bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2019–06–16
twelve papers selected by
Viktor Korolchuk, Newcastle University
  1. PHB2 (prohibitin 2) promotes PINK1-PRKN/Parkin-dependent mitophagy by the PARL-PGAM5-PINK1 axis.
  2. IRGM restrains NLRP3 inflammasome activation by mediating its SQSTM1/p62-dependent selective autophagy.
  3. The innate immune sensor Toll-like receptor 2 controls the senescence-associated secretory phenotype.
  4. A reversible autophagy inhibitor blocks autophagosome-lysosome fusion by preventing Stx17 loading onto autophagosomes.
  5. Rapamycin activates mammalian microautophagy.
  6. Restoring brain cholesterol turnover improves autophagy and has therapeutic potential in mouse models of spinocerebellar ataxia.
  7. Autophagy-Independent Functions of the Autophagy Machinery.
  8. Mitochondrial and autophagic alterations in skin fibroblasts from Parkinson disease patients with Parkin mutations.
  9. Ribosome Abundance Control Via the Ubiquitin-Proteasome System and Autophagy.
  10. AMPK directly activates mTORC2 to promote cell survival during acute energetic stress.
  11. Adiponectin receptor PAQR-2 signaling senses low temperature to promote C. elegans longevity by regulating autophagy.
  12. Preserving Lysosomal Function in the Aging Brain: Insights from Neurodegeneration.
  1. Autophagy. 2019 Jun 10.
    PHB2 (prohibitin 2) promotes PINK1-PRKN/Parkin-dependent mitophagy by the PARL-PGAM5-PINK1 axis.
    Chaojun Yan, Longlong Gong, Li Chen, Meng Xu, Hussein Abou-Hamdan, Mingliang Tang, Laurent Désaubry, Zhiyin Song.
      Mitophagy, which is a conserved cellular process for selectively removing damaged or unwanted mitochondria, is critical for mitochondrial quality control and the maintenance of normal cellular physiology. However, the precise mechanisms underlying mitophagy remain largely unknown. Prior studies on mitophagy focused on the events in the mitochondrial outer membrane. PHB2 (prohibitin 2), which is a highly conserved membrane scaffold protein, was recently identified as a novel inner membrane mitophagy receptor that mediates mitophagy. Here, we report a new signaling pathway for PHB2-mediated mitophagy. Upon mitochondrial membrane depolarization or misfolded protein aggregation, PHB2 depletion destabilizes PINK1 in the mitochondria, which blocks the mitochondrial recruitment of PRKN/Parkin, ubiquitin and OPTN (optineurin), leading to an inhibition of mitophagy. In addition, PHB2 overexpression directly induces PRKN recruitment to the mitochondria. Moreover, PHB2-mediated mitophagy is dependent on the mitochondrial inner membrane protease PARL, which interacts with PHB2 and is activated upon PHB2 depletion. Furthermore, PGAM5, which is processed by PARL, participates in PHB2-mediated PINK1 stabilization. Finally, a ligand of PHB proteins that we synthesized, called FL3, was found to strongly inhibit PHB2-mediated mitophagy and to effectively block cancer cell growth and energy production at nanomolar concentrations. Thus, our findings reveal that the PHB2-PARL-PGAM5-PINK1 axis is a novel pathway of PHB2-mediated mitophagy and that targeting PHB2 with the chemical compound FL3 is a promising strategy for cancer therapy.
    Keywords:  PARL; PGAM5; PHB2; PINK1-PRKN; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2019.1628520
  2. Autophagy. 2019 Jun 10.
    IRGM restrains NLRP3 inflammasome activation by mediating its SQSTM1/p62-dependent selective autophagy.
    Subhash Mehto, Swati Chauhan, Kautilya Kumar Jena, Nishant Ranjan Chauhan, Parej Nath, Rinku Sahu, Kollori Dhar, Saroj Kumar Das, Santosh Chauhan.
