bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2020–07–19
28 papers selected by
Viktor Korolchuk, Newcastle University
  1. TGF-β Promotes Metabolic Reprogramming in Lung Fibroblasts via mTORC1-dependent ATF4 Activation.
  2. CDK4/6 regulate lysosome biogenesis through TFEB/TFE3.
  3. Mitophagy, Mitochondrial Homeostasis, and Cell Fate.
  4. Genetic dissection of Ragulator structure and function in amino acid-dependent regulation of mTORC1.
  5. Mitochondria-Associated Degradation Pathway (MAD) Function beyond the Outer Membrane.
  6. An FGF15/19-TFEB regulatory loop controls hepatic cholesterol and bile acid homeostasis.
  7. Ribosome profiling reveals a functional role for autophagy in mRNA translational control.
  8. Ornithine-A urea cycle metabolite enhances autophagy and controls Mycobacterium tuberculosis infection.
  9. Melatonin pretreatment alleviates renal ischemia-reperfusion injury by promoting autophagic flux via TLR4/MyD88/MEK/ERK/mTORC1 signaling.
  10. Autophagy and Parkinson's Disease.
  11. Ribosome Recycling by ABCE1 Links Lysosomal Function and Iron Homeostasis to 3' UTR-Directed Regulation and Nonsense-Mediated Decay.
  12. Phospho-HDAC6 Gathers Into Protein Aggregates in Parkinson's Disease and Atypical Parkinsonisms.
  13. Role of FIP200 in inflammatory processes beyond its canonical autophagy function.
  14. C9orf72-associated SMCR8 protein binds in the ubiquitin pathway and with proteins linked with neurological disease.
  15. The Cdc48 Complex Alleviates the Cytotoxicity of Misfolded Proteins by Regulating Ubiquitin Homeostasis.
  16. Nuclear Factor-Erythroid 2-Related Factor 2 (Nrf2) and Mitochondrial Dynamics/Mitophagy in Neurological Diseases.
  17. Autophagy regulates the localization and degradation of p16INK4a.
  18. Progress of Anti-aging Drugs Targeting Autophagy.
  19. Autophagy and Polyglutamine Disease.
  20. Ubiquilin-2 differentially regulates polyglutamine disease proteins.
  21. Autophagy and Mitochondrial Encephalomyopathies.
  22. Drug Development and Treatment of Autophagy in Other Diseases.
  23. Zinc and Autophagy in Age-Related Macular Degeneration.
  24. Autophagy and Acute Kidney Injury.
  25. Lysosomal dysfunction of corneal fibroblasts underlies the pathogenesis of Granular Corneal Dystrophy Type 2 and can be rescued by TFEB.
  26. α-Synuclein aggregation and transmission in Parkinson's disease: a link to mitochondria and lysosome.
  27. The role of lipids in autophagy and its implication in neurodegeneration.
  28. Application of Autophagy in Cardiovascular Diseases.
  1. Am J Respir Cell Mol Biol. 2020 Jul 15.
    TGF-β Promotes Metabolic Reprogramming in Lung Fibroblasts via mTORC1-dependent ATF4 Activation.
    Erin M O'Leary, Yufeng Tian, Recep Nigdelioglu, Leah J Witt, Rengul Cetin-Atalay, Angelo Y Meliton, Parker S Woods, Lucas M Kimmig, Kaitlyn A Sun, Gizem A Gökalp, Gökhan M Mutlu, Robert B Hamanaka.
      Idiopathic pulmonary fibrosis is a fatal disease characterized by the TGF-β-dependent differentiation of lung fibroblasts into myofibroblasts, leading to excessive deposition of collagen proteins and progressive scarring. We have previously shown that synthesis of collagen by myofibroblasts requires de novo synthesis of glycine, the most abundant amino acid found in collagen protein. TGF-β upregulates the expression of the enzymes of the de novo serine/glycine synthesis pathway in lung fibroblasts; however, the transcriptional and signaling regulators of this pathway remain incompletely understood. Here we demonstrate that TGF-β promotes accumulation of Activating Transcription Factor 4 (ATF4) which is required for increased expression of the serine/glycine synthesis pathway enzymes in response to TGF-β. We found that induction of the Integrated Stress Response (ISR) contributes to TGF-β-induced ATF4 activity; however, the primary driver of ATF4 downstream of TGF-β is activation of the Mechanistic Target of Rapamycin Complex 1 (mTORC1). TGF-β activates the PI3-kinase-Akt-mTOR pathway, and inhibition of PI3-kinase prevents activation of downstream signaling and induction of ATF4. Using a panel of mTOR inhibitors, we found that ATF4 activation is dependent on mTORC1, independent of mTORC2. Rapamycin, which incompletely and allosterically inhibits mTORC1 had no effect on TGF-β-mediated induction of ATF4; however, Rapalink-1, which specifically targets the kinase domain of mTORC1 completely inhibited ATF4 induction and metabolic reprogramming downstream of TGF-β. Our results provide insight into the mechanisms of metabolic reprogramming in myofibroblasts and clarify contradictory published findings on the role of mTOR inhibition in myofibroblast differentiation.
    Keywords:  Fibrosis; Glycolysis; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1165/rcmb.2020-0143OC
  2. J Cell Biol. 2020 Aug 03. pii: e201911036. [Epub ahead of print]219(8):
    CDK4/6 regulate lysosome biogenesis through TFEB/TFE3.
    Qiuyuan Yin, Youli Jian, Meng Xu, Xiahe Huang, Niya Wang, Zhifang Liu, Qian Li, Jinglin Li, Hejiang Zhou, Lin Xu, Yingchun Wang, Chonglin Yang.
