bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2019‒04‒14
sixteen papers selected by
Viktor Korolchuk, Newcastle University
  1. Dhh1 promotes autophagy-related protein translation during nitrogen starvation.
  2. The PARK10 gene USP24 is a negative regulator of autophagy and ULK1 protein stability.
  3. Transmembrane 4 L Six Family Member 5 Senses Arginine for mTORC1 Signaling.
  4. Development of GABARAP family protein-sensitive LIR-based probes for neuronal autophagy.
  5. FOXO3 directly regulates an autophagy network to functionally regulate proteostasis in adult neural stem cells.
  6. ATG8-Binding UIM Proteins Define a New Class of Autophagy Adaptors and Receptors.
  7. RAB2 regulates the formation of autophagosome and autolysosome in mammalian cells.
  8. ULK1 and ULK2 Regulate Stress Granule Disassembly Through Phosphorylation and Activation of VCP/p97.
  9. α-Synuclein toxicity in yeast and human cells is caused by cell cycle re-entry and autophagy degradation of ribonucleotide reductase 1.
  10. Enhanced autophagic-lysosomal activity and increased BAG3-mediated selective macroautophagy as adaptive response of neuronal cells to chronic oxidative stress.
  11. A mutation in the major autophagy gene, WIPI2, associated with global developmental abnormalities.
  12. Extracellular vesicles degradation pathway based autophagy lysosome pathway.
  13. Somatic autophagy of axonal mitochondria in ischemic neurons.
  14. Transcriptional regulation of autophagy-lysosomal function in BRAF-driven melanoma progression and chemoresistance.
  15. TGFβ2-induced senescence during early inner ear development.
  16. Metformin promotes autophagy in ischemia/reperfusion myocardium via cytoplasmic AMPKα1 and nuclear AMPKα2 pathways.
  1. PLoS Biol. 2019 Apr;17(4): e3000219
    Dhh1 promotes autophagy-related protein translation during nitrogen starvation.
    Xu Liu, Zhiyuan Yao, Meiyan Jin, Sim Namkoong, Zhangyuan Yin, Jun Hee Lee, Daniel J Klionsky.
      Macroautophagy (hereafter autophagy) is a well-conserved cellular process through which cytoplasmic components are delivered to the vacuole/lysosome for degradation and recycling. Studies have revealed the molecular mechanism of transcriptional regulation of autophagy-related (ATG) genes upon nutrient deprivation. However, little is known about their translational regulation. Here, we found that Dhh1, a DExD/H-box RNA helicase, is required for efficient translation of Atg1 and Atg13, two proteins essential for autophagy induction. Dhh1 directly associates with ATG1 and ATG13 mRNAs under nitrogen-starvation conditions. The structured regions shortly after the start codons of the two ATG mRNAs are necessary for their translational regulation by Dhh1. Both the RNA-binding ability and helicase activity of Dhh1 are indispensable to promote Atg1 translation and autophagy. Moreover, eukaryotic translation initiation factor 4E (EIF4E)-associated protein 1 (Eap1), a target of rapamycin (TOR)-regulated EIF4E binding protein, physically interacts with Dhh1 after nitrogen starvation and facilitates the translation of Atg1 and Atg13. These results suggest a model for how some ATG genes bypass the general translational suppression that occurs during nitrogen starvation to maintain a proper level of autophagy.
    DOI:  https://doi.org/10.1371/journal.pbio.3000219
  2. Autophagy. 2019 Apr 07. 1-14
    The PARK10 gene USP24 is a negative regulator of autophagy and ULK1 protein stability.
    Julia A Thayer, Ola Awad, Nivedita Hegdekar, Chinmoy Sarkar, Henok Tesfay, Cameran Burt, Xianmin Zeng, Ricardo A Feldman, Marta M Lipinski.
