bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2020–03–22
twenty papers selected by
Viktor Korolchuk, Newcastle University
  1. GSK-3-TSC axis governs lysosomal acidification through autophagy and endocytic pathways.
  2. Rap1-GTPases control mTORC1 activity by coordinating lysosome organization with amino acid availability.
  3. The Journey of the Synaptic Autophagosome: A Cell Biological Perspective.
  4. Non-lethal sonodynamic therapy facilitates the M1-to-M2 transition in advanced atherosclerotic plaques via activating the ROS-AMPK-mTORC1-autophagy pathway.
  5. The mammalian cytosolic thioredoxin reductase pathway acts via a membrane protein to reduce ER-localised proteins.
  6. Autophagy promotes mammalian survival by suppressing oxidative stress and p53.
  7. Mitochondrial DNA stress triggers autophagy-dependent ferroptotic death.
  8. The NEDD4-USP13 axis facilitates autophagy via deubiquitinating PIK3C3.
  9. Upregulation of Neuronal Rheb(S16H) for Hippocampal Protection in the Adult Brain.
  10. ATM-CHK2-Beclin 1 axis promotes autophagy to maintain ROS homeostasis under oxidative stress.
  11. CYLD is a causative gene for frontotemporal dementia - amyotrophic lateral sclerosis.
  12. Autophagy compensates for defects in mitochondrial dynamics.
  13. Cryo-EM reconstruction of a VPS13 fragment reveals a long groove to channel lipids between membranes.
  14. PINK1/Parkin mediated mitophagy ameliorates palmitic acid-induced apoptosis through reducing mitochondrial ROS production in podocytes.
  15. p62 as a therapeutic target for tumor.
  16. Detection of mitophagy in mammalian cells, mice, and yeast.
  17. A three-dimensional dementia model reveals spontaneous cell cycle re-entry and a senescence-associated secretory phenotype.
  18. The Role of Autophagy and Autophagy Receptor NDP52 in Microbial Infections.
  19. Endoplasmic reticulum-associated degradation regulates mitochondrial dynamics in brown adipocytes.
  20. Autophagy and Stem Cells: Self-Eating for Self-Renewal.
  1. Cell Signal. 2020 Mar 12. pii: S0898-6568(20)30074-7. [Epub ahead of print] 109597
    GSK-3-TSC axis governs lysosomal acidification through autophagy and endocytic pathways.
    Limor Avrahami, Rom Paz, Kristina Dominko, Silva Hecimovic, Cecilia Bucci, Hagit Eldar-Finkelman.
      Impaired lysosomal activity, which results in defective protein processing, waste accumulation, and protein aggregation, is implicated in a number of disease pathologies. Acidification of lysosomes is a crucial process required for lysosome function. Previously we showed that inhibition of glycogen synthase kinase-3 (GSK-3) enhanced lysosomal acidification in both normal and pathological conditions. However, how GSK-3 integrates into the lysosome networking is unknown. Here we show that inhibition of mTORC1 and increased autophagic activity are downstream to GSK-3 inhibition and contribute to lysosomal acidification. Strikingly, lysosomal acidification is also restored by GSK-3 inhibition in the absence of functional autophagy, and, independently of mTORC1. This is facilitated by increased endocytic traffic: We show that GSK-3 inhibition enhanced material internalization, increased recruitment of active Rab5 into endosomes, and increased Rab7/RILP clustering into lysosomes, all processes required for late endosome maturation. Consistently, in cells defective in endocytic traffic caused by either constitutively active Rab5, or, deletion of the Niemann-Pick C1 protein, GSK-3 inhibition could not restore lysosomal acidification. Finally we found that the tuberous sclerosis complex, TSC, is required for lysosomal acidification and is activated by GSK-3 inhibition. Thus, the GSK-3/TSC axis regulates lysosomal acidification via both the autophagic and endocytic pathways. Our study provides new insights into the therapeutic potential of GSK-3 inhibitors in treating pathological conditions associated with impaired cellular clearance.
    Keywords:  Acidification; Autophagy; Endocytosis; GSK-3; GSK-3 inhibitors; L803-mts; Lysosomes; Rab5; Rab7; TSC; mTOR
    DOI:  https://doi.org/10.1016/j.cellsig.2020.109597
  2. Nat Commun. 2020 Mar 17. 11(1): 1416
    Rap1-GTPases control mTORC1 activity by coordinating lysosome organization with amino acid availability.
    Anders P Mutvei, Michal J Nagiec, Jens C Hamann, Sang Gyun Kim, C Theresa Vincent, John Blenis.