      Lysosomes are degradation and signaling organelles that adapt their biogenesis to meet many different cellular demands; however, it is unknown how lysosomes change their numbers for cell division. Here, we report that the cyclin-dependent kinases CDK4/6 regulate lysosome biogenesis during the cell cycle. Chemical or genetic inactivation of CDK4/6 increases lysosomal numbers by activating the lysosome and autophagy transcription factors TFEB and TFE3. CDK4/6 interact with and phosphorylate TFEB/TFE3 in the nucleus, thereby inactivating them by promoting their shuttling to the cytoplasm. During the cell cycle, lysosome numbers increase in S and G2/M phases when cyclin D turnover diminishes CDK4/6 activity. These findings not only uncover the molecular events that direct the nuclear export of TFEB/TFE3, but also suggest a mechanism that controls lysosome biogenesis in the cell cycle. CDK4/6 inhibitors promote autophagy and lysosome-dependent degradation, which has important implications for the therapy of cancer and lysosome-related disorders.
    DOI:  https://doi.org/10.1083/jcb.201911036
  3. Front Cell Dev Biol. 2020 ;8 467
    Mitophagy, Mitochondrial Homeostasis, and Cell Fate.
    Kaili Ma, Guo Chen, Wenhui Li, Oliver Kepp, Yushan Zhu, Quan Chen.
      Mitochondria are highly plastic and dynamic organelles that have graded responses to the changing cellular, environmental, and developmental cues. Mitochondria undergo constant mitochondrial fission and fusion, mitochondrial biogenesis, and mitophagy, which coordinately control mitochondrial morphology, quantity, quality, turnover, and inheritance. Mitophagy is a cellular process that selectively removes the aged and damaged mitochondria via the specific sequestration and engulfment of mitochondria for subsequent lysosomal degradation. It plays a pivotal role in reinstating cellular homeostasis in normal physiology and conditions of stress. Damaged mitochondria may either instigate innate immunity through the overproduction of ROS or the release of mtDNA, or trigger cell death through the release of cytochrome c and other apoptogenic factors when mitochondria damage is beyond repair. Distinct molecular machineries and signaling pathways are found to regulate these mitochondrial dynamics and behaviors. It is less clear how mitochondrial behaviors are coordinated at molecular levels. BCL2 family proteins interact within family members to regulate mitochondrial outer membrane permeabilization and apoptosis. They were also described as global regulators of mitochondrial homeostasis and mitochondrial fate through their interaction with distinct partners including Drp1, mitofusins, PGAM5, and even LC3 that involved mitochondrial dynamics and behaviors. In this review, we summarize recent findings on molecular pathways governing mitophagy and its coordination with other mitochondrial behaviors, which together determine cellular fate.
    Keywords:  cell fate; mitochondrial apoptosis; mitochondrial dynamics; mitophagy; mitophagy receptors
    DOI:  https://doi.org/10.3389/fcell.2020.00467
  4. J Biochem. 2020 Jul 11. pii: mvaa076. [Epub ahead of print]
    Genetic dissection of Ragulator structure and function in amino acid-dependent regulation of mTORC1.
    Shigeyuki Nada, Masato Okada.
      Ragulator is a heteropentameric protein complex consisting of two roadblock heterodimers wrapped by the membrane anchor p18/Lamtor1. The Ragulator complex functions as a lysosomal membrane scaffold for Rag GTPases to recruit and activate mTORC1. However, the roles of Ragulator structure in the regulation of mTORC1 function remain elusive. In this study, we disrupted Ragulator structure by directly anchoring RagC to lysosomes and monitored the effect on amino acid-dependent mTORC1 activation. Expression of lysosome-anchored RagC in p18-deficient cells resulted in constitutive lysosomal localization and amino acid-independent activation of mTORC1. Co-expression of Ragulator in this system restored the amino acid dependency of mTORC1 activation. Furthermore, ablation of Gator1, a suppressor of Rag GTPases, induced amino acid-independent activation of mTORC1 even in the presence of Ragulator. These results demonstrate that Ragulator structure is essential for amino acid-dependent regulation of Rag GTPases via Gator1. In addition, our genetic analyses revealed new roles of amino acids in the regulation of mTORC1 as follows: amino acids could activate a fraction of mTORC1 in a Rheb-independent manner, and could also drive negative-feedback regulation of mTORC1 signaling via protein phosphatases. These intriguing findings contribute to our overall understanding of the regulatory mechanisms of mTORC1 signaling.
    Keywords:  Rag; Ragulator; Rheb; lysosome; mTORC1; p18
    DOI:  https://doi.org/10.1093/jb/mvaa076
  5. Cell Rep. 2020 Jul 14. pii: S2211-1247(20)30883-4. [Epub ahead of print]32(2): 107902
    Mitochondria-Associated Degradation Pathway (MAD) Function beyond the Outer Membrane.
    Pin-Chao Liao, Dana M Alessi Wolken, Edith Serrano, Pallavi Srivastava, Liza A Pon.
      The mitochondria-associated degradation pathway (MAD) mediates ubiquitination and degradation of mitochondrial outer membrane (MOM) proteins by the proteasome. We find that the MAD, but not other quality-control pathways including macroautophagy, mitophagy, or mitochondrial chaperones and proteases, is critical for yeast cellular fitness under conditions of paraquat (PQ)-induced oxidative stress in mitochondria. Specifically, inhibition of the MAD increases PQ-induced defects in growth and mitochondrial quality and decreases chronological lifespan. We use mass spectrometry analysis to identify possible MAD substrates as mitochondrial proteins that exhibit increased ubiquitination in response to PQ treatment and inhibition of the MAD. We identify candidate substrates in the mitochondrial matrix and inner membrane and confirm that two matrix proteins are MAD substrates. Our studies reveal a broader function for the MAD in mitochondrial protein surveillance beyond the MOM and a major role for the MAD in cellular and mitochondrial fitness in response to chronic, low-level oxidative stress in mitochondria.
    Keywords:  Saccharomyces cerevisiae; chronological lifespan; mitochondrial quality control; mitophagy; oxidative stress; paraquat; proteasome; proteostasis; reactive oxygen species; ubiquitin
    DOI:  https://doi.org/10.1016/j.celrep.2020.107902
  6. Nat Commun. 2020 Jul 17. 11(1): 3612
    An FGF15/19-TFEB regulatory loop controls hepatic cholesterol and bile acid homeostasis.
