bims-auttor Biomed news
on Autophagy and mTOR
Issue of 2019‒02‒17
sixteen papers selected by
Viktor Korolchuk
Newcastle University


  1. Cell. 2019 Jan 29. pii: S0092-8674(19)30051-0. [Epub ahead of print]
    Neurohr GE, Terry RL, Lengefeld J, Bonney M, Brittingham GP, Moretto F, Miettinen TP, Vaites LP, Soares LM, Paulo JA, Harper JW, Buratowski S, Manalis S, van Werven FJ, Holt LJ, Amon A.
      Cell size varies greatly between cell types, yet within a specific cell type and growth condition, cell size is narrowly distributed. Why maintenance of a cell-type specific cell size is important remains poorly understood. Here we show that growing budding yeast and primary mammalian cells beyond a certain size impairs gene induction, cell-cycle progression, and cell signaling. These defects are due to the inability of large cells to scale nucleic acid and protein biosynthesis in accordance with cell volume increase, which effectively leads to cytoplasm dilution. We further show that loss of scaling beyond a certain critical size is due to DNA becoming limiting. Based on the observation that senescent cells are large and exhibit many of the phenotypes of large cells, we propose that the range of DNA:cytoplasm ratio that supports optimal cell function is limited and that ratios outside these bounds contribute to aging.
    DOI:  https://doi.org/10.1016/j.cell.2019.01.018
  2. Sci Rep. 2019 Feb 14. 9(1): 2102
    Wang Y, Liu J, Ma X, Cui C, Deenik PR, Henderson PKP, Sigler AL, Cui L.
      Detection of cellular senescence is important not only in the study of senescence in various biological systems, but also in various practical applications such as image-guided surgical removal of senescent cells, as well as the monitoring of drug-responsiveness during cancer therapies. Due to the lack of suitable imaging probes for senescence detection, particularly in living subjects, we have developed an activatable near-infrared (NIR) molecular probe with far-red excitation, NIR emission, and high "turn-on" ratio upon senescence-associated β-galactosidase (SABG) activation. We present here the first successful demonstration of NIR imaging of DNA damage-induced senescence both in vitro and in human tumor xenograft models.
    DOI:  https://doi.org/10.1038/s41598-019-38511-z
  3. Autophagy. 2019 Feb 15.
    Birgisdottir ÅB, Mouilleron S, Bhujabal Z, Wirth M, Sjøttem E, Evjen G, Zhang W, Lee R, O'Reilly N, Tooze SA, Lamark T, Johansen T.
      Autophagosome formation depends on a carefully orchestrated interplay between membrane-associated protein complexes. Initiation of macroautophagy/autophagy is mediated by the ULK1 (unc-51 like autophagy activating kinase 1) protein kinase complex and the autophagy-specific class III phosphatidylinositol 3-kinase complex I (PtdIns3K-C1). The latter contains PIK3C3/VPS34, PIK3R4/VPS15, BECN1/Beclin 1 and ATG14 and phosphorylates phosphatidylinositol to generate phosphatidylinositol 3-phosphate (PtdIns3P). Here, we show that PIK3C3, BECN1 and ATG14 contain functional LIR motifs and interact with the Atg8-family proteins with a preference for GABARAP and GABARAPL1. High resolution crystal structures of the functional LIR motifs of these core components of PtdIns3K-C1were obtained. Variation in hydrophobic pocket 2 (HP2) may explain the specificity for the GABARAP family. Mutation of the LIR motif in ATG14 did not prevent formation of the PtdIns3K-C1 complex, but blocked colocalization with MAP1LC3B/LC3B and impaired mitophagy. The ULK-mediated phosphorylation of S29 in ATG14 was strongly dependent on a functional LIR motif in ATG14. GABARAP-preferring LIR motifs in PIK3C3, BECN1 and ATG14 may, via coincidence detection, contribute to scaffolding of PtdIns3K-C1 on membranes for efficient autophagosome formation.