      Recent studies indicate a causative relationship between defects in autophagy and dopaminergic neuron degeneration in Parkinson disease (PD). However, it is not fully understood how autophagy is regulated in the context of PD. Here we identify USP24 (ubiquitin specific peptidase 24), a gene located in the PARK10 (Parkinson disease 10 [susceptibility]) locus associated with late onset PD, as a novel negative regulator of autophagy. Our data indicate that USP24 regulates autophagy by affecting ubiquitination and stability of the ULK1 protein. Knockdown of USP24 in cell lines and in human induced-pluripotent stem cells (iPSC) differentiated into dopaminergic neurons resulted in elevated ULK1 protein levels and increased autophagy flux in a manner independent of MTORC1 but dependent on the class III phosphatidylinositol 3-kinase (PtdIns3K) activity. Surprisingly, USP24 knockdown also improved neurite extension and/or maintenance in aged iPSC-derived dopaminergic neurons. Furthermore, we observed elevated levels of USP24 in the substantia nigra of a subpopulation of idiopathic PD patients, suggesting that USP24 may negatively regulate autophagy in PD. Abbreviations: Bafilomycin/BafA: bafilomycin A1; DUB: deubiquitinating enzyme; iPSC: induced pluripotent stem cells; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; nt: non-targeting; PD: Parkinson disease; p-ATG13: phospho-ATG13; PtdIns3P: phosphatidylinositol 3-phosphate; RPS6: ribosomal protein S6; SNPs: single nucleotide polymorphisms; TH: tyrosine hydroxylase; USP24: ubiquitin specific peptidase 24.
    Keywords:  Autophagy; Parkinson disease; USP24; dopaminergic neurons; induced-pluripotent stem cells
    DOI:  https://doi.org/10.1080/15548627.2019.1598754
  3. Cell Metab. 2019 Apr 01. pii: S1550-4131(19)30133-0. [Epub ahead of print]
    Transmembrane 4 L Six Family Member 5 Senses Arginine for mTORC1 Signaling.
    Jae Woo Jung, Stephani Joy Y Macalino, Minghua Cui, Ji Eon Kim, Hye-Jin Kim, Dae-Geun Song, Seo Hee Nam, Semi Kim, Sun Choi, Jung Weon Lee.
      The mechanistic target of rapamycin complex (mTORC1) is a signaling hub on the lysosome surface, responding to lysosomal amino acids. Although arginine is metabolically important, the physiological arginine sensor that activates mTOR remains unclear. Here, we show that transmembrane 4 L six family member 5 (TM4SF5) translocates from plasma membrane to lysosome upon arginine sufficiency and senses arginine, culminating in mTORC1/S6K1 activation. TM4SF5 bound active mTOR upon arginine sufficiency and constitutively bound amino acid transporter SLC38A9. TM4SF5 binding to the cytosolic arginine sensor Castor1 decreased upon arginine sufficiency, thus allowing TM4SF5-mediated sensing of metabolic amino acids. TM4SF5 directly bound free L-arginine via its extracellular loop possibly for the efflux, being supported by mutant study and homology and molecular docking modeling. Therefore, we propose that lysosomal TM4SF5 senses and enables arginine efflux for mTORC1/S6K1 activation, and arginine-auxotroph in hepatocellular carcinoma may be targeted by blocking the arginine sensing using anti-TM4SF5 reagents.
    Keywords:  TM4SF5; amino acid transporter; arginine sensor; homology modeling; lysosome; mTOR; metabolism; molecular docking modeling; protein interaction; tetraspanin trafficking
    DOI:  https://doi.org/10.1016/j.cmet.2019.03.005
  4. Mol Brain. 2019 04 08. 12(1): 33
    Development of GABARAP family protein-sensitive LIR-based probes for neuronal autophagy.
    Pureum Jeon, Ju-Hui Park, Yong-Woo Jun, You-Kyung Lee, Deok-Jin Jang, Jin-A Lee.