    Yifeng Wang, Sumedha Gunewardena, Feng Li, David J Matye, Cheng Chen, Xiaojuan Chao, Taeyoon Jung, Yuxia Zhang, Maciej Czerwiński, Hong-Min Ni, Wen-Xing Ding, Tiangang Li.
      Bile acid synthesis plays a key role in regulating whole body cholesterol homeostasis. Transcriptional factor EB (TFEB) is a nutrient and stress-sensing transcriptional factor that promotes lysosomal biogenesis. Here we report a role of TFEB in regulating hepatic bile acid synthesis. We show that TFEB induces cholesterol 7α-hydroxylase (CYP7A1) in human hepatocytes and mouse livers and prevents hepatic cholesterol accumulation and hypercholesterolemia in Western diet-fed mice. Furthermore, we find that cholesterol-induced lysosomal stress feed-forward activates TFEB via promoting TFEB nuclear translocation, while bile acid-induced fibroblast growth factor 19 (FGF19), acting via mTOR/ERK signaling and TFEB phosphorylation, feedback inhibits TFEB nuclear translocation in hepatocytes. Consistently, blocking intestinal bile acid uptake by an apical sodium-bile acid transporter (ASBT) inhibitor decreases ileal FGF15, enhances hepatic TFEB nuclear localization and improves cholesterol homeostasis in Western diet-fed mice. This study has identified a TFEB-mediated gut-liver signaling axis that regulates hepatic cholesterol and bile acid homeostasis.
    DOI:  https://doi.org/10.1038/s41467-020-17363-6
  7. Commun Biol. 2020 Jul 17. 3(1): 388
    Ribosome profiling reveals a functional role for autophagy in mRNA translational control.
    Juliet Goldsmith, Timothy Marsh, Saurabh Asthana, Andrew M Leidal, Deepthisri Suresh, Adam Olshen, Jayanta Debnath.
      Autophagy promotes protein degradation, and therefore has been proposed to maintain amino acid pools to sustain protein synthesis during metabolic stress. To date, how autophagy influences the protein synthesis landscape in mammalian cells remains unclear. Here, we utilize ribosome profiling to delineate the effects of genetic ablation of the autophagy regulator, ATG12, on translational control. In mammalian cells, genetic loss of autophagy does not impact global rates of cap dependent translation, even under starvation conditions. Instead, autophagy supports the translation of a subset of mRNAs enriched for cell cycle control and DNA damage repair. In particular, we demonstrate that autophagy enables the translation of the DNA damage repair protein BRCA2, which is functionally required to attenuate DNA damage and promote cell survival in response to PARP inhibition. Overall, our findings illuminate that autophagy impacts protein translation and shapes the protein landscape.
    DOI:  https://doi.org/10.1038/s42003-020-1090-2
  8. Nat Commun. 2020 Jul 15. 11(1): 3535
    Ornithine-A urea cycle metabolite enhances autophagy and controls Mycobacterium tuberculosis infection.
    Ramya Sivangala Thandi, Rajesh Kumar Radhakrishnan, Deepak Tripathi, Padmaja Paidipally, Abul K Azad, Larry S Schlesinger, Buka Samten, Sachin Mulik, Ramakrishna Vankayalapati.
      Macrophages are professional phagocytes known to play a vital role in controlling Mycobacterium tuberculosis (Mtb) infection and disease progression. Here we compare Mtb growth in mouse alveolar (AMs), peritoneal (PMs), and liver (Kupffer cells; KCs) macrophages and in bone marrow-derived monocytes (BDMs). KCs restrict Mtb growth more efficiently than all other macrophages and monocytes despite equivalent infections through enhanced autophagy. A metabolomics comparison of Mtb-infected macrophages indicates that ornithine and imidazole are two top-scoring metabolites in Mtb-infected KCs and that acetylcholine is the top-scoring in Mtb-infected AMs. Ornithine, imidazole and atropine (acetylcholine inhibitor) inhibit Mtb growth in AMs. Ornithine enhances AMPK mediated autophagy whereas imidazole directly kills Mtb by reducing cytochrome P450 activity. Intranasal delivery of ornithine or imidazole or the two together restricts Mtb growth. Our study demonstrates that the metabolic differences between Mtb-infected AMs and KCs lead to differences in the restriction of Mtb growth.
    DOI:  https://doi.org/10.1038/s41467-020-17310-5
  9. FASEB J. 2020 Jul 14.
    Melatonin pretreatment alleviates renal ischemia-reperfusion injury by promoting autophagic flux via TLR4/MyD88/MEK/ERK/mTORC1 signaling.
    Jinghui Yang, Hao Liu, Shu Han, Zhiren Fu, Jiyuan Wang, Yu Chen, Liming Wang.
      Autophagy is an important mechanism for cellular homeostasis and survival during pathologic stress conditions in the kidney, such as ischemia-reperfusion (IR) injury. In this study, renal IR was induced in female C57BL/6 mice after melatonin administration. Renal function, histological damage, inflammatory infiltration, cytokine production, oxidative stress, antioxidant capacity, autophagy changing, apoptosis levels, and autophagy-associated intracellular signaling pathway were assessed to evaluate the impact of antecedent melatonin treatment on IR-induced renal injury. The administration of melatonin resulted in significantly preserved renal function, and the protective effect was associated with ameliorated oxidative stress, limited pro-inflammatory cytokine production, and neutrophil and macrophage infiltration. Moreover, autophagic flux was increased after melatonin administration while the apoptosis levels were decreased in the melatonin-pretreated mice. Using TAK-242 and CRX-527, we confirmed that MyD88-dependent TLR4 and MEK/ERK/mTORC1 signaling participated in melatonin-induced autophagy in IR mice. Collectively, our results provide novel evidence that antecedent melatonin treatment provides protection for the kidney against IR injury by enhancing autophagy, as regulated by the TLR4/MyD88/MEK/ERK/mTORC1 signaling pathway. Therefore, melatonin preconditioning offers a potential therapeutic approach to prevent renal IR injury related to various clinical conditions.
