bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2019–03–03
25 papers selected by
Viktor Korolchuk, Newcastle University
  1. The "other" mTOR complex: new insights into mTORC2 immunobiology and their implications.
  2. Ubiquilins regulate autophagic flux through mTOR signalling and lysosomal acidification.
  3. The mTORC1-autophagy pathway is a target for senescent cell elimination.
  4. Two distinct mechanisms target the autophagy-related E3 complex to the pre-autophagosomal structure.
  5. Regulation of LC3 Lipidation by the Autophagy-Specific Class III Phosphatidylinostitol-3 Kinase Complex.
  6. TORC1 regulates autophagy induction in response to proteotoxic stress in yeast and human cells.
  7. Methods for Monitoring Matrix-Induced Autophagy.
  8. Cytoplasmic control of Rab family small GTPases through BAG6.
  9. Gamma secretase orthologs are required for lysosomal activity and autophagic degradation in Dictyostelium discoideum, independent of PSEN (presenilin) proteolytic function.
  10. Mitochondrial transport proteins RHOT1 and RHOT2 serve as docking sites for PRKN-mediated mitophagy.
  11. Autophagy-Mediated Cholesterol Trafficking Controls Steroid Production.
  12. Omegasome-proximal PtdIns(4,5)P2 couples F-actin mediated mitoaggregate disassembly with autophagosome formation during mitophagy.
  13. An autophagy-independent role for ATG16L1: promoting lysosome-mediated plasma membrane repair.
  14. Targeting autophagy in cardiac ischemia/reperfusion injury: A novel therapeutic strategy.
  15. The epg5 knockout zebrafish line: a model to study Vici syndrome.
  16. TRAF6 inhibits colorectal cancer metastasis through regulating selective autophagic CTNNB1/β-catenin degradation and is targeted for GSK3B/GSK3β-mediated phosphorylation and degradation.
  17. Targetome Analysis of Chaperone-Mediated Autophagy in Cancer Cells.
  18. Hyperactivation of mTORC1 disrupts cellular homeostasis in cerebellar Purkinje cells.
  19. Novel therapeutic strategies for stroke: The role of autophagy.
  20. Autophagy in the Heart.
  21. An autophagy deficiency promotes methylmercury-induced multinuclear cell formation.
  22. The selective autophagy receptors Optineurin and p62 are both required for zebrafish host resistance to mycobacterial infection.
  23. Cell penetrable, clickable and tagless activity-based probe of human cathepsin L.
  24. Down-regulated TMED10 in Alzheimer disease induces autophagy via ATG4B activation.
  25. Mammalian Target of Rapamycin: A Metabolic Rheostat for Regulating Adipose Tissue Function and Cardiovascular Health.
  1. Am J Transplant. 2019 Feb 23.
    The "other" mTOR complex: new insights into mTORC2 immunobiology and their implications.
    Helong Dai, Angus W Thomson.
      A central role of the mechanistic target of rapamycin (mTOR) in regulation of fundamental cell processes is well-recognized. mTOR functions in two distinct complexes: rapamycin-sensitive mTOR complex (C) 1 and rapamycin-insensitive mTORC2. While the role of mTORC1 in shaping immune responses, including transplant rejection, and the influence of its antagonism in promoting allograft tolerance have been studied extensively using rapamycin, lack of selective small molecule inhibitors has limited understanding of mTORC2 biology. Within the past few years, however, intracellular localization of mTORC2, its contribution to mitochondrial fitness, cell metabolism, cytoskeletal modeling and cell migration, and its role in differentiation and function of immune cells have been described. Studies in mTORC2 knockdown/knockout mouse models and a new class of dual mTORC1/2 inhibitors, have shed light on the immune regulatory functions of mTORC2. These include regulation of antigen-presenting cell, NK cell, T cell subset and B cell differentiation and function. mTORC2 has been implicated in regulation of ischemia/reperfusion injury and graft rejection. Potential therapeutic benefits of antagonizing mTORC2 to inhibit chronic rejection have also been described, while selective in vivo targeting strategies using nanotechnology have been developed. We briefly review and discuss these developments and their implications. This article is protected by copyright. All rights reserved.
    DOI:  https://doi.org/10.1111/ajt.15320
  2. Nat Cell Biol. 2019 Mar;21(3): 384-396
    Ubiquilins regulate autophagic flux through mTOR signalling and lysosomal acidification.
    Mümine Şentürk, Guang Lin, Zhongyuan Zuo, Dongxue Mao, Emma Watson, Antonios G Mikos, Hugo J Bellen.
      Although the aetiology of amyotrophic lateral sclerosis (ALS) remains poorly understood, impaired proteostasis is a common feature of different forms of ALS. Mutations in genes encoding ubiquilins, UBQLN2 and UBQLN4, cause familial ALS. The role of ubiquilins in proteasomal degradation is well established, but their role in autophagy-lysosomal clearance is poorly defined. Here, we describe a crosstalk between endoplasmic reticulum stress, mTOR signalling and autophagic flux in Drosophila and mammalian cells lacking ubiquilins. We found that loss of ubiquilins leads to endoplasmic reticulum stress, impairs mTORC1 activity, promotes autophagy and causes the demise of neurons. We show that ubiquilin mutants display defective autophagic flux due to reduced lysosome acidification. Ubiquilins are required to maintain proper levels of the V0a/V100 subunit of the vacuolar H+-ATPase and lysosomal pH. Feeding flies acidic nanoparticles alleviates defective autophagic flux in ubiquilin mutants. Hence, our studies reveal a conserved role for ubiquilins as regulators of autophagy by controlling vacuolar H+-ATPase activity and mTOR signalling.