      The kinase mTOR complex 1 (mTORC1) promotes cellular growth and is frequently dysregulated in cancers. In response to nutrients, mTORC1 is activated on lysosomes by Rag and Rheb guanosine triphosphatases (GTPases) and drives biosynthetic processes. How limitations in nutrients suppress mTORC1 activity remains poorly understood. We find that when amino acids are limited, the Rap1-GTPases confine lysosomes to the perinuclear region and reduce lysosome abundance, which suppresses mTORC1 signaling. Rap1 activation, which is independent of known amino acid signaling factors, limits the lysosomal surface available for mTORC1 activation. Conversely, Rap1 depletion expands the lysosome population, which markedly increases association between mTORC1 and its lysosome-borne activators, leading to mTORC1 hyperactivity. Taken together, we establish Rap1 as a critical coordinator of the lysosomal system, and propose that aberrant changes in lysosomal surface availability can impact mTORC1 signaling output.
    DOI:  https://doi.org/10.1038/s41467-020-15156-5
  3. Neuron. 2020 Mar 18. pii: S0896-6273(20)30044-1. [Epub ahead of print]105(6): 961-973
    The Journey of the Synaptic Autophagosome: A Cell Biological Perspective.
    Sarah E Hill, Daniel A Colón-Ramos.
      Autophagy is a key cellular degradative pathway, important for neuronal homeostasis and function. Disruption of autophagy is associated with neuronal dysfunction and neurodegeneration. Autophagy is compartmentalized in neurons, with specific stages of the pathway occurring in distinct subcellular compartments. Coordination of these stages drives progression of autophagy and enables clearance of substrates. Yet, we are only now learning how these distributed processes are integrated across the neuron. In this review, we focus on the cell biological course of autophagy in neurons, from biogenesis at the synapse to degradation in the soma. We describe how the steps of autophagy are distributed across neuronal subcellular compartments, how local machinery regulates autophagy, and the impact of coordinated regulation on neuronal physiology and disease. We also discuss how recent advances in our understanding of neuronal autophagic mechanisms have reframed how we think about the role of local regulation of autophagy in all tissues.
    DOI:  https://doi.org/10.1016/j.neuron.2020.01.018
  4. Redox Biol. 2020 Mar 09. pii: S2213-2317(20)30047-1. [Epub ahead of print]32 101501
    Non-lethal sonodynamic therapy facilitates the M1-to-M2 transition in advanced atherosclerotic plaques via activating the ROS-AMPK-mTORC1-autophagy pathway.
    Yang Yang, Jiayu Wang, Shuyuan Guo, Shirin Pourteymour, Qiulian Xu, Jie Gong, Zhen Huang, Zhaoqian Shen, Kamal Diabakte, Zhengyu Cao, Guodong Wu, Sukhareva Natalia, Zhen Tian, Hong Jin, Ye Tian.
      Emerging evidence indicates that macrophage functional polarization is critically involved in the development of atherosclerosis (AS). Here, we examined the role of 5-aminolaevulinic acid (ALA)-mediated non-lethal sonodynamic therapy (NL-SDT) in macrophage-subset polarization and atherosclerotic lesion stability and explored the potential underlying mechanisms. Using Western diet-fed apolipoprotein E (apoE)-/- and green fluorescent protein (GFP)-positive bone marrow (BM) chimeric mouse models, we demonstrated that NL-SDT promoted phenotypic switching of both BM-derived and resident macrophages from M1 to M2 and significantly inhibited AS progression. Further mechanistic studies indicated that NL-SDT enhanced macrophage differentiation toward the M2 phenotype by activating the reactive oxygen species (ROS)-5' AMP-activated protein kinase (AMPK)-mammalian target of rapamycin complex 1 (mTORC1)-autophagy signaling pathway in murine BM-derived M1 macrophages (BMDM1s). Moreover, NL-SDT drastically reduced lipid droplets, mainly by promoting apoAI-mediated cholesterol efflux in vitro. Specifically, administration of pharmacological inhibitors to the animal model showed a reciprocal effect on NL-SDT-induced macrophage polarization. These findings indicate that NL-SDT engages a virtuous cycle that enhances M1-to-M2 polarization, cholesterol efflux, and anti-inflammatory reactions in advanced plaque in vivo and in BMDM1s in vitro by activating the ROS-AMPK-mTORC1-autophagy pathway. This discovery might help elucidate the mechanism underlying NL-SDT as a potential treatment to prevent atherothrombotic events.