    Keywords:  autophagy; ischemia-reperfusion injury; melatonin
    DOI:  https://doi.org/10.1096/fj.202001252R
  10. Adv Exp Med Biol. 2020 ;1207 21-51
    Autophagy and Parkinson's Disease.
    Jiahong Lu, Mingyue Wu, Zhenyu Yue.
      Parkinson's disease (PD) is the second most common neurodegenerative disease characterized by motor system dysfunction. The etiology of PD has been linked with aging, environmental toxins and genetic mutation, while molecular pathogenesis of PD includes various factors, such as impaired protein homeostasis, oxidative stress, mitochondria dysfunction, synaptic transmission impairment, calcium homeostasis imbalance, prion-like α-synuclein transmission and neuron inflammation. Autophagy is a conserved bulk degradation process to maintain cellular homeostasis. Impairment of autophagy has been reported to be involved in the pathogenesis of PD. Coding proteins of several PD-related genes, such as SNCA, LRRK2, GBA, ATP13A2, VPS35 and FBXO7, are implicated in or affected by autophagy process. Furthermore, various pathogenic events during PD directly or indirectly interfere with the autophagy pathway, and dysregulation of autophagy has been observed in different neurotoxic PD models. Autophagy has been regarded as a potential therapeutic target for PD treatment. Indeed, modulations of autophagy-regulated genes (BECN1 and TFEB) expression exerted neuroprotection against PD models, and various autophagy regulators, such as rapamycin, trehalose, lysosome modulators and other small molecule autophagy inducers, have displayed neuroprotective effects in experimental PD models. Taken together, autophagy dysfunction has been implicated in the pathogenesis of PD, and pharmacological modulation of autophagy may be a new therapeutic strategy for the PD treatment.
    Keywords:  Autophagy; Parkinson disease; α-synuclein
    DOI:  https://doi.org/10.1007/978-981-15-4272-5_2
  11. Cell Rep. 2020 Jul 14. pii: S2211-1247(20)30876-7. [Epub ahead of print]32(2): 107895
    Ribosome Recycling by ABCE1 Links Lysosomal Function and Iron Homeostasis to 3' UTR-Directed Regulation and Nonsense-Mediated Decay.
    Xiaoqiang Zhu, He Zhang, Joshua T Mendell.
      Nonsense-mediated decay (NMD) is a pathway that degrades mRNAs containing premature termination codons. Here we describe a genome-wide screen for NMD factors that uncovers an unexpected mechanism that broadly governs 3' untranslated region (UTR)-directed regulation. The screen reveals that NMD requires lysosomal acidification, which allows transferrin-mediated iron uptake, which, in turn, is necessary for iron-sulfur (Fe-S) cluster biogenesis. This pathway maintains the activity of the Fe-S cluster-containing ribosome recycling factor ABCE1, whose impaired function results in movement of ribosomes into 3' UTRs, where they displace exon junction complexes, abrogating NMD. Importantly, these effects extend beyond NMD substrates, with ABCE1 activity required to maintain the accessibility of 3' UTRs to diverse regulators, including microRNAs and RNA binding proteins. Because of the sensitivity of the Fe-S cluster of ABCE1 to iron availability and reactive oxygen species, these findings reveal an unanticipated vulnerability of 3' UTR-directed regulation to lysosomal dysfunction, iron deficiency, and oxidative stress.
    Keywords:  3' UTR; 3' untranslated region; ABCE1; iron homeostasis; iron-sulfur cluster; lysosome; nonsense-mediated decay; post-transcriptional regulation
    DOI:  https://doi.org/10.1016/j.celrep.2020.107895
  12. Front Neurosci. 2020 ;14 624
    Phospho-HDAC6 Gathers Into Protein Aggregates in Parkinson's Disease and Atypical Parkinsonisms.
    Samanta Mazzetti, Mara De Leonardis, Gloria Gagliardi, Alessandra Maria Calogero, Milo Jarno Basellini, Laura Madaschi, Ilaria Costa, Francesca Cacciatore, Sonia Spinello, Manuela Bramerio, Roberto Cilia, Chiara Rolando, Giorgio Giaccone, Gianni Pezzoli, Graziella Cappelletti.
      HDAC6 is a unique histone deacetylase that targets cytoplasmic non-histone proteins and has a specific ubiquitin-binding activity. Both of these activities are required for HDAC6-mediated formation of aggresomes, which contain misfolded proteins that will ultimately be degraded via autophagy. HDAC6 deacetylase activity is increased following phosphorylation on serine 22 (phospho-HDAC6). In human, HDAC6 localizes in neuronal Lewy bodies in Parkinson's disease (PD) and in oligodendrocytic Papp-Lantos bodies in multiple system atrophy (MSA). However, the expression of phospho-HDAC6 in post-mortem human brains is currently unexplored. Here, we evaluate and compare the distribution of HDAC6 and its phosphorylated form in human brains obtained from patients affected by three forms of parkinsonism: two synucleinopathies (PD and MSA) and a tauopathy (progressive supranuclear palsy, PSP). We find that both HDAC6 and its phosphorylated form localize with pathological protein aggregates, including α-synuclein-positive Lewy bodies in PD and Papp-Lantos bodies in MSA, and phospho-tau-positive neurofibrillary tangles in PSP. We further find a direct interaction of HDAC6 with α-synuclein with proximity ligation assay (PLA) in neuronal cell of PD patients. Taken together, our findings suggest that both HDAC6 and phospho-HDAC6 regulate the homeostasis of intra-neuronal proteins in parkinsonism.