    DOI:  https://doi.org/10.1038/s41556-019-0281-x
  3. Biogerontology. 2019 Feb 23.
    The mTORC1-autophagy pathway is a target for senescent cell elimination.
    Olena Kucheryavenko, Glyn Nelson, Thomas von Zglinicki, Viktor I Korolchuk, Bernadette Carroll.
      Cellular senescence has recently been established as a key driver of organismal ageing. The state of senescence is controlled by extensive rewiring of signalling pathways, at the heart of which lies the mammalian Target of Rapamycin Complex I (mTORC1). Here we discuss recent publications aiming to establish the mechanisms by which mTORC1 drives the senescence program. In particular, we highlight our data indicating that mTORC1 can be used as a target for senescence cell elimination in vitro. Suppression of mTORC1 is known to extend lifespan of yeast, worms, flies and some mouse models and our proof-of-concept experiments suggest that it can also act by reducing senescent cell load in vivo.
    Keywords:  Ageing; DNA damage; Senescence; Torin1; mTOR
    DOI:  https://doi.org/10.1007/s10522-019-09802-9
  4. Elife. 2019 Feb 27. pii: e43088. [Epub ahead of print]8
    Two distinct mechanisms target the autophagy-related E3 complex to the pre-autophagosomal structure.
    Kumi Harada, Tetsuya Kotani, Hiromi Kirisako, Machiko Sakoh-Nakatogawa, Yu Oikawa, Yayoi Kimura, Hisashi Hirano, Hayashi Yamamoto, Yoshinori Ohsumi, Hitoshi Nakatogawa.
      In autophagy, Atg proteins organize the pre-autophagosomal structure (PAS) to initiate autophagosome formation. Previous studies in yeast revealed that the autophagy-related E3 complex Atg12-Atg5-Atg16 is recruited to the PAS via Atg16 interaction with Atg21, which binds phosphatidylinositol 3-phosphate (PI3P) produced at the PAS, to stimulate conjugation of the ubiquitin-like protein Atg8 to phosphatidylethanolamine. Here, we discover a novel mechanism for the PAS targeting of Atg12-Atg5-Atg16, which is mediated by the interaction of Atg12 with the Atg1 kinase complex that serves as a scaffold for PAS organization. While autophagy is partially defective without one of these mechanisms, cells lacking both completely lose the PAS localization of Atg12-Atg5-Atg16 and show no autophagic activity. As with the PI3P-dependent mechanism, Atg12-Atg5-Atg16 recruited via the Atg12-dependent mechanism stimulates Atg8 lipidation, but also has the specific function of facilitating PAS scaffold assembly. Thus, this study significantly advances our understanding of the nucleation step in autophagosome formation.
    Keywords:  S. cerevisiae; cell biology
    DOI:  https://doi.org/10.7554/eLife.43088
  5. Mol Biol Cell. 2019 Feb 27. mbcE18110743
    Regulation of LC3 Lipidation by the Autophagy-Specific Class III Phosphatidylinostitol-3 Kinase Complex.
    Livia W Brier, Liang Ge, Goran Stjepanovic, Ashley M Thelen, James Hurley, Randy Schekman.
      Autophagy is a conserved eukaryotic pathway critical for cellular adaptation to changes in nutrition levels and stress. The class III phosphatidylinositol 3-kinase complexes I and II (PI3KC3-C1 and C2) are essential for autophagosome initiation and maturation, respectively, from highly curved vesicles. We used a cell-free reaction that reproduces a key autophagy initiation step, LC3 lipidation, as a biochemical readout to probe the role of ATG14, a PI3KC3-C1-specific subunit implicated in targeting the complex to autophagy initiation sites. We reconstituted LC3 lipidation with recombinant PI3KC3-C1, -C2 or various mutant derivatives added to extracts derived from a CRISPR/Cas9-generated ATG14-knockout cell line. Both complexes C1 and C2 require the C-terminal helix of VPS34 for activity on highly curved membranes. However, only complex C1 supports LC3 lipidation through the curvature-targeting ALPS motif of ATG14. Furthermore, the ALPS motif and VPS34 catalytic activity are required for downstream recruitment of WIPI2, a protein that binds PtdIns3P and its product PtdIns(3,5)P2, and a WIPI-binding protein, ATG2A, but do not affect membrane association of ATG3 and ATG16L1, enzymes contributing directly to LC3 lipidation. These data reveal the nuanced role of the ATG14 ALPS in membrane curvature sensing, suggesting that the ALPS has additional roles in supporting LC3 lipidation.
    DOI:  https://doi.org/10.1091/mbc.E18-11-0743
  6. Biochem Biophys Res Commun. 2019 Feb 21. pii: S0006-291X(19)30272-4. [Epub ahead of print]
    TORC1 regulates autophagy induction in response to proteotoxic stress in yeast and human cells.
    Kazuki Suda, Atsuki Kaneko, Mitsugu Shimobayashi, Akio Nakashima, Maeda Tatsuya, Michael N Hall, Takashi Ushimaru.
