bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2021–08–01
fifty-five papers selected by
Viktor Korolchuk, Newcastle University
  1. ATG4s: above and beyond the Atg8-family protein lipidation system.
  2. All cells are created equal in the sight of autophagy: selective autophagy maintains homeostasis in senescent cells.
  3. MDVs to the rescue: How autophagy-deficient cancer cells adapt to defective mitophagy.
  4. Monitoring autophagy-dependent ferroptosis.
  5. Gαq activation modulates autophagy by promoting mTORC1 signaling.
  6. Monitoring selective autophagy of mitochondria using super-resolution microscopy.
  7. Mitophagy in Huntington's disease.
  8. ATG7 safeguards human neural integrity.
  9. Exploring selective autophagy in Drosophila: Methods to identify Atg8-interacting proteins.
  10. Hepatic mTORC1 signaling activates ATF4 as part of its metabolic response to feeding and insulin.
  11. Leucyl-tRNA synthetase 1 is required for proliferation of TSC-null cells.
  12. Lipid metabolism, inflammation, and foam cell formation in health and metabolic disorders: targeting mTORC1.
  13. Monitoring autophagy using super-resolution structured illumination and direct stochastic optical reconstruction microscopy.
  14. A Dictyostelium model for BPAN disease reveals a functional relationship between the WDR45/WIPI4 homolog Wdr45l and Vmp1 in the regulation of autophagy-associated PtdIns3P and ER stress.
  15. ER-Phagy: A New Regulator of ER Homeostasis.
  16. Monitoring autophagic flux in Caenorhabditis elegans using a p62/SQST-1 reporter.
  17. Host autophagy mediates organ wasting and nutrient mobilization for tumor growth.
  18. Determination of mitophagy by electron microscope.
  19. miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact proteotoxicity and muscle function during aging.
  20. ubtor Mutation Causes Motor Hyperactivity by Activating mTOR Signaling in Zebrafish.
  21. FTLD Patient-Derived Fibroblasts Show Defective Mitochondrial Function and Accumulation of p62.
  22. Development of a specific live-cell assay for native autophagic flux.
  23. Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans.
  24. Intranasal insulin rescues repeated anesthesia-induced deficits in synaptic plasticity and memory and prevents apoptosis in neonatal mice via mTORC1.
  25. Pink1/PARK2/mROS-Dependent Mitophagy Initiates the Sensitization of Cancer Cells to Radiation.
  26. Simultaneous determination of intraluminal lysosomal calcium and pH by dextran-conjugated fluorescent dyes.
  27. A novel tool for detecting lysosomal membrane permeabilization by high-throughput fluorescence microscopy.
  28. The role of mTOR in age-related diseases.
  29. Stress-primed secretory autophagy promotes extracellular BDNF maturation by enhancing MMP9 secretion.
  30. Move it to lose it: Mitocytosis expels damaged mitochondria.
  31. Assessment of EGFP-Q74 degradation for the measurement of autophagic flux.
  32. Current insights into the implications of m6A RNA methylation and autophagy interaction in human diseases.
  33. High throughput screening for autophagy.
  34. Endo-lysosomal Aβ concentration and pH trigger formation of Aβ oligomers that potently induce Tau missorting.
  35. Autophagy: A Novel Horizon for Hair Cell Protection.
  36. Advances in autophagy as a target in the treatment of tumors.
  37. PICALM regulates cathepsin D processing and lysosomal function.
  38. Mitochondrial and Organellar Crosstalk in Parkinson's Disease.
  39. Towards a better understanding of the neuro-developmental role of autophagy in sickness and in health.
  40. Quantification of intracellular ACBP/DBI levels.
  41. Post-ER degradation of misfolded GPI-anchored proteins is linked with microautophagy.
  42. Immunoblot-based assays for assessing autophagy in the turquoise killifish Nothobranchius furzeri.
  43. Multimodal assessment of autophagy in mammalian cells with a novel, LC3-based tandem reporter.
  44. Atg5 knockdown induces age-dependent cardiomyopathy which can be rescued by repeated remote ischemic conditioning.
  45. Autophagy induction regulates aquaporin 3-mediated skin fibroblasts aging.
  46. Identification of a new autophagy inhibitor targeting lipid droplets in vascular endothelial cells.
  47. Autophagic defects observed in fibroblasts from a patient with β-propeller protein-associated neurodegeneration.
  48. IRF1 inhibits autophagy-mediated proliferation of colorectal cancer via targeting ATG13.
  49. Autophagy balances the zinc-iron seesaw caused by Zn-stress.
  50. LRRK2 is required for CD38-mediated NAADP-Ca2+ signaling and the downstream activation of TFEB (transcription factor EB) in immune cells.
  51. Inhibitors of VPS34 and fatty-acid metabolism suppress SARS-CoV-2 replication.
  52. ATF3 induces RAB7 to govern autodegradation in paligenosis, a conserved cell plasticity program.
  53. miR‑214 ameliorates sepsis‑induced acute kidney injury via PTEN/AKT/mTOR‑regulated autophagy.
  54. Brain-specific inhibition of mTORC1 eliminates side effects resulting from mTORC1 blockade in the periphery and reduces alcohol intake in mice.
  55. SNX19 restricts endolysosome motility through contacts with the endoplasmic reticulum.
  1. Autophagy. 2021 Jul 25. 1-3
    ATG4s: above and beyond the Atg8-family protein lipidation system.
    Thanh Ngoc Nguyen, Benjamin Scott Padman, Michael Lazarou.
      The sole proteases of the macroautophagy/autophagy machinery, the ATG4s, contribute to autophagosome formation by cleaving Atg8-family protein members (LC3/GABARAPs) which enables Atg8-family protein lipidation and de-lipidation. Our recent work reveals that ATG4s can also promote phagophore growth independently of their protease activity and of Atg8-family proteins. ATG4s and their proximity partners including ARFIP2 and LRBA function to promote trafficking of ATG9A to mitochondria during PINK1-PRKN mitophagy. Through the development of a 3D electron microscopy framework utilizing FIB-SEM and artificial intelligence (termed AIVE: Artificial Intelligence-directed Voxel Extraction), we show that ATG4s promote ER-phagophore contacts during the lipid-transfer phase of autophagosome biogenesis, which requires ATG2B and ATG9A to support phagophore growth. We also discovered that ATG4s are not essential for removal of Atg8-family proteins from autolysosomes, but they can function as deubiquitinase-like enzymes to counteract the conjugation of Atg8-family proteins to other proteins, a process that we have termed ATG8ylation (also known as LC3ylation). These discoveries demonstrate the duality of the ATG4 family in driving autophagosome formation by functioning as both autophagy proteases and trafficking factors, while simultaneously raising questions about the putative roles of ATG8ylation in cell biology.
    Keywords:  ATG4; ATG8; ATG8ylation; PINK1-PRKN mitophagy; Parkinson’s disease; autophagy; de-lipidation; immune disease; mitochondrial dysfunction; ubiquitin-like
    DOI:  https://doi.org/10.1080/15548627.2021.1953263
  2. Autophagy. 2021 Jul 27. 1-2
    All cells are created equal in the sight of autophagy: selective autophagy maintains homeostasis in senescent cells.
    Jaejin Kim, Yeonghyeon Lee, Taerang Jeon, Mi-Sung Kim, Chanhee Kang.
      Macroautophagy/autophagy is a sophisticated quality control program that limits cellular damage and maintains homeostasis, being an essential part of several lifespan-promoting interventions. However, autophagy is also necessary for full establishment of cellular senescence, a causal factor for many age-related diseases and aging. What lies ahead of us to unravel such a paradoxical role of autophagy in senescence is to identify specific targets degraded by autophagy during senescence and determine their importance in the senescence regulatory network. Recently, we developed the "Selective autophagy substrates Identification Platform (SIP)" to advance these goals, providing a rich set of autophagy substrate proteins involved in senescence. Our study demonstrated that selective autophagy coordinates the stress support networks in senescent cells by degrading multiple regulatory components, echoing its homeostatic roles in normal cells. Targeting this type of selective autophagy might provide a unique opportunity to develop non-senescence addiction-based therapeutic strategies for senotherapy by disturbing the homeostatic state of senescent cells.
    Keywords:  Autophagy interactome; cellular senescence; inflammation; oxidative stress; proteostasis; regulated protein stability; selective autophagy; stress support networks
    DOI:  https://doi.org/10.1080/15548627.2021.1953848
  3. Dev Cell. 2021 Jul 26. pii: S1534-5807(21)00529-3. [Epub ahead of print]56(14): 2010-2012
    MDVs to the rescue: How autophagy-deficient cancer cells adapt to defective mitophagy.
    Laura Poillet-Perez, Eileen White.
      Cancers are dependent on mitochondria, the powerhouse of the cell, and autophagy, the mechanism to preserve mitochondrial quality and function. In this issue of Developmental Cell, Towers et al. identify mitochondria-derived vesicles (MDVs) as a new adaptive mechanism enabling cancer cells to compensate for autophagy loss and to maintain mitochondrial function.
    DOI:  https://doi.org/10.1016/j.devcel.2021.06.022
  4. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30195-3. [Epub ahead of print]165 163-176
    Monitoring autophagy-dependent ferroptosis.
    Jingbo Li, Rui Kang, Daolin Tang.
      Ferroptosis is an iron-dependent form of regulated cell death, driven by the accumulation of lipid peroxidation. Autophagy is a lysosome-dependent degradation process that can be used to remove and recover intracellular components, such as dysfunctional proteins and damaged organelles. By regulating iron storage and oxidative stress, excessive autophagy is involved in the induction and execution of ferroptosis. In particular, several types of selective autophagy (e.g., ferritinophagy, lipophagy, clockophagy, and chaperone-mediated autophagy) increase the susceptibility to ferroptotic cell death by degrading anti-ferroptotic regulators (e.g., ferritin, GPX4, ARNTL, and lipid droplets). These two integrated biological processes play a pathological role in the occurrence and development of human diseases, such as cancer, neurodegenerative disorders, ischemia and reperfusion injury. Therefore, it is important to develop reliable methods to evaluate the kinetics of autophagosome formation, iron accumulation, and lipid peroxidation. Here, we introduce some protocols (such as western blotting, lipid peroxidation assay kits and probes, and iron probes) to monitor the process of autophagy-dependent ferroptosis.
    Keywords:  Autophagy; Cell death; Ferroptosis; Lipid peroxidation; Metabolism
    DOI:  https://doi.org/10.1016/bs.mcb.2020.10.012
  5. Nat Commun. 2021 07 27. 12(1): 4540
    Gαq activation modulates autophagy by promoting mTORC1 signaling.
    Sofía Cabezudo, Maria Sanz-Flores, Alvaro Caballero, Inmaculada Tasset, Elena Rebollo, Antonio Diaz, Anna M Aragay, Ana María Cuervo, Federico Mayor, Catalina Ribas.