    Keywords:  ATG14; BECN1; GABARAP; LIR; PIK3C3; autophagy
    DOI:  https://doi.org/10.1080/15548627.2019.1581009
  4. Autophagy. 2019 Feb 15.
    Liu Y, Wang J.
      Cellular adaption to nutrient stress is exquisitely regulated, and its dysregulation could underlie human diseases including neurodegeneration. C9orf72 is linked to the most common forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) as well as rare cases of other neurological disorders. Recent studies have implicated C9orf72 functions in the autophagy-lysosome pathway, but the exact roles of C9orf72 remain unclear. We found that C9orf72 is required for the lysosomal targeting and degradation of CARM1, which is an important epigenetic regulator of macroautophagy/autophagy and lipid metabolism. In cells with C9orf72 deficiency including those derived from ALS-FTD patients, CARM1 is abnormally accumulated especially under glucose starvation stress, leading to dysregulated autophagy and lipid metabolism. These findings suggest that C9orf72 is a key regulator in the negative feedback control of the autophagy-lysosome pathway during nutrient stress responses.
    Keywords:  ALS; C9orf72; CARM1; FTD; NOX2; autophagy; fatty acid; lipid droplet; lipid metabolism; lysosome
    DOI:  https://doi.org/10.1080/15548627.2019.1580106
  5. Br J Pharmacol. 2019 Feb 10.
    Chia LY, Evans BA, Mukaida S, Bengtsson T, Hutchinson DS, Sato M.
      A vital role of adrenoceptors in metabolism and energy balance has been well-documented in heart, skeletal muscle, and adipose tissue. It has been only recently demonstrated, however, that activation of mechanistic/mammalian target of rapamycin (mTOR) makes a significant contribution to various metabolic and physiological responses to adrenoceptor agonists. mTOR exists as two distinct complexes named mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2), and has been shown to play a critical role in protein synthesis, cell proliferation, hypertrophy, mitochondrial function, and glucose uptake. This review will describe the physiological significance of mTORC1/2 as a novel paradigm of adrenoceptor signalling in heart, skeletal muscle and adipose tissue. Understanding the detailed signalling cascades of adrenoceptors and how they regulate physiological responses is important for identifying new therapeutic targets and identifying novel therapeutic interventions.
    Keywords:  Adrenoceptor; GLUT4; cardiomyocyte; glucose uptake; mTOR; skeletal muscle
    DOI:  https://doi.org/10.1111/bph.14616
  6. Ann Transl Med. 2018 Dec;6(24): 471
    Aliu E, Kanungo S, Arnold GL.
      Amino acids serve as key building blocks and as an energy source for cell repair, survival, regeneration and growth. Each amino acid has an amino group, a carboxylic acid, and a unique carbon structure. Human utilize 21 different amino acids; most of these can be synthesized endogenously, but 9 are "essential" in that they must be ingested in the diet. In addition to their role as building blocks of protein, amino acids are key energy source (ketogenic, glucogenic or both), are building blocks of Kreb's (aka TCA) cycle intermediates and other metabolites, and recycled as needed. A metabolic defect in the metabolism of tyrosine (homogentisic acid oxidase deficiency) historically defined Archibald Garrod as key architect in linking biochemistry, genetics and medicine and creation of the term 'Inborn Error of Metabolism' (IEM). The key concept of a single gene defect leading to a single enzyme dysfunction, leading to "intoxication" with a precursor in the metabolic pathway was vital to linking genetics and metabolic disorders and developing screening and treatment approaches as described in other chapters in this issue. Amino acid disorders also led to the evolution of the field of metabolic nutrition and offending amino acid restricted formula and foods. This review will discuss the more common disorders caused by inborn errors in amino acid metabolism.
    Keywords:  Phenylketonuria (PKU); amino acids; dietary protein; intoxication; metabolic formula
    DOI:  https://doi.org/10.21037/atm.2018.12.12
  7. J Biol Chem. 2019 Feb 12. pii: jbc.RA118.005698. [Epub ahead of print]
    Iwama R, Ohsumi Y.