      IRGM is an established genetic risk factor for Crohn disease (CD) and several other inflammatory disorders. However, the mechanisms employed by IRGM to restrain the inflammation are not known. In our recent study, we showed that IRGM negatively regulates NLRP3 inflammasome activation. IRGM employs 2 parallel approaches to constrain inflammasome activation. First, IRGM directly interacts with NLRP3 and PYCARD/ASC, and mediates their SQSTM1/p62-dependent macroautophagic/autophagic degradation. Second, IRGM impedes inflammasome assembly by blocking the polymerization of NLRP3 and PYCARD. We also found that IRGM suppresses NLRP3-mediated exacerbated outcomes of dextran sodium sulfate (DSS)-induced colitis in a mouse model. Taken together, this study presents evidence that IRGM can directly regulate inflammation and protect from inflammatory diseases.
    Keywords:  Crohn disease; IRGM; IRGM1; NLRP3 inflammasome; autophagy; inflammatory bowel disease
    DOI:  https://doi.org/10.1080/15548627.2019.1628544
  3. Sci Adv. 2019 Jun;5(6): eaaw0254
    The innate immune sensor Toll-like receptor 2 controls the senescence-associated secretory phenotype.
    Priya Hari, Fraser R Millar, Nuria Tarrats, Jodie Birch, Andrea Quintanilla, Curtis J Rink, Irene Fernández-Duran, Morwenna Muir, Andrew J Finch, Valerie G Brunton, João F Passos, Jennifer P Morton, Luke Boulter, Juan Carlos Acosta.
      Cellular senescence is a stress response program characterized by a robust cell cycle arrest and the induction of a proinflammatory senescence-associated secretory phenotype (SASP) that is triggered through an unknown mechanism. Here, we show that, during oncogene-induced senescence (OIS), the Toll-like receptor 2 (TLR2) and its partner TLR10 are key mediators of senescence in vitro and in murine models. TLR2 promotes cell cycle arrest by regulating the tumor suppressors p53-p21CIP1, p16INK4a, and p15INK4b and regulates the SASP through the induction of the acute-phase serum amyloids A1 and A2 (A-SAAs) that, in turn, function as the damage-associated molecular patterns (DAMPs) signaling through TLR2 in OIS. Last, we found evidence that the cGAS-STING cytosolic DNA sensing pathway primes TLR2 and A-SAAs expression in OIS. In summary, we report that innate immune sensing of senescence-associated DAMPs by TLR2 controls the SASP and reinforces the cell cycle arrest program in OIS.
    DOI:  https://doi.org/10.1126/sciadv.aaw0254
  4. Mol Biol Cell. 2019 Jun 12. mbcE18080482
    A reversible autophagy inhibitor blocks autophagosome-lysosome fusion by preventing Stx17 loading onto autophagosomes.
    Somya Vats, Ravi Manjithaya.
      Autophagy is an evolutionarily conserved intracellular lysosomal degradation pathway. It is a multi-step process involving de novo formation of double membrane autophagosomes that capture cytosolic constituents (cargo) and eventually fuse with lysosomes wherein the cargo gets degraded and resulting simpler biomolecules get recycled. In addition to their autophagy function, several of the autophagy related proteins work at the interface of other vesicular trafficking pathways. Hence, development of specific autophagy modulators that do not perturb general endo-lysosomal traffic possesses unique challenges. In this paper, we report a novel small molecule EACC which inhibits autophagic flux by blocking autophagosome-lysosome fusion. Strikingly, unlike other late stage inhibitors, EACC does not have any effect on lysosomal properties or on endocytosis mediated degradation of EGF receptor. EACC affects the translocation of SNAREs Stx17 and SNAP29 on autophagosomes without impeding the completion of autophagosomes. EACC treatment also reduces the interaction of Stx17 with the HOPS subunit VPS33A and the cognate lysosomal R-SNARE VAMP8. Interestingly, this effect of EACC although quite robust is reversible and hence EACC can be used as a tool to study autophagosomal SNARE trafficking. Our results put forward a novel method to block autophagic flux by impeding the action of the autophagosomal SNAREs.
    DOI:  https://doi.org/10.1091/mbc.E18-08-0482
  5. J Pharmacol Sci. 2019 May 24. pii: S1347-8613(19)34062-9. [Epub ahead of print]
    Rapamycin activates mammalian microautophagy.
    Masahiro Sato, Takahiro Seki, Ayumu Konno, Hirokazu Hirai, Yuki Kurauchi, Akinori Hisatsune, Hiroshi Katsuki.