      Autophagy allows for lysosomal cellular degradation of cytosolic components. In particular, neuronal autophagy is essential for cellular homeostasis and neuronal survival and is tightly regulated by several autophagy-related (ATG) proteins in post-mitotic neurons. Among these ATG proteins, the LC3/GABARAP proteins are known to regulate autophagosome biogenesis/maturation and cargo recognition. However, little is known about the role of GABARAP family proteins in neuronal autophagy despite their abundant expression in post-mitotic neurons. We have previously developed HyD (Hydrophobic Domain)-LIR (LC3-interacting region)-based autophagosome markers. In this study, to monitor GABARAP family proteins in autophagosomes of post-mitotic neurons, we improved the sensitivity of the probes for specifically detecting endogenous GABARAP family proteins by adding one more LIR motif to the LIR probes. We have tested the efficiency of two different LIRs, from ULK2 and Stbd1, in regard to their cellular localization to autophagosomes. HyD-2xLIR(ULK2)-GFP and HyD-2xLIR(Stbd1)-GFP demonstrated specific localization to GABARAP-positive autophagosomes relative to LC3B-positive autophagosomes in MEF/HeLa cells in an autophagy-dependent manner. Indeed, HyD-2xLIR(Stbd1)-GFP could efficiently detect GABARAP-positive autophagosomes in cultured cortical neurons. Our improved GABARAP-sensitive probes will contribute toward understanding the specific role of GABARAP family proteins in regard to neuronal autophagy.
    Keywords:  Autophagy; GABARAP; LC3; LIR motif
    DOI:  https://doi.org/10.1186/s13041-019-0458-z
  5. PLoS Genet. 2019 Apr 11. 15(4): e1008097
    FOXO3 directly regulates an autophagy network to functionally regulate proteostasis in adult neural stem cells.
    Amanda J Audesse, Shleshma Dhakal, Lexi-Amber Hassell, Zachary Gardell, Yuliya Nemtsova, Ashley E Webb.
      Maintenance of a healthy proteome is essential for cellular homeostasis and loss of proteostasis is associated with tissue dysfunction and neurodegenerative disease. The mechanisms that support proteostasis in healthy cells and how they become defective during aging or in disease states are not fully understood. Here, we investigate the transcriptional programs that are essential for neural stem and progenitor cell (NSPC) function and uncover a program of autophagy genes under the control of the transcription factor FOXO3. Using genomic approaches, we observe that FOXO3 directly binds a network of target genes in adult NSPCs that are involved in autophagy, and find that FOXO3 functionally regulates induction of autophagy in these cells. Interestingly, in the absence of FOXO activity, aggregates accumulate in NSPCs, and this effect is reversed by TOR (target of rapamycin) inhibition. Surprisingly, enhancing FOXO3 causes nucleation of protein aggregates, but does not increase their degradation. The work presented here identifies a genomic network under the direct control of a key transcriptional regulator of aging that is critical for maintaining a healthy mammalian stem cell pool to support lifelong neurogenesis.
    DOI:  https://doi.org/10.1371/journal.pgen.1008097
  6. Cell. 2019 Mar 19. pii: S0092-8674(19)30158-8. [Epub ahead of print]
    ATG8-Binding UIM Proteins Define a New Class of Autophagy Adaptors and Receptors.
    Richard S Marshall, Zhihua Hua, Sujina Mali, Fionn McLoughlin, Richard D Vierstra.
      During autophagy, vesicle dynamics and cargo recruitment are driven by numerous adaptors and receptors that become tethered to the phagophore through interactions with lipidated ATG8/LC3 decorating the expanding membrane. Most currently described ATG8-binding proteins exploit a well-defined ATG8-interacting motif (AIM, or LC3-interacting region [LIR]) that contacts a hydrophobic patch on ATG8 known as the LIR/AIM docking site (LDS). Here we describe a new class of ATG8 interactors that exploit ubiquitin-interacting motif (UIM)-like sequences for high-affinity binding to an alternative ATG8 interaction site. Assays with candidate UIM-containing proteins together with unbiased screens identified a large collection of UIM-based ATG8 interactors in plants, yeast, and humans. Analysis of a subset also harboring ubiquitin regulatory X (UBX) domains revealed a role for UIM-directed autophagy in clearing non-functional CDC48/p97 complexes, including some impaired in human disease. With this new class of adaptors and receptors, we greatly extend the reach of selective autophagy and identify new factors regulating autophagic vesicle dynamics.
