bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2021‒02‒14
38 papers selected by
Viktor Korolchuk
Newcastle University


  1. Autophagy. 2021 Feb 11.
      Mitochondria are dynamic, multifunctional cellular organelles that play a fundamental role in maintaining cellular homeostasis. Keeping the quality of mitochondria in check is of essential importance for functioning and survival of the cells. Selective autophagic clearance of flawed mitochondria, a process termed mitophagy, is one of the most prominent mechanisms through which cells maintain a healthy mitochondrial pool. The best-studied pathway through which mitophagy is exerted is the PINK1-PRKN pathway. However, an increasing number of studies have shown an existence of alternative pathways, where different proteins and lipids are able to recruit autophagic machinery independently of PINK1 and PRKN. The significance of PRKN-independent mitophagy pathways is reflected in various physiological and pathophysiological processes, but many questions regarding the regulation and the interplay between these pathways remain open. Here we review the current knowledge and recent progress made in the field of PRKN-independent mitophagy. Particularly we focus on the regulation of various receptors that participate in targeting impaired mitochondria to autophagosomes independently of PRKN.
    Keywords:  autophagy receptors; mitochondria; mitochondrial dysfunction; mitophagy; selective autophagy
    DOI:  https://doi.org/10.1080/15548627.2021.1888244
  2. Cell Death Discov. 2020 Apr 22. 6(1): 27
      Glucose is a major requirement for biological life. Its concentration is constantly sensed at the cellular level, allowing for adequate responses to any changes of glucose availability. Such responses are mediated by key sensors and signaling pathway components that adapt cellular metabolism to glucose levels. One of the major hubs of these responses is mechanistic target of rapamycin (mTOR) kinase, which forms the mTORC1 and mTORC2 protein complexes. Under physiological glucose concentrations, mTORC1 is activated and stimulates a number of proteins and enzymes involved in anabolic processes, while restricting the autophagic process. Conversely, when glucose levels are low, mTORC1 is inhibited, in turn leading to the repression of numerous anabolic processes, sparing ATP and antioxidants. Understanding how mTORC1 activity is regulated by glucose is not only important to better delineate the biological function of mTOR, but also to highlight potential therapeutic strategies for treating diseases characterized by deregulated glucose availability, as is the case of cancer. In this perspective, we depict the different sensors and upstream proteins responsible of controlling mTORC1 activity in response to changes in glucose concentration. This includes the major energy sensor AMP-activated protein kinase (AMPK), as well as other independent players. The impact of such modes of regulation of mTORC1 on cellular processes is also discussed.
    DOI:  https://doi.org/10.1038/s41420-020-0260-9
  3. Cell Discov. 2020 Feb 11. 6(1): 6
      Autophagy is a major intracellular degradation system that derives its degradative abilities from the lysosome. The most well-studied form of autophagy is macroautophagy, which delivers cytoplasmic material to lysosomes via the double-membraned autophagosome. Other forms of autophagy, namely chaperone-mediated autophagy and microautophagy, occur directly on the lysosome. Besides providing the means for degradation, lysosomes are also involved in autophagy regulation and can become substrates of autophagy when damaged. During autophagy, they exhibit notable changes, including increased acidification, enhanced enzymatic activity, and perinuclear localization. Despite their importance to autophagy, details on autophagy-specific regulation of lysosomes remain relatively scarce. This review aims to provide a summary of current understanding on the behaviour of lysosomes during autophagy and outline unexplored areas of autophagy-specific lysosome research.