      The mTORC1 node plays a major role in autophagy modulation. We report a role of the ubiquitous Gαq subunit, a known transducer of plasma membrane G protein-coupled receptors signaling, as a core modulator of mTORC1 and autophagy. Cells lacking Gαq/11 display higher basal autophagy, enhanced autophagy induction upon different types of nutrient stress along with a decreased mTORC1 activation status. They are also unable to reactivate mTORC1 and thus inactivate ongoing autophagy upon nutrient recovery. Conversely, stimulation of Gαq/11 promotes sustained mTORC1 pathway activation and reversion of autophagy promoted by serum or amino acids removal. Gαq is present in autophagic compartments and lysosomes and is part of the mTORC1 multi-molecular complex, contributing to its assembly and activation via its nutrient status-sensitive interaction with p62, which displays features of a Gαq effector. Gαq emerges as a central regulator of the autophagy machinery required to maintain cellular homeostasis upon nutrient fluctuations.
    DOI:  https://doi.org/10.1038/s41467-021-24811-4
  6. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30193-X. [Epub ahead of print]165 153-161
    Monitoring selective autophagy of mitochondria using super-resolution microscopy.
    Ziyue Li, Nicholas T Ktistakis.
      Selective elimination of damaged mitochondria via macroautophagy (mitophagy) is a conserved cellular process that plays an important role in organismal health. In recent years mitophagy has been studied in parallel to the more general, non-selective autophagy pathway induced in response to amino acid starvation with important similarities and differences noted between the two. The elaborate sequence of membrane rearrangements that give rise to autophagosomes in the non-selective pathway have their counterpart in mitophagy, but with the addition of other factors, such as a ubiquitin mark and mitophagy receptors, which mediate cargo recognition. In some types of mitophagy such as the one induced by ivermectin, the forming autophagosomal structure contains six different elements: the targeted mitochondrial fragment, a section of endoplasmic reticulum that provides a cradle, a ubiquitin layer, the mitophagy receptors and the early and late autophagosomal proteins/membranes. Super-resolution microscopy is ideally suited to investigate the spatial relationships between these elements that converge together but retain some distinctive localization, and we provide here a general protocol that can be used for mammalian cells.
    Keywords:  Autophagy; Endoplasmic reticulum; Ivermectin; Mitochondria; Mitophagy; Structured illumination microscopy
    DOI:  https://doi.org/10.1016/bs.mcb.2020.10.010
  7. Neurochem Int. 2021 Jul 27. pii: S0197-0186(21)00193-5. [Epub ahead of print] 105147
    Mitophagy in Huntington's disease.
    I Šonský, P Vodička, K Vodičková Kepková, H Hansíková.
      Huntington's disease (HD), as well as Parkinson's disease and Alzheimer's disease, belong to a group of neurodegenerative diseases characterized by common features, such as the progressive loss of neurons and the presence of pathogenic forms of misfolded protein aggregates. A quality control system such as autophagy is crucial for the clearance of protein aggregates and dysfunctional organelles and thus essential for the maintenance of neuronal homeostasis. The constant high energy demand of neuronal tissue links neurodegeneration to mitochondria. Inefficient removal of damaged mitochondria is thought to contribute to the pathogenesis of neurodegenerative diseases such as HD. In addition, direct involvement of the huntingtin protein in the autophagic machinery has been described. In this review, we focus on mitophagy, a selective form of autophagy responsible for mitochondrial turnover. We also discuss the relevance of pharmacological regulation of mitophagy in the future therapeutic approach to neurodegenerations, including HD.
    Keywords:  Huntington's disease; Mitochondria; Mitophagy; Mitophagy adaptors; Pharmacological induction of mitophagy
    DOI:  https://doi.org/10.1016/j.neuint.2021.105147
  8. Autophagy. 2021 Jul 27. 1-3
    ATG7 safeguards human neural integrity.
    Jack J Collier, Monika Oláhová, Thomas G McWilliams, Robert W Taylor.
      ATG7 drives macroautophagy, hereafter "autophagy", by generating ATG12-ATG5 conjugates and lipidating Atg8 homologs including LC3. A pioneering body of work has defined the requirement of ATG7 for survival in mice and shown that neural-specific atg7 deletion causes neurodegeneration, but it has not been ascertained whether human life is compatible with ATG7 dysfunction. Recently, we defined the importance of ATG7 in human physiology by identifying twelve patients from five families harboring pathogenic, biallelic ATG7 variants causing a neurodevelopmental disorder. Patient fibroblasts show undetectable or severely diminished ATG7 protein levels, and biochemical assessment via autophagic flux and long-lived protein degradation assays demonstrated that attenuated autophagy underpins the pathology. Confirming the pathogenicity of patient variants, mouse cells expressing mutated ATG7 are unable to rescue LC3/Atg8 lipidation to wild-type levels. Our work defines mutated ATG7 as an important cause of human neurological disease and expands our understanding of autophagy in longevity and human health. We demonstrated that in certain circumstances, human survival with relatively mild phenotypes is possible even with undetectable levels of a nonredundant core autophagy protein.
    Keywords:  Autophagy; atg7; cell biology; disease; macroautophagy; molecular genetics; neurodegeneration
    DOI:  https://doi.org/10.1080/15548627.2021.1953267
  9. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30191-6. [Epub ahead of print]165 13-29
    Exploring selective autophagy in Drosophila: Methods to identify Atg8-interacting proteins.
    Stavroula Petridi, Anne-Claire Jacomin, Zambarlal Bhujabal, Terje Johansen, Ioannis P Nezis.
      Autophagy has been described as a catabolic process in which cytoplasmic material is being recycled under various conditions of cellular stress, preventing cell damage and promoting cell survival. Drosophila has been demonstrated to provide an excellent animal model for the study of autophagy. Here, we provide a detailed experimental procedure for the identification of Atg8a interactors, exploiting the iLIR database, followed by the in vitro confirmation of interactions and in situ detection of the respective proteins.
    Keywords:  Autophagy; Drosophila; GST pull-down assay; Macroauptophagy; Mosaic analysis; Selective autophagy
    DOI:  https://doi.org/10.1016/bs.mcb.2020.10.008
  10. Mol Metab. 2021 Jul 22. pii: S2212-8778(21)00156-3. [Epub ahead of print] 101309
    Hepatic mTORC1 signaling activates ATF4 as part of its metabolic response to feeding and insulin.
    Vanessa Byles, Yann Cormerais, Krystle Kalafut, Victor Barrera, James E Hughes Hallett, Shannan Ho Sui, John M Asara, Christopher M Adams, Gerta Hoxhaj, Issam Ben-Sahra, Brendan D Manning.
       OBJECTIVE: The mechanistic target of rapamycin complex 1 (mTORC1) is dynamically regulated by fasting and feeding cycles in the liver to promote protein and lipid synthesis while suppressing autophagy. However, beyond these functions, the metabolic response of the liver to feeding and insulin signaling orchestrated by mTORC1 remains poorly defined. Here, we determine whether ATF4, a stress responsive transcription factor recently found to be independently regulated by mTORC1 signaling in proliferating cells, is responsive to hepatic mTORC1 signaling to alter hepatocyte metabolism.
    METHODS: ATF4 protein levels and expression of canonical gene targets were analyzed in the liver following fasting and physiological feeding in the presence or absence of the mTORC1 inhibitor rapamycin. Primary hepatocytes from wild-type or liver-specific Atf4 knockout (LAtf4KO) mice were used to characterize the effects of insulin-stimulated mTORC1-ATF4 function on hepatocyte gene expression and metabolism. Both unbiased steady-state metabolomics and stable-isotope tracing methods were employed to define mTORC1 and ATF4-dependent metabolic changes. RNA-sequencing was used to determine global changes in feeding-induced transcripts in the livers of wild-type versus LAtf4KO mice.
    RESULTS: We demonstrate that ATF4 and its metabolic gene targets are stimulated by mTORC1 signaling in the liver in response to feeding and in a hepatocyte-intrinsic manner by insulin. While we demonstrate that de novo purine and pyrimidine synthesis is stimulated by insulin through mTORC1 signaling in primary hepatocytes, this regulation was independent of ATF4. Metabolomics and metabolite tracing studies revealed that insulin-mTORC1-ATF4 signaling stimulates pathways of non-essential amino acid synthesis in primary hepatocytes, including those of alanine, aspartate, methionine, and cysteine, but not serine.
    CONCLUSION: The results demonstrate that ATF4 is a novel metabolic effector of mTORC1 in liver, extending the molecular consequences of feeding and insulin-induced mTORC1 signaling in this key metabolic tissue to the control of amino acid metabolism.
    Keywords:  ATF4; feeding; insulin; liver; mTORC1; methionine metabolism
    DOI:  https://doi.org/10.1016/j.molmet.2021.101309
  11. Biochem Biophys Res Commun. 2021 Jul 26. pii: S0006-291X(21)01119-0. [Epub ahead of print]571 159-166
    Leucyl-tRNA synthetase 1 is required for proliferation of TSC-null cells.
    Ji-Hyun Bae, Jong Hyun Kim.
      Uncontrolled cell proliferation associated with cancer depends on the functional abrogation of at least one of tumor suppressor. In response to nutrient cue, tuberous sclerosis complex (TSC) works as a tumor suppressor which inhibits cell growth via negative regulation of the mammalian target of rapamycin complex (mTORC1). However, the regulation mechanism of nutrient-dependent cell proliferation in TSC-null cells remains unclear. Here, we demonstrate that leucine is required for cell proliferation through the activation of leucyl-tRNA synthetase (LARS1)-mTORC1 pathway in TSC-null cells. Cell proliferation and survival were attenuated by LARS1 knock-down or inhibitors in TSC-null cells. In addition, either rapamycin or LARS1 inhibitors significantly decreased colony formation ability while their combined treatment drastically attenuated it. Taken together, we suggest that LARS1 inhibitors might considered as novel tools for the regression of tumor growth and proliferation in TSC-null tumor cells which regrow upon discontinuation of the mTORC1 inhibition.
    Keywords:  Amino acids; Cell proliferation; LARS1; TSC; mTORC1
    DOI:  https://doi.org/10.1016/j.bbrc.2021.07.080
  12. J Mol Med (Berl). 2021 Jul 26.
    Lipid metabolism, inflammation, and foam cell formation in health and metabolic disorders: targeting mTORC1.
    So Yeong Cheon, KyoungJoo Cho.
