bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2020‒07‒26
thirty papers selected by
Viktor Korolchuk
Newcastle University


  1. Proc Natl Acad Sci U S A. 2020 Jul 20. pii: 202008923. [Epub ahead of print]
    Chen S, Mari M, Parashar S, Liu D, Cui Y, Reggiori F, Novick PJ, Ferro-Novick S.
      Endoplasmic reticulum (ER) macroautophagy (hereafter called ER-phagy) uses autophagy receptors to selectively degrade ER domains in response to starvation or the accumulation of aggregation-prone proteins. Autophagy receptors package the ER into autophagosomes by binding to the ubiquitin-like yeast protein Atg8 (LC3 in mammals), which is needed for autophagosome formation. In budding yeast, cortical and cytoplasmic ER-phagy requires the autophagy receptor Atg40. While different ER autophagy receptors have been identified, little is known about other components of the ER-phagy machinery. In an effort to identify these components, we screened the genome-wide library of viable yeast deletion mutants for defects in the degradation of cortical ER following treatment with rapamycin, a drug that mimics starvation. Among the mutants we identified was vps13Δ. While yeast has one gene that encodes the phospholipid transporter VPS13, humans have four vacuolar protein-sorting (VPS) protein 13 isoforms. Mutations in all four human isoforms have been linked to different neurological disorders, including Parkinson's disease. Our findings have shown that Vps13 acts after Atg40 engages the autophagy machinery. Vps13 resides at contact sites between the ER and several organelles, including late endosomes. In the absence of Vps13, the cortical ER marker Rtn1 accumulated at late endosomes, and a dramatic decrease in ER packaging into autophagosomes was observed. Together, these studies suggest a role for Vps13 in the sequestration of the ER into autophagosomes at late endosomes. These observations may have important implications for understanding Parkinson's and other neurological diseases.
    Keywords:  ER-phagy; Vps13; autophagy; contact site; lipid transporter
    DOI:  https://doi.org/10.1073/pnas.2008923117
  2. Dose Response. 2020 Jul-Sep;18(3):18(3): 1559325820934227
    Moore MN.
      Autophagy has been strongly linked with hormesis, however, it is only relatively recently that the mechanistic basis underlying this association has begun to emerge. Lysosomal autophagy is a group of processes that degrade proteins, protein aggregates, membranes, organelles, segregated regions of cytoplasm, and even parts of the nucleus in eukaryotic cells. These degradative processes are evolutionarily very ancient and provide a survival capability for cells that are stressed or injured. Autophagy and autophagic dysfunction have been linked with many aspects of cell physiology and pathology in disease processes; and there is now intense interest in identifying various therapeutic strategies involving its regulation. The main regulatory pathway for augmented autophagy is the mechanistic target of rapamycin (mTOR) cell signaling, although other pathways can be involved, such as 5'-adenosine monophosphate-activated protein kinase. Mechanistic target of rapamycin is a key player in the many highly interconnected intracellular signaling pathways and is responsible for the control of cell growth among other processes. Inhibition of mTOR (specifically dephosphorylation of mTOR complex 1) triggers augmented autophagy and the search is on the find inhibitors that can induce hormetic responses that may be suitable for treating many diseases, including many cancers, type 2 diabetes, and age-related neurodegenerative conditions.
    Keywords:  AMPK; aging; autophagy; cancers; cell signaling; hormesis; lysosomes; mTOR; neurodegenerative diseases; therapeutics
    DOI:  https://doi.org/10.1177/1559325820934227
  3. Autophagy. 2020 Jul 20.
    He A, Dean JM, Lu D, Chen Y, Lodhi IJ.
      Hepatic lipid homeostasis is controlled by a coordinated regulation of various metabolic pathways involved in de novo synthesis, uptake, storage, and catabolism of lipids. Disruption of this balance could lead to hepatic steatosis. Peroxisomes play an essential role in lipid metabolism, yet their importance is often overlooked. In a recent study, we demonstrated a role for hepatic peroxisomal β-oxidation in autophagic degradation of lipid droplets. ACOX1 (acyl-Coenzyme A oxidase 1, palmitoyl), the rate-limiting enzyme of peroxisomal β-oxidation, increases with fasting or high-fat diet (HFD). Liver-specific acox1 knockout (acox1-LKO) protects mice from hepatic steatosis induced by starvation or HFD via induction of lipophagy. Mechanistically, we showed that hepatic ACOX1 deficiency decreases the total cytosolic acetyl-CoA levels, which leads to reduced acetylation of RPTOR/RAPTOR, a component of MTORC1, which is a key regulator of macroautophagy/autophagy. These results identify peroxisome-derived acetyl-CoA as a critical metabolic regulator of autophagy that controls hepatic lipid homeostasis.
    Keywords:  ACOX1; MTORC1; NAFLD; autophagy; lipids; lipophagy; lysosome; peroxisome
    DOI:  https://doi.org/10.1080/15548627.2020.1797288
  4. Methods Mol Biol. 2020 ;2171 115-125
    Asano J, Sato T, Ohteki T.
      Autophagy is a lysosomal degradation pathway with important roles in physiological homeostasis and disease. We previously showed that intrinsic autophagy in intestinal stem cells (ISCs) is important for ISC homeostasis. Here we describe the detailed methods for detecting autophagy in ISCs by observing autophagosomes in GFP-LC3 transgenic mice and quantifying the p62 protein levels. We also describe methods for detecting mitophagy in these cells, by analyzing the mitochondrial transmembrane potential and reactive oxygen species (ROS) level by MitoTracker and CellROX solution, respectively.