    Keywords:  AMPK; Atherosclerosis; Autophagy; Macrophage polarization; Non-lethal sonodynamic therapy; mTORC1
    DOI:  https://doi.org/10.1016/j.redox.2020.101501
  5. J Cell Sci. 2020 Mar 17. pii: jcs.241976. [Epub ahead of print]
    The mammalian cytosolic thioredoxin reductase pathway acts via a membrane protein to reduce ER-localised proteins.
    Xiaofei Cao, Sergio Lilla, Zhenbo Cao, Marie Anne Pringle, Ojore B V Oka, Philip J Robinson, Tomasz Szmaja, Marcel van Lith, Sara Zanivan, Neil J Bulleid.
      Folding of proteins entering the mammalian secretory pathway requires the insertion of the correct disulfides. Disulfide formation involves both an oxidative pathway for their insertion and a reductive pathway to remove incorrectly formed disulfides. Reduction of these disulfides is critical for correct folding and degradation of misfolded proteins. Previously, we showed that the reductive pathway is driven by NADPH generated in the cytosol. Here, by reconstituting the pathway using purified proteins and ER microsomal membranes, we demonstrate that the thioredoxin reductase system provides the minimal cytosolic components required for reducing proteins within the ER lumen. In particular, saturation of the pathway and its protease sensitivity demonstrates the requirement for a membrane protein to shuttle electrons from the cytosol to the ER. These results provide compelling evidence for the critical role of the cytosol in regulating ER redox homeostasis ensuring correct protein folding and facilitating the degradation of misfolded ER proteins.
    Keywords:  Disulfide formation; Endoplasmic reticulum; Protein folding; Thioredoxin pathway
    DOI:  https://doi.org/10.1242/jcs.241976
  6. Genes Dev. 2020 Mar 19.
    Autophagy promotes mammalian survival by suppressing oxidative stress and p53.
    Yang Yang, Gizem Karsli-Uzunbas, Laura Poillet-Perez, Akshada Sawant, Zhixian Sherrie Hu, Yuhan Zhao, Dirk Moore, Wenwei Hu, Eileen White.
      Autophagy captures intracellular components and delivers them to lysosomes for degradation and recycling. Conditional autophagy deficiency in adult mice causes liver damage, shortens life span to 3 mo due to neurodegeneration, and is lethal upon fasting. As autophagy deficiency causes p53 induction and cell death in neurons, we sought to test whether p53 mediates the lethal consequences of autophagy deficiency. Here, we conditionally deleted Trp53 (p53 hereafter) and/or the essential autophagy gene Atg7 throughout adult mice. Compared with Atg7 Δ/Δ mice, the life span of Atg7 Δ/Δ p53 Δ/Δ mice was extended due to delayed neurodegeneration and resistance to death upon fasting. Atg7 also suppressed apoptosis induced by p53 activator Nutlin-3, suggesting that autophagy inhibited p53 activation. To test whether increased oxidative stress in Atg7 Δ/Δ mice was responsible for p53 activation, Atg7 was deleted in the presence or absence of the master regulator of antioxidant defense nuclear factor erythroid 2-related factor 2 (Nrf2). Nrf2-/-Atg7 Δ/Δ mice died rapidly due to small intestine damage, which was not rescued by p53 codeletion. Thus, Atg7 limits p53 activation and p53-mediated neurodegeneration. In turn, NRF2 mitigates lethal intestine degeneration upon autophagy loss. These findings illustrate the tissue-specific roles for autophagy and functional dependencies on the p53 and NRF2 stress response mechanisms.
    Keywords:  ATG7; DNA damage; NRF2; apoptosis; autophagy; oxidative stress; p53
    DOI:  https://doi.org/10.1101/gad.335570.119
  7. Autophagy. 2020 Mar 18. 1-13
    Mitochondrial DNA stress triggers autophagy-dependent ferroptotic death.
    Changfeng Li, Ying Zhang, Jiao Liu, Rui Kang, Daniel J Klionsky, Daolin Tang.