      Metabolic homeostasis is important for maintaining a healthy lifespan. Lipid metabolism is particularly necessary for the maintenance of metabolic energy sources and their storage, and the structure and function of cell membranes, as well as for the regulation of nutrition through lipogenesis, lipolysis, and lipophagy. Dysfunctional lipid metabolism leads to the development of metabolic disorders, such as atherosclerosis, diabetes mellitus, and non-alcoholic fatty liver disease (NAFLD). Furthermore, dyslipidaemia causes inflammatory responses and foam cell formation. Mechanistic target of rapamycin (mTOR) signalling is a key regulator of diverse cellular processes, including cell metabolism and cell fate. mTOR complex 1 (mTORC1) is involved in lipid metabolism and immune responses in the body. Therefore, the mTORC1 signalling pathway has been suggested as a potential therapeutic target for the treatment of metabolic disorders. In this review, we focus on the roles of mTORC1 in lipid metabolism and inflammation, and present current evidence on its involvement in the development and progression of metabolic disorders.
    Keywords:  Foam cells; Inflammation; Lipid metabolism; Mechanistic target of rapamycin (mTOR); Metabolic disorders
    DOI:  https://doi.org/10.1007/s00109-021-02117-8
  13. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30211-9. [Epub ahead of print]165 139-152
    Monitoring autophagy using super-resolution structured illumination and direct stochastic optical reconstruction microscopy.
    Dumisile Lumkwana, Lize Engelbrecht, Ben Loos.
      Autophagy is a major protein degradation pathway responsible for the removal of primarily long-lived and misfolded proteins, contributing to cellular homeostasis. Autophagy dysfunction has been associated with the onset of various human pathologies. Visualizing key proteins that govern autophagy pathway activity, the molecular machinery and cargo is essential to elucidate roles and mechanisms of autophagy function. Although multiple fluorescence-based microscopy approaches exist to assess autophagy, the limit of resolution associated with light microscopy makes precise intracellular protein localization, interaction and molecular distribution challenging. Here we describe a detailed protocol for both super-resolution structured illumination microscopy (SR-SIM) as well as direct stochastic optical reconstruction microscopy (dSTORM) for the visualization of key proteins associated with the autophagy molecular machinery and cargo. The presented method enables to achieve increased resolving power to assess localization and molecular density profiles, typically not achievable with standard confocal or wide field fluorescence microcopy.
    Keywords:  Autophagosome; Autophagy; Direct stochastic optical reconstruction; Fluorescence microscopy; Lysosome; Structured illumination
    DOI:  https://doi.org/10.1016/bs.mcb.2020.12.005
  14. Autophagy. 2021 Jul 27. 1-17
    A Dictyostelium model for BPAN disease reveals a functional relationship between the WDR45/WIPI4 homolog Wdr45l and Vmp1 in the regulation of autophagy-associated PtdIns3P and ER stress.
    Alba Tornero-Écija, Luis-Carlos Tábara, Miranda Bueno-Arribas, Laura Antón-Esteban, Cristina Navarro-Gómez, Irene Sánchez, Olivier Vincent, Ricardo Escalante.
      PROPPINs are conserved PtdIns3P-binding proteins required for autophagosome biogenesis that fold into a characteristic group of seven-bladed beta-propellers. Mutations in WDR45/WIPI4, a human member of this family, lead to BPAN, a rare form of neurodegeneration. We have generated mutants for the two PROPPIN proteins present in the model system Dictyostelium discoideum (Atg18 and Wdr45l) and characterized their function. Lack of Wdr45l greatly impairs autophagy, while Atg18 only causes subtle defects in the maturation of autolysosomes. The strong phenotype of the Wdr45l mutant is strikingly similar to that observed in Dictyostelium cells lacking Vmp1, an ER protein required for omegasome formation. Common phenotypes include impaired growth in axenic medium, lack of aggregation, and local enrichment of PtdIns3P as determined by the use of lipid reporters. In addition, Vmp1 and Wdr45l mutants show a chronically active response to ER stress. For both mutants, this altered PtdIns3P localization can be prevented by the additional mutation of the upstream regulator Atg1, which also leads to recovery of axenic growth and reduction of ER stress. We propose that, in addition to an autophagy defect, local autophagy-associated PtdIns3P accumulation might contribute to the pathogenesis of BPAN by disrupting ER homeostasis. The introduction of BPAN-associated mutations in Dictyostelium Wdr45l reveals the impact of pathogenic residues on the function and localization of the protein.
    Keywords:  Atg18; autophagosome; membrane contact site; omegasome; proppin proteins
    DOI:  https://doi.org/10.1080/15548627.2021.1953262
  15. Front Cell Dev Biol. 2021 ;9 684526
    ER-Phagy: A New Regulator of ER Homeostasis.
    Ming Yang, Shilu Luo, Xi Wang, Chenrui Li, Jinfei Yang, Xuejing Zhu, Li Xiao, Lin Sun.
      The endoplasmic reticulum (ER) is one of the most important cellular organelles and is essential for cell homeostasis. Upon external stimulation, ER stress induces the unfolded protein response (UPR) and ER-associated degradation (ERAD) to maintain ER homeostasis. However, persistent ER stress can lead to cell damage. ER-phagy is a selective form of autophagy that ensures the timely removal of damaged ER, thereby protecting cells from damage caused by excessive ER stress. As ER-phagy is a newly identified form of autophagy, many receptor-mediated ER-phagy pathways have been discovered in recent years. In this review, we summarize our understanding of the maintenance of ER homeostasis and describe the receptors identified to date. Finally, the relationships between ER-phagy and diseases are also discussed.
    Keywords:  ER-phagy; ERAD; autophagy; endoplasmic reticulum (ER); unfolded protein response (UPR)
    DOI:  https://doi.org/10.3389/fcell.2021.684526
  16. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30194-1. [Epub ahead of print]165 73-87
    Monitoring autophagic flux in Caenorhabditis elegans using a p62/SQST-1 reporter.
    Christina Ploumi, Aggeliki Sotiriou, Nektarios Tavernarakis.
      Autophagy is a well-conserved self-degrading mechanism, which involves the elimination of unnecessary or damaged cellular constituents. Although extensively studied, many aspects regarding its tight regulation and its implication in health and disease remain elusive. The nematode Caenorhabditis elegans has been widely used as a simple multicellular model organism for studying the autophagic machinery per se, and uncover its multidimensional roles in the maintenance of cellular and organismal homeostasis. The current protocol describes the in vivo detection and biochemical analysis of the autophagic substrate SQST-1, as an indicator of autophagic flux in C. elegans.
    Keywords:  Autophagic flux; Autophagy; Caenorhabditis elegans; LC3; SQST-1; Sequestosome; p62
    DOI:  https://doi.org/10.1016/bs.mcb.2020.10.011
  17. EMBO J. 2021 Jul 26. e107336
    Host autophagy mediates organ wasting and nutrient mobilization for tumor growth.
    Rojyar Khezri, Petter Holland, Todd Andrew Schoborg, Ifat Abramovich, Szabolcs Takáts, Caroline Dillard, Ashish Jain, Fergal O'Farrell, Sebastian Wolfgang Schultz, William M Hagopian, Eduardo Martin Quintana, Rachel Ng, Nadja Sandra Katheder, Mohammed Mahidur Rahman, José Gerardo Teles Reis, Andreas Brech, Heinrich Jasper, Nasser M Rusan, Anne Hope Jahren, Eyal Gottlieb, Tor Erik Rusten.
      During tumor growth-when nutrient and anabolic demands are high-autophagy supports tumor metabolism and growth through lysosomal organelle turnover and nutrient recycling. Ras-driven tumors additionally invoke non-autonomous autophagy in the microenvironment to support tumor growth, in part through transfer of amino acids. Here we uncover a third critical role of autophagy in mediating systemic organ wasting and nutrient mobilization for tumor growth using a well-characterized malignant tumor model in Drosophila melanogaster. Micro-computed X-ray tomography and metabolic profiling reveal that RasV12 ; scrib-/- tumors grow 10-fold in volume, while systemic organ wasting unfolds with progressive muscle atrophy, loss of body mass, -motility, -feeding, and eventually death. Tissue wasting is found to be mediated by autophagy and results in host mobilization of amino acids and sugars into circulation. Natural abundance Carbon 13 tracing demonstrates that tumor biomass is increasingly derived from host tissues as a nutrient source as wasting progresses. We conclude that host autophagy mediates organ wasting and nutrient mobilization that is utilized for tumor growth.
    Keywords:   Drosophila ; autophagy; cancer cachexia; muscle; tumor; wasting
    DOI:  https://doi.org/10.15252/embj.2020107336
  18. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30198-9. [Epub ahead of print]165 103-110
    Determination of mitophagy by electron microscope.
    Zhiyu Li, Qi Wu, Le Liu, Si Sun, Shengrong Sun, Zhong Wang, Juanjuan Li.
      Mitophagy is an autophagic mechanism for targeting damaged or unnecessary mitochondria and responsible for mitochondria quality control. Emerging evidence revealed that mitophagy is associated with many physiological processes and cellular activities. Therefore, the determination of mitophagy may provide insights into human physiological and pathological processes. Electron microscopy, one of the best approaches, can directly provide the ultrastructure evidence for mitophagy. Here, we detail an experiment protocol for electron microscopy preparation, so as to detect mitophagy in biological samples. Compare with other biochemical techmology, conventional electron microscopy are still essential for strengthening or replacing biochemical methods, and a better understanding of this method could be important to investigate mitophagy.
    Keywords:  Biological sample preparation; Detection; Electron microscope; Method; Mitophagy
    DOI:  https://doi.org/10.1016/bs.mcb.2020.10.015
  19. Elife. 2021 Jul 27. pii: e66768. [Epub ahead of print]10
    miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact proteotoxicity and muscle function during aging.
    Isabelle Schiffer, Birgit Gerisch, Kazuto Kawamura, Raymond Laboy, Jennifer Hewitt, Martin Sebastian Denzel, Marcelo A Mori, Siva Vanapalli, Yidong Shen, Orsolya Symmons, Adam Antebi.
      Muscle function relies on the precise architecture of dynamic contractile elements, which must be fine-tuned to maintain motility throughout life. Muscle is also plastic, and remodeled in response to stress, growth, neural and metabolic inputs. The conserved muscle-enriched microRNA, miR-1, regulates distinct aspects of muscle development, but whether it plays a role during aging is unknown. Here we investigated Caenorhabditis elegans miR-1 in muscle function in response to proteostatic stress. mir-1 deletion improved mid-life muscle motility, pharyngeal pumping, and organismal longevity upon polyQ35 proteotoxic challenge. We identified multiple vacuolar ATPase subunits as subject to miR-1 control, and the regulatory subunit vha-13/ATP6V1A as a direct target downregulated via its 3'UTR to mediate miR-1 physiology. miR-1 further regulates nuclear localization of lysosomal biogenesis factor HLH-30/TFEB and lysosomal acidification. Our studies reveal that miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact muscle function and health during aging.
    Keywords:  C. elegans; genetics; genomics; lysosomal v-ATPase; miR-1; polyglutamine; proteostasis; vha-13
    DOI:  https://doi.org/10.7554/eLife.66768
  20. Neurosci Bull. 2021 Jul 26.
    ubtor Mutation Causes Motor Hyperactivity by Activating mTOR Signaling in Zebrafish.