    DOI:  https://doi.org/10.1038/s41421-020-0141-7
  4. Autophagy. 2021 Feb 08.
      Macroautophagy/autophagy plays a critical role in restoring/maintaining skeletal muscle function under normal conditions as well as during damage-induced regeneration. This homeostatic degradation mechanism, however, rapidly declines with aging leading to functional deterioration of skeletal muscles. ARHGEF3 is a RHOA- and RHOB-specific GEF capable of inhibiting myogenic AKT signaling independently of its GEF function. Our recent study reveals that ARHGEF3 negatively regulates skeletal muscle autophagy during injury-induced regeneration and normal aging. By enhancing autophagy, arhgef3 knockout augments the regenerative capacity of muscles in both young and regeneration-defective middle-aged mice and prevents age-related loss of muscle strength. We further show that the GEF activity of ARHGEF3 toward ROCK, but not its downstream target AKT, mediates its function in muscle regeneration. These findings suggest that ARHGEF3 may be a candidate therapeutic target for impaired muscle regeneration, age-related muscle weakness, and potentially other diseases arising from aberrant regulation of autophagy.
    Keywords:  AKT; ARHGEF3; Aging; RHOA; ROCK; autophagy; injury; regeneration; skeletal muscle; strength
    DOI:  https://doi.org/10.1080/15548627.2021.1886721
  5. Cells. 2021 Feb 10. pii: 365. [Epub ahead of print]10(2):
      Ferroptosis is one of the recently described types of cell death which is dependent on many factors, including the accumulation of iron and lipid peroxidation. Its induction requires various signaling pathways. Recent discovery of ferroptosis induction pathways stimulated by autophagy, so called autophagy-dependent ferroptosis, put our attention on the role of ferroptosis in lysosomal storage diseases (LSD). Lysosome dysfunction, observed in these diseases, may influence ferroptosis efficiency, with as yet unknown consequences for the function of cells, tissues, and organisms, due to the effects of ferroptosis on physiological and pathological metabolic processes. Modulation of levels of ferrous ions and enhanced oxidative stress, which are primary markers of ferroptosis, are often described as processes associated with the pathology of LSD. Inhibition of autophagy flux and resultant accumulation of autophagosomes in neuronopathic LSD may induce autophagy-dependent ferroptosis, indicating a considerable contribution of this process in neurodegeneration. In this review article, we describe molecular mechanisms of ferroptosis in light of LSD, underlining the modulation of levels of ferroptosis markers in these diseases. Furthermore, we propose a hypothesis about the possible involvement of autophagy-dependent ferroptosis in these disorders.
    Keywords:  autophagy-dependent ferroptosis; ferroptosis; lysosomal storage diseases; programmed cell death
    DOI:  https://doi.org/10.3390/cells10020365
  6. J Biol Chem. 2021 Feb 09. pii: S0021-9258(21)00177-0. [Epub ahead of print] 100405
      Components of the autophagy machinery are subject to regulation by various post-translational modifications. Previous studies have shown that monoubiquitination of LC3B catalyzed by the ubiquitin-activating enzyme UBA6 and ubiquitin-conjugating enzyme/ubiquitin ligase BIRC6 targets LC3B for proteasomal degradation, thus reducing LC3B levels and autophagic activity under conditions of stress. However, mechanisms capable of counteracting this process are not known. Herein, we report that LC3B ubiquitination is reversed by the action of the deubiquitinating enzyme USP10. We identified USP10 in a CRISPR-Cas9 knockout screen for ubiquitination-related genes that regulate LC3B levels. Biochemical analyses showed that silencing of USP10 reduces the levels of both the LC3B-I and LC3B-II forms of LC3B through increased ubiquitination and proteasomal degradation. In turn, the reduced LC3B levels result in slower degradation of the autophagy receptors SQSTM1 and NBR1, and an increased accumulation of puromycin-induced aggresome-like structures. Taken together, these findings indicate that the levels of LC3B and autophagic activity are controlled through cycles of LC3B ubiquitination and deubiquitination.