    Keywords:  Atg5; Autophagosome; Autophagy; GFP-LC3; Intestinal epithelial cells (IECs); Intestinal stem cells (ISCs); Lgr5; Mitochondria; Reactive oxygen species (ROS); p62
    DOI:  https://doi.org/10.1007/978-1-0716-0747-3_7
  5. Circ Res. 2020 Jul 22.
    Gu S, Tan J, Li Q, Liu S, Ma J, Zheng Y, Liu J, Bi W, Sha P, Li X, Wei M, Cao N, Yang HT.
      Rationale: Impaired autophagic flux contributes to ischemia/reperfusion (I/R)-induced cardiomyocyte death, but the underlying molecular mechanisms remain largely unexplored. Objective: To determine the role of lysosomal-associated transmembrane protein 4B (LAPTM4B) in the regulation of autophagic flux and myocardial I/R injury. Methods and Results: LAPTM4B was expressed in murine hearts but downregulated in hearts with I/R (30 minutes/2 hours) injury and neonatal rat cardiomyocytes (NRCMs) with hypoxia/reoxygenation (6 hours/2 hours) injury. During myocardial reperfusion, LAPTM4B knockout (LAPTM4B-/-) mice had a significantly increased infarct size and lactate dehydrogenase release, while adenovirus-mediated LAPTM4B-overexpression was cardioprotective. Concomitantly, LAPTM4B-/- mice showed higher accumulation of the autophagy markers LC3-II, but not P62, in the I/R heart, while they did not alter chloroquine-induced further increases of LC3-II and P62 in both Sham and I/R hearts. Conversely, LAPTM4B-overexpression had opposite effects. The hypoxia/reoxygenation-reduced viability of NRCMs, ratio of autolysosomes/autophagosomes, and function of lysosomes were further decreased by LAPTM4B-knockdown but reversed by LAPTM4B-overexpression. Moreover, the LAPTM4B-overexpression-mediated benefits were abolished by knockdown of lysosome-associated membrane protein-2 (an autophagosome-lysosome fusion protein) in vitro and by the autophagy inhibitor bafilomycin A1 in vivo. In contrast, rapamycin successfully restored the impaired autophagic flux in LAPTM4B-/- mice and the subsequent myocardial I/R injury. Mechanistically, LAPTM4B regulated the activity of mammalian target of rapamycin complex 1 (mTORC1) via interacting with mTOR through its EC3 domain. Thus, mTORC1 was overactivated in LAPTM4B-/- mice, leading to the repression of transcription factor EB (TFEB), a master regulator of lysosomal and autophagic genes, during myocardial I/R. The mTORC1 inhibition or TFEB-overexpression rescued the LAPTM4B-/--induced impairment in autophagic flux and I/R injury, whereas TFEB-knockdown abolished the LAPTM4B-overexpression-mediated recovery of autophagic flux and cardioprotection. Conclusions: The downregulation of LAPTM4B contributes to myocardial I/R-induced impairment of autophagic flux via modulation of the mTORC1/TFEB pathway.
    Keywords:  LAPTM4B; autophagic flux; autophagosome-lysosome fusion; mTORC1/TFEB pathway
    DOI:  https://doi.org/10.1161/CIRCRESAHA.119.316388
  6. Autophagy. 2020 Jul 20.
    Nthiga TM, Shrestha BK, Lamark T, Johansen T.
      The endoplasmic reticulum (ER) is the largest membrane-bound organelle in eukaryotic cells and plays critical roles in diverse processes in metabolism, signaling and intracellular organization. In response to stress stimuli such as nutrient deprivation, accumulation of misfolded proteins or exposure to chemicals, the ER increases in size through upregulated synthesis of its components to counteract the stress. To restore physiological size, the excess ER components are continuously dismantled and degraded by reticulophagy, a form of autophagy that targets, via adaptor molecules called reticulophagy receptors, specific ER portions to the lysosome for degradation. Previous studies have identified several ER resident proteins as reticulophagy receptors. In a recent study, we identified CALCOCO1 as a soluble reticulophagy receptor for the degradation of tubular ER in response to proteotoxic and starvation-induced stress. On the ER membrane, CALCOCO1 interacts with VAPA and VAPB via a FFAT-like motif and recruits autophagy machinery by binding directly to Atg8-family proteins via LIR and UDS interacting region (UIR) motifs acting co-dependently. Depletion of CALCOCO1 in cultured cells led to an impaired ER degradation during stress.
    Keywords:  Autophagy receptor; CALCOCO1; ER-phagy; FFAT motif; VAPA
    DOI:  https://doi.org/10.1080/15548627.2020.1797289
  7. Autophagy. 2020 Jul 20.
    López-Hernández T, Maritzen T, Haucke V.
      Osmotic stress is a critical challenge for mammalian cells as loss of water triggered by a hyperosmotic environment promotes harmful protein aggregation and impairs cell survival. How the degradative capacity of cells, in particular the macroautophagy/autophagy-lysosome system, is adapted to meet the proteolytic demands induced by osmotic challenge remains poorly understood. We have identified a hitherto unknown pathway that is activated by hyperosmotic stress and serves to link alterations in cellular ion homeostasis to the induction of autophagy and lysosomal gene expression and, thereby, to lysosome biogenesis.
    Keywords:  CLEAR network; TFEB; endocytosis; ion honeostasis; lysosome; macroautophagy; osmotic stress; proteostasis
    DOI:  https://doi.org/10.1080/15548627.2020.1798065
  8. Autophagy. 2020 Jul 21.
    Zhang H, Zhou J, Xiao P, Lin Y, Gong X, Liu S, Xu Q, Wang M, Ren H, Lu M, Wang Y, Zhu J, Xie Z, Li H, Lu K.