      Autophagy-lysosome proteolysis is classified into macroautophagy (MA), microautophagy (mA) and chaperone-mediated autophagy (CMA). In contrast to MA and CMA, mA have been mainly studied in yeast. In 2011, mammalian mA was identified as a pathway to deliver cytosolic proteins into multivesicular bodies. However, its molecular mechanism is quite different from yeast mA. Using a cell-based method to evaluate mA and CMA, we revealed that rapamycin, an activator of yeast mA, significantly activated mammalian mA. Although rapamycin activates MA, mA was also activated by rapamycin in MA-deficient cells. These findings suggest that rapamycin is a first-identified activator of mammalian mA.
    Keywords:  Chaperone-mediated autophagy; Microautophagy; Rapamycin
    DOI:  https://doi.org/10.1016/j.jphs.2019.05.007
  6. Acta Neuropathol. 2019 Jun 14.
    Restoring brain cholesterol turnover improves autophagy and has therapeutic potential in mouse models of spinocerebellar ataxia.
    Clévio Nóbrega, Liliana Mendonça, Adriana Marcelo, Antonin Lamazière, Sandra Tomé, Gaetan Despres, Carlos A Matos, Fatich Mechmet, Dominique Langui, Wilfred den Dunnen, Luis Pereira de Almeida, Nathalie Cartier, Sandro Alves.
      Spinocerebellar ataxias (SCAs) are devastating neurodegenerative disorders for which no curative or preventive therapies are available. Deregulation of brain cholesterol metabolism and impaired brain cholesterol turnover have been associated with several neurodegenerative diseases. SCA3 or Machado-Joseph disease (MJD) is the most prevalent ataxia worldwide. We show that cholesterol 24-hydroxylase (CYP46A1), the key enzyme allowing efflux of brain cholesterol and activating brain cholesterol turnover, is decreased in cerebellar extracts from SCA3 patients and SCA3 mice. We investigated whether reinstating CYP46A1 expression would improve the disease phenotype of SCA3 mouse models. We show that administration of adeno-associated viral vectors encoding CYP46A1 to a lentiviral-based SCA3 mouse model reduces mutant ataxin-3 accumulation, which is a hallmark of SCA3, and preserves neuronal markers. In a transgenic SCA3 model with a severe motor phenotype we confirm that cerebellar delivery of AAVrh10-CYP46A1 is strongly neuroprotective in adult mice with established pathology. CYP46A1 significantly decreases ataxin-3 protein aggregation, alleviates motor impairments and improves SCA3-associated neuropathology. In particular, improvement in Purkinje cell number and reduction of cerebellar atrophy are observed in AAVrh10-CYP46A1-treated mice. Conversely, we show that knocking-down CYP46A1 in normal mouse brain impairs cholesterol metabolism, induces motor deficits and produces strong neurodegeneration with impairment of the endosomal-lysosomal pathway, a phenotype closely resembling that of SCA3. Remarkably, we demonstrate for the first time both in vitro, in a SCA3 cellular model, and in vivo, in mouse brain, that CYP46A1 activates autophagy, which is impaired in SCA3, leading to decreased mutant ataxin-3 deposition. More broadly, we show that the beneficial effect of CYP46A1 is also observed with mutant ataxin-2 aggregates. Altogether, our results confirm a pivotal role for CYP46A1 and brain cholesterol metabolism in neuronal function, pointing to a key contribution of the neuronal cholesterol pathway in mechanisms mediating clearance of aggregate-prone proteins. This study identifies CYP46A1 as a relevant therapeutic target not only for SCA3 but also for other SCAs.
    Keywords:  24-Cholesterol hydroxylase; Ataxia; Autophagy; Cholesterol metabolism; SCA animal models; SCA patients
    DOI:  https://doi.org/10.1007/s00401-019-02019-7
  7. Cell. 2019 Jun 13. pii: S0092-8674(19)30554-9. [Epub ahead of print]177(7): 1682-1699
    Autophagy-Independent Functions of the Autophagy Machinery.
    Lorenzo Galluzzi, Douglas R Green.
      Macroautophagy (herein referred to as autophagy) is an evolutionary ancient mechanism that culminates with the lysosomal degradation of superfluous or potentially dangerous cytosolic entities. Over the past 2 decades, the molecular mechanisms underlying several variants of autophagy have been characterized in detail. Accumulating evidence suggests that most, if not all, components of the molecular machinery for autophagy also mediate autophagy-independent functions. Here, we discuss emerging data on the non-autophagic functions of autophagy-relevant proteins.