    Keywords:  CRISPR/Cas; LC3; USP10; autophagy; deubiquitination; protein aggregation; ubiquitin
    DOI:  https://doi.org/10.1016/j.jbc.2021.100405
  7. Cell Death Discov. 2020 Jun 08. 6(1): 45
      The Parkinson's disease (PD)-associated kinase Leucine-Rich Repeat Kinase 2 (LRRK2) is a crucial modulator of the autophagy-lysosome pathway, but unclarity exists on the precise mechanics of its role and the direction of this modulation. In particular, LRRK2 is involved in the degradation of pathological alpha-synuclein, with pathogenic mutations precipitating neuropathology in cellular and animal models of PD, and a significant proportion of LRRK2 patients presenting Lewy neuropathology. Defects in autophagic processing and lysosomal degradation of alpha-synuclein have been postulated to underlie its accumulation and onset of neuropathology. Thus, it is critical to obtain a comprehensive knowledge on LRRK2-associated pathology. Here, we investigated a G2019S-LRRK2 recombinant cell line exhibiting accumulation of endogenous, phosphorylated alpha-synuclein. We found that G2019S-LRRK2 leads to accumulation of LC3 and abnormalities in lysosome morphology and proteolytic activity in a kinase-dependent fashion, but independent from constitutively active Rab10. Notably, LRRK2 inhibition was ineffective upon upstream blockade of autophagosome-lysosome fusion events, highlighting this step as critical for alpha-synuclein clearance.
    DOI:  https://doi.org/10.1038/s41420-020-0279-y
  8. Cell Death Discov. 2020 May 01. 6(1): 32
      The transcription factor EB (TFEB) regulates the expression of target genes bearing the Coordinated Lysosomal Expression and Regulation (CLEAR) motif, thereby modulating autophagy and lysosomal biogenesis. Furthermore, TFEB can bind to the promoter of autophagy-associated genes and induce the formation of autophagosomes, autophagosome-lysosome fusion, and lysosomal cargo degradation. An increasing number of studies have shown that TFEB stimulates the intracellular clearance of pathogenic factors by enhancing autophagy and lysosomal function in multiple kidney diseases, such as cystinosis, acute kidney injury, and diabetic nephropathy. Taken together, this highlights the importance of developing novel therapeutic strategies against kidney diseases based on TFEB regulation. In this review, we present an overview of the current data on TFEB and its implication in kidney disease.
    DOI:  https://doi.org/10.1038/s41420-020-0265-4
  9. Autophagy. 2021 Feb 08. 1-3
      Together with the proteasome, macroautophagy is a main pathway for the degradation of intracellular elements. Endoplasmic reticulum (ER)-autophagy i.e. reticulophagy/ER-phagy leads to the encapsulation of pieces of the ER in forming autophagosomes. This is generally followed by fusion with lysosomes and degradation of these ER components by lysosomal hydrolases. Recent work by our group shows that ER elements could also be incorporated into late endosomes and later be released by a secretory mechanism which we will herein refer to as secretory reticulophagy/ER-phagy (SERP). In the absence of macroautophagy, such as by knocking out Atg5, SERP is more efficient, leading to an increased secretion of MAP1LC3B-II and LC3-interacting region (LIR)-containing proteins of the ER, reticulons and atlastins. In this scenario, neurites grow longer and neuronal polarity is altered. In the absence of SERP, such as by knocking out Vamp7, secretion of MAP1LC3B-II, ER-LIR containing proteins and neurite growth are severely inhibited. We argue that SERP might be a main secretory mechanism bypassing the Golgi apparatus, and that it is particularly active and important in neurite growth.
    Keywords:  ATG5; ER-phagy; VAMP7; atlastins; autophagy; extracellular vesicles; late-endosome; reticulons; secretion
    DOI:  https://doi.org/10.1080/15548627.2021.1883886
  10. Int J Mol Sci. 2021 Feb 09. pii: 1743. [Epub ahead of print]22(4):
      The aim of this review was to summarize current available information about the role of phosphatidylinositol-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling in cancer as a potential target for new therapy options. The mTOR and PI3K/AKT/mTORC1 (mTOR complex 1) signaling are critical for the regulation of many fundamental cell processes including protein synthesis, cell growth, metabolism, survival, catabolism, and autophagy, and deregulated mTOR signaling is implicated in cancer, metabolic dysregulation, and the aging process. In this review, we summarize the information about the structure and function of the mTOR pathway and discuss the mechanisms of its deregulation in human cancers including genetic alterations of PI3K/AKT/mTOR pathway components. We also present recent data regarding the PI3K/AKT/mTOR inhibitors in clinical studies and the treatment of cancer, as well the attendant problems of resistance and adverse effects.