      Biogenesis of autophagosomes is the early step of macroautophagy/autophagy and requires membrane acquisition mainly from ER-Golgi-sourced precursor vesicles. Matured autophagosomes fuse with lysosomes for final degradation. However, how this selective fusion is determined remains elusive. Here, we identified Sac1 by a high throughput screen in Saccharomyces cerevisiae to show it was critical for autophagosome-lysosome fusion through its PtdIns4P phosphatase activity. Sac1 deficiency caused a dramatic increase of PtdIns4P at early Golgi apparatus and abnormal incorporation of PtdIns4P into Atg9 vesicles and autophagosomes, which caused failure to recruit SNARE proteins for autophagosome fusion with vacuoles. Sac1 function in autophagy was highly conserved from yeast to mammalian cells. Our work thus suggested that correct upstream lipid incorporation was important for downstream fusion step of autophagy and that Sac1 played a critical and ancient role in this surveillance of lipid integration.
    Keywords:  Atg9; ER; Golgi; PtdIns3P; PtdIns4P; SNARE; Sac1; autophagosome-lysosome fusion; hydrolase
    DOI:  https://doi.org/10.1080/15548627.2020.1796321
  9. Autophagy. 2020 Jul 18.
    Richard P, Feng S, Tsai YL, Li W, Rinchetti P, Muhith U, Irizarry-Cole J, Stolz K, Sanz LA, Hartono S, Hoque M, Tadesse S, Seitz H, Lotti F, Hirano M, Chédin F, Tian B, Manley JL.
      SETX (senataxin) is an RNA/DNA helicase that has been implicated in transcriptional regulation and the DNA damage response through resolution of R-loop structures. Mutations in SETX result in either of two distinct neurodegenerative disorders. SETX dominant mutations result in a juvenile form of amyotrophic lateral sclerosis (ALS) called ALS4, whereas recessive mutations are responsible for ataxia called ataxia with oculomotor apraxia type 2 (AOA2). How mutations in the same protein can lead to different phenotypes is still unclear. To elucidate AOA2 disease mechanisms, we first examined gene expression changes following SETX depletion. We observed the effects on both transcription and RNA processing, but surprisingly observed decreased R-loop accumulation in SETX-depleted cells. Importantly, we discovered a strong connection between SETX and the macroautophagy/autophagy pathway, reflecting a direct effect on transcription of autophagy genes. We show that SETX depletion inhibits the progression of autophagy, leading to an accumulation of ubiquitinated proteins, decreased ability to clear protein aggregates, as well as mitochondrial defects. Analysis of AOA2 patient fibroblasts also revealed a perturbation of the autophagy pathway. Our work has thus identified a novel function for SETX in the regulation of autophagy, whose modulation may have a therapeutic impact for AOA2.
    Keywords:  AOA2; DRIP; LC3; R loop; R-loop; SETX; autophagy; lysosomal degradation; senataxin; transcription regulation
    DOI:  https://doi.org/10.1080/15548627.2020.1796292
  10. Dev Cell. 2020 Jul 20. pii: S1534-5807(20)30507-4. [Epub ahead of print]54(2): 140-141
    Katsumoto K, Grapin-Botton A.
      A major trigger of adult β-cell insulin secretion is glucose. In a recent issue of Cell Metabolism, Helman and colleagues show that in fetuses insulin secretion depends on the activation of mTOR by amino acids and that reducing amino acids promotes maturation of β-cells derived from pluripotent stem cells.
    DOI:  https://doi.org/10.1016/j.devcel.2020.06.028
  11. Autophagy. 2020 Jul 18. 1-3
    Jacomin AC, Petridi S, Di Monaco M, Nezis IP.
      Despite the growing evidence that the macroautophagy/autophagy-related protein LC3 is localized in the nucleus, why and how it is targeted to the nucleus are poorly understood. In our recent study, we found that transcription factor seq (sequoia) interacts via its LIR motif with Atg8a, the Drosophila homolog of LC3, to negatively regulate the transcription of autophagy genes. Atg8a was found to also interact with the nuclear acetyltransferase complex subunit YL-1 and deacetylase Sirt2. Modulation of the acetylation status of Atg8a by YL-1 and Sirt2 affects the interaction between seq and Atg8a, and controls the induction of autophagy. Our work revealed a novel nuclear role for Atg8a, which is linked with the transcriptional regulation of autophagy genes.
    Keywords:  Acetylation; LC3/Atg8; LIR motif; autophagy; nucleus; transcription
    DOI:  https://doi.org/10.1080/15548627.2020.1794356
  12. Nat Metab. 2019 Mar;1(3): 321-333
    Valvezan AJ, Manning BD.
      The protein kinase complex mechanistic target of rapamycin complex 1 (mTORC1) serves as a key conduit between growth signals and the metabolic processes underlying cell growth. The activation state of mTORC1 is controlled by intracellular nutrients and energy, as well as exogenous hormones and growth factors, thereby integrating local and systemic growth signals. Here we discuss the molecular logic of the mTORC1 signalling network and its importance in coupling growth signals to the control of cellular metabolism. After activation, mTORC1 promotes the conversion of available nutrients and energy into the major macromolecular species contributing to cellular mass, including proteins, nucleic acids and lipids, while suppressing the autophagic recycling of these macromolecules back into their nutrient constituents. Given that uncoupling of mTORC1 from its normal regulatory inputs contributes to many diseases-including cancer, genetic tumour syndromes, metabolic diseases, autoimmune diseases and neurological disorders-understanding the molecular logic of the mTORC1 network and how to modulate it may present therapeutic opportunities for treatment of a broad range of diseases and potentially even for the extension of lifespan.
    DOI:  https://doi.org/10.1038/s42255-019-0038-7
  13. Breast Cancer Res Treat. 2020 Jul 20.
    Bortnik S, Tessier-Cloutier B, Leung S, Xu J, Asleh K, Burugu S, Magrill J, Greening K, Derakhshan F, Yip S, Ng T, Gelmon KA, Nielsen TO, Gorski SM.