    Keywords:  AIM; ATG8; ATG8-interacting motif; Arabidopsis; CDC48/p97; LC3-interacting region; LDS; LIR; LIR/AIM-docking site; UDS; UIM; UIM-docking site; autophagy; ubiquitin-interacting motif; yeast
    DOI:  https://doi.org/10.1016/j.cell.2019.02.009
  7. Autophagy. 2019 Apr 06. 1-13
    RAB2 regulates the formation of autophagosome and autolysosome in mammalian cells.
    Xianming Ding, Xiao Jiang, Rui Tian, Pengwei Zhao, Lin Li, Xinyi Wang, She Chen, Yushan Zhu, Mei Mei, Shilai Bao, Wei Liu, Zaiming Tang, Qiming Sun.
      Multiple sources contribute membrane and protein machineries to construct functional macroautophagic/autophagic structures. However, the underlying molecular mechanisms remain elusive. Here, we show that RAB2 connects the Golgi network to autophagy pathway by delivering membrane and by sequentially engaging distinct autophagy machineries. In unstressed cells, RAB2 resides primarily in the Golgi apparatus, as evidenced by its interaction and colocalization with GOLGA2/GM130. Importantly, autophagy stimuli dissociate RAB2 from GOLGA2 to interact with ULK1 complex, which facilitates the recruitment of ULK1 complex to form phagophores. Intriguingly, RAB2 appears to modulate ULK1 kinase activity to propagate signals for autophagosome formation. Subsequently, RAB2 switches to interact with autophagosomal RUBCNL/PACER and STX17 to further specify the recruitment of HOPS complex for autolysosome formation. Together, our study reveals a multivalent pathway in bulk autophagy regulation, and provides mechanistic insights into how the Golgi apparatus contributes to the formation of different autophagic structures. Abbreviations: ACTB: actin beta; ATG9: autophagy related 9A; ATG14: autophagy related 14; ATG16L1: autophagy related 16 like 1; BCAP31: B cell receptor associated protein 31; BECN1: beclin 1; Ctrl: control; CQ: chloroquine; CTSD: cathepsin D; DMSO: dimethyl sulfoxide; EBSS: Earle's balanced salt solution; EEA1: early endosome antigen 1; GDI: guanine nucleotide dissociation inhibitor; GFP: green fluorescent protein; GOLGA2: golgin A2; HOPS: homotypic fusion and protein sorting complex; IP: immunoprecipitation; KD: knockdown; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LC3: microtubule-associated protein 1 light chain 3; OE: overexpression; PtdIns3K: class III phosphatidylinositol 3-kinase; SQSTM1/p62: sequestosome 1; RAB2: RAB2A, member RAS oncogene family; RAB7: RAB7A, member RAS oncogene family; RAB11: RAB11A, member RAS oncogene family; RUBCNL/PACER: rubicon like autophagy enhancer; STX17: syntaxin 17; TBC1D14: TBC1 domain family member 14; TFRC: transferrin receptor; TGOLN2: trans-golgi network protein 2; TUBB: tubulin beta class I; ULK1: unc-51 like autophagy activating kinase 1; VPS41: VPS41, HOPS complex subunit; WB: western blot; WT: wild type; YPT1: GTP-binding protein YPT1.
    Keywords:  Autophagosome; GOLGA2; Golgi apparatus; RAB2; RUBCNL; autolysosome
    DOI:  https://doi.org/10.1080/15548627.2019.1596478
  8. Mol Cell. 2019 Apr 03. pii: S1097-2765(19)30231-X. [Epub ahead of print]
    ULK1 and ULK2 Regulate Stress Granule Disassembly Through Phosphorylation and Activation of VCP/p97.
    Bo Wang, Brian A Maxwell, Joung Hyuck Joo, Youngdae Gwon, James Messing, Ashutosh Mishra, Timothy I Shaw, Amber L Ward, Honghu Quan, Sadie Miki Sakurada, Shondra M Pruett-Miller, Tulio Bertorini, Peter Vogel, Hong Joo Kim, Junmin Peng, J Paul Taylor, Mondira Kundu.