      Autophagy is a conserved intracellular degradation system in eukaryotes. Recent studies have revealed that autophagy can be induced not only by nitrogen starvation, but also by many other stimuli. However, questions persist regarding the types of conditions that induce autophagy, as well as the particular kinds of autophagy that are induced under these specific conditions. In experimental studies, abrupt nutrient changes are often used to induce autophagy. In this study, we investigated autophagy induction in batch culture on low-glucose medium, in which growth of yeast (Saccharomyces cerevisiae) cells is clearly reflected exclusively by carbon source state. In this medium, cells pass sequentially through three stages: glucose-utilizing, ethanol-utilizing, and ethanol-depleted phases. Using GFP cleavage assay by immunoblotting methods, fluorescence microscopy, and TEM ultrastructural analysis, we found that bulk autophagy and ER-phagy are induced starting at the ethanol-utilizing phase and bulk autophagy is activated to a greater extent in the ethanol-depleted phase. Furthermore, we found that mitophagy is induced by ethanol depletion. Microautophagy occurred after glucose depletion and involved incorporation of cytosolic components and lipid droplets into the vacuolar lumen. Moreover, we observed that autophagy-deficient cells grow more slowly in the ethanol-utilizing phase and exhibit a delay in growth resumption when they are shifted to fresh medium from the ethanol-depleted phase. Our findings suggest that distinct types of autophagy are induced in yeast cells undergoing gradual changes in carbon source availability.
    Keywords:  ER-phagy; autophagy; autophagy-related protein 8 (Atg8); diauxie; ethanol; glucose; mitophagy; nutrient starvation; physiology; yeast
    DOI:  https://doi.org/10.1074/jbc.RA118.005698
  8. MBio. 2019 Feb 12. pii: e02323-18. [Epub ahead of print]10(1):
    Bossler F, Kuhn BJ, Günther T, Kraemer SJ, Khalkar P, Adrian S, Lohrey C, Holzer A, Shimobayashi M, Dürst M, Mayer A, Rösl F, Grundhoff A, Krijgsveld J, Hoppe-Seyler K, Hoppe-Seyler F.
      Hypoxia is linked to therapeutic resistance and poor clinical prognosis for many tumor entities, including human papillomavirus (HPV)-positive cancers. Notably, HPV-positive cancer cells can induce a dormant state under hypoxia, characterized by a reversible growth arrest and strong repression of viral E6/E7 oncogene expression, which could contribute to therapy resistance, immune evasion and tumor recurrence. The present work aimed to gain mechanistic insights into the pathway(s) underlying HPV oncogene repression under hypoxia. We show that E6/E7 downregulation is mediated by hypoxia-induced stimulation of AKT signaling. Ablating AKT function in hypoxic HPV-positive cancer cells by using chemical inhibitors efficiently counteracts E6/E7 repression. Isoform-specific activation or downregulation of AKT1 and AKT2 reveals that both AKT isoforms contribute to hypoxic E6/E7 repression and act in a functionally redundant manner. Hypoxic AKT activation and consecutive E6/E7 repression is dependent on the activities of the canonical upstream AKT regulators phosphoinositide 3-kinase (PI3K) and mechanistic target of rapamycin (mTOR) complex 2 (mTORC2). Hypoxic downregulation of E6/E7 occurs, at least in part, at the transcriptional level. Modulation of E6/E7 expression by the PI3K/mTORC2/AKT cascade is hypoxia specific and not observed in normoxic HPV-positive cancer cells. Quantitative proteome analyses identify additional factors as candidates to be involved in hypoxia-induced activation of the PI3K/mTORC2/AKT signaling cascade and in the AKT-dependent repression of the E6/E7 oncogenes under hypoxia. Collectively, these data uncover a functional key role of the PI3K/mTORC2/AKT signaling cascade for viral oncogene repression in hypoxic HPV-positive cancer cells and provide new insights into the poorly understood cross talk between oncogenic HPVs and their host cells under hypoxia.IMPORTANCE Oncogenic HPV types are major human carcinogens. Under hypoxia, HPV-positive cancer cells can repress the viral E6/E7 oncogenes and induce a reversible growth arrest. This response could contribute to therapy resistance, immune evasion, and tumor recurrence upon reoxygenation. Here, we uncover evidence that HPV oncogene repression is mediated by hypoxia-induced activation of canonical PI3K/mTORC2/AKT signaling. AKT-dependent downregulation of E6/E7 is only observed under hypoxia and occurs, at least in part, at the transcriptional level. Quantitative proteome analyses identify additional factors as candidates to be involved in AKT-dependent E6/E7 repression and/or hypoxic PI3K/mTORC2/AKT activation. These results connect PI3K/mTORC2/AKT signaling with HPV oncogene regulation, providing new mechanistic insights into the cross talk between oncogenic HPVs and their host cells.