      PURPOSE: Previous studies indicate that breast cancer molecular subtypes differ with respect to their dependency on autophagy, but our knowledge of the differential expression and prognostic significance of autophagy-related biomarkers in breast cancer is limited.METHODS: Immunohistochemistry (IHC) was performed on tissue microarrays from a large population of 3992 breast cancer patients divided into training and validation cohorts. Consensus staining scores were used to evaluate the expression levels of autophagy proteins LC3B, ATG4B, and GABARAP and determine the associations with clinicopathological variables and molecular biomarkers. Survival analyses were performed using the Kaplan-Meier function and Cox proportional hazards regression models.
    RESULTS: We found subtype-specific expression differences for ATG4B, with its expression lowest in basal-like breast cancer and highest in Luminal A, but there were no significant associations with patient prognosis. LC3B and GABARAP levels were highest in basal-like breast cancers, and high levels were associated with worse outcomes across all subtypes (DSS; GABARAP: HR 1.43, LC3B puncta: HR 1.43). High ATG4B levels were associated with ER, PR, and BCL2 positivity, while high LC3B and GABARAP levels were associated with ER, PR, and BCL2 negativity, as well as EGFR, HER2, HER3, CA-IX, PD-L1 positivity, and high Ki67 index (p < 0.05 for all associations). Exploratory multi-marker analysis indicated that the combination of ATG4B and GABARAP with LC3B could be useful for further stratifying patient outcomes.
    CONCLUSIONS: ATG4B levels varied across breast cancer subtypes but did not show prognostic significance. High LC3B expression and high GABARAP expression were both associated with poor prognosis and with clinicopathological characteristics of aggressive disease phenotypes in all breast cancer subtypes.
    Keywords:  ATG4B; Autophagy; Biomarker; Breast cancer; GABARAP; Immunohistochemistry; LC3B; Prognosis; Subtype
    DOI:  https://doi.org/10.1007/s10549-020-05795-z
  14. Life Sci. 2020 Jul 20. pii: S0024-3205(20)30867-5. [Epub ahead of print] 118116
    Liu T, Yang Q, Zhang X, Qin R, Shan W, Zhang H, Chen X.
      Emerging evidence implicates accelerated renal tubular epithelial cell (RTEC) senescence in renal fibrosis progression. Mitophagy protects against kidney injury. However, the mechanistic interplay between cell senescence and mitophagy in RTECs is not clearly defined. The purpose of this study was to evaluate the inhibition of RTEC senescence and renal fibrosis by quercetin and explore the underlying mechanisms. We found that quercetin attenuated RTEC senescence induced by angiotensin II (AngII) in vitro and unilateral ureteral obstruction in vivo. Moreover, we demonstrated that mitochondrial abnormalities such as elevated reactive oxygen species, decreased membrane potential, and fragmentation and accumulation of mitochondrial mass, occurred in AngII-treated RTECs. Quercetin treatment reversed these effects. Furthermore, quercetin enhanced mitophagy in AngII-treated RTECs, which was markedly reduced by treatment with mitophagy-specific inhibitors. Sirtuin-1 (SIRT1) was involved in quercetin-mediated PTEN-induced kinase 1 (PINK1)/Parkin-associated mitophagy activation. Pharmacological antagonism of SIRT1 in AngII-treated RTECs blocked the effects of quercetin on mitophagy and cellular senescence. Finally, quercetin alleviated kidney fibrosis by reducing RTEC senescence via mitophagy. Collectively, the antifibrotic effect of quercetin involved inhibition of RTEC senescence, possibly through activation of SIRT1/PINK1/Parkin-mediated mitophagy. These findings suggest that pharmacological elimination of senescent cells and stimulation of mitophagy represent effective therapeutic strategies to prevent kidney fibrosis.
    Keywords:  Fibrosis; Mitochondria; Mitophagy; Quercetin; Senescence
    DOI:  https://doi.org/10.1016/j.lfs.2020.118116
  15. Dev Cell. 2020 Jul 20. pii: S1534-5807(20)30538-4. [Epub ahead of print]54(2): 268-281
    Sebastián D, Zorzano A.
      Cellular processes that sense and transmit metabolic changes are crucial for adaptation to external signals. In this regard, autophagy provides energy upon nutrient deprivation and represents a quality control mechanism that eliminates damaged organelles or proteins. Here, we review recent findings on the metabolic pathways controlling autophagy in skeletal muscle, a plastic tissue that undergoes major changes in energy demands. We also analyze the implications of autophagy in the regulation of energy metabolism in muscle and how alterations in this process affect energy homeostasis at the whole-body level and the development of metabolic diseases and aging.
    DOI:  https://doi.org/10.1016/j.devcel.2020.06.030
  16. Chembiochem. 2020 Jul 20.
    Yang A, Pantoom S, Wu Y.
      Autophagy is a conserved catabolic process involved in the elimination of proteins, organelles and pathogens. Lipidated LC3 proteins that are conjugated to phosphatidylethanolamine (PE) play a key role in autophagosome biogenesis. Endogenous ATG4-mediated deconjugation of LC3-PE is required for LC3 recycling. However, the Legionella effector RavZ irreversibly deconjugates LC3-PE to inhibit autophagy. It is not clear how ATG4 and RavZ process LC3-PE with distinct modes. Herein, a series of semi-synthetic LC3-PE proteins containing C-terminal mutations or insertions were used to investigate the relationship of the C-terminal structure of LC3-PE with ATG4/RavZ-mediated deconjugation. Using a combination of molecular docking and biochemical assays, we found that Gln 116 , Phe 119 and Gly 120 of LC3-PE are required for the cleavage by both RavZ and ATG4B, while Glu 117 (LC3) is specific for the cleavage by RavZ. The molecular ruler mechanism exists in the active site of ATG4B but not in RavZ. Met 63 and Gln 64 at the active site of RavZ are involved in accommodating LC3 C-terminal motif. Our findings show that the distinct binding modes of LC3 C-terminal motif (116-120) with ATG4 and RavZ may determine the specificity of cleavage site.