      Pancreatic cancer tends to be highly resistant to current therapy and remains one of the great challenges in biomedicine with very low 5-year survival rates. Here, we report that zalcitabine, an antiviral drug for human immunodeficiency virus infection, can suppress the growth of primary and immortalized human pancreatic cancer cells through the induction of ferroptosis, an iron-dependent form of regulated cell death. Mechanically, this effect relies on zalcitabine-induced mitochondrial DNA stress, which activates the STING1/TMEM173-mediated DNA sensing pathway, leading to macroautophagy/autophagy-dependent ferroptotic cell death via lipid peroxidation, but not a type I interferon response. Consequently, the genetic and pharmacological inactivation of the autophagy-dependent ferroptosis pathway diminishes the anticancer effects of zalcitabine in cell culture and animal models. Together, these findings not only provide a new approach for pancreatic cancer therapy but also increase our understanding of the interplay between autophagy and DNA damage response in shaping cell death.Abbreviations: ALOX: arachidonate lipoxygenase; ARNTL/BMAL1: aryl hydrocarbon receptor nuclear translocator-like; ATM: ATM serine/threonine kinase; ATG: autophagy-related; cGAMP: cyclic GMP-AMP; CGAS: cyclic GMP-AMP synthase; ER: endoplasmic reticulum; FANCD2: FA complementation group D2; GPX4: glutathione peroxidase 4; IFNA1/IFNα: interferon alpha 1; IFNB1/IFNβ: interferon beta 1; MAP1LC3B/LC3: microtubule-associated protein 1 light chain 3 beta; MDA: malondialdehyde; mtDNA: mitochondrial DNA; NCOA4: nuclear receptor coactivator 4; PDAC: pancreatic ductal adenocarcinoma; POLG: DNA polymerase gamma, catalytic subunit; qRT-PCR: quantitative polymerase chain reaction; RCD: regulated cell death; ROS: reactive oxygen species; SLC7A11: solute carrier family 7 member 11; STING1/TMEM173: stimulator of interferon response cGAMP interactor 1; TFAM: transcription factor A, mitochondrial.
    Keywords:  Antiviral drug; CGAS; DNA damage; POLG; STING1; TFAM; autophagy; ferroptosis; mitochondria; tumor therapy
    DOI:  https://doi.org/10.1080/15548627.2020.1739447
  8. Autophagy. 2020 Mar 18. 1-2
    The NEDD4-USP13 axis facilitates autophagy via deubiquitinating PIK3C3.
    Weihong Xie, Shouheng Jin, Jun Cui.
      Macroautophagy/autophagy, an evolutionarily conserved eukaryotic bioprocess, plays an important role in the bulk degradation of intracellular macromolecules, organelles, and invading pathogens. PIK3C3/VPS34 (phosphatidylinositol 3-kinase catalytic subunit type 3) functions as a key protein in autophagy initiation and progression. The activity of PIK3C3 is tightly regulated by multiple post-translational modifications, including ubiquitination, however, the regulatory mechanisms underpinning the reversible deubiquitination of PIK3C3 remain poorly understood. Recently, we identified the E3 ubiquitin ligase NEDD4/NEDD4-1 as a positive regulator of autophagy through decreasing the K48-linked ubiquitination of PIK3C3 by recruiting USP13.
    Keywords:  Auto-ubiquitination; NEDD4; PIK3C3; USP13; autophagy; deubiquitination complex
    DOI:  https://doi.org/10.1080/15548627.2020.1743071
  9. Int J Mol Sci. 2020 Mar 16. pii: E2023. [Epub ahead of print]21(6):
    Upregulation of Neuronal Rheb(S16H) for Hippocampal Protection in the Adult Brain.
    Gyeong Joon Moon, Minsang Shin, Sang Ryong Kim.
      Ras homolog protein enriched in brain (Rheb) is a key activator of mammalian target of rapamycin complex 1 (mTORC1). The activation of mTORC1 by Rheb is associated with various processes such as protein synthesis, neuronal growth, differentiation, axonal regeneration, energy homeostasis, autophagy, and amino acid uptake. In addition, Rheb-mTORC1 signaling plays a crucial role in preventing the neurodegeneration of hippocampal neurons in the adult brain. Increasing evidence suggests that the constitutive activation of Rheb has beneficial effects against neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). Our recent studies revealed that adeno-associated virus serotype 1 (AAV1) transduction with Rheb(S16H), a constitutively active form of Rheb, exhibits neuroprotective properties through the induction of various neurotrophic factors, promoting neurotrophic interactions between neurons and astrocytes in the hippocampus of the adult brain. This review provides compelling evidence for the therapeutic potential of AAV1-Rheb(S16H) transduction in the hippocampus of the adult brain by exploring its neuroprotective effects and mechanisms.
    Keywords:  Alzheimer’s disease; Rheb(S16H); neurotrophic factor; neurotrophic interaction
    DOI:  https://doi.org/10.3390/ijms21062023
  10. EMBO J. 2020 Mar 18. e103111
    ATM-CHK2-Beclin 1 axis promotes autophagy to maintain ROS homeostasis under oxidative stress.