    Tiantian Wang, Mingshan Zhou, Quan Zhang, Cuizhen Zhang, Gang Peng.
      Mechanistic target of rapamycin (mTOR) signaling governs important physiological and pathological processes key to cellular life. Loss of mTOR negative regulators and subsequent over-activation of mTOR signaling are major causes underlying epileptic encephalopathy. Our previous studies showed that UBTOR/KIAA1024/MINAR1 acts as a negative regulator of mTOR signaling, but whether UBTOR plays a role in neurological diseases remains largely unknown. We therefore examined a zebrafish model and found that ubtor disruption caused increased spontaneous embryonic movement and neuronal activity in spinal interneurons, as well as the expected hyperactivation of mTOR signaling in early zebrafish embryos. In addition, mutant ubtor larvae showed increased sensitivity to the convulsant pentylenetetrazol, and both the motor activity and the neuronal activity were up-regulated. These phenotypic abnormalities in zebrafish embryos and larvae were rescued by treatment with the mTORC1 inhibitor rapamycin. Taken together, our findings show that ubtor regulates motor hyperactivity and epilepsy-like behaviors by elevating neuronal activity and activating mTOR signaling.
    Keywords:  Epilepsy; Hyperactivity; Ubtor; Zebrafish; mTOR
    DOI:  https://doi.org/10.1007/s12264-021-00755-z
  21. Mol Neurobiol. 2021 Jul 30.
    FTLD Patient-Derived Fibroblasts Show Defective Mitochondrial Function and Accumulation of p62.
    Stina Leskelä, Dorit Hoffmann, Hannah Rostalski, Nadine Huber, Rebekka Wittrahm, Päivi Hartikainen, Ville Korhonen, Ville Leinonen, Mikko Hiltunen, Eino Solje, Anne M Remes, Annakaisa Haapasalo.
      Frontotemporal lobar degeneration (FTLD) is a clinically, genetically, and neuropathologically heterogeneous group of neurodegenerative syndromes, leading to progressive cognitive dysfunction and frontal and temporal atrophy. C9orf72 hexanucleotide repeat expansion (C9-HRE) is the most common genetic cause of FTLD, but pathogenic mechanisms underlying FTLD are not fully understood. Here, we compared cellular features and functional properties, especially related to protein degradation pathways and mitochondrial function, of FTLD patient-derived skin fibroblasts from C9-HRE carriers and non-carriers and healthy donors. Fibroblasts from C9-HRE carriers were found to produce RNA foci, but no dipeptide repeat proteins, and they showed unchanged levels of C9orf72 mRNA transcripts. The main protein degradation pathways, the ubiquitin-proteasome system and autophagy, did not show alterations between the fibroblasts from C9-HRE-carrying and non-carrying FTLD patients and compared to healthy controls. An increase in the number and size of p62-positive puncta was evident in fibroblasts from both C9-HRE carriers and non-carriers. In addition, several parameters of mitochondrial function, namely, basal and maximal respiration and respiration linked to ATP production, were significantly reduced in the FTLD patient-derived fibroblasts from both C9-HRE carriers and non-carriers. Our findings suggest that FTLD patient-derived fibroblasts, regardless of whether they carry the C9-HRE expansion, show unchanged proteasomal and autophagic function, but significantly impaired mitochondrial function and increased accumulation of p62 when compared to control fibroblasts. These findings suggest the possibility of utilizing FTLD patient-derived fibroblasts as a platform for biomarker discovery and testing of drugs targeted to specific cellular functions, such as mitochondrial respiration.
    Keywords:  Amyotrophic lateral sclerosis; Autophagy; C9orf72; Frontotemporal lobar degeneration; Mitochondrial function; Ubiquitin–proteasome system
    DOI:  https://doi.org/10.1007/s12035-021-02475-x
  22. J Biol Chem. 2021 Jul 22. pii: S0021-9258(21)00805-X. [Epub ahead of print] 101003
    Development of a specific live-cell assay for native autophagic flux.
    Nathaniel Safren, Elizabeth M Tank, Ahmed M Malik, Jason P Chua, Nicholas Santoro, Sami J Barmada.
      Autophagy is an evolutionarily conserved pathway mediating the breakdown of cellular proteins and organelles. Emphasizing its pivotal nature, autophagy dysfunction contributes to many diseases; nevertheless, development of effective autophagy modulating drugs is hampered by fundamental deficiencies in available methods for measuring autophagic activity, or flux. To overcome these limitations, we introduced the photoconvertible protein Dendra2 into the MAP1LC3B locus of human cells via CRISPR/Cas9 genome editing, enabling accurate and sensitive assessments of autophagy in living cells by optical pulse labeling. We used this assay to perform high throughput drug screens of four chemical libraries comprising over 30,000 diverse compounds, identifying several clinically relevant drugs and novel autophagy modulators. A select series of candidate compounds also modulated autophagy flux in human motor neurons modified by CRISPR/Cas9 to express GFP-labeled LC3. Using automated microscopy, we tested the therapeutic potential of autophagy induction in several distinct neuronal models of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). In doing so, we found that autophagy induction exhibited discordant effects, improving survival in disease models involving the RNA binding protein TDP-43, while exacerbating toxicity in neurons expressing mutant forms of UBQLN2 and C9ORF72 associated with familial ALS/FTD. These studies confirm the utility of the Dendra2-LC3 assay, while illustrating the contradictory effects of autophagy induction in different ALS/FTD subtypes.
    Keywords:  ALS; FTD; autophagy; high-content; high-throughput; neurodegeneration; photoconvertible; repurposing; screen; stem cell
    DOI:  https://doi.org/10.1016/j.jbc.2021.101003
  23. Nat Commun. 2021 07 27. 12(1): 4568
    Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans.
    Wen-Jun Li, Chen-Wei Wang, Li Tao, Yong-Hong Yan, Mei-Jun Zhang, Ze-Xian Liu, Yu-Xin Li, Han-Qing Zhao, Xue-Mei Li, Xian-Dong He, Yu Xue, Meng-Qiu Dong.
      Insulin/IGF-1 Signaling (IIS) is known to constrain longevity by inhibiting the transcription factor FOXO. How phosphorylation mediated by IIS kinases regulates lifespan beyond FOXO remains unclear. Here, we profile IIS-dependent phosphorylation changes in a large-scale quantitative phosphoproteomic analysis of wild-type and three IIS mutant Caenorhabditis elegans strains. We quantify more than 15,000 phosphosites and find that 476 of these are differentially phosphorylated in the long-lived daf-2/insulin receptor mutant. We develop a machine learning-based method to prioritize 25 potential lifespan-related phosphosites. We perform validations to show that AKT-1 pT492 inhibits DAF-16/FOXO and compensates the loss of daf-2 function, that EIF-2α pS49 potently inhibits protein synthesis and daf-2 longevity, and that reduced phosphorylation of multiple germline proteins apparently transmits reduced DAF-2 signaling to the soma. In addition, an analysis of kinases with enriched substrates detects that casein kinase 2 (CK2) subunits negatively regulate lifespan. Our study reveals detailed functional insights into longevity.
    DOI:  https://doi.org/10.1038/s41467-021-24816-z
  24. Sci Rep. 2021 Jul 29. 11(1): 15490
    Intranasal insulin rescues repeated anesthesia-induced deficits in synaptic plasticity and memory and prevents apoptosis in neonatal mice via mTORC1.
    Patricia Soriano Roque, Mehdi Hooshmandi, Laura Neagu-Lund, Shelly Yin, Noosha Yousefpour, Hiroaki Sato, Tamaki Sato, Yosuke Nakadate, Akiko Kawakami, Soroush Tahmasebi, Alfredo Ribeiro-da-Silva, Christos G Gkogkas, Masha Prager-Khoutorsky, Thomas Schricker, Linda Wykes, Arkady Khoutorsky.
      Long-lasting cognitive impairment in juveniles undergoing repeated general anesthesia has been observed in numerous preclinical and clinical studies, yet, the underlying mechanisms remain unknown and no preventive treatment is available. We found that daily intranasal insulin administration to juvenile mice for 7 days prior to repeated isoflurane anesthesia rescues deficits in hippocampus-dependent memory and synaptic plasticity in adulthood. Moreover, intranasal insulin prevented anesthesia-induced apoptosis of hippocampal cells, which is thought to underlie cognitive impairment. Inhibition of the mechanistic target of rapamycin complex 1 (mTORC1), a major intracellular effector of insulin receptor, blocked the beneficial effects of intranasal insulin on anesthesia-induced apoptosis. Consistent with this finding, mice lacking mTORC1 downstream translational repressor 4E-BP2 showed no induction of repeated anesthesia-induced apoptosis. Our study demonstrates that intranasal insulin prevents general anesthesia-induced apoptosis of hippocampal cells, and deficits in synaptic plasticity and memory, and suggests that the rescue effect is mediated via mTORC1/4E-BP2 signaling.
    DOI:  https://doi.org/10.1038/s41598-021-94849-3
  25. Oxid Med Cell Longev. 2021 ;2021 5595652
    Pink1/PARK2/mROS-Dependent Mitophagy Initiates the Sensitization of Cancer Cells to Radiation.
    Lei Yu, Xiangshan Yang, Xin Li, Lijing Qin, Weiqiang Xu, Hongli Cui, Zhen Jia, Qiang He, Zhicheng Wang.
      Autophagy plays a double-edged sword for cancer; particularly, mitophagy plays important roles in the selective degradation of damaged mitochondria. However, whether mitophagy is involved in killing effects of tumor cells by ionizing radiation (IR) and its underlying mechanism remain elusive. The purpose is to evaluate the effects of mitochondrial ROS (mROS) on autophagy after IR; furthermore, we hypothesized that KillerRed (KR) targeting mitochondria could induce mROS generation, subsequent mitochondrial depolarization, accumulation of Pink1, and recruitment of PARK2 to promote the mitophagy. Thereby, we would achieve a new strategy to enhance mROS accumulation and clarify the roles and mechanisms of radiosensitization by KR and IR. Our data demonstrated that IR might cause autophagy of both MCF-7 and HeLa cells, which is related to mitochondria and mROS, and the ROS scavenger N-acetylcysteine (NAC) could reduce the effects. Based on the theory, mitochondrial targeting vector sterile α- and HEAT/armadillo motif-containing protein 1- (Sarm1-) mtKR has been successfully constructed, and we found that ROS levels have significantly increased after light exposure. Furthermore, mitochondrial depolarization of HeLa cells was triggered, such as the decrease of Na+K+ ATPase, Ca2+Mg2+ ATPase, and mitochondrial respiratory complex I and III activities, and mitochondrial membrane potential (MMP) has significantly decreased, and voltage-dependent anion channel 1 (VDAC1) protein has significantly increased in the mitochondria. Additionally, HeLa cell proliferation was obviously inhibited, and the cell autophagic rates dramatically increased, which referred to the regulation of the Pink1/PARK2 pathway. These results indicated that mitophagy induced by mROS can initiate the sensitization of cancer cells to IR and might be regulated by the Pink1/PARK2 pathway.