    Keywords:  ATG4; Autophagy; LC3; RavZ; expressed protein ligation
    DOI:  https://doi.org/10.1002/cbic.202000359
  17. Sci Rep. 2020 Jul 20. 10(1): 11952
    Chen YC, Navarrete MS, Wang Y, McClintock NC, Sakurai R, Wang F, Chen KT, Chou TF, Rehan VK, Lee DJ, Diaz B.
      N-myristoyltransferase-1 (NMT1) catalyzes protein myristoylation, a lipid modification that is elevated in cancer cells. NMT1 sustains proliferation and/or survival of cancer cells through mechanisms that are not completely understood. We used genetic and pharmacological inhibition of NMT1 to further dissect the role of this enzyme in cancer, and found an unexpected essential role for NMT1 at promoting lysosomal metabolic functions. Lysosomes mediate enzymatic degradation of vesicle cargo, and also serve as functional platforms for mTORC1 activation. We show that NMT1 is required for both lysosomal functions in cancer cells. Inhibition of NMT1 impaired lysosomal degradation leading to autophagy flux blockade, and simultaneously caused the dissociation of mTOR from the surface of lysosomes leading to decreased mTORC1 activation. The regulation of lysosomal metabolic functions by NMT1 was largely mediated through the lysosomal adaptor LAMTOR1. Accordingly, genetic targeting of LAMTOR1 recapitulated most of the lysosomal defects of targeting NMT1, including defective lysosomal degradation. Pharmacological inhibition of NMT1 reduced tumor growth, and tumors from treated animals had increased apoptosis and displayed markers of lysosomal dysfunction. Our findings suggest that compounds targeting NMT1 may have therapeutic benefit in cancer by preventing mTORC1 activation and simultaneously blocking lysosomal degradation, leading to cancer cell death.
    DOI:  https://doi.org/10.1038/s41598-020-68615-w
  18. Toxicology. 2020 Jul 18. pii: S0300-483X(20)30177-3. [Epub ahead of print] 152538
    Ran D, Ma Y, Liu W, Luo T, Zheng J, Wang D, Song R, Zhao H, Zou H, Gu J, Yuan Y, Bian J, Liu Z.
      Cadmium (Cd) is one of worldwide environmental pollutants that causes bone homeostasis, which depends on the resorption of bones by osteoclasts and formation of bones by the osteoblasts (OB). However, the Cd toxicity on OB and its mechanism are unclear. Autophagy is an evolutionarily conserved degradation process in which domestic intracellular components are selectively digested for the recycling of nutrients and energy. This process is indispensable for cell homeostasis maintenance and stress responses. Dysregulation at the level of autophagic activity consequently disturbs the balance between bone formation and bone resorption and mediates the onset and progression of multiple bone diseases, including osteoporosis. TAK1 has been recently emerged as an activator of AMPK and hence an autophagy inducer. AMPK is a key molecule that induces autophagy and regulates cellular metabolism to maintain energy homeostasis. Conversely, autophagy is inhibited by mTORC1. In this study, we found that Cd treatment caused the formation of autophagosomes, LC3-II lipidation and p62 downregulation, and the increased autophagic flux, indicating that Cd treatment induced autophagy in OBs. Cd treatment induced TAK1 activation mediated AMPK phosphorylation, which promoted autophagy via phosphorylation of ULK1 at S317. Meanwhile, Cd treatment dramatically decreased mTORC1, S6K1, 4E-BP1, S6, ULK1S555 and ULK1S757 phosphorylation, suggesting that mTORC1 activity was inhibited and inactive mTORC1 prevents ULK1 activation by phosphorylating ULK1 at SerS555 and Ser757. Our data strongly suggest that TAK1 mediates AMPK activation, which activates ULK1 by phosphorylating ULK1S317 and suppressing mTORC1-mediated ULK1S555 and ULK1S757 phosphorylation. Our study has revealed a signaling mechanism for TAK1 in Cd-induced autophagy in OBs.
    Keywords:  AMPK/mTORC1/ULK1 pathway; Autophagy; Cadmium; Osteoblast; TAK1
    DOI:  https://doi.org/10.1016/j.tox.2020.152538
  19. Chem Biol Interact. 2020 Jul 17. pii: S0009-2797(20)30779-1. [Epub ahead of print] 109196
    Xu Z, Feng J, Li Y, Guan D, Chen H, Zhai X, Zhang L, Li C, Li C.