      Misfolded and aggregated proteins are eliminated to maintain protein homeostasis. Autophagy contributes to the removal of protein aggregates. However, if and how proteotoxic stress induces autophagy is poorly understood. Here we show that proteotoxic stress after treatment with azetidine-2-carboxylic acid (AZC), a toxic proline analog, induces autophagy in budding yeast. AZC treatment attenuated target of rapamycin complex 1 (TORC1) activity, resulting in the dephosphorylation of Atg13, a key factor of autophagy. By contrast, AZC treatment did not affect target of rapamycin complex 2 (TORC2). Proteotoxic stress also induced TORC1 inactivation and autophagy in fission yeast and human cells. This study suggested that TORC1 is a conserved key factor to cope with proteotoxic stress in eukaryotic cells.
    Keywords:  Autophagy; Azetidine-2-carboxylic acid (AZC); Proteotoxic stress; Target of rapamycin complex 1 (TORC1)
    DOI:  https://doi.org/10.1016/j.bbrc.2019.02.077
  7. Methods Mol Biol. 2019 ;1952 157-191
    Methods for Monitoring Matrix-Induced Autophagy.
    Carolyn Chen, Aastha Kapoor, Renato V Iozzo.
      A growing body of research demonstrates modulation of autophagy by a variety of matrix constituents, including decorin, endorepellin, and endostatin. These matrix proteins are both pro-autophagic and anti-angiogenic. Here, we detail a series of methods to monitor matrix-induced autophagy and its concurrent effects on angiogenesis. We first discuss cloning and purifying proteoglycan fragment and core proteins in the laboratory and review relevant techniques spanning from cell culture to treatment with these purified proteoglycans in vitro and ex vivo. Further, we cover protocols in monitoring autophagic progression via morphological and microscopic characterization, biochemical western blot analysis, and signaling pathway investigation. Downstream angiogenic effects using in vivo approaches are then discussed using wild-type mice and the GFP-LC3 transgenic mouse model. Finally, we explore matrix-induced mitophagy via monitoring changes in mitochondrial DNA and permeability.
    Keywords:  Angiogenesis; Beclin 1; Decorin; Endorepellin; LC3; LC3-GFP; Mitophagy; Starvation
    DOI:  https://doi.org/10.1007/978-1-4939-9133-4_14
  8. EMBO Rep. 2019 Feb 25. pii: e46794. [Epub ahead of print]
    Cytoplasmic control of Rab family small GTPases through BAG6.
    Toshiki Takahashi, Setsuya Minami, Yugo Tsuchiya, Kazu Tajima, Natsumi Sakai, Kei Suga, Shin-Ichi Hisanaga, Norihiko Ohbayashi, Mitsunori Fukuda, Hiroyuki Kawahara.
      Rab family small GTPases are master regulators of distinct steps of intracellular vesicle trafficking in eukaryotic cells. GDP-bound cytoplasmic forms of Rab proteins are prone to aggregation due to the exposure of hydrophobic groups but the machinery that determines the fate of Rab species in the cytosol has not been elucidated in detail. In this study, we find that BAG6 (BAT3/Scythe) predominantly recognizes a cryptic portion of GDP-associated Rab8a, while its major GTP-bound active form is not recognized. The hydrophobic residues of the Switch I region of Rab8a are essential for its interaction with BAG6 and the degradation of GDP-Rab8a via the ubiquitin-proteasome system. BAG6 prevents the excess accumulation of inactive Rab8a, whose accumulation impairs intracellular membrane trafficking. BAG6 binds not only Rab8a but also a functionally distinct set of Rab family proteins, and is also required for the correct distribution of Golgi and endosomal markers. From these observations, we suggest that Rab proteins represent a novel set of substrates for BAG6, and the BAG6-mediated pathway is associated with the regulation of membrane vesicle trafficking events in mammalian cells.
    Keywords:  BAG6; Rab GTP‐binding proteins; Rab8a; membrane trafficking; ubiquitin‐proteasome system
    DOI:  https://doi.org/10.15252/embr.201846794
  9. Autophagy. 2019 Feb 26.
    Gamma secretase orthologs are required for lysosomal activity and autophagic degradation in Dictyostelium discoideum, independent of PSEN (presenilin) proteolytic function.
    Devdutt Sharma, Grant Otto, Eleanor Warren, Philip Beesley, Jason S King, Robin S B Williams.
      Mutations in the g-secretase complex are strongly associated with familial Alzheimer disease. Both proteolytic and non-proteolytic functions for the γ-secretase complex have been previously described in mammalian model organisms, but their relative contributions to disease pathology remain unclear. Here, we dissect the roles of orthologs of the γ-secretase components in the model system Dictyostelium, focusing on endocytosis, lysosomal activity and autophagy. In this model, we show that the orthologs of PSEN (psenA and psenB), Ncstn (nicastrin) and Aph-1 (gamma-secretase subunit Aph-1), are necessary for optimal fluid-phase uptake by macropinocytosis and in multicellular development under basic condition. Disruption of either psenA/B or Aph-1 proteins also leads disrupted phagosomal proteolysis as well as decreased autophagosomal acidification and autophagic flux. This indicates a general defect in lysosomal trafficking and degradation, which we show leads to the accumulation of ubiquitinated protein aggregates in cells lacking psenA/B and Aph-1 proteins. Importantly, we find that all the endocytic defects observed in Dictyostelium PSEN ortholog mutants can be fully rescued by proteolytically inactive Dictyostelium psenB and human PSEN1 proteins. Our data therefore demonstrates an evolutionarily conserved non-proteolytic role for presenilin, and γ-secretase component orthologs, in maintaining Dictyostelium lysosomal trafficking and autophagy.