    Keywords:  HDAC6; Parkinson’s disease; parkinsonism; phosphorylated-HDCA6; protein aggregation; tau; α-synuclein
    DOI:  https://doi.org/10.3389/fnins.2020.00624
  13. Biochem Soc Trans. 2020 Jul 14. pii: BST20191156. [Epub ahead of print]
    Role of FIP200 in inflammatory processes beyond its canonical autophagy function.
    Syn Kok Yeo, Chenran Wang, Jun-Lin Guan.
      FIP200 (RB1CC1) is a critical regulator of canonical macroautophagy and has also emerged as a crucial regulator of selective autophagy as well as inflammatory processes. The illumination of FIP200's role in autophagy at the molecular level has been accompanied by studies demonstrating the importance of its autophagy function in physiological processes in mammals and pathological contexts such as cancer. However, there is an increasing appreciation that most, if not all of the autophagy genes, also play a role in other processes such as LC3-associated phagocytosis, vesicle trafficking and protein secretion. Consequently, this has led to efforts in generating specific mutants of autophagy genes that are more amenable to dissecting their autophagy versus non-autophagy functions. In this aspect, we have generated a FIP200 knock-in mouse allele that is defective for canonical macroautophagy. This has revealed a canonical-autophagy-independent function of FIP200 that is responsible for limiting pro-inflammatory signaling. In this review, we will discuss FIP200's role in this process, the implications with regards to cancer immunotherapy and highlight key prospective avenues to specifically dissect the distinct functions of FIP200.
    Keywords:  autophagy; breast cancer; inflammatory process
    DOI:  https://doi.org/10.1042/BST20191156
  14. Acta Neuropathol Commun. 2020 Jul 16. 8(1): 110
    C9orf72-associated SMCR8 protein binds in the ubiquitin pathway and with proteins linked with neurological disease.
    John L Goodier, Alisha O Soares, Gavin C Pereira, Lauren R DeVine, Laura Sanchez, Robert N Cole, Jose Luis García-Pérez.
      A pathogenic GGGCCC hexanucleotide expansion in the first intron/promoter region of the C9orf72 gene is the most common mutation associated with amyotrophic lateral sclerosis (ALS). The C9orf72 gene product forms a complex with SMCR8 (Smith-Magenis Syndrome Chromosome Region, Candidate 8) and WDR41 (WD Repeat domain 41) proteins. Recent studies have indicated roles for the complex in autophagy regulation, vesicle trafficking, and immune response in transgenic mice, however a direct connection with ALS etiology remains unclear. With the aim of increasing understanding of the multi-functional C9orf72-SMCR8-WDR41 complex, we determined by mass spectrometry analysis the proteins that directly associate with SMCR8. SMCR8 protein binds many components of the ubiquitin-proteasome system, and we demonstrate its poly-ubiquitination without obvious degradation. Evidence is also presented for localization of endogenous SMCR8 protein to cytoplasmic stress granules. However, in several cell lines we failed to reproduce previous observations that C9orf72 protein enters these granules. SMCR8 protein associates with many products of genes associated with various Mendelian neurological disorders in addition to ALS, implicating SMCR8-containing complexes in a range of neuropathologies. We reinforce previous observations that SMCR8 and C9orf72 protein levels are positively linked, and now show in vivo that SMCR8 protein levels are greatly reduced in brain tissues of C9orf72 gene expansion carrier individuals. While further study is required, these data suggest that SMCR8 protein level might prove a useful biomarker for the C9orf72 expansion in ALS.
    Keywords:  Amyotrophic lateral sclerosis; Autophagy; Biomarker; Mass spectrometry; Proteasome; Stress granules; Ubiquitin
    DOI:  https://doi.org/10.1186/s40478-020-00982-x
  15. Cell Rep. 2020 Jul 14. pii: S2211-1247(20)30879-2. [Epub ahead of print]32(2): 107898
    The Cdc48 Complex Alleviates the Cytotoxicity of Misfolded Proteins by Regulating Ubiquitin Homeostasis.
    Ryan Higgins, Marie-Helene Kabbaj, Delaney Sherwin, Lauren A Howell, Alexa Hatcher, Robert J Tomko, Yanchang Wang.
      The accumulation of misfolded proteins is associated with multiple neurodegenerative disorders, but it remains poorly defined how this accumulation causes cytotoxicity. Here, we demonstrate that the Cdc48/p97 segregase machinery drives the clearance of ubiquitinated model misfolded protein Huntingtin (Htt103QP) and limits its aggregation. Nuclear ubiquitin ligase San1 acts upstream of Cdc48 to ubiquitinate Htt103QP. Unexpectedly, deletion of SAN1 and/or its cytosolic counterpart UBR1 rescues the toxicity associated with Cdc48 deficiency, suggesting that ubiquitin depletion, rather than compromised proteolysis of misfolded proteins, causes the growth defect in cells with Cdc48 deficiency. Indeed, Cdc48 deficiency leads to elevated protein ubiquitination levels and decreased free ubiquitin, which depends on San1/Ubr1. Furthermore, enhancing free ubiquitin levels rescues the toxicity in various Cdc48 pathway mutants and restores normal turnover of a known Cdc48-independent substrate. Our work highlights a previously unappreciated function for Cdc48 in ensuring the regeneration of monoubiquitin that is critical for normal cellular function.
    Keywords:  Cdc48; San1/Ubr1 E3 ligases; mutated Huntingtin; proteotoxicity; ubiquitin homeostasis
    DOI:  https://doi.org/10.1016/j.celrep.2020.107898
  16. Antioxidants (Basel). 2020 Jul 15. pii: E617. [Epub ahead of print]9(7):
    Nuclear Factor-Erythroid 2-Related Factor 2 (Nrf2) and Mitochondrial Dynamics/Mitophagy in Neurological Diseases.
    Tae-Cheon Kang.