    Keywords:  AKT; PI3K; cancer; mTOR; mutation; therapy
    DOI:  https://doi.org/10.3390/ijms22041743
  11. Biochem Cell Biol. 2021 Feb 09.
      Autophagy plays a key role in the metabolism of macromolecules by the lysosomal degradative machinery. The transcription factor EB (TFEB) regulates autophagosome biogenesis and lysosome function, and promoting TFEB activity has emerged as a potential strategy for the treatment of metabolic disorders. Here, we describe that cetrimonium bromide (CTAB), a quaternary ammonium compound, promotes autophagy and lysosomal biogenesis by inducing the nuclear translocation of TFEB in hepatic cells. shRNA-mediated TFEB knockdown inhibits CTAB-induced autophagy and lysosomal biogenesis. Mechanistically, CTAB treatment inhibits the Akt-mTORC1 signaling pathway. Moreover, CTAB treatment markedly promotes lipid metabolism in both palmitate and oleate-treated HepG2 cells, and this promotion was attenuated by the depletion of TFEB. Altogether, our results indicate that CTAB activates the autophagy-lysosome pathway by inducing the nuclear translocation of TFEB via the inhibition of mTORC1 signaling. These results deepen our understanding of TFEB function and provide new insights into CTAB-mediated lipid metabolism.
    DOI:  https://doi.org/10.1139/bcb-2020-0570
  12. Molecules. 2021 Feb 06. pii: 854. [Epub ahead of print]26(4):
      Expression levels of the major mammalian autophagy regulator Beclin 1 and its interaction with Bcl-2 regulate the switch between autophagic cell survival and apoptotic cell death pathways. However, some of the regulators and the precise mechanisms of these processes still remain elusive. Bag-1 (Bcl-2 associated athanogene-1), a member of BAG family proteins, is a multifunctional pro-survival molecule that possesses critical functions in vital cellular pathways. Herein, we report the role of Bag-1 on Bcl-2/Beclin 1 crosstalk through indirectly interacting with Beclin 1. Pull-down experiments suggested a molecular interaction between Bag-1 and Beclin 1 in breast cancer cell lines. On the other hand, in vitro binding assays showed that Bag-1/Beclin 1 interaction does not occur directly but occurs through a mediator molecule. Bag-1 interaction with p-Beclin 1 (T119), indicator of early autophagy, is increased during nutrient starvation suggesting involvement of Bag-1 in the autophagic regulation. Furthermore, CRISPR/Cas9-mediated Bag-1 knock-out in MCF-7 cells hampered cell survival and proliferation and resulted in decreased levels of total LC3 under starvation. Collectively, we suggest that Bag-1 modulates cell survival/death decision through maintaining macroautophagy as a component of Beclin 1-associated complexes.
    Keywords:  Bag-1; Bcl-2; Beclin 1; autophagy; breast cancer
    DOI:  https://doi.org/10.3390/molecules26040854
  13. Cell Death Discov. 2020 Aug 05. 6(1): 70
      Authophagy and G2/M arrest are two important mechanistic responses of cells to ionizing radiation (IR), in particular the IR-induced fibrosis. However, what interplayer and how it links the autophagy and the G2/M arrest remains elusive. Here, we demonstrate that the autophagy-related protein BECN1 plays a critical role in ionizing radiation-induced G2/M arrest. The treatment of cells with autophagy inhibitor 3-methyladenine (3-MA) at 0-12 h but not 12 h postirradiation significantly sensitized them to IR, indicating a radio-protective role of autophagy in the early response of cells to radiation. 3-MA and BECN1 disruption inactivated the G2/M checkpoint following IR by abrogating the IR-induced phosphorylation of phosphatase CDC25C and its target CDK1, a key mediator of the G2/M transition in coordination with CCNB1. Irradiation increased the nuclear translocation of BECN1, and this process was inhibited by 3-MA. We confirmed that BECN1 interacts with CDC25C and CHK2, and which is mediated the amino acids 89-155 and 151-224 of BECN1, respectively. Importantly, BECN1 deficiency disrupted the interaction of CHK2 with CDC25C and the dissociation of CDC25C from CDK1 in response to irradiation, resulting in the dephosphorylation of CDK1 and overexpression of CDK1. In summary, IR induces the translocation of BECN1 to the nucleus, where it mediates the interaction between CDC25C and CHK2, resulting in the phosphorylation of CDC25C and its dissociation from CDK1. Consequently, the mitosis-promoting complex CDK1/CCNB1 is inactivated, resulting in the arrest of cells at the G2/M transition. Our findings demonstrated that BECN1 plays a role in promotion of radiation-induced G2/M arrest through regulation of CDK1 activity. Whether such functions of BECN1 in G2/M arrest is dependent or independent on its autophagy-related roles is necessary to further identify.