    Keywords:  ; Alzheimer disease; autophagy; development; lysosomal trafficking; nicastrin; presenilin; γ-secretase
    DOI:  https://doi.org/10.1080/15548627.2019.1586245
  10. Autophagy. 2019 Feb 26.
    Mitochondrial transport proteins RHOT1 and RHOT2 serve as docking sites for PRKN-mediated mitophagy.
    Dzhamilja Safiulina, Malle Kuum, Vinay Choubey, Miriam A Hickey, Allen Kaasik.
      The Parkinson disease-associated proteins PINK1 and PRKN coordinate the ubiquitination of mitochondrial outer membrane proteins to tag them either for degradation or for autophagic clearance of the mitochondrion. The proteins include the mitochondrial trafficking proteins RHOT1 and RHOT2, the removal of which may be required for immobilization of mitochondria prior to mitophagy. Here, we demonstrate that RHOT1 and RHOT2 are not only substrates for PINK1-PRKN-dependent degradation but that they also play an active role in the process of mitophagy. RHOT1, and likely also RHOT2, may act as a docking site for inactive PRKN prior to mitochondrial damage, thus keeping PRKN in close proximity to its potential substrates and thereby facilitating mitophagy. We also show that RHOT1 functions as a calcium-sensing docking site for PRKN, and we suggest that calcium binding to RHOT is a key step in the calcium-dependent activation of mitophagy machinery.
    Keywords:  PRKN translocation; cytosolic calcium; mitochondrial trafficking; mitophagy; neuron
    DOI:  https://doi.org/10.1080/15548627.2019.1586260
  11. Dev Cell. 2019 Feb 13. pii: S1534-5807(19)30007-3. [Epub ahead of print]
    Autophagy-Mediated Cholesterol Trafficking Controls Steroid Production.
    Michael J Texada, Alina Malita, Christian F Christensen, Kathrine B Dall, Nils J Faergeman, Stanislav Nagy, Kenneth A Halberg, Kim Rewitz.
      Steroid hormones are important signaling molecules that regulate growth and drive the development of many cancers. These factors act as long-range signals that systemically regulate the growth of the entire organism, whereas the Hippo/Warts tumor-suppressor pathway acts locally to limit organ growth. We show here that autophagy, a pathway that mediates the degradation of cellular components, also controls steroid production. This process is regulated by Warts (in mammals, LATS1/2) signaling, via its effector microRNA bantam, in response to nutrients. Specifically, autophagy-mediated mobilization and trafficking of the steroid precursor cholesterol from intracellular stores controls the production of the Drosophila steroid ecdysone. Furthermore, we also show that bantam regulates this process via the ecdysone receptor and Tor signaling, identifying pathways through which bantam regulates autophagy and growth. The Warts pathway thus promotes nutrient-dependent systemic growth during development by autophagy-dependent steroid hormone regulation (ASHR). These findings uncover an autophagic trafficking mechanism that regulates steroid production.
    Keywords:  Drosophila; EcR; Tor; autophagy; bantam; cholesterol; ecdysone; prothoracic gland; steroid; steroidogenesis; warts
    DOI:  https://doi.org/10.1016/j.devcel.2019.01.007
  12. Nat Commun. 2019 Feb 27. 10(1): 969
    Omegasome-proximal PtdIns(4,5)P2 couples F-actin mediated mitoaggregate disassembly with autophagosome formation during mitophagy.
    Cheng-Wei Hsieh, Wei Yuan Yang.
      Cells govern their homeostasis through autophagy by sequestering substrates, ranging from proteins to aggregates and organelles, into autophagosomes for lysosomal degradation. In these processes cells need to coordinate between substrate remodeling and autophagosome formation for efficient engulfment. We found that in Parkin-mediated mitophagy, mitochondria to be turned over first become grape-like mitoaggregates, followed by their disassembly into smaller pieces via the actinomyosin system. At the disassembly step, we observed spatially-associated, synchronous formation of circular F-actin and BATS-labeled autophagy initiation sites near mitochondria, suggesting coordination between substrate downsizing and autophagosome formation during mitophagy. Interestingly, PtdIns(4,5)P2, instead of PtdIns(3)P, regulates this mitophagy-associated formation of circular F-actin and BATS-sites. Selective depletion of PtdIns(4,5)P2 near omegasomes, the endoplasmic reticulum (ER) subdomains involved in autophagosome formation, impaired mitoaggregate disassembly. Our findings demonstrate the presence of a pool of PtdIns(4,5)P2 adjacent to omegasomes, and that they coordinate mitoaggregate disassembly with autophagy initiation during Parkin-mediated mitophagy.
    DOI:  https://doi.org/10.1038/s41467-019-08924-5
  13. Autophagy. 2019 Feb 26. 1-2
    An autophagy-independent role for ATG16L1: promoting lysosome-mediated plasma membrane repair.
    Joel M J Tan, Nora Mellouk, John H Brumell.