      Mitochondria play an essential role in bioenergetics and respiratory functions for cell viability through numerous biochemical processes. To maintain mitochondria quality control and homeostasis, mitochondrial morphologies change rapidly in response to external insults and changes in metabolic status through fusion and fission (so called mitochondrial dynamics). Furthermore, damaged mitochondria are removed via a selective autophagosomal process, referred to as mitophagy. Although mitochondria are one of the sources of reactive oxygen species (ROS), they are themselves vulnerable to oxidative stress. Thus, endogenous antioxidant defense systems play an important role in cell survival under physiological and pathological conditions. Nuclear factor-erythroid 2-related factor 2 (Nrf2) is a redox-sensitive transcription factor that maintains redox homeostasis by regulating antioxidant-response element (ARE)-dependent transcription and the expression of antioxidant defense enzymes. Although the Nrf2 system is positively associated with mitochondrial biogenesis and mitochondrial quality control, the relationship between Nrf2 signaling and mitochondrial dynamics/mitophagy has not been sufficiently addressed in the literature. This review article describes recent clinical and experimental observations on the relationship between Nrf2 and mitochondrial dynamics/mitophagy in various neurological diseases.
    Keywords:  Alzheimer’s disease; Huntington’s disease; Parkinson’s disease; cerebrovascular disease; epilepsy; mitochondrial fission; mitochondrial fusion
    DOI:  https://doi.org/10.3390/antiox9070617
  17. Aging Cell. 2020 Jul 13. e13171
    Autophagy regulates the localization and degradation of p16INK4a.
    Philip R Coryell, Supreet K Goraya, Katherine A Griffin, Margaret A Redick, Samuel R Sisk, Jeremy E Purvis.
      The tumor suppressor protein p16INK4a (p16) is a well-established hallmark of aging that induces cellular senescence in response to stress. Previous studies have focused primarily on p16 regulation at the transcriptional level; comparatively little is known about the protein's intracellular localization and degradation. The autophagy-lysosomal pathway has been implicated in the subcellular trafficking and turnover of various stress-response proteins and has also been shown to attenuate age-related pathologies, but it is unclear whether p16 is involved in this pathway. Here, we investigate the role of autophagy, vesicular trafficking, and lysosomal degradation on p16 expression and localization in human epithelial cells. Time-lapse fluorescence microscopy using an endogenous p16-mCherry reporter revealed that serum starvation, etoposide, and hydrogen peroxide stimulate autophagy and drive p16 recruitment to acidic cytoplasmic vesicles within 4 hr. Blocking lysosomal proteases with leupeptin and ammonium chloride resulted in the accumulation of p16 within lysosomes and increased total p16 levels suggesting that p16 is degraded by this pathway. Furthermore, autophagy blockers chloroquine and bafilomycin A1 caused p16 aggregation within stalled vesicles containing autophagosome marker LC3. Increase of p16 within these vesicles coincided with the accumulation of LC3-II. Knockdown of autophagosome chaperone p62 attenuated the formation of p16 aggregates in lysosomes, suggesting that p16 is targeted to these vesicles by p62. Taken together, these results implicate the autophagy pathway as a novel regulator of p16 degradation and localization, which could play a role in the etiology of cancer and age-related diseases.
    Keywords:  Ink4a; autophagy; lysosomes; p16
    DOI:  https://doi.org/10.1111/acel.13171
  18. Adv Exp Med Biol. 2020 ;1207 681-688
    Progress of Anti-aging Drugs Targeting Autophagy.
    Jinku Bao, Bo Liu, Chuanfang Wu.
      Senescence is a progressive process of degeneration that occurs when cells and organisms mature. Many studies have shown that autophagy is closely related to senescence. Autophagy gradually decreases with the senescence activity of cells, and vice versa. Therefore, moderate autophagy can protect the body and inhibit cell senescence. The inactivation of genes encoding nematode insulin-like tyrosine kinase receptor (daf-2) inhibited the activity of type I PI3K (age-1), Akt molecules (akt1, akt2), PDK (pdk-1), and TOR, and increased the lifespan and autophagy of Caenorhabditis elegans.
    Keywords:  Autophagy; Insulin-like/PI3K pathway; Senescence
    DOI:  https://doi.org/10.1007/978-981-15-4272-5_50
  19. Adv Exp Med Biol. 2020 ;1207 149-161
    Autophagy and Polyglutamine Disease.
    Haigang Ren, Zongbing Hao, Guanghui Wang.
      Polyglutamine (polyQ) disease is a type of fatal neurodegenerative disease caused by an expansion of CAG repeats in a specific gene, resulting in a protein with an abnormal polyQ fragment. The age of onset and the degree of pathological deterioration are related to the length of the polyQ fragment. At least 9 kinds of polyglutamine diseases have been discovered, including Huntington disease (HD), dentatorubral pallidoluysian atrophy (DRPLA), spinobulbar muscular atrophy (SBMA) and six spinocerebellar ataxia (SCA) such as SCA1, 2, 3, 6, 7 and 17 subtypes (Table 9.1). Previous studies suggest that autophagy plays a major role in the quality control of disease proteins in polyQ diseases. In this chapter, we majorly focused on three representative polyQ diseases, including spinocerebellar Ataxia type 3 (SCA3), spinocerebellar ataxia type 7 (SCA7) and Huntington's disease (HD). The relationship of the ubiquitin-proteasome system and autophagy involved in disease protein accumulation were summarized.
    Keywords:  Autophagy; Huntington’s disease; Polyglutamine disease; SCA3; SCA7
    DOI:  https://doi.org/10.1007/978-981-15-4272-5_9
  20. Hum Mol Genet. 2020 Jul 18. pii: ddaa152. [Epub ahead of print]
    Ubiquilin-2 differentially regulates polyglutamine disease proteins.
    Julia E Gerson, Nathaniel Safren, Svetlana Fischer, Ronak Patel, Emily V Crowley, Jacqueline P Welday, Alexandra K Windle, Sami Barmada, Henry L Paulson, Lisa M Sharkey.