    DOI:  https://doi.org/10.1155/2021/5595652
  26. Methods Cell Biol. 2021 ;pii: S0091-679X(21)00020-0. [Epub ahead of print]165 199-208
    Simultaneous determination of intraluminal lysosomal calcium and pH by dextran-conjugated fluorescent dyes.
    Philippe Pihán, Paula Nunes-Hasler, Nicolas Demaurex, Claudio Hetz.
      The lysosome is the main catabolic organelle in the cell, also serving as a signaling platform. Lysosomes maintain a low intraluminal pH where dozens of hydrolytic enzymes degrade a wide variety of macromolecules. Besides degradation of polymers, the lysosome is involved in various cellular processes, including energy metabolism, plasma membrane repair and antigen presentation. Recent work has shown that the lysosome is an important calcium store, modulating diverse cellular functions such as membrane fusion and fission, autophagy and lysosomal biogenesis. Precise measurement of free lysosomal calcium concentration has been hampered by its low luminal pH, since the affinity of most calcium probes decreases with higher proton concentration. Here we detailed an adapted protocol for the simultaneous measurement of lysosomal pH and calcium using dextran-conjugated ratiometric fluorescent dyes. As compared with indirect measurements of lysosomal calcium release using genetically-encoded calcium indicators (GECIs), the present method offers the possibility of obtaining pH-corrected, intraluminal calcium concentrations at single lysosome resolution. It also enables simultaneous temporal resolution of lysosomal calcium and pH.
    Keywords:  Confocal microscopy; Lysosomal calcium; Lysosomal signaling; Ratiometric fluorescent probes
    DOI:  https://doi.org/10.1016/bs.mcb.2021.02.007
  27. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30187-4. [Epub ahead of print]165 1-12
    A novel tool for detecting lysosomal membrane permeabilization by high-throughput fluorescence microscopy.
    Karla Alvarez-Valadez, Allan Sauvat, Hélène Fohrer-Ting, Christophe Klein, Oliver Kepp, Guido Kroemer, Mojgan Djavaheri-Mergny.
      Lysosomes are placed at the center of cellular trafficking and degradative pathways. They also function as a signaling platform for nutrient sensing and metabolic reprogramming. Lysosomes play crucial roles in cellular adaptation in response to stress and are tightly connected to a variety of cell death modalities. Several stimuli can initiate the permeabilization of the lysosome membrane, thus causing cell death when the cellular adaptive system fail to repair or replace damaged lysosomes. The induction of lysosomal membrane permeabilization (LMP) triggers the rapid translocation of Galectin 3/LGALS3 from the cytosol to the lysosomal lumen, making it a valuable marker of LMP. However, Galectin 3 can also be recruited to damaged endo/phagosomal membranes. To make sure that Galectin 3 labels damaged lysosomes, it is therefore important to verify its colocalization with lysosomal markers such as lysosome-associated membrane protein 1 (LAMP1). Here, we describe a simple, fast and robust protocol that allows the detection of LMP of individual lysosomes in U2OS cells expressing mCherry-tagged Galectin 3 and mGFP-tagged LAMP1. This method permits the high-throughput detection and quantification of damaged lysosomes by fluorescence microscopy. It also offers the advantage of studying, in the same experiment, the alterations in size, shape and subcellular localization of intact and damaged lysosomes.
    Keywords:  Autophagy; Cell death; Galectin 3; High-throughput fluorescence microscopy; LAMP1; Lysosomal membrane permeabilization; Lysosomes; Stress responses
    DOI:  https://doi.org/10.1016/bs.mcb.2020.10.004
  28. J Enzyme Inhib Med Chem. 2021 Dec;36(1): 1679-1693
    The role of mTOR in age-related diseases.
    Zofia Chrienova, Eugenie Nepovimova, Kamil Kuca.
      The ageing population is becoming a significant socio-economic issue. To address the expanding health gap, it is important to deepen our understanding of the mechanisms underlying ageing in various organisms at the single-cell level. The discovery of the antifungal, immunosuppressive, and anticancer drug rapamycin, which possesses the ability to extend the lifespan of several species, has prompted extensive research in the areas of cell metabolic regulation, development, and senescence. At the centre of this research is the mTOR pathway, with key roles in cell growth, proteosynthesis, ribosomal biogenesis, transcriptional regulation, glucose and lipid metabolism, and autophagy. Recently, it has become obvious that mTOR dysregulation is involved in several age-related diseases, such as cancer, neurodegenerative diseases, and type 2 diabetes mellitus. Additionally, mTOR hyperactivation affects the process of ageing per se. In this review, we provide an overview of recent insights into the mTOR signalling pathway, including its regulation and its influence on various hallmarks of ageing at the cellular level.
    Keywords:  Ageing; age-related disease; mTORC1; mTORC2; rapamycin
    DOI:  https://doi.org/10.1080/14756366.2021.1955873
  29. Nat Commun. 2021 Jul 30. 12(1): 4643
    Stress-primed secretory autophagy promotes extracellular BDNF maturation by enhancing MMP9 secretion.
    Silvia Martinelli, Elmira A Anderzhanova, Thomas Bajaj, Svenja Wiechmann, Frederik Dethloff, Katja Weckmann, Daniel E Heinz, Tim Ebert, Jakob Hartmann, Thomas M Geiger, Michael Döngi, Kathrin Hafner, Max L Pöhlmann, Lee Jollans, Alexandra Philipsen, Susanne V Schmidt, Ulrike Schmidt, Giuseppina Maccarrone, Valentin Stein, Felix Hausch, Christoph W Turck, Mathias V Schmidt, Anne-Kathrin Gellner, Bernhard Kuster, Nils C Gassen.
      The stress response is an essential mechanism for maintaining homeostasis, and its disruption is implicated in several psychiatric disorders. On the cellular level, stress activates, among other mechanisms, autophagy that regulates homeostasis through protein degradation and recycling. Secretory autophagy is a recently described pathway in which autophagosomes fuse with the plasma membrane rather than with lysosomes. Here, we demonstrate that glucocorticoid-mediated stress enhances secretory autophagy via the stress-responsive co-chaperone FK506-binding protein 51. We identify the matrix metalloproteinase 9 (MMP9) as one of the proteins secreted in response to stress. Using cellular assays and in vivo microdialysis, we further find that stress-enhanced MMP9 secretion increases the cleavage of pro-brain-derived neurotrophic factor (proBDNF) to its mature form (mBDNF). BDNF is essential for adult synaptic plasticity and its pathway is associated with major depression and posttraumatic stress disorder. These findings unravel a cellular stress adaptation mechanism that bears the potential of opening avenues for the understanding of the pathophysiology of stress-related disorders.
    DOI:  https://doi.org/10.1038/s41467-021-24810-5
  30. Dev Cell. 2021 Jul 26. pii: S1534-5807(21)00546-3. [Epub ahead of print]56(14): 2014-2015
    Move it to lose it: Mitocytosis expels damaged mitochondria.
    Chahat Mehra, Lena Pernas.
      Mechanisms by which cells remove damaged mitochondria extracellularly are unclear. Recent work by Jiao and colleagues in Cell shows that migrating cells expel dysfunctional mitochondria in membrane-bound structures called migrasomes to maintain mitochondrial homeostasis.
    DOI:  https://doi.org/10.1016/j.devcel.2021.07.001
  31. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30201-6. [Epub ahead of print]165 31-38
    Assessment of EGFP-Q74 degradation for the measurement of autophagic flux.
    Yan Wang, Jiao Meng, Qi Wu, Guo Chen, Wei Xie, Zhen Zhang, Guido Kroemer, Oliver Kepp.
      Autophagy plays a major role in physiological and pathological processes. The quantitation of the abundance of autophagy-specific substrates constitutes an efficient strategy for assessing autophagic activity. Here, we provide a detailed protocol for quantifying the decay of a fusion protein composed by enhanced green fluorescent protein (EGFP) and glutamine repeats (Q74) using regular or high-throughput fluorescence microscopy. This method provides a direct measurement of autophagic flux in a Huntington's disease model.
    Keywords:  Autophagy; EGFP-Q74; Fluorescence microscopy; Huntington's disease
    DOI:  https://doi.org/10.1016/bs.mcb.2020.10.018
  32. Cell Biosci. 2021 Jul 27. 11(1): 147
    Current insights into the implications of m6A RNA methylation and autophagy interaction in human diseases.
    Xuechai Chen, Jianan Wang, Muhammad Tahir, Fangfang Zhang, Yuanyuan Ran, Zongjian Liu, Juan Wang.
      Autophagy is a conserved degradation process crucial to maintaining the primary function of cellular and organismal metabolism. Impaired autophagy could develop numerous diseases, including cancer, cardiomyopathy, neurodegenerative disorders, and aging. N6-methyladenosine (m6A) is the most common RNA modification in eukaryotic cells, and the fate of m6A modified transcripts is controlled by m6A RNA binding proteins. m6A modification influences mRNA alternative splicing, stability, translation, and subcellular localization. Intriguingly, recent studies show that m6A RNA methylation could alter the expression of essential autophagy-related (ATG) genes and influence the autophagy function. Thus, both m6A modification and autophagy could play a crucial role in the onset and progression of various human diseases. In this review, we summarize the latest studies describing the impact of m6A modification in autophagy regulation and discuss the role of m6A modification-autophagy axis in different human diseases, including obesity, heart disease, azoospermatism or oligospermatism, intervertebral disc degeneration, and cancer. The comprehensive understanding of the m6A modification and autophagy interplay may help in interpreting their impact on human diseases and may aid in devising future therapeutic strategies.
    Keywords:  Autophagy; Azoospermatism; Cancer; Ischemic heart disease; Obesity; RNA methylation; m6A
    DOI:  https://doi.org/10.1186/s13578-021-00661-x
  33. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30217-X. [Epub ahead of print]165 89-101
    High throughput screening for autophagy.
    Sabrina Forveille, Marion Leduc, Allan Sauvat, Giulia Cerrato, Guido Kroemer, Oliver Kepp.
      Robotized high throughput screening allows for the assessment of autophagy in a large number of samples. Here, we describe a drug discovery platform for the phenotypic identification of novel autophagy inducers by means of automated cell biology workflows employing robotized cell culture, sample preparation and data acquisition. In this setting, fluorescent biosensor cells that express microtubule-associated proteins 1A/1B light chain 3B (best known as LC3) conjugated to green fluorescent protein (GFP), are utilized together with automated high content microscopy for the image-based assessment of autophagy. In sum, we detail a drug discovery screening workflow from high throughput sample preparation and processing to data acquisition and analysis.