    Qi-Qiang Guo, Shan-Shan Wang, Shan-Shan Zhang, Hong-De Xu, Xiao-Man Li, Yi Guan, Fei Yi, Ting-Ting Zhou, Bo Jiang, Ning Bai, Meng-Tao Ma, Zhuo Wang, Yan-Ling Feng, Wen-Dong Guo, Xuan Wu, Gui-Feng Zhao, Guang-Jian Fan, Sheng-Ping Zhang, Chuan-Gui Wang, Long-Yue Cao, Brian P O'Rourke, Shi-Hui Liu, Ping-Yuan Wang, Shuai Han, Xiao-Yu Song, Liu Cao.
      The homeostatic link between oxidative stress and autophagy plays an important role in cellular responses to a wide variety of physiological and pathological conditions. However, the regulatory pathway and outcomes remain incompletely understood. Here, we show that reactive oxygen species (ROS) function as signaling molecules that regulate autophagy through ataxia-telangiectasia mutated (ATM) and cell cycle checkpoint kinase 2 (CHK2), a DNA damage response (DDR) pathway activated during metabolic and hypoxic stress. We report that CHK2 binds to and phosphorylates Beclin 1 at Ser90/Ser93, thereby impairing Beclin 1-Bcl-2 autophagy-regulatory complex formation in a ROS-dependent fashion. We further demonstrate that CHK2-mediated autophagy has an unexpected role in reducing ROS levels via the removal of damaged mitochondria, which is required for cell survival under stress conditions. Finally, CHK2-/- mice display aggravated infarct phenotypes and reduced Beclin 1 p-Ser90/Ser93 in a cerebral stroke model, suggesting an in vivo role of CHK2-induced autophagy in cell survival. Taken together, these results indicate that the ROS-ATM-CHK2-Beclin 1-autophagy axis serves as a physiological adaptation pathway that protects cells exposed to pathological conditions from stress-induced tissue damage.
    Keywords:   ROS ; Beclin 1; CHK2; autophagy; oxidative stress
    DOI:  https://doi.org/10.15252/embj.2019103111
  11. Brain. 2020 Mar 18. pii: awaa039. [Epub ahead of print]
    CYLD is a causative gene for frontotemporal dementia - amyotrophic lateral sclerosis.
    Carol Dobson-Stone, Marianne Hallupp, Hamideh Shahheydari, Audrey M G Ragagnin, Zac Chatterton, Francine Carew-Jones, Claire E Shepherd, Holly Stefen, Esmeralda Paric, Thomas Fath, Elizabeth M Thompson, Peter Blumbergs, Cathy L Short, Colin D Field, Peter K Panegyres, Jane Hecker, Garth Nicholson, Alex D Shaw, Janice M Fullerton, Agnes A Luty, Peter R Schofield, William S Brooks, Neil Rajan, Mark F Bennett, Melanie Bahlo, John E Landers, Olivier Piguet, John R Hodges, Glenda M Halliday, Simon D Topp, Bradley N Smith, Christopher E Shaw, Emily McCann, Jennifer A Fifita, Kelly L Williams, Julie D Atkin, Ian P Blair, John B Kwok.
      Frontotemporal dementia and amyotrophic lateral sclerosis are clinically and pathologically overlapping disorders with shared genetic causes. We previously identified a disease locus on chromosome 16p12.1-q12.2 with genome-wide significant linkage in a large European Australian family with autosomal dominant inheritance of frontotemporal dementia and amyotrophic lateral sclerosis and no mutation in known amyotrophic lateral sclerosis or dementia genes. Here we demonstrate the segregation of a novel missense variant in CYLD (c.2155A>G, p.M719V) within the linkage region as the genetic cause of disease in this family. Immunohistochemical analysis of brain tissue from two CYLD p.M719V mutation carriers showed widespread glial CYLD immunoreactivity. Primary mouse neurons transfected with CYLDM719V exhibited increased cytoplasmic localization of TDP-43 and shortened axons. CYLD encodes a lysine 63 deubiquitinase and CYLD cutaneous syndrome, a skin tumour disorder, is caused by mutations that lead to reduced deubiquitinase activity. In contrast with CYLD cutaneous syndrome-causative mutations, CYLDM719V exhibited significantly increased lysine 63 deubiquitinase activity relative to the wild-type enzyme (paired Wilcoxon signed-rank test P = 0.005). Overexpression of CYLDM719V in HEK293 cells led to more potent inhibition of the cell signalling molecule NF-κB and impairment of autophagosome fusion to lysosomes, a key process in autophagy. Although CYLD mutations appear to be rare, CYLD's interaction with at least three other proteins encoded by frontotemporal dementia and/or amyotrophic lateral sclerosis genes (TBK1, OPTN and SQSTM1) suggests that it may play a central role in the pathogenesis of these disorders. Mutations in several frontotemporal dementia and amyotrophic lateral sclerosis genes, including TBK1, OPTN and SQSTM1, result in a loss of autophagy function. We show here that increased CYLD activity also reduces autophagy function, highlighting the importance of autophagy regulation in the pathogenesis of frontotemporal dementia and amyotrophic lateral sclerosis.