      Divergent protein context helps explain why polyglutamine expansion diseases differ clinically and pathologically. This heterogeneity may also extend to how polyglutamine disease proteins are handled by cellular pathways of proteostasis. Studies suggest, for example, that the ubiquitin-proteasome shuttle protein Ubiquilin-2 (UBQLN2) selectively interacts with specific polyglutamine disease proteins. Here we employ cellular models, primary neurons and mouse models to investigate the potential differential regulation by UBQLN2 of two polyglutamine disease proteins, huntingtin (HTT) and ataxin-3 (ATXN3). In cells, overexpressed UBQLN2 selectively lowered levels of full-length pathogenic HTT but not of HTT exon 1 fragment or full-length ATXN3. Consistent with these results, UBQLN2 specifically reduced accumulation of aggregated mutant HTT but not mutant ATXN3 in mouse models of Huntington's disease (HD) and spinocerebellar ataxia type 3 (SCA3), respectively. Normally a cytoplasmic protein, UBQLN2 translocated to the nuclei of neurons in HD mice but not in SCA3 mice. Remarkably, instead of reducing the accumulation of nuclear mutant ATXN3, UBQLN2 induced an accumulation of cytoplasmic ATXN3 aggregates in neurons of SCA3 mice. Together these results reveal a selective action of UBQLN2 toward polyglutamine disease proteins, indicating that polyglutamine expansion alone is insufficient to promote UBQLN2-mediated clearance of this class of disease proteins. Additional factors, including nuclear translocation of UBQLN2, may facilitate its action to clear intranuclear, aggregated disease proteins like HTT.
    DOI:  https://doi.org/10.1093/hmg/ddaa152
  21. Adv Exp Med Biol. 2020 ;1207 103-110
    Autophagy and Mitochondrial Encephalomyopathies.
    Xiangnan Zhang, Yanrong Zheng, Zhong Chen.
      Mitochondrial encephalomyopathies are a group of disorders affecting skeletal muscles and brain. Although the symptoms vary among these disorders, mitochondrial DNA mutation or loss is the common characteristic. The abnormality of mitochondrial genome usually causes the dysfunction of mitochondrial respiratory and even mitochondrial damage. As a critical way of degradation, attention has been paid to the involvement of autophagy in encephalomyopathies. Autophagy is found activated in these encephalomyopathies-relevant cells as a compensatory manner to eliminate these damaged and dysfunctional mitochondria. However, accumulating evidences indicate that autophagy is incompetent to clear them. The insufficient mitophagy may ultimately accelerate cell death. Here we discuss the involvement of autophagy in encephalomyopathies based on the current evidence. We further look into the future to rescue encephalomyopathies by regulating autophagy. Only five encephalomyopathies are included in this chapter due to the availability of evidence. Nevertheless, these encephalomyopathies share a variety of common features and autophagy may also be regulated in the other encephalomyopathies.
    Keywords:  Autophagy; Encephalomyopathy; Mitochondria; Mitophagy
    DOI:  https://doi.org/10.1007/978-981-15-4272-5_6
  22. Adv Exp Med Biol. 2020 ;1207 689-697
    Drug Development and Treatment of Autophagy in Other Diseases.
    Jinku Bao, Bo Liu, Chuanfang Wu.
      In addition to tumors and aging that are associated with autophagy, many other diseases are also regulated by autophagy, including liver disease, myopathy, immune pathogen infection, cardiovascular disease, and so on. This chapter will detail the relationship between autophagy and these diseases and their underlying molecular mechanisms. We summarized the current research status of autophagy as a target for the treatment of related diseases, and prospected the development of related drugs and therapeutic strategies. We hope to provide new ideas for finding new therapeutic targets through the autophagic signaling pathways.
    Keywords:  Autophagy; Cardiovascular disease; Immune pathogen infection; Liver disease; Myopathy
    DOI:  https://doi.org/10.1007/978-981-15-4272-5_51
  23. Int J Mol Sci. 2020 Jul 15. pii: E4994. [Epub ahead of print]21(14):
    Zinc and Autophagy in Age-Related Macular Degeneration.
    Janusz Blasiak, Elzbieta Pawlowska, Jan Chojnacki, Joanna Szczepanska, Cezary Chojnacki, Kai Kaarniranta.
      Zinc supplementation is reported to slow down the progression of age-related macular degeneration (AMD), but there is no general consensus on the beneficiary effect on zinc in AMD. As zinc can stimulate autophagy that is declined in AMD, it is rational to assume that it can slow down its progression. As melanosomes are the main reservoir of zinc in the retina, zinc may decrease the number of lipofuscin granules that are substrates for autophagy. The triad zinc-autophagy-AMD could explain some controversies associated with population studies on zinc supplementation in AMD as the effect of zinc on AMD may be modulated by genetic background. This aspect was not determined in many studies regarding zinc in AMD. Zinc deficiency induces several events associated with AMD pathogenesis, including increased oxidative stress, lipid peroxidation and the resulting lipofuscinogenesis. The latter requires autophagy, which is impaired. This is a vicious cycle-like reaction that may contribute to AMD progression. Promising results with zinc deficiency and supplementation in AMD patients and animal models, as well as emerging evidence of the importance of autophagy in AMD, are the rationale for future research on the role of autophagy in the role of zinc supplementation in AMD.
    Keywords:  AMD; age-related macular degeneration; autophagy; lipofuscin; melanosomes; zinc
    DOI:  https://doi.org/10.3390/ijms21144994
  24. Adv Exp Med Biol. 2020 ;1207 469-480
    Autophagy and Acute Kidney Injury.
    Jing Cui, Xueyuan Bai, Xiangmei Chen.