      There is growing evidence in the literature for unconventional roles of autophagy-related (ATG) proteins, outside of their function in canonical autophagy. Here we discuss our recent study that revealed a novel ATG16L1-dependent pathway that promotes plasma membrane repair upon bacterial pore-forming toxin damage. Disruption of the ATG16L1-dependent pathway leads to an accumulation of cholesterol in lysosomes, which affects lysosomal exocytosis required for efficient membrane repair. Our study provides insights into the role of ATG16L1 in cholesterol homeostasis and plasma membrane integrity.
    Keywords:  Autophagy; bacterial infection; cholesterol; inflammatory bowel disease; lysosome; plasma membrane repair
    DOI:  https://doi.org/10.1080/15548627.2019.1586261
  14. J Cell Physiol. 2019 Feb 26.
    Targeting autophagy in cardiac ischemia/reperfusion injury: A novel therapeutic strategy.
    Mehrdad Aghaei, Morteza Motallebnezhad, Sajjad Ghorghanlu, Ali Jabbari, Ayesheh Enayati, Maryam Rajaei, Mona Pourabouk, Alireza Moradi, Ali Mohammad Alizadeh, Vahid Khori.
      Acute myocardial infarction (AMI) is one of the leading causes of morbidity worldwide. Myocardial reperfusion is known as an effective therapeutic choice against AMI. However, reperfusion of blood flow induces ischemia/reperfusion (I/R) injury through different complex processes including ion accumulation, disruption of mitochondrial membrane potential, the formation of reactive oxygen species, and so forth. One of the processes that gets activated in response to I/R injury is autophagy. Indeed, autophagy acts as a "double-edged sword" in the pathology of myocardial I/R injury and there is a controversy about autophagy being beneficial or detrimental. On the basis of the autophagy effect and regulation on myocardial I/R injury, many studies targeted it as a therapeutic strategy. In this review, we discuss the role of autophagy in I/R injury and its targeting as a therapeutic strategy.
    Keywords:  acute myocardial infarction; autophagy; ischemia/reperfusion injury
    DOI:  https://doi.org/10.1002/jcp.28345
  15. Autophagy. 2019 Feb 26.
    The epg5 knockout zebrafish line: a model to study Vici syndrome.
    Giacomo Meneghetti, Tatjana Skobo, Martina Chrisam, Nicola Facchinello, Camilla Maria Fontana, Stefania Bellesso, Patrizia Sabatelli, Flavia Raggi, Francesco Cecconi, Paolo Bonaldo, Luisa Dalla Valle.
      The EPG5 protein is a RAB7A effector involved in fusion specificity between autophagosomes and late endosomes or lysosomes during macroautophagy/autophagy. Mutations in the human EPG5 gene cause a rare and severe multisystem disorder called Vici syndrome. In this work, we show that zebrafish epg5-/- mutants from both heterozygous and incrossed homozygous matings are viable and can develop to the age of sexual maturity without conspicuous defects in external appearance. In agreement with the dysfunctional autophagy of Vici syndrome, western blot revealed higher levels of the Lc3-II autophagy marker in epg5-/- mutants with respect to wild type controls. Moreover, starvation elicited higher accumulation of Lc3-II in epg5-/- than in wild type larvae, together with a significant reduction of skeletal muscle birefringence. Accordingly, muscle ultrastructural analysis revealed accumulation of degradation-defective autolysosomes in starved epg5-/- mutants. By aging, epg5-/- mutants showed impaired motility and muscle thinning, together with accumulation of non-degradative autophagic vacuoles. Furthermore, epg5-/- adults displayed morphological alterations in gonads and heart. These findings point at the zebrafish epg5 mutant as a valuable model for EPG5-related disorders, thus providing a new tool for dissecting the contribution of EPG5 on the onset and progression of Vici syndrome as well as for the screening of autophagy-stimulating drugs.
    Keywords:  ; CRISPR-Cas9; Vici syndrome; autophagic flux; autophagy; zebrafish mutant line
    DOI:  https://doi.org/10.1080/15548627.2019.1586247
  16. Autophagy. 2019 Feb 26.
    TRAF6 inhibits colorectal cancer metastasis through regulating selective autophagic CTNNB1/β-catenin degradation and is targeted for GSK3B/GSK3β-mediated phosphorylation and degradation.
    Hua Wu, Xing-Xing Lu, Jing-Ru Wang, Tian-Yu Yang, Xiu-Ming Li, Xiao-Shun He, Yi Li, Wen-Long Ye, Yong Wu, Wen-Juan Gan, Peng-Da Guo, Jian-Ming Li.
      Aberrant CTNNB1 signaling is one of the fundamental processes in cancers, especially colorectal cancer (CRC). Here, we reported that TRAF6, an E3 ubiquitin ligase important for inflammatory signaling, inhibited epithelial-mesenchymal transition (EMT) and CRC metastasis through driving a selective autophagic CTNNB1 degradation machinery. Mechanistically, TRAF6 interacted with MAP1LC3B/LC3B through its LC3-interacting region 'YxxL' and catalyzed K63-linked polyubiquitination of LC3B. The K63-linked ubiquitination of LC3B promoted the formation of the LC3B-ATG7 complex and was critical to the subsequent recognition of CTNNB1 by LC3B for the selective autophagic degradation. However, TRAF6 was phosphorylated at Thr266 by GSK3B in most clinical CRC, which triggered K48-linked polyubiquitination and degradation of TRAF6 and thereby attenuated its inhibitory activity towards the autophagy-dependent CTNNB1 signaling. Clinically, decreased expression of TRAF6 was associated with elevated GSK3B protein levels and activity and reduced overall survival in CRC patients. Pharmacological inhibition of GSK3B activity stabilized the TRAF6 protein, promoted CTNNB1 degradation, and effectively suppressed EMT and CRC metastasis. Thus, targeting TRAF6 and its pathway may be meaningful for treating advanced CRC.
