M6P; alpha-galactosidase A; chloroquine; clathrin; endocytosis; enzyme replacement therapy; lysosome
    DOI:  https://doi.org/10.3390/biom10060837