      Disturbances in autophagy and stress granule dynamics have been implicated as potential mechanisms underlying inclusion body myopathy (IBM) and related disorders. Yet the roles of core autophagy proteins in IBM and stress granule dynamics remain poorly characterized. Here, we demonstrate that disrupted expression of the core autophagy proteins ULK1 and ULK2 in mice causes a vacuolar myopathy with ubiquitin and TDP-43-positive inclusions; this myopathy is similar to that caused by VCP/p97 mutations, the most common cause of familial IBM. Mechanistically, we show that ULK1/2 localize to stress granules and phosphorylate VCP, thereby increasing VCP's activity and ability to disassemble stress granules. These data suggest that VCP dysregulation and defective stress granule disassembly contribute to IBM-like disease in Ulk1/2-deficient mice. In addition, stress granule disassembly is accelerated by an ULK1/2 agonist, suggesting ULK1/2 as targets for exploiting the higher-order regulation of stress granules for therapeutic intervention of IBM and related disorders.
    Keywords:  ATG1; ATG7; ULK1; ULK2; VCP; amyotrophic lateral sclerosis; autophagy; inclusion body myopathy; p97; stress granules
    DOI:  https://doi.org/10.1016/j.molcel.2019.03.027
  9. Aging Cell. 2019 Apr 11. e12922
    α-Synuclein toxicity in yeast and human cells is caused by cell cycle re-entry and autophagy degradation of ribonucleotide reductase 1.
    Belém Sampaio-Marques, Ana Guedes, Igor Vasilevskiy, Susana Gonçalves, Tiago F Outeiro, Joris Winderickx, William C Burhans, Paula Ludovico.
      α-Synuclein (aSyn) toxicity is associated with cell cycle alterations, activation of DNA damage responses (DDR), and deregulation of autophagy. However, the relationships between these phenomena remain largely unknown. Here, we demonstrate that in a yeast model of aSyn toxicity and aging, aSyn expression induces Ras2-dependent growth signaling, cell cycle re-entry, DDR activation, autophagy, and autophagic degradation of ribonucleotide reductase 1 (Rnr1), a protein required for the activity of ribonucleotide reductase and dNTP synthesis. These events lead to cell death and aging, which are abrogated by deleting RAS2, inhibiting DDR or autophagy, or overexpressing RNR1. aSyn expression in human H4 neuroglioma cells also induces cell cycle re-entry and S-phase arrest, autophagy, and degradation of RRM1, the human homologue of RNR1, and inhibiting autophagic degradation of RRM1 rescues cells from cell death. Our findings represent a model for aSyn toxicity that has important implications for understanding synucleinopathies and other age-related neurodegenerative diseases.
    Keywords:  DNA damage responses; alpha-synuclein; autophagy; cell cycle re-entry; chronological aging; ribonuclease reductase
    DOI:  https://doi.org/10.1111/acel.12922
  10. Redox Biol. 2019 Apr 02. pii: S2213-2317(19)30047-3. [Epub ahead of print]24 101181
    Enhanced autophagic-lysosomal activity and increased BAG3-mediated selective macroautophagy as adaptive response of neuronal cells to chronic oxidative stress.
    Debapriya Chakraborty, Vanessa Felzen, Christof Hiebel, Elisabeth Stürner, Natarajan Perumal, Caroline Manicam, Elisabeth Sehn, Franz Grus, Uwe Wolfrum, Christian Behl.