    Keywords:  CTNNB1; GSK3B; TRAF6; autophagy; colorectal cancer; metastasis
    DOI:  https://doi.org/10.1080/15548627.2019.1586250
  17. Autophagy. 2019 Mar 01.
    Targetome Analysis of Chaperone-Mediated Autophagy in Cancer Cells.
    Yuqing Hao, Merve Kacal, Amanda Tomie Ouchida, Boxi Zhang, Erik Norberg, Helin Vakifahmetoglu-Norberg.
      Chaperone-mediated autophagy is a lysosomal degradation pathway of select soluble proteins. Nearly one-third of the soluble proteins are predicted to be recognized by this pathway, yet only a minor fraction of this proteome has been identified as CMA substrates in cancer cells. Here, we undertook a quantitative multiplex mass spectrometry approach to study the proteome of isolated lysosomes in cancer cells during CMA-activated conditions. By integrating bioinformatics analyses, we identified and categorized proteins of multiple cellular pathways that were specifically targeted by CMA. Beyond verifying metabolic pathways, we showed that multiple components involved in select biological processes, including cellular translation, was specifically targeted for degradation by CMA. In particular, several proteins of the translation initiation complex were identified as bona fide CMA substrates in multiple cancer cell lines of distinct origin and we showed that CMA suppresses cellular translation. We further showed that the identified CMA substrates display high expression in multiple primary cancers compared to their normal counterparts. Combined, these findings uncover cellular processes affected by CMA and reveal a new role for CMA in the control of translation in cancer cells.
    Keywords:  autophagy; degradome; lysosome; proteome; translation
    DOI:  https://doi.org/10.1080/15548627.2019.1586255
  18. Sci Rep. 2019 Feb 26. 9(1): 2799
    Hyperactivation of mTORC1 disrupts cellular homeostasis in cerebellar Purkinje cells.
    Yusuke Sakai, Hidetoshi Kassai, Hisako Nakayama, Masahiro Fukaya, Tatsuya Maeda, Kazuki Nakao, Kouichi Hashimoto, Hiroyuki Sakagami, Masanobu Kano, Atsu Aiba.
      Mammalian target of rapamycin (mTOR) is a central regulator of cellular metabolism. The importance of mTORC1 signaling in neuronal development and functions has been highlighted by its strong relationship with many neurological and neuropsychiatric diseases. Previous studies demonstrated that hyperactivation of mTORC1 in forebrain recapitulates tuberous sclerosis and neurodegeneration. In the mouse cerebellum, Purkinje cell-specific knockout of Tsc1/2 has been implicated in autistic-like behaviors. However, since TSC1/2 activity does not always correlate with clinical manifestations as evident in some cases of tuberous sclerosis, the intriguing possibility is raised that phenotypes observed in Tsc1/2 knockout mice cannot be attributable solely to mTORC1 hyperactivation. Here we generated transgenic mice in which mTORC1 signaling is directly hyperactivated in Purkinje cells. The transgenic mice exhibited impaired synapse elimination of climbing fibers and motor discoordination without affecting social behaviors. Furthermore, mTORC1 hyperactivation induced prominent apoptosis of Purkinje cells, accompanied with dysregulated cellular homeostasis including cell enlargement, increased mitochondrial respiratory activity, and activation of pseudohypoxic response. These findings suggest the different contributions between hyperactivated mTORC1 and Tsc1/2 knockout in social behaviors, and reveal the perturbations of cellular homeostasis by hyperactivated mTORC1 as possible underlying mechanisms of neuronal dysfunctions and death in tuberous sclerosis and neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s41598-019-38730-4
  19. Crit Rev Clin Lab Sci. 2019 Mar 01. 1-18
    Novel therapeutic strategies for stroke: The role of autophagy.
    Seyed Fazel Nabavi, Antoni Sureda, Ana Sanches-Silva, Kasi Pandima Devi, Touqeer Ahmed, Momina Shahid, Eduardo Sobarzo-Sánchez, Marco Dacrema, Maria Daglia, Nady Braidy, Rosa Anna Vacca, Ioana Berindan-Neagoe, Diana Gulei, Davide Barreca, Maciej Banach, Seyed Mohammad Nabavi, Ahmad Reza Dehpour, Samira Shirooie.
      Autophagy is an important biological mechanism involved in the regulation of numerous fundamental cellular processes that are mainly associated with cellular growth and differentiation. Autophagic pathways are vital for maintaining cellular homeostasis by enhancing the turnover of nonfunctional proteins and organelles. Neuronal cells, like other eukaryotic cells, are dependent on autophagy for neuroprotection in response to stress, but can also induce cell death in cerebral ischemia. Recent studies have demonstrated that autophagy may induce neuroprotection following acute brain injury, including ischemic stroke. However in some special circumstances, activation of autophagy can induce cell death, playing a deleterious role in the etiology and progression of ischemic stroke. Currently, there are no therapeutic options against stroke that demonstrate efficient neuroprotective abilities. In the present work, we will review the significance of autophagy in the context of ischemic stroke by first outlining its role in ischemic neuronal death. We will also highlight the potential therapeutic applications of pharmacological modulators of autophagy, including some naturally occurring polyphenolic compounds that can target this catabolic process. Our findings provide renewed insight on the mechanism of action of autophagy in stroke together with potential neuroprotective compounds, which may partially exert their function through enhancing mitochondrial function and attenuating damaging autophagic processes.