      Acute kidney injury (AKI) is one of the major kidney diseases associated with poor clinical outcomes both in short- and long-term, which caused by toxins, transient ischemia, and so on. Autophagy is a cellular stress response that plays important roles in the pathogenesis of various diseases, including kidney diseases. Autophagy is induced in proximal tubules during AKI. It has been demonstrated that autophagy plays a renoprotective role in AKI by pharmacological and genetic inhibitory studies. However, the role of autophagy in kidney recovery and repair from AKI remains unknown mostly. In many studies, a dynamic change of autophagy was important for tubular proliferation and repair in the recovery phase of AKI. Moreover, autophagy may not only promote renal fibrosis through inducing tubular atrophy and decomposition but also prevent it by mediating intracellular degradation of excessive collagen in terms of renal fibrosis. In further researches, we expect to clarify the regulation of autophagy in kidney injury and repair, and find out therapeutic drugs for treating AKI and preventing its progression to chronic kidney disease.
    Keywords:  Acute kidney injury; Autophagy; Ischemia-reperfusion; Reactive oxygen species
    DOI:  https://doi.org/10.1007/978-981-15-4272-5_34
  25. J Cell Mol Med. 2020 Jul 15.
    Lysosomal dysfunction of corneal fibroblasts underlies the pathogenesis of Granular Corneal Dystrophy Type 2 and can be rescued by TFEB.
    Seung-Il Choi, Jong Hwan Woo, Eung Kweon Kim.
      Granular corneal dystrophy type 2 (GCD2) is the most common form of transforming growth factor β-induced (TGFBI) gene-linked corneal dystrophy and is pathologically characterized by the corneal deposition of mutant-TGFBIp. The defective autophagic degradation of pathogenic mutant-TGFBIp has been shown in GCD2; however, its exact mechanisms are unknown. To address this, we investigated lysosomal functions using corneal fibroblasts. Levels of cathepsins K and L (CTSK and CTSL) were significantly decreased in GCD2 cells, but of cathepsins B and D (CTSB and CTSD) did not change. The maturation of the pro-enzymes to their active forms (CTSB, CTSK and CTSL) was inhibited in GCD2 cells. CTSL enzymes directly degraded both LC3 (autophagosomes marker) and mutant-TGFBIp. Exogenous CTSL expression dramatically reduced mutant-TGFBIp in GCD2 cells, but not TGFBIp in WT cells. An increased lysosomal pH and clustered lysosomal perinuclear position were found in GCD2 cells. Transcription factor EB (TFEB) levels were significantly reduced in GCD2 cells, compared to WT. Notably, exogenous TFEB expression improved mutant-TGFBIp clearance and lysosomal abnormalities in GCD2 cells. Taken together, lysosomal dysfunction in the corneal fibroblasts underlies the pathogenesis of GCD2, and TFEB has a therapeutic potential in the treatment of GCD2.
    Keywords:  LC3 degradation; TGFBIp; autophagy; cathepsin; corneal fibroblasts; granular corneal dystrophy type 2; lysosomal pH
    DOI:  https://doi.org/10.1111/jcmm.15646
  26. Sci China Life Sci. 2020 Jul 15.
    α-Synuclein aggregation and transmission in Parkinson's disease: a link to mitochondria and lysosome.
    Rui Wang, Hongyang Sun, Haigang Ren, Guanghui Wang.
      The presence of intraneuronal Lewy bodies (LBs) and Lewy neurites (LNs) in the substantia nigra (SN) composed of aggregated α-synuclein (α-syn) has been recognized as a hallmark of pathological changes in Parkinson's disease (PD). Numerous studies have shown that aggregated α-syn is necessary for neurotoxicity. Meanwhile, the mitochondrial and lysosomal dysfunctions are associated with α-syn pathogenicity The hypothesis that α-syn transmission in the human brain contributes to the instigation and progression of PD has provided insights into PD pathology. This review will provide a brief overview of increasing researches that shed light on the relationship of α-syn aggregation with mitochondrial and lysosomal dysfunctions, and highlight recent understanding of α-syn transmission in PD pathology.
    Keywords:  Lewy pathology; aggregation; lysosome; mitochondria; transmission; α-synuclein
    DOI:  https://doi.org/10.1007/s11427-020-1756-9
  27. Cell Stress. 2020 May 19. 4(7): 167-186
    The role of lipids in autophagy and its implication in neurodegeneration.
    Sergio Hernandez-Diaz, Sandra-Fausia Soukup.
      Neurodegenerative diseases are, at present, major socio-economic burdens without effective treatments and their increasing prevalence means that these diseases will be a challenge for future generations. Neurodegenerative diseases may differ in etiology and pathology but are often caused by the accumulation of dysfunctional and aggregation-prone proteins. Autophagy, a conserved cellular mechanism, deals with cellular stress and waste product build-up and has been shown to reduce the accumulation of dysfunctional proteins in animal models of neurodegenerative diseases. Historically, progress in understanding the precise function of lipids has traditionally been far behind other biological molecules (like proteins) but emerging works demonstrate the importance of lipids in the autophagy pathway and how the disturbance of lipid metabolism is connected to neurodegeneration. Here we review how altered autophagy and the disturbance of lipid metabolism, particularly of phosphoinositols and sphingolipids, feature in neurodegenerative diseases and address work from the field that suggests that these potentially offer an opportunity of therapeutic intervention.
    Keywords:  Alzheimer's disease; Parkinson's disease; autophagy; lipids; neurodegeneration; phosphoinositols; sphingolipids
    DOI:  https://doi.org/10.15698/cst2020.07.225
  28. Adv Exp Med Biol. 2020 ;1207 265-270
    Application of Autophagy in Cardiovascular Diseases.
    Jie Du, Yulin Li, Congcong Zhang.
      Autophagy is closely related to the pathogenesis and progression of cardiovascular diseases. Autophagy may be a therapeutic target for many cardiovascular diseases. In this chapter, we will summarize autophagy activators and inhibitors as potential drugs for cardiovascular diseases.
    Keywords:  Autophagy activators; Autophagy inhibitors; Drug
    DOI:  https://doi.org/10.1007/978-981-15-4272-5_19
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