      Oxidative stress and a disturbed cellular protein homeostasis (proteostasis) belong to the most important hallmarks of aging and of neurodegenerative disorders. The proteasomal and autophagic-lysosomal degradation pathways are key measures to maintain proteostasis. Here, we report that hippocampal cells selected for full adaptation and resistance to oxidative stress induced by hydrogen peroxide (oxidative stress-resistant cells, OxSR cells) showed a massive increase in the expression of components of the cellular autophagic-lysosomal network and a significantly higher overall autophagic activity. A comparative expression analysis revealed that distinct key regulators of autophagy are upregulated in OxSR cells. The observed adaptive autophagic response was found to be independent of the upstream autophagy regulator mTOR but is accompanied by a significant upregulation of further downstream components of the canonical autophagy network such as Beclin1, WIPI1 and the transmembrane ATG9 proteins. Interestingly, the expression of the HSP70 co-chaperone BAG3, mediator of BAG3-mediated selective macroautophagy and highly relevant for the clearance of aggregated proteins in cells, was found to be increased in OxSR cells that were consequently able to effectively overcome proteotoxic stress. Overexpression of BAG3 in oxidative stress-sensitive HT22 wildtype cells partly established the vesicular phenotype and the enhanced autophagic flux seen in OxSR cells suggesting that BAG3 takes over an important part in the adaptation process. A full proteome analysis demonstrated additional changes in the expression of mitochondrial proteins, metabolic enzymes and different pathway regulators in OxSR cells as consequence of the adaptation to oxidative stress in addition to autophagy-related proteins. Taken together, this analysis revealed a wide variety of pathways and players that act as adaptive response to chronic redox stress in neuronal cells.
    Keywords:  Adaptation; Autophagy; BAG3; Oxidative stress; Protein homeostasis
    DOI:  https://doi.org/10.1016/j.redox.2019.101181
  11. Brain. 2019 Apr 10. pii: awz075. [Epub ahead of print]
    A mutation in the major autophagy gene, WIPI2, associated with global developmental abnormalities.
    Musharraf Jelani, Hannah C Dooley, Andrea Gubas, Hussein Sheikh Ali Mohamoud, Muhammad Tariq Masood Khan, Zahir Ali, Changsoo Kang, Fazal Rahim, Amin Jan, Nirmal Vadgama, Muhammad Ismail Khan, Jumana Yousuf Al-Aama, Asifullah Khan, Sharon A Tooze, Jamal Nasir.
      We describe a large consanguineous pedigree from a remote area of Northern Pakistan, with a complex developmental disorder associated with wide-ranging symptoms, including mental retardation, speech and language impairment and other neurological, psychiatric, skeletal and cardiac abnormalities. We initially carried out a genetic study using the HumanCytoSNP-12 v2.1 Illumina gene chip on nine family members and identified a single region of homozygosity shared amongst four affected individuals on chromosome 7p22 (positions 3059377-5478971). We performed whole-exome sequencing on two affected individuals from two separate branches of the extended pedigree and identified a novel nonsynonymous homozygous mutation in exon 9 of the WIPI2 (WD-repeat protein interacting with phosphoinositide 2) gene at position 5265458 (c.G745A;pV249M). WIPI2 plays a critical role in autophagy, an evolutionary conserved cellular pathway implicated in a growing number of medical conditions. The mutation is situated in a highly conserved and critically important region of WIPI2, responsible for binding PI(3)P and PI(3,5)P2, an essential requirement for autophagy to proceed. The mutation is absent in all public databases, is predicted to be damaging and segregates with the disease phenotype. We performed functional studies in vitro to determine the potential effects of the mutation on downstream pathways leading to autophagosome assembly. Binding of the V231M mutant of WIPI2b to ATG16L1 (as well as ATG5-12) is significantly reduced in GFP pull-down experiments, and fibroblasts derived from the patients show reduced WIPI2 puncta, reduced LC3 lipidation and reduced autophagic flux.
    Keywords:  LC3; WIPI2; autophagy; exome sequencing; gene
    DOI:  https://doi.org/10.1093/brain/awz075
  12. Am J Transl Res. 2019 ;11(3): 1170-1183
    Extracellular vesicles degradation pathway based autophagy lysosome pathway.
    Jun Zheng, Jin Tan, Yu-Yang Miao, Qiang Zhang.