    Keywords:  AKT; cervical cancer; human papillomavirus; tumor virus
    DOI:  https://doi.org/10.1128/mBio.02323-18
  9. Autophagy. 2019 Feb 13.
    Zhou XJ, Klionsky DJ, Zhang H.
      Recent studies suggest that defects in macroautophagy/autophagy contribute to the pathogenesis of systemic lupus erythamatosus (SLE), especially in adaptive immunity. The occurrence and progression of lupus nephritis (LN) is the end result of complex interactions between regulation of immune responses and pathological process by renal resident cells, but there is still a lot of missing information for establishing the role of autophagy in the pathogenesis of LN, and as a therapy target. In our recent study, we observed that autophagy is activated in LN, especially in podocytes. Based on in vitro assays, many of the most important mediators of the disease-patients' sera, patients' IgG and IFNA/IFN-α-can induce autophagy in both murine and human podocytes, by reactive oxygen species production or MTORC1 inhibition; autophagy activation negatively associates with podocyte injury. With regard to intervention, autophagy activators can protect against podocyte injury, whereas autophagy inhibitors aggravate injury. Taken together, our findings suggest that podocyte autophagy is involved in lupus renal protection and may be a therapeutic target. These data shed new light on the role of rapamycin and autophagy inducers in the treatment of SLE.
    Keywords:  MTORC1; autophagy; lupus nephritis; podocyte; rapamycin
    DOI:  https://doi.org/10.1080/15548627.2019.1580512
  10. Cancer. 2019 Feb 12.
    Deng S, Shanmugam MK, Kumar AP, Yap CT, Sethi G, Bishayee A.
      Autophagy, also known as macroautophagy, is a tightly regulated process involved in the stress responses, such as starvation. It is a vacuolar, lysosomal pathway for the degradation of damaged proteins and organelles in eukaryotic cells. Autophagy also plays a key role in various tissue processes and immune responses and in the regulation of inflammation. Over the past decade, three levels of autophagy regulation have been identified in mammalian cells: 1) signaling, 2) autophagosome formation, and 3) autophagosome maturation and lysosomal degradation. Any deregulation of the autophagy processes can lead to the development of diverse chronic diseases, such as diabetes, obesity, cardiovascular disease, neurodegenerative disease, and malignancies. However, the potential role of autophagy in cancer is rather complex and has been associated with both the induction and the inhibition of neoplasia. Several synthetic autophagy modulators have been identified as promising candidates for cancer therapy. In addition, diverse phytochemicals derived from natural sources, such as curcumin, ursolic acid, resveratrol, thymoquinone, and γ-tocotrienol, also have attracted attention as promising autophagy modulators with minimal side effects. In this review, the authors discuss the importance of autophagy regulators and various natural compounds that induce and/or inhibit autophagy in the prevention and therapy of cancer.