    Keywords:  CYLD; autophagy; deubiquitinase; genome-wide linkage analysis; whole-exome sequencing
    DOI:  https://doi.org/10.1093/brain/awaa039
  12. PLoS Genet. 2020 Mar 19. 16(3): e1008638
    Autophagy compensates for defects in mitochondrial dynamics.
    Simon Haeussler, Fabian Köhler, Michael Witting, Madeleine F Premm, Stéphane G Rolland, Christian Fischer, Laetitia Chauve, Olivia Casanueva, Barbara Conradt.
      Compromising mitochondrial fusion or fission disrupts cellular homeostasis; however, the underlying mechanism(s) are not fully understood. The loss of C. elegans fzo-1MFN results in mitochondrial fragmentation, decreased mitochondrial membrane potential and the induction of the mitochondrial unfolded protein response (UPRmt). We performed a genome-wide RNAi screen for genes that when knocked-down suppress fzo-1MFN(lf)-induced UPRmt. Of the 299 genes identified, 143 encode negative regulators of autophagy, many of which have previously not been implicated in this cellular quality control mechanism. We present evidence that increased autophagic flux suppresses fzo-1MFN(lf)-induced UPRmt by increasing mitochondrial membrane potential rather than restoring mitochondrial morphology. Furthermore, we demonstrate that increased autophagic flux also suppresses UPRmt induction in response to a block in mitochondrial fission, but not in response to the loss of spg-7, which encodes a mitochondrial metalloprotease. Finally, we found that blocking mitochondrial fusion or fission leads to increased levels of certain types of triacylglycerols and that this is at least partially reverted by the induction of autophagy. We propose that the breakdown of these triacylglycerols through autophagy leads to elevated metabolic activity, thereby increasing mitochondrial membrane potential and restoring mitochondrial and cellular homeostasis.
    DOI:  https://doi.org/10.1371/journal.pgen.1008638
  13. J Cell Biol. 2020 May 04. pii: e202001161. [Epub ahead of print]219(5):
    Cryo-EM reconstruction of a VPS13 fragment reveals a long groove to channel lipids between membranes.
    PeiQi Li, Joshua Aaron Lees, C Patrick Lusk, Karin M Reinisch.
      A single particle cryo-EM reconstruction of an ∼160-kD N-terminal fragment of the lipid transport protein VPS13 reveals an ∼160-Å long channel lined with hydrophobic residues suitable for solubilizing multiple lipid fatty acid moieties. The structure suggests that VPS13 and related proteins, like the autophagy protein ATG2, can act as bridges between organelle membranes to allow bulk lipid flow between organelles.
    DOI:  https://doi.org/10.1083/jcb.202001161
  14. Biochem Biophys Res Commun. 2020 Mar 12. pii: S0006-291X(20)30484-8. [Epub ahead of print]
    PINK1/Parkin mediated mitophagy ameliorates palmitic acid-induced apoptosis through reducing mitochondrial ROS production in podocytes.
    Xu-Shun Jiang, Xue-Mei Chen, Wei Hua, Jun-Ling He, Ting Liu, Xun-Jia Li, Jiang-Min Wan, Hua Gan, Xiao-Gang Du.
      Diabetic nephropathy (DN), the primary cause of end-stage renal disease (ESRD), is often accompanied by dyslipidemia, which is closely related to the occurrence and development of DN and even the progression to ESRD. Mitophagy, the selective degradation of damaged and dysfunctional mitochondria by autophagy, is a crucial mitochondrial quality control mechanism, and largely regulated by PINK1 (PTEN-induced putative kinase 1)/Parkin signaling pathway. In the present study, we demonstrated that PA induced mitochondrial damage and excessive mitoROS generation in podocytes. We also found PA treatment resulted in the activation of mitophagy by increasing co-localization of GFP-LC3 with mitochondria and enhancing the formation of mitophagosome, stabilization of PINK1 and mitochondrial translocation of Parkin, which indicated that PINK1/Parkin pathway was involved in PA-induced mitophagy in podocytes. Furthermore, inhibition of mitophagy by silencing Parkin dramatically aggravated PA-induced mitochondrial dysfunction, mitoROS production, and further enhanced PA-induced apoptosis of podocytes. Finally, we showed that PINK1/Parkin pathway were up-regulated in kidney of high fat diet (HFD)-induced obese rats. Taken together, our results suggest that PINK1/Parkin mediated mitophagy plays a protective role in PA-induced podocytes apoptosis through reducing mitochondrial ROS production and that enhancing mitophagy provides a potential therapeutic strategy for kidney diseases with hyperlipidemia, such as DN.