    DOI:  https://doi.org/10.1038/s41420-020-00301-2
  14. Cells. 2021 Feb 05. pii: 333. [Epub ahead of print]10(2):
      Autophagy is a critical regulator of cellular survival, differentiation, development, and homeostasis, dysregulation of which is associated with diverse diseases including cancer and neurodegenerative diseases. Transcription factor EB (TFEB), a master transcriptional regulator of autophagy and lysosome, can enhance autophagic and lysosomal biogenesis and function. TFEB has attracted a lot of attention owing to its ability to induce the intracellular clearance of pathogenic factors in a variety of disease models, suggesting that novel therapeutic strategies could be based on the modulation of TFEB activity. Therefore, TFEB agonists are a promising strategy to ameliorate diseases implicated with autophagy dysfunction. Recently, several TFEB agonists have been identified and preclinical or clinical trials are applied. In this review, we present an overview of the latest research on TFEB biology and TFEB agonists.
    Keywords:  TFEB agonists; autophagy; lysosome; rapamycin; resveratrol
    DOI:  https://doi.org/10.3390/cells10020333
  15. FASEB J. 2021 Mar;35(3): e21403
      The retinal pigment epithelium (RPE) undergoes characteristic structural changes and epithelial-mesenchymal transition (EMT) during normal aging, which are exacerbated in age-related macular degeneration (AMD). Although the pathogenic mechanisms of aging and AMD remain unclear, transforming growth factor-β1 (TGF-β1) is known to induce oxidative stress, morphometric changes, and EMT as a senescence-promoting factor. In this study, we examined whether intravitreal injection of TGF-β1 into the mouse eye elicits senescence-like morphological alterations in the RPE and if this can be prevented by suppressing mammalian target of rapamycin complex 1 (mTORC1) or NADPH oxidase (NOX) signaling. We verified that intravitreal TGF-β1-induced stress fiber formation and EMT in RPE cells, along with age-associated morphometric changes, including increased variation in cell size and reduced cell density. In RPE cells, exogenous TGF-β1 increased endogenous expression of TGF-β1 and upregulated Smad3-ERK1/2-mTORC1 signaling, increasing reactive oxygen species (ROS) production and EMT. We demonstrated that inhibition of the mTORC1-NOX4 pathway by pretreatment with 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), an activator of AMP-dependent protein kinase, or GKT137831, a NOX1/4 inhibitor, decreased ROS generation, prevented stress fiber formation, attenuated EMT, and improved the regularity of the RPE structure in vitro and in vivo. These results suggest that intravitreal TGF-β1 injection could be used as a screening model to investigate the aging-related structural and functional changes to the RPE. Furthermore, the regulation of TGF-β-mTORC1-NOX signaling could be a potential therapeutic target for reducing pathogenic alterations in aged RPE and AMD.