    Keywords:  Autophagy; intervention; ischemia; neuroprotection; stroke
    DOI:  https://doi.org/10.1080/10408363.2019.1575333
  20. Circ J. 2019 Feb 28.
    Autophagy in the Heart.
    Osamu Yamaguchi.
      The autophagic machinery is a well-conserved degradation system in eukaryotes from yeast to mammals. Autophagy has been thought of as a nonselective degradation process in which cytoplasmic proteins and organelles are degraded by fusion with lysosome. Recent studies have revealed selective forms of autophagy, such as mitochondria-specific autophagy, termed "mitophagy". Research over the past decade has revealed that autophagy in cardiomyocytes plays a protective role, not only during hemodynamic stress but in homeostasis during aging. Hemodynamic stress and aging induce mitochondrial damage, leading to increased oxidative stress and decreased ATP production. Damaged mitochondria are generally degraded through mitophagy, which might be the main protective function of autophagy in the heart. Complete digestion of mitochondrial DNA through mitophagy is important to avoid inflammatory responses that can induce heart failure. A polyamine, spermidine, is reported to bring about an extension of lifespan and to protect the heart from age-related cardiac dysfunction, both of which are mediated through induction of autophagy. Therefore, appropriate induction of autophagy could be a novel therapeutic target for cardiovascular diseases, including heart failure. However, precise evaluation of autophagic activity in the human heart is difficult at this time, but exploitation of the novel technique of autophagy evaluation is expected for both drug discovery and clinical application.
    Keywords:  Autophagy; Heart failure; Inflammation; Mitochondria; Mitophagy
    DOI:  https://doi.org/10.1253/circj.CJ-18-1065
  21. Biochem Biophys Res Commun. 2019 Feb 20. pii: S0006-291X(19)30279-7. [Epub ahead of print]
    An autophagy deficiency promotes methylmercury-induced multinuclear cell formation.
    Yasukazu Takanezawa, Ryosuke Nakamura, Yuka Sone, Shimpei Uraguchi, Masako Kiyono.
      Methylmercury (MeHg) is a highly toxic pollutant, and is considered hazardous to human health. In our previous study, we found that MeHg induces autophagy and that Atg5-dependent autophagy plays a protective role against MeHg toxicity. To further characterize the role of autophagy in MeHg-induced toxicity, we examined the impact of autophagy on microtubules and nuclei under MeHg exposure using Atg5KO mouse embryonic fibroblasts (MEFs). Low concentrations of MeHg induced a decrease in α-tubulin and acetylated-tubulin in both wild-type and Atg5KO cells. While α-tubulin acetylation was promoted by treatment with tubacin, a selective inhibitor of histone deacetylase 6, MeHg treatment inhibits the increase of tubacin-induced acetylated-tubulin. However, similar effects were observed for treatment with either tubacin or tubacin + MeHg in wild-type and Atg5KO cells. We also found a significant increase in the number of multinuclear cells upon MeHg exposure in Atg5KO MEFs compared to wild-type MEFs. In addition, DNA double strand breaks (DSBs), measured by phosphorylation of the core histone H2A variant (H2AX) on serine 139 (γH2AX), markedly increased in Atg5KO MEFs compared to wild-type MEFs. Our results therefore suggest that autophagy is not a simple elimination pathway of MeHg-induced damaged proteins, but that it also plays a protective role in the context of MeHg-associated DSBs.
    Keywords:  Autophagy; Double strand breaks; Methylmercury; Multinuclear cells; Tubulin
    DOI:  https://doi.org/10.1016/j.bbrc.2019.02.084
  22. PLoS Pathog. 2019 Feb 28. 15(2): e1007329
    The selective autophagy receptors Optineurin and p62 are both required for zebrafish host resistance to mycobacterial infection.
    Rui Zhang, Monica Varela, Wies Vallentgoed, Gabriel Forn-Cuni, Michiel van der Vaart, Annemarie H Meijer.
      Mycobacterial pathogens are the causative agents of chronic infectious diseases like tuberculosis and leprosy. Autophagy has recently emerged as an innate mechanism for defense against these intracellular pathogens. In vitro studies have shown that mycobacteria escaping from phagosomes into the cytosol are ubiquitinated and targeted by selective autophagy receptors. However, there is currently no in vivo evidence for the role of selective autophagy receptors in defense against mycobacteria, and the importance of autophagy in control of mycobacterial diseases remains controversial. Here we have used Mycobacterium marinum (Mm), which causes a tuberculosis-like disease in zebrafish, to investigate the function of two selective autophagy receptors, Optineurin (Optn) and SQSTM1 (p62), in host defense against a mycobacterial pathogen. To visualize the autophagy response to Mm in vivo, optn and p62 zebrafish mutant lines were generated in the background of a GFP-Lc3 autophagy reporter line. We found that loss-of-function mutation of optn or p62 reduces autophagic targeting of Mm, and increases susceptibility of the zebrafish host to Mm infection. Transient knockdown studies confirmed the requirement of both selective autophagy receptors for host resistance against Mm infection. For gain-of-function analysis, we overexpressed optn or p62 by mRNA injection and found this to increase the levels of GFP-Lc3 puncta in association with Mm and to reduce the Mm infection burden. Taken together, our results demonstrate that both Optn and p62 are required for autophagic host defense against mycobacterial infection and support that protection against tuberculosis disease may be achieved by therapeutic strategies that enhance selective autophagy.