    Keywords:  Apoptosis; Mitophagy; PINK1/Parkin; Palmitic acid; Podocytes
    DOI:  https://doi.org/10.1016/j.bbrc.2020.02.170
  15. Eur J Med Chem. 2020 Mar 17. pii: S0223-5234(20)30198-7. [Epub ahead of print]193 112231
    p62 as a therapeutic target for tumor.
    Mengmin Tao, Tian Liu, Qidong You, Zhengyu Jiang.
      p62/SQSTM1 (hereafter as p62) is a stress-inducible cellular protein, which interacts with various signaling proteins to regulate a variety of cellular functions. Growing lines of evidence supported a critical role of p62 in tumorigenesis, and p62 may become a therapeutic target for tumor. In this review, we summarize biological functions of structural domains of p62, reported bioactive molecules targeting p62, and the relationship between p62 and tumorigenesis.
    Keywords:  Autophagy; NF-κB; Nrf2; Tumor; mTORC1; p62/SQSTM1
    DOI:  https://doi.org/10.1016/j.ejmech.2020.112231
  16. Methods Cell Biol. 2020 ;pii: S0091-679X(19)30123-2. [Epub ahead of print]155 557-579
    Detection of mitophagy in mammalian cells, mice, and yeast.
    Hannah Calvelli, Judith Krigman, Mashun Onishi, Derek P Narendra, Nuo Sun, Koji Okamoto.
      Selective elimination of superfluous or dysfunctional mitochondria is a fundamental process conserved among both uni- and multicellular eukaryotes, contributing to mitochondrial quality and quantity control. This process depends on autophagy, a cellular self-eating membrane trafficking system, and is thus called mitophagy. In this chapter, we describe methods to detect mitophagy in mammalian cells, mice, and yeast.
    Keywords:  Autophagy; Lysosome; Macroautophagy; Mitochondria; Park2; Park6
    DOI:  https://doi.org/10.1016/bs.mcb.2019.10.006
  17. Neurobiol Aging. 2020 Feb 19. pii: S0197-4580(20)30038-5. [Epub ahead of print]
    A three-dimensional dementia model reveals spontaneous cell cycle re-entry and a senescence-associated secretory phenotype.
    Veronica Porterfield, Shahzad S Khan, Erin P Foff, Mehmet Murat Koseoglu, Isabella K Blanco, Sruthi Jayaraman, Eric Lien, Michael J McConnell, George S Bloom, John S Lazo, Elizabeth R Sharlow.
      A hexanucleotide repeat expansion on chromosome 9 open reading frame 72 (C9orf72) is associated with familial amyotrophic lateral sclerosis (ALS) and a subpopulation of patients with sporadic ALS and frontotemporal dementia. We used inducible pluripotent stem cells from neurotypic and C9orf72+ (C9+) ALS patients to derive neuronal progenitor cells. We demonstrated that C9+ and neurotypic neuronal progenitor cells differentiate into neurons. The C9+ neurons, however, spontaneously re-expressed cyclin D1 after 12 weeks, suggesting cell cycle re-engagement. Gene profiling revealed significant increases in senescence-associated genes in C9+ neurons. Moreover, C9+ neurons expressed high levels of mRNA for CXCL8, a chemokine overexpressed by senescent cells, while media from C9+ neurons contained significant levels of CXCL8, CXCL1, IL13, IP10, CX3CL1, and reactive oxygen species, which are components of the senescence-associated secretory phenotype. Thus, re-engagement of cell cycle-associated proteins and a senescence-associated secretory phenotype could be fundamental components of neuronal dysfunction in ALS and frontotemporal dementia.
    Keywords:  Amyotrophic lateral sclerosis; Cell cycle re-entry; Frontotemporal dementia; Senescence; Senescence-associated secretory phenotype
    DOI:  https://doi.org/10.1016/j.neurobiolaging.2020.02.011
  18. Int J Mol Sci. 2020 Mar 16. pii: E2008. [Epub ahead of print]21(6):
    The Role of Autophagy and Autophagy Receptor NDP52 in Microbial Infections.