      Cancer metastasis and resistance for chemotherapeutic agent correlate with epithelial-mesenchymal transition (EMT), while ROS production also involves in the EMT process, However, how autophagy mediated ROS production affects EMT remains unclear. Previous study showed that DpdtC (2,2'-di-pyridylketone hydrazone dithiocarbamate) could induce ferritinophagy in HepG2 cell. To insight into more details that how ferritinophagy affects cellular feature, the SGC-7901and BGC-823 gastric cancer cell lines were used. Interestingly DpdtC treatment resulted in EMT inhibition and was ROS dependent. Similar situation occurred in TGF-β1 induced EMT model, supporting that DpdtC was able to inhibit EMT. Next the ability of DpdtC in ferritinophagy induction was further evaluated. As expected, DpdtC induced ferritinophagy in the absence and presence of TGF-β1. The correlation analysis revealed that an enhanced ferritinophagic flux contributed to the EMT inhibition. In addition, ferritinophagy triggers Fenton reaction, resulting in ROS production which give rise of p53 response, thus the role of p53 was further investigated. DpdtC treatment resulted in upregulation of p53, but, the addition of p53 inhibitor, PFT-α could significantly neutralize the action of DpdtC on ferritinophagy induction and EMT inhibition. Furthermore, autophagy inhibitors or NAC could counteract the action of DpdtC, indicating that ferrtinophagy-mediated ROS played an important role in the cellular events. In addition to upregulation of p53, its down-stream targets, AKT/mTor were also downregulated, supporting that DpdtC induced EMT inhibition was achieved through ferritinophagy-ROS vicious cycle mediated p53/AKT/mTor pathway. And the activation of ferritinophagic flux was the dominant driving force in action of DpdtC in gastric cancer cells.
    Keywords:  Dithiocarbamate derivative; Epithelial-mesenchymal transition (EMT); Ferritinophagy; Iron chelator; ROS; p53/AKT/mTor
    DOI:  https://doi.org/10.1016/j.cbi.2020.109196
  20. Proc Natl Acad Sci U S A. 2020 Jul 23. pii: 202003236. [Epub ahead of print]
    Peng W, Wong YC, Krainc D.
      Mitochondria and lysosomes are critical for cellular homeostasis, and dysfunction of both organelles has been implicated in numerous diseases. Recently, interorganelle contacts between mitochondria and lysosomes were identified and found to regulate mitochondrial dynamics. However, whether mitochondria-lysosome contacts serve additional functions by facilitating the direct transfer of metabolites or ions between the two organelles has not been elucidated. Here, using high spatial and temporal resolution live-cell microscopy, we identified a role for mitochondria-lysosome contacts in regulating mitochondrial calcium dynamics through the lysosomal calcium efflux channel, transient receptor potential mucolipin 1 (TRPML1). Lysosomal calcium release by TRPML1 promotes calcium transfer to mitochondria, which was mediated by tethering of mitochondria-lysosome contact sites. Moreover, mitochondrial calcium uptake at mitochondria-lysosome contact sites was modulated by the outer and inner mitochondrial membrane channels, voltage-dependent anion channel 1 and the mitochondrial calcium uniporter, respectively. Since loss of TRPML1 function results in the lysosomal storage disorder mucolipidosis type IV (MLIV), we examined MLIV patient fibroblasts and found both altered mitochondria-lysosome contact dynamics and defective contact-dependent mitochondrial calcium uptake. Thus, our work highlights mitochondria-lysosome contacts as key contributors to interorganelle calcium dynamics and their potential role in the pathophysiology of disorders characterized by dysfunctional mitochondria or lysosomes.
    Keywords:  TRPML1; calcium; lysosomal storage disorder; mitochondria–lysosome contacts; interorganelle membrane contact sites
    DOI:  https://doi.org/10.1073/pnas.2003236117
  21. Dev Cell. 2020 Jul 20. pii: S1534-5807(20)30544-X. [Epub ahead of print]54(2): 156-170
    Figlia G, Willnow P, Teleman AA.
      Metabolites affect cell growth in two different ways. First, they serve as building blocks for biomass accumulation. Second, metabolites regulate the activity of growth-relevant signaling pathways. They do so in part by covalently attaching to proteins, thereby generating post-translational modifications (PTMs) that affect protein function, the focus of this Perspective. Recent advances in mass spectrometry have revealed a wide variety of such metabolites, including lipids, amino acids, Coenzyme-A, acetate, malonate, and lactate to name a few. An active area of research is to understand which modifications affect protein function and how they do so. In many cases, the cellular levels of these metabolites affect the stoichiometry of the corresponding PTMs, providing a direct link between cell metabolism and the control of cell signaling, transcription, and cell growth.
    Keywords:  O-GlcNAc; YAP; acetylation; autophagy; crotonylation; glutathionylation; hippo; mTORC1; malonylation; methylation; palmitoylation
    DOI:  https://doi.org/10.1016/j.devcel.2020.06.036
  22. iScience. 2020 Jul 04. pii: S2589-0042(20)30531-9. [Epub ahead of print]23(7): 101344
    Zhang Z, Liu Z, Tian Y.
      pH and Ca2+ play important roles in regulating lysosomal activity and lysosome-mediated physiological and pathological processes. However, effective methods for simultaneous determination of pH and Ca2+ is the bottleneck. Herein, a single DNA-based FLIM reporter was developed for real-time imaging and simultaneous quantification of pH and Ca2+ in lysosomes with high affinity, in which a specific probe for recognition of Ca2+ was assembled onto a DNA nanostructure together with pH-responsive and lysosome-targeted molecules. The developed DNA reporter showed excellent biocompatibility and long-term stability up to ∼56 h in lysosomes. Using this powerful tool, it was discovered that pH was closely related to Ca2+ concentration in lysosome, whereas autophagy can be regulated by lysosomal pH and Ca2+. Furthermore, Aβ-induced neuronal death resulted from autophagy abnormal through lysosomal pH and Ca2+ changes. In addition, lysosomal pH and Ca2+ were found to regulate the transformation of NSCs, resulting in Rapamycin-induced antiaging.
    Keywords:  Cellular Neuroscience; Optical Imaging; Technical Aspects of Cell Biology
    DOI:  https://doi.org/10.1016/j.isci.2020.101344
  23. Nat Rev Nephrol. 2020 Jul 23.
    Tang C, Livingston MJ, Liu Z, Dong Z.