    Keywords:  5′-adenosine monophosphate-activated protein kinase; Beclin-1; autophagosome; autophagy; autophagy-related; cancer; lysosome; phytochemicals
    DOI:  https://doi.org/10.1002/cncr.31978
  11. Chem Sci. 2019 Jan 07. 10(1): 56-66
    Park SH, Hyun JY, Shin I.
      Lysosomal pHs are maintained at low values by the cooperative action of a proton pump and a chloride channel to maintain electroneutrality. Owing to the biological significance of lysosomal chloride ions, measurements of their levels are of great importance to understand lysosome-associated biological events. However, appropriate probes to selectively detect Cl- ions within acidic lysosomes have not been developed to date. In this study, we prepared MQAE-MP, a lysosomal Cl--selective fluorescent probe, and applied it to gain information about biological processes associated with lysosomes. The fluorescence of MQAE-MP is pH-insensitive over physiological pH ranges and is quenched by Cl- with a Stern-Volmer constant of 204 M-1. Because MQAE-MP detects lysosomal Cl- selectively, it was employed to assess the effects of eleven substances on lysosomal Cl- concentrations. The results show that lysosomal Cl- concentrations decrease in cells treated with substances that inhibit proteins responsible for lysosomal membrane stabilization, induce lysosomal membrane permeabilization, and transport lysosomal Cl- to the cytosol. In addition, we investigated the effect of lysosomal chloride ions on the fusion of autophagosomes with lysosomes to generate autolysosomes during autophagy inhibition promoted by substances. It was found that changes in lysosomal Cl- concentrations did not affect the fusion of autophagosomes with lysosomes but an increase in the cytosolic Ca2+ concentration blocked the fusion process. We demonstrate from the current study that MQAE-MP has great potential as a lysosomal Cl--selective fluorescent probe for studies of biological events associated with lysosomes.
    DOI:  https://doi.org/10.1039/c8sc04084b
  12. Elife. 2019 Feb 12. pii: e40811. [Epub ahead of print]8
    Ling SC, Dastidar SG, Tokunaga S, Ho WY, Lim K, Ilieva H, Parone PA, Tyan SH, Tse TM, Chang JC, Platoshyn O, Bui NB, Bui A, Vetto A, Sun S, McAlonis-Downes M, Han JS, Swing D, Kapeli K, Yeo GW, Tessarollo L, Marsala M, Shaw CE, Tucker-Kellogg G, La Spada AR, Lagier-Tourenne C, Da Cruz S, Cleveland DW.
      Mutations in coding and non-coding regions of FUS cause amyotrophic lateral sclerosis (ALS). The latter mutations may exert toxicity by increasing FUS accumulation. We show here that broad expression within the nervous system of wild-type or either of two ALS-linked mutants of human FUS in mice produces progressive motor phenotypes accompanied by characteristic ALS-like pathology. FUS levels are autoregulated by a mechanism in which human FUS downregulates endogenous FUS at mRNA and protein levels. Increasing wild-type human FUS expression achieved by saturating this autoregulatory mechanism produces a rapidly progressive phenotype and dose-dependent lethality. Transcriptome analysis reveals mis-regulation of genes that are largely not observed upon FUS reduction. Likely mechanisms for FUS neurotoxicity include autophagy inhibition and defective RNA metabolism. Thus, our results reveal that overriding FUS autoregulation will trigger gain-of-function toxicity via altered autophagy-lysosome pathway and RNA metabolism function, highlighting a role for protein and RNA dyshomeostasis in FUS-mediated toxicity.
    Keywords:  mouse; neuroscience
    DOI:  https://doi.org/10.7554/eLife.40811
  13. Crit Rev Biochem Mol Biol. 2018 Dec;53(6): 623-651
    Parakh S, Perri ER, Jagaraj CJ, Ragagnin AMG, Atkin JD.