    Keywords:  ATG5; BECN1; LC3-associated phagocytosis; proliferation; regulated cell death; vesicular trafficking
    DOI:  https://doi.org/10.1016/j.cell.2019.05.026
  8. Aging (Albany NY). 2019 Jun 09.
    Mitochondrial and autophagic alterations in skin fibroblasts from Parkinson disease patients with Parkin mutations.
    Ingrid González-Casacuberta, Diana-Luz Juárez-Flores, Mario Ezquerra, Raquel Fucho, Marc Catalán-García, Mariona Guitart-Mampel, Ester Tobías, Carmen García-Ruiz, José Carlos Fernández-Checa, Eduard Tolosa, María-José Martí, Josep Maria Grau, Rubén Fernández-Santiago, Francesc Cardellach, Constanza Morén, Glòria Garrabou.
      PRKN encodes an E3-ubiquitin-ligase involved in multiple cell processes including mitochondrial homeostasis and autophagy. Previous studies reported alterations of mitochondrial function in fibroblasts from patients with PRKN mutation-associated Parkinson's disease (PRKN-PD) but have been only conducted in glycolytic conditions, potentially masking mitochondrial alterations. Additionally, autophagy flux studies in this cell model are missing.We analyzed mitochondrial function and autophagy in PRKN-PD skin-fibroblasts (n=7) and controls (n=13) in standard (glucose) and mitochondrial-challenging (galactose) conditions.In glucose, PRKN-PD fibroblasts showed preserved mitochondrial bioenergetics with trends to abnormally enhanced mitochondrial respiration that, accompanied by decreased CI, may account for the increased oxidative stress. In galactose, PRKN-PD fibroblasts exhibited decreased basal/maximal respiration vs. controls and reduced mitochondrial CIV and oxidative stress compared to glucose, suggesting an inefficient mitochondrial oxidative capacity to meet an extra metabolic requirement. PRKN-PD fibroblasts presented decreased autophagic flux with reduction of autophagy substrate and autophagosome synthesis in both conditions.The alterations exhibited under neuron-like oxidative environment (galactose), may be relevant to the disease pathogenesis potentially explaining the increased susceptibility of dopaminergic neurons to undergo degeneration. Abnormal PRKN-PD phenotype supports the usefulness of fibroblasts to model disease and the view of PD as a systemic disease where molecular alterations are present in peripheral tissues.
    Keywords:  Parkin mutation; Parkinson’s disease; autophagy; fibroblasts; mitochondrial function
    DOI:  https://doi.org/10.18632/aging.102014
  9. J Mol Biol. 2019 Jun 10. pii: S0022-2836(19)30353-5. [Epub ahead of print]
    Ribosome Abundance Control Via the Ubiquitin-Proteasome System and Autophagy.
    Heeseon An, J Wade Harper.
      Ribosomes are central to the life of a cell, as they translate the genetic code into the amino acid language of proteins. Moreover, ribosomal abundance within the cell is coordinated with protein production required for cell function or processes such as cell division. As such, it is not surprising that these elegant machines are both highly regulated at the level of both their output of newly translated proteins but also at the level of ribosomal protein expression, ribosome assembly, and ribosome turnover. In this review, we focus on mechanisms that regulate ribosome abundance through both the ubiquitin-proteasome system and forms of autophagy referred to as "ribophagy". We discussed mechanisms employed in both yeast and mammalian cells, including the various machinery that is important for recognition and degradation of ribosomal components. In addition, we discussed controversies in the field and how the development of new approaches for examining flux through the proteasomal and autophagic systems in the context of a systematic inventory of ribosomal components is necessary to fully understand how ribosome abundance is controlled under various physiological conditions.
    Keywords:  autophagy; degradation; ribosome; ubiquitin
    DOI:  https://doi.org/10.1016/j.jmb.2019.06.001
  10. Sci Signal. 2019 Jun 11. pii: eaav3249. [Epub ahead of print]12(585):
    AMPK directly activates mTORC2 to promote cell survival during acute energetic stress.
    Dubek Kazyken, Brian Magnuson, Cagri Bodur, Hugo A Acosta-Jaquez, Deqiang Zhang, Xin Tong, Tammy M Barnes, Gabrielle K Steinl, Nicole E Patterson, Christopher H Altheim, Naveen Sharma, Ken Inoki, Gregory D Cartee, Dave Bridges, Lei Yin, Steven M Riddle, Diane C Fingar.