      Autophagy is a conserved lysosomal pathway for the degradation of cytoplasmic components. Basal autophagy in kidney cells is essential for the maintenance of kidney homeostasis, structure and function. Under stress conditions, autophagy is altered as part of the adaptive response of kidney cells, in a process that is tightly regulated by signalling pathways that can modulate the cellular autophagic flux - mammalian target of rapamycin, AMP-activated protein kinase and sirtuins are key regulators of autophagy. Dysregulated autophagy contributes to the pathogenesis of acute kidney injury, to incomplete kidney repair after acute kidney injury and to chronic kidney disease of varied aetiologies, including diabetic kidney disease, focal segmental glomerulosclerosis and polycystic kidney disease. Autophagy also has a role in kidney ageing. However, questions remain about whether autophagy has a protective or a pathological role in kidney fibrosis, and about the precise mechanisms and signalling pathways underlying the autophagy response in different types of kidney cells and across the spectrum of kidney diseases. Further research is needed to gain insights into the regulation of autophagy in the kidneys and to enable the discovery of pathway-specific and kidney-selective therapies for kidney diseases and anti-ageing strategies.
    DOI:  https://doi.org/10.1038/s41581-020-0309-2
  24. Nat Metab. 2020 May;2(5): 387-396
    Tharyan RG, Annibal A, Schiffer I, Laboy R, Atanassov I, Weber AL, Gerisch B, Antebi A.
      Mitochondria are multidimensional organelles whose activities are essential to cellular vitality and organismal longevity, yet underlying regulatory mechanisms spanning these different levels of organization remain elusive1-5. Here we show that Caenorhabditis elegans nuclear transcription factor Y, beta subunit (NFYB-1), a subunit of the NF-Y transcriptional complex6-8, is a crucial regulator of mitochondrial function. Identified in RNA interference (RNAi) screens, NFYB-1 loss leads to perturbed mitochondrial gene expression, reduced oxygen consumption, mitochondrial fragmentation, disruption of mitochondrial stress pathways, decreased mitochondrial cardiolipin levels and abolition of organismal longevity triggered by mitochondrial impairment. Multi-omics analysis reveals that NFYB-1 is a potent repressor of lysosomal prosaposin, a regulator of glycosphingolipid metabolism. Limiting prosaposin expression unexpectedly restores cardiolipin production, mitochondrial function and longevity in the nfyb-1 background. Similarly, cardiolipin supplementation rescues nfyb-1 phenotypes. These findings suggest that the NFYB-1-prosaposin axis coordinates lysosomal to mitochondria signalling via lipid pools to enhance cellular mitochondrial function and organismal health.
    DOI:  https://doi.org/10.1038/s42255-020-0200-2
  25. Cell Death Dis. 2020 Jul 18. 11(7): 545
    Song KY, Guo XM, Wang HQ, Zhang L, Huang SY, Huo YC, Zhang G, Feng JZ, Zhang RR, Ma Y, Hu QZ, Qin XY.
      Skeletal muscle atrophy is one of the clinical symptoms of myotonic dystrophy type 1 (DM1). A decline in skeletal muscle regeneration is an important contributor to muscle atrophy. Skeletal muscle satellite cells (SSCs) drive skeletal muscle regeneration. Increased autophagy can reduce the proliferative capacity of SSCs, which plays an important role in the early regeneration of damaged skeletal muscle in DM1. Discovering new ways to restore SSC proliferation may aid in the identification of new therapeutic targets for the treatment of skeletal muscle atrophy in DM1. In the pathogenesis of DM1, muscleblind-like 1 (MBNL1) protein is generally considered to form nuclear RNA foci and disturb the RNA-splicing function. However, the role of MBNL1 in SSC proliferation in DM1 has not been reported. In this study, we obtained SSCs differentiated from normal DM1-04-induced pluripotent stem cells (iPSCs), DM1-03 iPSCs, and DM1-13-3 iPSCs edited by transcription activator-like (TAL) effector nucleases (TALENs) targeting CTG repeats, and primary SSCs to study the pathogenesis of DM1. DM1 SSC lines and primary SSCs showed decreased MBNL1 expression and elevated autophagy levels. However, DM1 SSCs edited by TALENs showed increased cytoplasmic distribution of MBNL1, reduced levels of autophagy, increased levels of phosphorylated mammalian target of rapamycin (mTOR), and improved proliferation rates. In addition, we confirmed that after MBNL1 overexpression, the proliferative capability of DM1 SSCs and the level of phosphorylated mTOR were enhanced, while the autophagy levels were decreased. Our data also demonstrated that the proliferative capability of DM1 SSCs was enhanced after autophagy was inhibited by overexpressing mTOR. Finally, treatment with rapamycin (an mTOR inhibitor) was shown to abolish the increased proliferation capability of DM1 SSCs due to MBNL1 overexpression. Taken together, these data suggest that MBNL1 reverses the proliferation defect of SSCs in DM1 by inhibiting autophagy via the mTOR pathway.
    DOI:  https://doi.org/10.1038/s41419-020-02756-8
  26. Cell Rep. 2020 Jul 21. pii: S2211-1247(20)30892-5. [Epub ahead of print]32(3): 107911
    Imanishi T, Unno M, Kobayashi W, Yoneda N, Akira S, Saito T.
      Effector, but not naïve, T cells are activated by toll-like receptor-2 (TLR2) stimulation, leading to cytokine production and proliferation. We found that the differential response is attributable to the lack of expression of the adaptor protein TIRAP in naive T cells. TIRAP expression is induced upon T-cell receptor (TCR) stimulation and sustained by strong interleukin-2 (IL-2) signals. Expression of TIRAP requires TCR- and IL-2-induced mTORC1 activation. TLR2 stimulation induced the activation of nuclear factor κB (NF-κB) and ERK, leading to much higher production of interferon-γ (IFN-γ) by T helper 1 (Th1) cells cultured in a high concentration of IL-2 than by those cultured in a low concentration of IL-2. In contrast, TLR2 stimulation induces mTORC1 activation through TIRAP, which is essential for TLR2-mediated IFN-γ production. These data demonstrate that the mTORC1 signal confers the response to TLR2 signaling by inducing TIRAP expression and that the TIRAP-mTORC1 axis is critical for TLR2-mediated IFN-γ production by effector T cells.