    Keywords:  TGF-β1; epithelial-mesenchymal transition; mTORC1-NOX signaling; retinal pigment epithelium; senescence
    DOI:  https://doi.org/10.1096/fj.202001939RR
  16. Cell Mol Life Sci. 2021 Feb 13.
      Cells use mitophagy to remove dysfunctional or excess mitochondria, frequently in response to imposed stresses, such as hypoxia and nutrient deprivation. Mitochondrial cargo receptors (MCR) induced by these stresses target mitochondria to autophagosomes through interaction with members of the LC3/GABARAP family. There are a growing number of these MCRs, including BNIP3, BNIP3L, FUNDC1, Bcl2-L-13, FKBP8, Prohibitin-2, and others, in addition to mitochondrial protein targets of PINK1/Parkin phospho-ubiquitination. There is also an emerging link between mitochondrial lipid signaling and mitophagy where ceramide, sphingosine-1-phosphate, and cardiolipin have all been shown to promote mitophagy. Here, we review the upstream signaling mechanisms that regulate mitophagy, including components of the mitochondrial fission machinery, AMPK, ATF4, FoxOs, Sirtuins, and mtDNA release, and address the significance of these pathways for stress responses in tumorigenesis and metastasis. In particular, we focus on how mitophagy modulators intersect with cell cycle control and survival pathways in cancer, including following ECM detachment and during cell migration and metastasis. Finally, we interrogate how mitophagy affects tissue atrophy during cancer cachexia and therapy responses in the clinic.
    Keywords:  AMPK; ATF4; Autophagy; BCL2-L-13; BNIP3/BNIP3L; Cachexia; DRP1; Electron transport chain; FUNDC1; Fission; FoxOs; LC3/GABARAP; Metabolism; Metastasis; Mitochondria; Mitohormesis; Mitophagy; NAD+; PARP; PINK1/Parkin; ROS; Respiration; Sirtuins; UPRmt
    DOI:  https://doi.org/10.1007/s00018-021-03774-1
  17. EMBO Rep. 2021 Feb 10. e49097
      Parkin promotes cell survival by removing damaged mitochondria via mitophagy. However, although some studies have suggested that Parkin induces cell death, the regulatory mechanism underlying the dual role of Parkin remains unknown. Herein, we report that mitochondrial ubiquitin ligase (MITOL/MARCH5) regulates Parkin-mediated cell death through the FKBP38-dependent dynamic translocation from the mitochondria to the ER during mitophagy. Mechanistically, MITOL mediates ubiquitination of Parkin at lysine 220 residue, which promotes its proteasomal degradation, and thereby fine-tunes mitophagy by controlling the quantity of Parkin. Deletion of MITOL leads to accumulation of the phosphorylated active form of Parkin in the ER, resulting in FKBP38 degradation and enhanced cell death. Thus, we have shown that MITOL blocks Parkin-induced cell death, at least partially, by protecting FKBP38 from Parkin. Our findings unveil the regulation of the dual function of Parkin and provide a novel perspective on the pathogenesis of PD.
    Keywords:  E3 ubiquitin ligase; MITOL/MARCH5; Parkin; mitochondria; mitophagy
    DOI:  https://doi.org/10.15252/embr.201949097
  18. Matrix Biol. 2021 Feb 03. pii: S0945-053X(21)00013-5. [Epub ahead of print]
      Autophagy is a fundamental cellular process discovered as a response to nutrient deprivation. It provides the cellular and molecular machinery for catabolism of cellular constituents, generating energy and building blocks for continued survival. However, autophagy does much more than provide an entry into catabolic pathways, it provides a mechanism for intracellular quality control, removing damaged organelles and misfolded proteins, critical for cellular health. Autophagy serves as a counterpoint to cell growth and anabolic events, activated when growth is not possible or is suppressed. Hence, there is an inherent antagonism between autophagy and growth. Heparan sulfate modified proteins are important co-receptors that generally promote growth factor activity and are therefore positioned within signaling networks that inhibit, or negatively regulate autophagy levels. This review summarizes evidence that heparan sulfate modified proteins provide an evolutionarily conserved inhibitory modulation of autophagy that can have profound effects on cell physiology and organismal responses to stress.