      As an ancient intracellular degradation pathway, the autophagy lysosome pathway exists in various cells continuously and stably and maintains cellular homeostasis by degrading damaged organelles and misfolded proteins that are prejudicial to cells. Extracellular vesicles (EVs) including microparticles and exosomes, are derived from varieties of mammalian tissue cells such as platelets, endothelial cells, cardiomyocytes. Through large quantity of active substances carried by EVs, EVs exert momentous biological functions. Recent researches have revealed the molecular mechanism of the interaction between extracellular vesicles and autophagy. In this review, we first elaborate that extracellular vesicles are identified and internalized by target cells by means of receptor-ligand. Since extracellular vesicles contain multiple functional molecules, we subsequently describe the process of intracellular autophagy pathway induced by extracellular vesicles, which activates autophagy-related pathways or delivers autophagy-associated molecules. Finally, we introduced the effects of extracellular vesicle-induced autophagy on extracellular vesicles and target cells respectively. In conclusion, this article integrates relevant theoretical knowledge of autophagy caused by extracellular vesicles and provides a new direction for the study of extracellular vesicles in the future.
    Keywords:  Extracellular vesicles; autophagy; exosome; internalization; microparticle; signaling pathway
  13. J Cell Biol. 2019 Apr 12. pii: jcb.201804101. [Epub ahead of print]
    Somatic autophagy of axonal mitochondria in ischemic neurons.
    Yanrong Zheng, Xiangnan Zhang, Xiaoli Wu, Lei Jiang, Anil Ahsan, Shijia Ma, Ziyu Xiao, Feng Han, Zheng-Hong Qin, Weiwei Hu, Zhong Chen.
      Mitophagy protects against ischemic neuronal injury by eliminating damaged mitochondria, but it is unclear how mitochondria in distal axons are cleared. We find that oxygen and glucose deprivation-reperfusion reduces mitochondrial content in both cell bodies and axons. Axonal mitochondria elimination was not abolished in Atg7 fl/fl ;nes-Cre neurons, suggesting the absence of direct mitophagy in axons. Instead, axonal mitochondria were enwrapped by autophagosomes in soma and axon-derived mitochondria prioritized for elimination by autophagy. Intriguingly, axonal mitochondria showed prompt loss of anterograde motility but increased retrograde movement upon reperfusion. Anchoring of axonal mitochondria by syntaphilin blocked neuronal mitophagy and aggravated injury. Conversely, induced binding of mitochondria to dynein reinforced retrograde transport and enhanced mitophagy to prevent mitochondrial dysfunction and attenuate neuronal injury. Therefore, we reveal somatic autophagy of axonal mitochondria in ischemic neurons and establish a direct link of retrograde mitochondrial movement with mitophagy. Our findings may provide a new concept for reducing ischemic neuronal injury by correcting mitochondrial motility.
    DOI:  https://doi.org/10.1083/jcb.201804101
  14. Nat Commun. 2019 Apr 12. 10(1): 1693
    Transcriptional regulation of autophagy-lysosomal function in BRAF-driven melanoma progression and chemoresistance.
    Shun Li, Ying Song, Christine Quach, Hongrui Guo, Gyu-Beom Jang, Hadi Maazi, Shihui Zhao, Nathaniel A Sands, Qingsong Liu, Gino K In, David Peng, Weiming Yuan, Keigo Machida, Min Yu, Omid Akbari, Ashley Hagiya, Yongfei Yang, Vasu Punj, Liling Tang, Chengyu Liang.
      Autophagy maintains homeostasis and is induced upon stress. Yet, its mechanistic interaction with oncogenic signaling remains elusive. Here, we show that in BRAFV600E-melanoma, autophagy is induced by BRAF inhibitor (BRAFi), as part of a transcriptional program coordinating lysosome biogenesis/function, mediated by the TFEB transcription factor. TFEB is phosphorylated and thus inactivated by BRAFV600E via its downstream ERK independently of mTORC1. BRAFi disrupts TFEB phosphorylation, allowing its nuclear translocation, which is synergized by increased phosphorylation/inactivation of the ZKSCAN3 transcriptional repressor by JNK2/p38-MAPK. Blockade of BRAFi-induced transcriptional activation of autophagy-lysosomal function in melanoma xenografts causes enhanced tumor progression, EMT-transdifferentiation, metastatic dissemination, and chemoresistance, which is associated with elevated TGF-β levels and enhanced TGF-β signaling. Inhibition of TGF-β signaling restores tumor differentiation and drug responsiveness in melanoma cells. Thus, the "BRAF-TFEB-autophagy-lysosome" axis represents an intrinsic regulatory pathway in BRAF-mutant melanoma, coupling BRAF signaling with TGF-β signaling to drive tumor progression and chemoresistance.