      AMP-activated protein kinase (AMPK) senses energetic stress and, in turn, promotes catabolic and suppresses anabolic metabolism coordinately to restore energy balance. We found that a diverse array of AMPK activators increased mTOR complex 2 (mTORC2) signaling in an AMPK-dependent manner in cultured cells. Activation of AMPK with the type 2 diabetes drug metformin (GlucoPhage) also increased mTORC2 signaling in liver in vivo and in primary hepatocytes in an AMPK-dependent manner. AMPK-mediated activation of mTORC2 did not result from AMPK-mediated suppression of mTORC1 and thus reduced negative feedback on PI3K flux. Rather, AMPK associated with and directly phosphorylated mTORC2 (mTOR in complex with rictor). As determined by two-stage in vitro kinase assay, phosphorylation of mTORC2 by recombinant AMPK was sufficient to increase mTORC2 catalytic activity toward Akt. Hence, AMPK phosphorylated mTORC2 components directly to increase mTORC2 activity and downstream signaling. Functionally, inactivation of AMPK, mTORC2, and Akt increased apoptosis during acute energetic stress. By showing that AMPK activates mTORC2 to increase cell survival, these data provide a potential mechanism for how AMPK paradoxically promotes tumorigenesis in certain contexts despite its tumor-suppressive function through inhibition of growth-promoting mTORC1. Collectively, these data unveil mTORC2 as a target of AMPK and the AMPK-mTORC2 axis as a promoter of cell survival during energetic stress.
    DOI:  https://doi.org/10.1126/scisignal.aav3249
  11. Nat Commun. 2019 Jun 13. 10(1): 2602
    Adiponectin receptor PAQR-2 signaling senses low temperature to promote C. elegans longevity by regulating autophagy.
    Yuan-Li Chen, Jun Tao, Pei-Ji Zhao, Wei Tang, Jian-Ping Xu, Ke-Qin Zhang, Cheng-Gang Zou.
      Temperature is a key factor for determining the lifespan of both poikilotherms and homeotherms. It is believed that animals live longer at lower body temperatures. However, the precise mechanism remains largely unknown. Here, we report that autophagy serves as a boost mechanism for longevity at low temperature in the nematode Caenorhabditis elegans. The adiponectin receptor AdipoR2 homolog PAQR-2 signaling detects temperature drop and augments the biosynthesis of two ω-6 polyunsaturated fatty acids, γ-linolenic acid and arachidonic acid. These two polyunsaturated fatty acids in turn initiate autophagy in the epidermis, delaying an age-dependent decline in collagen contents, and extending the lifespan. Our findings reveal that the adiponectin receptor PAQR-2 signaling acts as a regulator linking low temperature with autophagy to extend lifespan, and suggest that such a mechanism may be evolutionally conserved among diverse organisms.
    DOI:  https://doi.org/10.1038/s41467-019-10475-8
  12. Neurotherapeutics. 2019 Jun 10.
    Preserving Lysosomal Function in the Aging Brain: Insights from Neurodegeneration.
    Wesley Peng, Georgia Minakaki, Maria Nguyen, Dimitri Krainc.
      Lysosomes are acidic, membrane-bound organelles that serve as the primary catabolic compartment of the cell. They are crucial to a variety of cellular processes from nutrient storage to autophagy. Given the diversity of lysosomal functions, it is unsurprising that lysosomes are also emerging as important players in aging. Lysosomal dysfunction is implicated in several aging-related neurodegenerative diseases including Alzheimer's, Parkinson's, amyotrophic lateral sclerosis/frontotemporal dementia, and Huntington's. Although the precise role of lysosomes in the aging brain is not well-elucidated, some insight into their function has been gained from our understanding of the pathophysiology of age-dependent neurodegenerative diseases. Therapeutic strategies targeting lysosomes and autophagic machinery have already been tested in several of these diseases with promising results, suggesting that improving lysosomal function could be similarly beneficial in preserving function in the aging brain.
    Keywords:  Lysosome; aging; autophagy; neurodegeneration; therapeutic targets
    DOI:  https://doi.org/10.1007/s13311-019-00742-3
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