    Keywords:  Automation; Cancer; Drug discovery; Imaging
    DOI:  https://doi.org/10.1016/bs.mcb.2020.12.011
  34. Nat Commun. 2021 Jul 30. 12(1): 4634
    Endo-lysosomal Aβ concentration and pH trigger formation of Aβ oligomers that potently induce Tau missorting.
    Marie P Schützmann, Filip Hasecke, Sarah Bachmann, Mara Zielinski, Sebastian Hänsch, Gunnar F Schröder, Hans Zempel, Wolfgang Hoyer.
      Amyloid-β peptide (Aβ) forms metastable oligomers >50 kDa, termed AβOs, that are more effective than Aβ amyloid fibrils at triggering Alzheimer's disease-related processes such as synaptic dysfunction and Tau pathology, including Tau mislocalization. In neurons, Aβ accumulates in endo-lysosomal vesicles at low pH. Here, we show that the rate of AβO assembly is accelerated 8,000-fold upon pH reduction from extracellular to endo-lysosomal pH, at the expense of amyloid fibril formation. The pH-induced promotion of AβO formation and the high endo-lysosomal Aβ concentration together enable extensive AβO formation of Aβ42 under physiological conditions. Exploiting the enhanced AβO formation of the dimeric Aβ variant dimAβ we furthermore demonstrate targeting of AβOs to dendritic spines, potent induction of Tau missorting, a key factor in tauopathies, and impaired neuronal activity. The results suggest that the endosomal/lysosomal system is a major site for the assembly of pathomechanistically relevant AβOs.
    DOI:  https://doi.org/10.1038/s41467-021-24900-4
  35. Neural Plast. 2021 ;2021 5511010
    Autophagy: A Novel Horizon for Hair Cell Protection.
    Chang Liu, Zhiwei Zheng, Pengjun Wang, Shuangba He, Yingzi He.
      As a general sensory disorder, hearing loss was a major concern worldwide. Autophagy is a common cellular reaction to stress that degrades cytoplasmic waste through the lysosome pathway. Autophagy not only plays major roles in maintaining intracellular homeostasis but is also involved in the development and pathogenesis of many diseases. In the auditory system, several studies revealed the link between autophagy and hearing protection. In this review, we aimed to establish the correlation between autophagy and hair cells (HCs) from the aspects of ototoxic drugs, aging, and acoustic trauma and discussed whether autophagy could serve as a potential measure in the protection of HCs.
    DOI:  https://doi.org/10.1155/2021/5511010
  36. J Drug Target. 2021 Jul 28. 1-61
    Advances in autophagy as a target in the treatment of tumors.
    Yingying Li, Shan Gao, Xiyou Du, Jianbo Ji, Yanwei Xi, Guangxi Zhai.
      Autophagy is a multi-step lysosomal degradation process, which regulates energy and material metabolism and has been used to maintain homeostasis. Autophagy has been shown to be involved in the regulation of health and disease. But at present, there is no consensus on the relationship between autophagy and tumor, and we consider that it plays a dual role in the occurrence and development of tumor. That is to say, under certain conditions, it can inhibit the occurrence of tumor, but it can also promote the process of tumor. Therefore, autophagy could be used as a target for tumor treatment. The regulation of autophagy plays a synergistic role in the radiotherapy, chemotherapy, phototherapy and immunotherapy of tumor, and nano drug delivery system provides a promising strategy for improving the efficacy of autophagy regulation. This review summarized the progress in the regulatory pathways and factors of autophagy as well as nanoformulations as carriers for the delivery of autophagy modulators.
    Keywords:  autophagy; autophagy regulation; cancer; nanoparticle; phototherapy immunotherapy
    DOI:  https://doi.org/10.1080/1061186X.2021.1961792
  37. Biochem Biophys Res Commun. 2021 Jul 23. pii: S0006-291X(21)01061-5. [Epub ahead of print]570 103-109
    PICALM regulates cathepsin D processing and lysosomal function.
    Kathryn J Hattersley, Julian M Carosi, Leanne K Hein, Julien Bensalem, Timothy J Sargeant.
      Degradation and clearance of cellular waste in the autophagic and endo-lysosomal systems is important for normal physiology and prevention of common late-onset diseases such as Alzheimer's disease (AD). Phosphatidylinostol-binding clathrin assembly protein (PICALM) is a robust AD risk factor gene and encodes an endosomal protein clathrin-binding cytosolic protein, reduction of which is known to exacerbate tauopathy. Although PICALM is known to regulate initiation of autophagy, its role in maturation of lysosomal enzymes required for proteolysis has not been studied. We sought to determine the importance of PICALM for cellular degradative function by disrupting exon 1 of PICALM using CRISPR/Cas9 in HeLa cells. PICALM disruption increased numbers of early endosomes. Proteomic analysis of endosome-enriched samples showed that disrupting exon 1 of PICALM increased the abundance of lysosomal enzymes in these organelles, and western blotting revealed disruption to processing and maturation of the lysosomal protease, cathepsin D, and a deficit in autophagy. This study shows PICALM is important for the correct maturation of lysosomal enzymes and efficient proteolytic function in the lysosome.
    Keywords:  Alzheimer's disease; Autophagy; Cathepsin D; Lysosomes; PICALM
    DOI:  https://doi.org/10.1016/j.bbrc.2021.07.024
  38. ASN Neuro. 2021 Jan-Dec;13:13 17590914211028364
    Mitochondrial and Organellar Crosstalk in Parkinson's Disease.
    Bipul Ray, Abid Bhat, Arehally Marappa Mahalakshmi, Sunanda Tuladhar, Muhammed Bishir, Surapaneni Krishna Mohan, Vishnu Priya Veeraraghavan, Ramesh Chandra, Musthafa Mohamed Essa, Saravana Babu Chidambaram, Meena Kishore Sakharkar.
      Mitochondrial dysfunction is a well-established pathological event in Parkinson's disease (PD). Proteins misfolding and its impaired cellular clearance due to altered autophagy/mitophagy/pexophagy contribute to PD progression. It has been shown that mitochondria have contact sites with endoplasmic reticulum (ER), peroxisomes and lysosomes that are involved in regulating various physiological processes. In pathological conditions, the crosstalk at the contact sites initiates alterations in intracellular vesicular transport, calcium homeostasis and causes activation of proteases, protein misfolding and impairment of autophagy. Apart from the well-reported molecular changes like mitochondrial dysfunction, impaired autophagy/mitophagy and oxidative stress in PD, here we have summarized the recent scientific reports to provide the mechanistic insights on the altered communications between ER, peroxisomes, and lysosomes at mitochondrial contact sites. Furthermore, the manuscript elaborates on the contributions of mitochondrial contact sites and organelles dysfunction to the pathogenesis of PD and suggests potential therapeutic targets.
    Keywords:  Parkinson’s disease; endoplasmic reticulum; lysosome; mitochondria; mitochondrial contact sites; peroxisome
    DOI:  https://doi.org/10.1177/17590914211028364
  39. Cell Stress. 2021 Jul;5(7): 99-118
    Towards a better understanding of the neuro-developmental role of autophagy in sickness and in health.
    Juan Zapata-Muñoz, Beatriz Villarejo-Zori, Pablo Largo-Barrientos, Patricia Boya.
      Autophagy is a critical cellular process by which biomolecules and cellular organelles are degraded in an orderly manner inside lysosomes. This process is particularly important in neurons: these post-mitotic cells cannot divide or be easily replaced and are therefore especially sensitive to the accumulation of toxic proteins and damaged organelles. Dysregulation of neuronal autophagy is well documented in a range of neurodegenerative diseases. However, growing evidence indicates that autophagy also critically contributes to neurodevelopmental cellular processes, including neurogenesis, maintenance of neural stem cell homeostasis, differentiation, metabolic reprogramming, and synaptic remodelling. These findings implicate autophagy in neurodevelopmental disorders. In this review we discuss the current understanding of the role of autophagy in neurodevelopment and neurodevelopmental disorders, as well as currently available tools and techniques that can be used to further investigate this association.
    Keywords:  autism spectrum disorder; developmental disorders; neurodevelopment; neurogenesis; neuronal autophagy
    DOI:  https://doi.org/10.15698/cst2021.07.253
  40. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30210-7. [Epub ahead of print]165 111-122
    Quantification of intracellular ACBP/DBI levels.
    Valentina Sica, Isabelle Martins, Federico Pietrocola, José Manuel Bravo-San Pedro.
      Acyl-CoA binding protein (ACBP), also called diazepam-binding inhibitor (DBI), is a ubiquitous protein that can be secreted from cells by an unconventional pathway. Depending on its levels and on its subcellular localization, ACBP/DBI can regulate lipid metabolism. Several studies have shown that ACBP/DBI is secreted by an autophagy-dependent mechanism, positioning this catabolic pathway as the mechanism that controls lipid metabolism through the intracellular modulation of the levels of this protein. Autophagy is activated, among other stimuli, when cells have increased energy requirements; this causes a drop in the intracellular ACBP/DBI levels due to its release into the extracellular space and triggers an increase in the lipid catabolism. Conversely, when autophagy is inhibited, during pathological (obesity) or physiological (after-meal) situations, the intracellular levels of ACBP/DBI increase resulting in the activation of lipid anabolism, this effect has been demonstrated to be the link between obesity and autophagy inhibition. Here, we detail three different protocols for the detection of the ACBP/DBI levels by immunofluorescence, image flow cytometry or immunoblot techniques, which allow the quantification of ACBP/DBI levels and, indirectly, its autophagy-dependent release.
    Keywords:  Autophagy; Imaging flow cytometry; Immunoblot; Immunofluorescence; Lipid-metabolism; Unconventional secretion
    DOI:  https://doi.org/10.1016/bs.mcb.2020.12.004
  41. Curr Biol. 2021 Jul 21. pii: S0960-9822(21)00907-6. [Epub ahead of print]
    Post-ER degradation of misfolded GPI-anchored proteins is linked with microautophagy.
    Leticia Lemus, Zrinka Matić, Lihi Gal, Amir Fadel, Maya Schuldiner, Veit Goder.
      Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are membrane-conjugated cell-surface proteins with diverse structural, developmental, and signaling functions and clinical relevance. Typically, after biosynthesis and attachment to the preassembled GPI anchor, GPI-APs rapidly leave the endoplasmic reticulum (ER) and rely on post-ER quality control. Terminally misfolded GPI-APs end up inside the vacuole/lysosome for degradation, but their trafficking itinerary to this organelle and the processes linked to their uptake by the vacuole/lysosome remain uncharacterized. In a yeast mutant that is lacking Pep4, a key vacuolar protease, several misfolded model GPI-APs accumulated in the vacuolar membrane. In the same mutant, macroautophagy and the multi-vesicular body (MVB) pathway were intact, hinting at a hitherto-unknown trafficking pathway for the degradation of misfolded GPI-APs. To unravel it, we used a genome-wide screen coupled to high-throughput fluorescence microscopy and followed the fate of the misfolded GPI-AP: Gas1∗. We found that components of the early secretory and endocytic pathways are involved in its targeting to the vacuole and that vacuolar transporter chaperones (VTCs), with roles in microautophagy, negatively affect the vacuolar uptake of Gas1∗. In support, we demonstrate that Gas1∗ internalizes from vacuolar membranes into membrane-bound intravacuolar vesicles prior to degradation. Our data link post-ER degradation with microautophagy.