    DOI:  https://doi.org/10.1038/s41467-019-09634-8
  15. Sci Rep. 2019 Apr 11. 9(1): 5912
    TGFβ2-induced senescence during early inner ear development.
    Alejandro Gibaja, María R Aburto, Sara Pulido, Manuel Collado, Juan M Hurle, Isabel Varela-Nieto, Marta Magariños.
      Embryonic development requires the coordinated regulation of apoptosis, survival, autophagy, proliferation and differentiation programs. Senescence has recently joined the cellular processes required to master development, in addition to its well-described roles in cancer and ageing. Here, we show that senescent cells are present in a highly regulated temporal pattern in the developing vertebrate inner ear, first, surrounding the otic pore and, later, in the otocyst at the endolymphatic duct. Cellular senescence is associated with areas of increased apoptosis and reduced proliferation consistent with the induction of the process when the endolymphatic duct is being formed. Modulation of senescence disrupts otic vesicle morphology. Transforming growth factor beta (TGFβ) signaling interacts with signaling pathways elicited by insulin-like growth factor type 1 (IGF-1) to jointly coordinate cellular dynamics required for morphogenesis and differentiation. Taken together, these results show that senescence is a natural occurring process essential for early inner ear development.
    DOI:  https://doi.org/10.1038/s41598-019-42040-0
  16. Life Sci. 2019 Apr 03. pii: S0024-3205(19)30252-8. [Epub ahead of print]
    Metformin promotes autophagy in ischemia/reperfusion myocardium via cytoplasmic AMPKα1 and nuclear AMPKα2 pathways.
    Yishi Wang, Zheng Yang, Guoxu Zheng, Lu Yu, Yue Yin, Nan Mu, Heng Ma.
      AIMS: In myocardial ischemia-reperfusion (MI/R) injury, impaired autophagy function worsens cardiomyocyte death. AMP-activated protein kinase (AMPK) is a heterotrimeric protein that plays an important role in cardioprotection and myocardial autophagic function. AMPKα1 and α2 are localized primarily in the cytoplasm and nucleus, respectively, in cardiomyocytes, but the isoform-specific autophagy regulation of AMPK during MI/R remains unclear.MATERIALS AND METHODS: An MI/R model was built, and the protein expression of AMPKα1/α2, p-AMPK, mTOR, p-mTOR, TFEB, p-FoxO3a, SKP2, CARM1, TBP, Atg5, LAMP2, LC3B, and p62 during ischemia and reperfusion was determined by western blotting. Recombinant adeno-associated virus (serotype 9) vectors carrying tandem fluorescent-tagged LC3 or mRFP-GFP-LC3/GFP-LC3 were used to evaluate the autophagy status. AMPKα2 knockout mice were used for in vivo studies.
    KEY FINDINGS: Both cytoplasmic AMPKα1 and nuclear α2 subunit expression decreased during the reperfusion period, which led to AMPKα1-mTOR-TFEB and AMPKα2-Skp2-CARM1-TFEB signaling inhibition, respectively. The decreased TFEB level during reperfusion suppressed autophagy. Metformin could activate both the AMPKα1- and α2- mediated pathways, thus restoring autophagy flux during reperfusion. Nevertheless, in AMPKα2 knockout mice, nuclear α2-regulated Skp2-CARM1-TFEB signaling was inhibited, while α1-related signaling was comparatively unaffected, which partially impaired metformin-enhanced autophagy.
    SIGNIFICANCE: Our study suggests that metformin had the dual effects of promoting both cytoplasmic AMPKα1- and nuclear AMPKα2-related signaling to improve autophagic flux and restore cardiac function during MI/R.
    Keywords:  AMPKα1/α2; Autophagy; Ischemia/reperfusion injury; Metformin; Myocardium
    DOI:  https://doi.org/10.1016/j.lfs.2019.04.002
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