    Shuangqi Fan, Keke Wu, Mengpo Zhao, Erpeng Zhu, Shengming Ma, Yuming Chen, Hongxing Ding, Lin Yi, Mingqiu Zhao, Jinding Chen.
      Autophagy is a general protective mechanism for maintaining homeostasis in eukaryotic cells, regulating cellular metabolism, and promoting cell survival by degrading and recycling cellular components under stress conditions. The degradation pathway that is mediated by autophagy receptors is called selective autophagy, also named as xenophagy. Autophagy receptor NDP52 acts as a 'bridge' between autophagy and the ubiquitin-proteasome system, and it also plays an important role in the process of selective autophagy. Pathogenic microbial infections cause various diseases in both humans and animals, posing a great threat to public health. Increasing evidence has revealed that autophagy and autophagy receptors are involved in the life cycle of pathogenic microbial infections. The interaction between autophagy receptor and pathogenic microorganism not only affects the replication of these microorganisms in the host cell, but it also affects the host's immune system. This review aims to discuss the effects of autophagy on pathogenic microbial infection and replication, and summarizes the mechanisms by which autophagy receptors interact with microorganisms. While considering the role of autophagy receptors in microbial infection, NDP52 might be a potential target for developing effective therapies to treat pathogenic microbial infections.
    Keywords:  NDP52; autophagy; autophagy receptor; microbial infection; ubiquitin-proteasome
    DOI:  https://doi.org/10.3390/ijms21062008
  19. Science. 2020 Mar 19. pii: eaay2494. [Epub ahead of print]
    Endoplasmic reticulum-associated degradation regulates mitochondrial dynamics in brown adipocytes.
    Zhangsen Zhou, Mauricio Torres, Haibo Sha, Christopher J Halbrook, Françoise Van den Bergh, Rachel B Reinert, Tatsuya Yamada, Siwen Wang, Yingying Luo, Allen H Hunter, Chunqing Wang, Thomas H Sanderson, Meilian Liu, Aaron Taylor, Hiromi Sesaki, Costas A Lyssiotis, Jun Wu, Sander Kersten, Daniel A Beard, Ling Qi.
      The endoplasmic reticulum (ER) engages mitochondria at specialized ER domains known as mitochondria-associated membranes (MAMs). Here, we used three-dimensional high-resolution imaging to investigate the formation of pleomorphic "megamitochondria" with altered MAMs in brown adipocytes lacking the Sel1L-Hrd1 protein complex of ER-associated protein degradation (ERAD). Mice with ERAD deficiency in brown adipocytes were cold sensitive and exhibited mitochondrial dysfunction. ERAD deficiency affected ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover of the MAM protein, sigma receptor 1 (SigmaR1). Thus, our study provides molecular insights into ER-mitochondrial crosstalk and expands our understanding of the physiological importance of Sel1L-Hrd1 ERAD.
    DOI:  https://doi.org/10.1126/science.aay2494
  20. Front Cell Dev Biol. 2020 ;8 138
    Autophagy and Stem Cells: Self-Eating for Self-Renewal.
    Natasha C Chang.
      Autophagy is a fundamental cell survival mechanism that allows cells to adapt to metabolic stress through the degradation and recycling of intracellular components to generate macromolecular precursors and produce energy. The autophagy pathway is critical for development, maintaining cellular and tissue homeostasis, as well as immunity and prevention of human disease. Defects in autophagy have been attributed to cancer, neurodegeneration, muscle and heart disease, infectious disease, as well as aging. While autophagy has classically been viewed as a passive quality control and general house-keeping mechanism, emerging evidence demonstrates that autophagy is an active process that regulates the metabolic status of the cell. Adult stem cells, which are long-lived cells that possess the unique ability to self-renew and differentiate into specialized cells throughout the body, have distinct metabolic requirements. Research in a variety of stem cell types have established that autophagy plays critical roles in stem cell quiescence, activation, differentiation, and self-renewal. Here, we will review the evidence demonstrating that autophagy is a key regulator of stem cell function and how defective stem cell autophagy contributes to degenerative disease, aging and the generation of cancer stem cells. Moreover, we will discuss the merits of targeting autophagy as a regenerative medicine strategy to promote stem cell function and improve stem cell-based therapies.
    Keywords:  aging; autophagy; cancer stem cell; mitochondria; quiescence; reprogramming; self-renewal; stem cells
    DOI:  https://doi.org/10.3389/fcell.2020.00138
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