    Keywords:  ESCRT machinery; GPI-anchored proteins; Pep4; VTCs; lysosome; microautophagy; post-ER quality control; protein internalization; protein trafficking; vacuolar membrane; vacuolar transporter chaperones; vacuole
    DOI:  https://doi.org/10.1016/j.cub.2021.06.078
  42. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30190-4. [Epub ahead of print]165 123-138
    Immunoblot-based assays for assessing autophagy in the turquoise killifish Nothobranchius furzeri.
    Gerasimos Anagnostopoulos, Léa Montégut, Hui Chen, Vincent Carbonnier, Isabelle Martins, Khady Mangane, Abdelkrim Mannioui, Alex Bois, Elisa Elena Baracco, Maria Chiara Maiuri, Guido Kroemer.
      Autophagy is an evolutionarily conserved biological process required for the turnover of the cytoplasm of eukaryotic cell. Beyond its catabolic nature, autophagy has a plethora of pro-survival functions, thus combatting hypoxia, nutrient shortage, and unfolded protein accumulation. Here, we introduce the naturally short-lived turquoise killifish Nothobranchius furzeri as an emerging model to study autophagic function in vivo, in response to environmental challenges. We show that starvation in killifish is sufficient to increase autophagic flux in the liver, thus enhancing the lipidation of microtubule-associated protein light chain 3 (LC3) and reducing the abundance of the autophagic substrate sequestosome-1 (SQSTM1). We describe an immunoblot-based comprehensive protocol to monitor fluctuations in autophagy in this model organism.
    Keywords:  Autophagy; Killifish
    DOI:  https://doi.org/10.1016/bs.mcb.2020.10.007
  43. Methods Cell Biol. 2021 ;pii: S0091-679X(21)00017-0. [Epub ahead of print]165 39-57
    Multimodal assessment of autophagy in mammalian cells with a novel, LC3-based tandem reporter.
    Dan F Lazar, Amani A Gillette, Samantha R Lewis, Braeden L Butler.
      Autophagy is an important intracellular pathway for the degradation of superfluous or harmful subcellular materials, thereby playing a critical role in the maintenance of cell health under normal and stress-related conditions. Researchers interrogating autophagic activity in mammalian cell lines often leverage complementary assay technologies to confirm observations. The Autophagy LC3 HiBiT Reporter assay system utilizes a tandem reporter module, HiBiT-HaloTag, fused to a key marker of autophagic activity, LC3B protein, to enable multiple, cell-based assay modalities. This novel autophagy reporter expressed in a single cell line supports (a) a bioluminescent, homogeneous, plate-reader assay for rapid and quantitative assessment of changes in the level of the LC3-based reporter, (b) a fluorescence-based imaging approach to monitor reporter subcellular distribution in live cells, and (c) an antibody-free, protein blotting method to detect the relative amounts of the LC3-I and LC-II forms of the reporter associated with modulation of autophagic flux. Here we detail protocols for all three assay modalities applied to a U2OS human osteosarcoma cell line stably expressing the novel autophagy reporter, enabling the identification of modulators of autophagic activity and subsequent confirmation of mechanism of action.
    Keywords:  Autophagic flux; Autophagy; Autophagy LC3 HiBiT reporter; HaloTag; HiBiT; LC3B
    DOI:  https://doi.org/10.1016/bs.mcb.2021.02.004
  44. Basic Res Cardiol. 2021 Jul 28. 116(1): 47
    Atg5 knockdown induces age-dependent cardiomyopathy which can be rescued by repeated remote ischemic conditioning.
    Fangfei Wang, Quan He, Zhiqian Gao, Andrew N Redington.
      Altered autophagy is implicated in several human cardiovascular diseases. Remote ischemic conditioning (RIC) is cardioprotective in multiple cardiovascular injury models and modifies autophagy signaling, but its effect in cardiomyopathy induced by gene manipulation has not been reported. To investigate the cardiac effects of chronically reduced autophagy as a result of Atg5 knockdown and assess whether RIC can rescue the phenotype. Atg5 knockdown was induced with tamoxifen for 14 days in cardiac-specific conditional Atg5 flox mice. Autophagy proteins and cardiac function were evaluated by Western blot and echocardiography, respectively. RIC was induced by cyclical hindlimb ischemia and reperfusion using a tourniquet. RIC or sham procedure was performed daily during tamoxifen induction and, in separate experiments, chronically 3 times per week for 8 weeks. Cardiac responses were assessed by end of the study. Cardiac-specific knockdown of Atg5 reduced protein levels by 70% and was associated with a significant increase in mTOR, a reduction of LC3-II and increased upstream autophagy proteins including LC3-I, P62, and Beclin. The changes in biochemical markers were associated with development of an age-related cardiomyopathy during the 17-month follow-up indicated by increased heart weight body weight ratio, progressive decline in cardiac function, and premature death. RIC increased cardiac ATG5 and rescued some of the Atg5 knockdown-induced cardiomyopathy phenotype and associated morphological remodeling. We conclude that cardiac-specific Atg5 knockdown leads to the development of age-related cardiomyopathy. RIC reverses the molecular and structural phenotype when administered both acutely and chronically.
    Keywords:  Autophagy; Cardiac function; Inducible gene ablation; Preconditioning
    DOI:  https://doi.org/10.1007/s00395-021-00888-2
  45. Br J Dermatol. 2021 Jul 28.
    Autophagy induction regulates aquaporin 3-mediated skin fibroblasts aging.
    H Xie, L Zhou, F Liu, J Long, S Yan, Y Xie, X Hu, Ji Li.
       BACKGROUND: Long- and short-term ultraviolet (UV) exposure have distinct biological effects on human fibroblasts.
    OBJECTIVES: This study aimed to elucidate the underlying mechanisms of the biological effects of UV exposure on human skin fibroblasts.
    METHOD: We subjected human skin fibroblast cells with or without AQP3, DEDD, or Beclin1 manipulation to UVA treatment and evaluated autophagy and senescence/aging in them.
    RESULTS: Short-term UVA irradiation induced autophagy and upregulated AQP3 but not senescence, whereas long-term UVA irradiation inhibited autophagy, AQP3, and senescence/aging in vitro and in vivo. Silencing AQP3 abolished short-term UVA irradiation-induced autophagy and led to cellular senescence, whereas AQP3 overexpression partially rescued the senescence and autophagy inhibition induced by long-term UVA exposure in vitro. Mechanistically, the transcription factor JUN was found to bind to the AQP3 promoter to activate its transcription following short-term UVA exposure. Subsequently, AQP3 interacted with DEDD to induce its ubiquitination-mediated degradation and promote autophagy, and bound to Beclin1 to directly activate autophagy. Finally, autophagy induced by AQP3 overexpression robustly prevented UVA-induced senescence/aging in vitro and in vivo.
    CONCLUSIONS: Thus, our study indicates that AQP3 controls skin fibroblasts photoaging by regulating autophagy and represents a potential target for future interventions against skin aging.
    Keywords:  AQP3; Autophagy; DEDD; Skin aging; UVA
    DOI:  https://doi.org/10.1111/bjd.20662
  46. Biochem Biophys Res Commun. 2021 Jul 27. pii: S0006-291X(21)01117-7. [Epub ahead of print]571 195-200
    Identification of a new autophagy inhibitor targeting lipid droplets in vascular endothelial cells.
    Hui Ren, Wen Yao, Qun Wei, Jun Zhang, BaoXiang Zhao, JunYing Miao.
      Autophagy of vascular endothelial cells (VECs) plays an important role in maintaining vascular homeostasis. Lipid droplets (LDs) are organelles that can be formed in response to various stimuli, including excessive lipid or various stresses. LDs sequester toxic lipids, thereby preventing lipotoxic cell damage and have a complex relationship with autophagy. In the previous study, we identified a novel Grp94 inhibitor HCP1 inhibited apoptosis in VECs. Here we found that HCP1 targeted LDs and promoted the accumulation of LDs in VECs. Our results showed that HCP1 upregulated the protein levels of autophagy-related proteins. We demonstrated that HCP1 upregulated the number of LDs and suppressed autophagy by inhibiting Grp94. Therefore, we provided HCP1 as a new VECs autophagy inhibitor targeting LDs, which might be a potential compound in the treatment of VECs autophagy related vascular diseases.
    Keywords:  Autophagy; Grp94; Lipid droplets; Vascular endothelial cells
    DOI:  https://doi.org/10.1016/j.bbrc.2021.07.078
  47. Am J Med Genet A. 2021 Jul 29.
    Autophagic defects observed in fibroblasts from a patient with β-propeller protein-associated neurodegeneration.
    Jae-Hyeok Lee, Sang Ook Nam, Eun Kyoung Kim, Jin-Hong Shin, Seung Hwan Oh, Dongryeol Ryu, Hye Eun Lee, Ji Young Mun.
      Beta-propeller protein-associated neurodegeneration (BPAN) is associated with mutations in the autophagy gene WDR45. The aim of this study was to demonstrate autophagic defects in a patient with BPAN. We assayed autophagic markers using western blot analysis and immunocytochemistry and applied transmission electron microscopy (TEM) to visualize the autophagic structures in fibroblasts from a 7-year-old Korean female with WDR45 splice-site mutation (c.977-1G>A; NM_007075.3). The protein and mRNA expression levels of WDR45 gene were decreased in the patient-derived fibroblasts. The amount of increase in LC3-II upon treatment with an autophagy inducer and inhibitor was reduced in mutant cells compared to control cells, suggesting decreased autophagic flux. TEM showed the accumulation of large vacuoles in mutant cells with a decrease of autophagosomes. Our study demonstrated that the WDR45 mutation in this patient impaired autophagy and provided additional insight into ultrastructural changes of autophagic structures.
    Keywords:  WDR45; autophagy; beta-propeller protein-associated neurodegeneration
    DOI:  https://doi.org/10.1002/ajmg.a.62442
  48. Cancer Invest. 2021 Jul 27. 1-18
    IRF1 inhibits autophagy-mediated proliferation of colorectal cancer via targeting ATG13.
    Li Yuan, Xiao Zhang, Kai Cheng, Liping Li, Zhongming Guo, Liang Zeng.