      Rab GTPases are becoming increasingly implicated in neurodegenerative disorders, although their role in amyotrophic lateral sclerosis (ALS) has been somewhat overlooked. However, dysfunction of intracellular transport is gaining increasing attention as a pathogenic mechanism in ALS. Many previous studies have focused axonal trafficking, and the extreme length of axons in motor neurons may contribute to their unique susceptibility in this disorder. In contrast, the role of transport defects within the cell body has been relatively neglected. Similarly, whilst Rab GTPases control all intracellular membrane trafficking events, their role in ALS is poorly understood. Emerging evidence now highlights this family of proteins in ALS, particularly the discovery that C9orf72 functions in intra transport in conjunction with several Rab GTPases. Here, we summarize recent updates on cellular transport defects in ALS, with a focus on Rab GTPases and how their dysfunction may specifically target neurons and contribute to pathophysiology. We discuss the molecular mechanisms associated with dysfunction of Rab proteins in ALS. Finally, we also discuss dysfunction in other modes of transport recently implicated in ALS, including nucleocytoplasmic transport and the ER-mitochondrial contact regions (MAM compartment), and speculate whether these may also involve Rab GTPases.
    Keywords:  Amyotrophic lateral sclerosis; Rab GTPases; cellular trafficking; motor neuron disease; neurodegeneration
    DOI:  https://doi.org/10.1080/10409238.2018.1553926
  14. Int J Mol Sci. 2019 Feb 11. pii: E755. [Epub ahead of print]20(3):
    Tian T, Li X, Zhang J.
      The mammalian or mechanistic target of rapamycin (mTOR) pathway plays a crucial role in regulation of cell survival, metabolism, growth and protein synthesis in response to upstream signals in both normal physiological and pathological conditions, especially in cancer. Aberrant mTOR signaling resulting from genetic alterations from different levels of the signal cascade is commonly observed in various types of cancers. Upon hyperactivation, mTOR signaling promotes cell proliferation and metabolism that contribute to tumor initiation and progression. In addition, mTOR also negatively regulates autophagy via different ways. We discuss mTOR signaling and its key upstream and downstream factors, the specific genetic changes in the mTOR pathway and the inhibitors of mTOR applied as therapeutic strategies in eight solid tumors. Although monotherapy and combination therapy with mTOR inhibitors have been extensively applied in preclinical and clinical trials in various cancer types, innovative therapies with better efficacy and less drug resistance are still in great need, and new biomarkers and deep sequencing technologies will facilitate these mTOR targeting drugs benefit the cancer patients in personalized therapy.
    Keywords:  PI3K; cancer; inhibitor; mTOR; therapy
    DOI:  https://doi.org/10.3390/ijms20030755
  15. Reprod Toxicol. 2019 Feb 12. pii: S0890-6238(18)30229-6. [Epub ahead of print]
    Xu C, Chen X, Sheng WB, Yang P.
      Autophagy is required for neurulation, and autophagy activators with minimal toxicity, such as the natural compound trehalose, a nonreducing disaccharide, possess high therapeutic value. To determine whether trehalose directly induces autophagy, FITC-labeled trehalose was used for tracing its presence in autophagosome complexes. Trehalose was as potent as rapamycin and starvation in inducing de novo autophagosome formation and increasing autophagosome flux in GFP-LC3 reporter cells and C17.2 neural stem cells. Trehalose effectively reversed high glucose-suppressed autophagy and reduced p62 protein expression. Trehalose abolished the disruption of autophagosome complexes under high glucose conditions in vitro and maternal diabetes in vivo. Autophagosomes induced by trehalose were functionally active, forming mitophagy and reticulophagy in removing damaged cellular organelles in neuroepithelial cells exposed to maternal diabetes. Thus, trehalose directly participated in functional autophagosome generation by incorporating itself into autophagosomes. These findings provide the mechanistic basis for the use of trehalose in preventing disruptive autophagy-associated pathogenesis.
    Keywords:  autophagosome; autophagy; high glucose; maternal p62diabetes; neural tube defects; trehalose
    DOI:  https://doi.org/10.1016/j.reprotox.2019.02.005