    DOI:  https://doi.org/10.1371/journal.ppat.1007329
  23. Bioorg Chem. 2019 Feb 14. pii: S0045-2068(18)31378-6. [Epub ahead of print]85 505-514
    Cell penetrable, clickable and tagless activity-based probe of human cathepsin L.
    Dibyendu Dana, Jeremy Garcia, Ashif I Bhuiyan, Pratikkumar Rathod, Laura Joo, Daniel A Novoa, Suneeta Paroly, Karl R Fath, Emmanuel J Chang, Sanjai K Pathak.
      Human cathepsin L is a ubiquitously expressed endopeptidase and is known to play critical roles in a wide variety of cellular signaling events. Its overexpression has been implicated in numerous human diseases, including highly invasive forms of cancer. Inhibition of cathepsin L is therefore considered a viable therapeutic strategy. Unfortunately, several redundant and even opposing roles of cathepsin L have recently emerged. Selective cathepsin L probes are therefore needed to dissect its function in context-specific manner before significant resources are directed into drug discovery efforts. Herein, the development of a clickable and tagless activity-based probe of cathepsin L is reported. The probe is highly efficient, active-site directed and activity-dependent, selective, cell penetrable, and non-toxic to human cells. Using zebrafish model, we demonstrate that the probe can inhibit cathepsin L function in vivo during the hatching process. It is anticipated that the probe will be a highly effective tool in dissecting cathepsin L biology at the proteome levels in both normal physiology and human diseases, thereby facilitating drug-discovery efforts targeting cathepsin L.
    Keywords:  Activity-based probe; Cathepsin L probe; Clickable probe; Copper-mediated azide-alkyne cycloaddition; Tagless cathepsin L probe
    DOI:  https://doi.org/10.1016/j.bioorg.2019.02.032
  24. Autophagy. 2019 Mar 01.
    Down-regulated TMED10 in Alzheimer disease induces autophagy via ATG4B activation.
    Ji Hyun Shin, So Jung Park, Doo Sin Jo, Na Yeon Park, Joon Bum Kim, Ji-Eun Bae, Yoon Kyung Jo, Jung Jin Hwang, Jin-A Lee, Dong-Gyu Jo, Jin Cheon Kim, Yong Keun Jung, Jae-Young Koh, Dong-Hyung Cho.
      Several studies have shown that dysfunction of macroautophagy/autophagy is associated with many human diseases, including neurodegenerative disease and cancer. To explore the molecular mechanisms of autophagy, we performed a cell-based functional screening with SH-SY5Y cells stably expressing GFP-LC3, using an siRNA library and identified TMED10 (transmembrane p24 trafficking protein 10), previously known as the γ-secretase-modulating protein, as a novel regulator of autophagy. Further investigations revealed that depletion of TMED10 induced the activation of autophagy. Interestingly, protein-protein interaction assays showed that TMED10 directly binds to ATG4B (autophagy related gene 4B cysteine peptidase), and the interaction is diminished under autophagy activation conditions such as rapamycin treatment and serum deprivation. In addition, inhibition of TMED10 significantly enhanced the proteolytic activity of ATG4B for LC3 cleavage. Importantly, the expression of TMED10 in AD (Alzheimer disease) patients was considerably decreased, and downregulation of TMED10 increased amyloid-β (Aβ) production. Treatment with Aβ increased ATG4B proteolytic activity as well as dissociation of TMED10 and ATG4B. Taken together, our results suggest that the AD-associated protein TMED10 negatively regulates autophagy by inhibiting ATG4B activity.
    Keywords:  ATG4B; Alzheimer disease; TMED10; autophagy; screening
    DOI:  https://doi.org/10.1080/15548627.2019.1586249
  25. Am J Pathol. 2019 Mar;pii: S0002-9440(18)30296-7. [Epub ahead of print]189(3): 492-501
    Mammalian Target of Rapamycin: A Metabolic Rheostat for Regulating Adipose Tissue Function and Cardiovascular Health.
    Matthew F Wipperman, David C Montrose, Antonio M Gotto, David P Hajjar.
      The complex relationship between diet and metabolism is an important contributor to cellular metabolism and health. Over the past few decades, a central role for mammalian target of rapamycin (mTOR) in the regulation of multiple cellular processes, including the response to food intake, maintaining homeostasis, and the pathogenesis of disease, has been shown. Herein, we first review our current understanding of the biochemical functions of mTOR and its response to fluctuations in hormone levels, like insulin. Second, we highlight the role of mTOR in lipogenesis, adipogenesis, β-oxidation of lipids, and ketosis of carbohydrates, lipids, and proteins. Special attention is paid to recent advances in mTOR signaling in white versus brown adipose tissues. Finally, we review how mTOR regulates cardiovascular health and disease. Together, these insights define a clearer picture of the connection between mTOR signaling, metabolic health, and disease.
    DOI:  https://doi.org/10.1016/j.ajpath.2018.11.013
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