      IRF1 is a nuclear transcription factor that mediates interferon effects and appears to have anti-tumor activity. To determine the roles of IRF1 in colorectal cancer (CRC), we investigated the effects of IRF1 in CRC cells. We found that IRF1 inhibit cell proliferation and tumor growth. Under starvation conditions, IRF1 enhanced apoptosis and reduced autophagic flux. ATG13, an important factors of autophagy complex, was confirmed as a target of IRF1. These findings indicated that IRF1 function as a tumor suppressor in CRC and inhibit autophagy through ATG13, targeting this pathway may provide new insights into the molecular mechanisms of CRC progression.
    Keywords:  Colorectal cancer; IRF1; autophagy; growth
    DOI:  https://doi.org/10.1080/07357907.2021.1961265
  49. Trends Plant Sci. 2021 Jul 17. pii: S1360-1385(21)00156-4. [Epub ahead of print]
    Autophagy balances the zinc-iron seesaw caused by Zn-stress.
    Daiki Shinozaki, Kohki Yoshimoto.
      Under zinc (Zn) deficiency, plants take up excess iron (Fe), but the uptake is inhibited under Zn excess. Coordination between intracellular recycling, transport, and sensing is essential for Zn-Fe homeostasis. A new study shows that autophagy resupplies Zn2+ and Fe2+ to correct intracellular Zn-Fe imbalances.
    Keywords:  Arabidopsis thaliana; autophagy; iron; metal homeostasis; zinc
    DOI:  https://doi.org/10.1016/j.tplants.2021.06.014
  50. Autophagy. 2021 Jul 27. 1-19
    LRRK2 is required for CD38-mediated NAADP-Ca2+ signaling and the downstream activation of TFEB (transcription factor EB) in immune cells.
    Neel R Nabar, Christopher N Heijjer, Chong-Shan Shi, Il-Young Hwang, Sundar Ganesan, Mikael C I Karlsson, John H Kehrl.
      CD38 is a cell surface receptor capable of generating calcium-mobilizing second messengers. It has been implicated in host defense and cancer biology, but signaling mechanisms downstream of CD38 remain unclear. Mutations in LRRK2 (leucine-rich repeat kinase 2) are the most common genetic cause of Parkinson disease; it is also a risk factor for Crohn disease, leprosy, and certain types of cancers. The pathogenesis of these diseases involves inflammation and macroautophagy/autophagy, processes both CD38 and LRRK2 are implicated in. Here, we mechanistically and functionally link CD38 and LRRK2 as upstream activators of TFEB (transcription factor EB), a host defense transcription factor and the master transcriptional regulator of the autophagy/lysosome machinery. In B-lymphocytes and macrophages, we show that CD38 and LRRK2 exist in a complex on the plasma membrane. Ligation of CD38 with the monoclonal antibody clone 90 results in internalization of the CD38-LRRK2 complex and its targeting to the endolysosomal system. This generates an NAADP-dependent calcium signal, which requires LRRK2 kinase activity, and results in the downstream activation of TFEB. lrrk2 KO macrophages accordingly have TFEB activation defects following CD38 or LPS stimulation and fail to switch to glycolytic metabolism after LPS treatment. In overexpression models, the pathogenic LRRK2G2019S mutant promotes hyperactivation of TFEB even in the absence of CD38, both by stabilizing TFEB and promoting its nuclear translocation via aberrant calcium signaling. In sum, we have identified a physiological CD38-LRRK2-TFEB signaling axis in immune cells. The common pathogenic mutant, LRRK2G2019S, appears to hijack this pathway.
    Keywords:  Autophagy; B cell; LRRK2; TFEB; calcium; endocytosis; immunometabolism; innate immunity; lysosome; macrophage
    DOI:  https://doi.org/10.1080/15548627.2021.1954779
  51. Cell Rep. 2021 Jul 20. pii: S2211-1247(21)00906-2. [Epub ahead of print] 109479
    Inhibitors of VPS34 and fatty-acid metabolism suppress SARS-CoV-2 replication.
    Caroline G Williams, Alexander S Jureka, Jesus A Silvas, Anthony M Nicolini, Stacie A Chvatal, Jared Carlson-Stevermer, Jennifer Oki, Kevin Holden, Christopher F Basler.
      Coronaviruses rely on host membranes for entry, establishment of replication centers, and egress. Compounds targeting cellular membrane biology and lipid biosynthetic pathways have previously shown promise as antivirals and are actively being pursued as treatments for other conditions. Here, we test small molecule inhibitors that target the PI3 kinase VPS34 or fatty acid metabolism for anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activity. Our studies determine that compounds targeting VPS34 are potent SARS-CoV-2 inhibitors. Mechanistic studies with compounds targeting multiple steps up- and downstream of fatty acid synthase (FASN) identify the importance of triacylglycerol production and protein palmitoylation as requirements for efficient viral RNA synthesis and infectious virus production. Further, FASN knockout results in significantly impaired SARS-CoV-2 replication that can be rescued with fatty acid supplementation. Together, these studies clarify roles for VPS34 and fatty acid metabolism in SARS-CoV-2 replication and identify promising avenues for the development of countermeasures against SARS-CoV-2.
    Keywords:  COVID-19; SARS coronavirus 2; antiviral; autophagy; coronavirus; fatty acid; membranes; phosphoinositol 3 kinase
    DOI:  https://doi.org/10.1016/j.celrep.2021.109479
  52. EMBO Rep. 2021 Jul 26. e51806
    ATF3 induces RAB7 to govern autodegradation in paligenosis, a conserved cell plasticity program.
    Megan D Radyk, Lillian B Spatz, Bianca L Peña, Jeffrey W Brown, Joseph Burclaff, Charles J Cho, Yan Kefalov, Chien-Cheng Shih, James Aj Fitzpatrick, Jason C Mills.
      Differentiated cells across multiple species and organs can re-enter the cell cycle to aid in injury-induced tissue regeneration by a cellular program called paligenosis. Here, we show that activating transcription factor 3 (ATF3) is induced early during paligenosis in multiple cellular contexts, transcriptionally activating the lysosomal trafficking gene Rab7b. ATF3 and RAB7B are upregulated in gastric and pancreatic digestive-enzyme-secreting cells at the onset of paligenosis Stage 1, when cells massively induce autophagic and lysosomal machinery to dismantle differentiated cell morphological features. Their expression later ebbs before cells enter mitosis during Stage 3. Atf3-/- mice fail to induce RAB7-positive autophagic and lysosomal vesicles, eventually causing increased death of cells en route to Stage 3. Finally, we observe that ATF3 is expressed in human gastric metaplasia and during paligenotic injury across multiple other organs and species. Thus, our findings indicate ATF3 is an evolutionarily conserved gene orchestrating the early paligenotic autodegradative events that must occur before cells are poised to proliferate and contribute to tissue repair.
    Keywords:  BHLHA15; RAB5; acinar-ductal metaplasia; plasticity; spasmolytic polypeptide-expressing metaplasia
    DOI:  https://doi.org/10.15252/embr.202051806
  53. Mol Med Rep. 2021 Oct;pii: 683. [Epub ahead of print]24(4):
    miR‑214 ameliorates sepsis‑induced acute kidney injury via PTEN/AKT/mTOR‑regulated autophagy.
    Zhenzhen Sang, Shimin Dong, Pu Zhang, Yunxia Wei.
      Previous studies have suggested that oxidative stress and autophagy results in acute kidney injury (AKI) during sepsis and microRNA (miR)‑214 serves a vital role in the protection of kidneys subjected to oxidative stress. The present study aimed to test whether the renoprotection of miR‑214 is related to autophagy in sepsis. The role of autophagy was investigated in a mouse model of cecal ligation and puncture (CLP). Reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) was used to analyze the expression of miR‑214. The structure and function of kidneys harvested from the mice were evaluated. Kidney autophagy levels were detected with immunohistochemical, immunofluorescent and western blotting. It was found that miR‑214 could alleviate AKI in septic mice by inhibiting the level of kidney autophagy. Furthermore, miR‑214 inhibited autophagy by silencing PTEN expression in the kidney tissues of septic mice. These findings indicated that miR‑214 ameliorated CLP‑induced AKI by reducing oxidative stress and inhibiting autophagy through the regulation of the PTEN/AKT/mTOR pathway.
    Keywords:  acute kidney injury; autophagy; microRNA‑214; sepsis
    DOI:  https://doi.org/10.3892/mmr.2021.12322
  54. Nat Commun. 2021 07 27. 12(1): 4407
    Brain-specific inhibition of mTORC1 eliminates side effects resulting from mTORC1 blockade in the periphery and reduces alcohol intake in mice.
    Yann Ehinger, Ziyang Zhang, Khanhky Phamluong, Drishti Soneja, Kevan M Shokat, Dorit Ron.
      Alcohol Use Disorder (AUD) affects a large portion of the population. Unfortunately, efficacious medications to treat the disease are limited. Studies in rodents suggest that mTORC1 plays a crucial role in mechanisms underlying phenotypes such as heavy alcohol intake, habit, and relapse. Thus, mTORC1 inhibitors, which are used in the clinic, are promising therapeutic agents to treat AUD. However, chronic inhibition of mTORC1 in the periphery produces undesirable side effects, which limit their potential use for the treatment of AUD. To overcome these limitations, we designed a binary drug strategy in which male mice were treated with the mTORC1 inhibitor RapaLink-1 together with a small molecule (RapaBlock) to protect mTORC1 activity in the periphery. We show that whereas RapaLink-1 administration blocked mTORC1 activation in the liver, RapaBlock abolished the inhibitory action of Rapalink-1. RapaBlock also prevented the adverse side effects produced by chronic inhibition of mTORC1. Importantly, co-administration of RapaLink-1 and RapaBlock inhibited alcohol-dependent mTORC1 activation in the nucleus accumbens and attenuated alcohol seeking and drinking.
    DOI:  https://doi.org/10.1038/s41467-021-24567-x
  55. Nat Commun. 2021 07 27. 12(1): 4552
    SNX19 restricts endolysosome motility through contacts with the endoplasmic reticulum.
    Amra Saric, Spencer A Freeman, Chad D Williamson, Michal Jarnik, Carlos M Guardia, Michael S Fernandopulle, David C Gershlick, Juan S Bonifacino.
      The ability of endolysosomal organelles to move within the cytoplasm is essential for the performance of their functions. Long-range movement involves coupling of the endolysosomes to motor proteins that carry them along microtubule tracks. This movement is influenced by interactions with other organelles, but the mechanisms involved are incompletely understood. Herein we show that the sorting nexin SNX19 tethers endolysosomes to the endoplasmic reticulum (ER), decreasing their motility and contributing to their concentration in the perinuclear area of the cell. Tethering depends on two N-terminal transmembrane domains that anchor SNX19 to the ER, and a PX domain that binds to phosphatidylinositol 3-phosphate on the endolysosomal membrane. Two other domains named PXA and PXC negatively regulate the interaction of SNX19 with endolysosomes. These studies thus identify a mechanism for controlling the motility and positioning of endolysosomes that involves tethering to the ER by a sorting nexin.
    DOI:  https://doi.org/10.1038/s41467-021-24709-1
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