    DOI:  https://doi.org/10.1016/j.celrep.2020.107911
  27. Biochem Pharmacol. 2020 Jul 17. pii: S0006-2952(20)30393-2. [Epub ahead of print] 114157
    Guo Q, Wang J, Weng Q.
      Optineurin is a widely expressed protein that possesses multiple functions. Growing evidence suggests that mutation or dysregulation of optineurin can cause several neurodegenerative diseases, including amyotrophic lateral sclerosis, primary open-angle glaucoma, and Huntington's disease, as well as inflammatory digestive disorders such as Crohn's disease. Optineurin engages in vesicular trafficking, receptor regulation, immune reactions, autophagy, and distinct signaling pathways including nuclear factor kappa beta, by which optineurin contributes to cellular death and related diseases, indicating its potential as a therapeutic target. In this review, we discuss the major functions and signaling pathways of optineurin. Furthermore, we illustrate the influence of optineurin mutation or dysregulation to region-specific pathogenesis as well as potential applications of optineurin in therapeutic strategies.
    Keywords:  NF-κB; autophagy; disease; optineurin; vesicular trafficking
    DOI:  https://doi.org/10.1016/j.bcp.2020.114157
  28. Int J Mol Sci. 2020 Jul 16. pii: E5029. [Epub ahead of print]21(14):
    Emanuele S, Lauricella M, D'Anneo A, Carlisi D, De Blasio A, Di Liberto D, Giuliano M.
      p62 is a versatile protein involved in the delicate balance between cell death and survival, which is fundamental for cell fate decision in the context of both cancer and neurodegenerative diseases. As an autophagy adaptor, p62 recognizes polyubiquitin chains and interacts with LC3, thereby targeting the selected cargo to the autophagosome with consequent autophagic degradation. Beside this function, p62 behaves as an interactive hub in multiple signalling including those mediated by Nrf2, NF-κB, caspase-8, and mTORC1. The protein is thus crucial for the control of oxidative stress, inflammation and cell survival, apoptosis, and metabolic reprogramming, respectively. As a multifunctional protein, p62 falls into the category of those factors that can exert opposite roles in the cells. Chronic p62 accumulation was found in many types of tumors as well as in stress granules present in different forms of neurodegenerative diseases. However, the protein seems to have a Janus behaviour since it may also serve protective functions against tumorigenesis or neurodegeneration. This review describes the diversified roles of p62 through its multiple domains and interactors and specifically focuses on its oncoJanus and neuroJanus roles.
    Keywords:  apoptosis; autophagy; cancer; neurodegenerative diseases; p62
    DOI:  https://doi.org/10.3390/ijms21145029
  29. Autophagy. 2020 Jul 18.
    Moscat J, Diaz-Meco MT.
      Hepatocellular carcinoma (HCC) is the consequence of chronic liver damage caused by the excessive generation of reactive oxygen species (ROS). To mitigate the deleterious effects of ROS, cells activate the transcription factor NFE2L2/NRF2, which is constitutively degraded through its partner KEAP1. The inactivation of KEAP1 by ROS results in the upregulation of NFE2L2, which leads to the upregulation of critical detoxifying molecules that serve to keep ROS at tolerable levels in order to maintain cell viability. It is thought that this mechanism allows cells to accumulate mutations, which together with the additional pro-tumorigenic and pro-survival effects of NFE2L2 activation, promote cancer initiation and progression. Germane to this phenomenon is macroautophagy/autophagy, which under homeostatic conditions has also been proposed to serve as a detoxifying mechanism by clearing up toxic aggregates and damaged organelles. Our recent data establish a new paradigm for the role that autophagy plays in HCC development.
    Keywords:  NRF2; atypical PKCs; autophagy; hepatocellular carcinoma; reactive oxygen species
    DOI:  https://doi.org/10.1080/15548627.2020.1797290
  30. Mol Med Rep. 2020 Sep;22(3): 2219-2226
    Wu Y, Li W, Hu Y, Liu Y, Sun X.
      Sirtuin 1 (SIRT1) is involved in the pathogenesis of allergic asthma. This study aimed to investigate whether EX‑527, a specific SIRT1 inhibitor, exerted suppressive effects on allergic airway inflammation in mice submitted to ovalbumin (OVA) inhalation. In addition, this study assessed whether such a protective role was mediated by autophagy suppression though mammalian target of rapamycin (mTOR) activation. Female C57BL/6 mice were sensitized to OVA and EX‑527 (10 mg/kg) was administered prior to OVA challenge. The study found that EX‑527 reversed OVA‑induced airway inflammation, and reduced OVA‑induced increases in inflammatory cytokine expression, and total cell and eosinophil counts in bronchoalveolar lavage fluid. In addition, EX‑527 enhanced mTOR activation, thereby suppressing autophagy in allergic mice. To assess whether EX‑527 inhibited airway inflammation in asthma through the mTOR‑mediated autophagy pathway, rapamycin was administered to mice treated with EX‑527 after OVA sensitization. All effects induced by EX‑527, including increased phosphorylated‑mTOR and decreased autophagy, were abrogated by rapamycin treatment. Taken together, the present findings indicated that EX‑527 may inhibit allergic airway inflammation by suppressing autophagy, an effect mediated by mTOR activation in allergic mice.
    DOI:  https://doi.org/10.3892/mmr.2020.11338