    Keywords:  Parkinson's Disease; TDP-43; autophagy; endocytosis; heparan sulfate modified proteins; mitophagy; neurodegenerative disease
    DOI:  https://doi.org/10.1016/j.matbio.2021.01.006
  19. J Biochem. 2021 Feb 12. pii: mvab017. [Epub ahead of print]
      Autophagy, which is an evolutionarily conserved intracellular degradation system, involves de novo generation of autophagosomes that sequester and deliver diverse cytoplasmic materials to the lysosome for degradation. Autophagosome formation is mediated by approximately 20 core autophagy-related (Atg) proteins, which collaborate to mediate complicated membrane dynamics during autophagy. To elucidate the molecular functions of these Atg proteins in autophagosome formation, many researchers have tried to determine the structures of Atg proteins by using various structural biological methods. Although not sufficient, the basic structural catalog of all core Atg proteins was established. In this review article, we summarize structural biological studies of core Atg proteins, with an emphasis on recently unveiled structures, and describe the mechanistic breakthroughs in autophagy research that have derived from new structural information.
    Keywords:  Atg proteins; autophagosome; autophagy; phase separation; structural biology
    DOI:  https://doi.org/10.1093/jb/mvab017
  20. Bone. 2021 Feb 09. pii: S8756-3282(21)00043-0. [Epub ahead of print] 115881
      Bone is an active organ that is continuously remodeled throughout life via formation and resorption; therefore, a fine-tuned bone (re)modeling is crucial for bone homeostasis and is closely connected with energy metabolism. Amino acids are essential for various cellular functions as well as an energy source, and their synthesis and catabolism (e.g., metabolism of carbohydrates and fatty acids) are regulated through numerous enzymatic cascades. In addition, the intracellular levels of amino acids are maintained by autophagy, a cellular recycling system for proteins and organelles; under nutrient deprivation conditions, autophagy is strongly induced to compensate for cellular demands and to restore the amino acid pool. Metabolites derived from amino acids are known to be precursors of bioactive molecules such as second messengers and neurotransmitters, which control various cellular processes, including cell proliferation, differentiation, and homeostasis. Thus, amino acid metabolism and autophagy are tightly and reciprocally regulated in our bodies. This review discusses the current knowledge and potential links between bone diseases and deficiencies in amino acid metabolism and autophagy.
    Keywords:  Amino acid metabolism; Autophagy; Bone; Bone formation; Bone homeostasis
    DOI:  https://doi.org/10.1016/j.bone.2021.115881
  21. Cells. 2021 Jan 29. pii: 262. [Epub ahead of print]10(2):
      Neurodegenerative disorders are spreading worldwide and are one of the greatest threats to public health. There is currently no adequate therapy for these disorders, and therefore there is an urgent need to accelerate the discovery and development of effective treatments. Although neurodegenerative disorders are broad ranging and highly complex, they may share overlapping mechanisms, and thus potentially manifest common targets for therapeutic interventions. Glycogen synthase kinase-3 (GSK-3) is now acknowledged to be a central player in regulating mood behavior, cognitive functions, and neuron viability. Indeed, many targets controlled by GSK-3 are critically involved in progressing neuron deterioration and disease pathogenesis. In this review, we focus on three pathways that represent prominent mechanisms linking GSK-3 with neurodegenerative disorders: cytoskeleton organization, the mammalian target of rapamycin (mTOR)/autophagy axis, and mitochondria. We also consider the challenges and opportunities in the development of GSK-3 inhibitors for treating neurodegeneration.
    Keywords:  GSK-3; GSK-3 inhibitors; autophagy; lysosome; mTOR; microtubules; mitochondria; neurodegeneration
    DOI:  https://doi.org/10.3390/cells10020262
  22. EMBO Rep. 2021 Feb 08. e50629
      Mitophagy is an essential cellular autophagic process that selectively removes superfluous and damaged mitochondria, and it is coordinated with mitochondrial biogenesis to fine tune the quantity and quality of mitochondria. Coordination between these two opposing processes to maintain the functional mitochondrial network is of paramount importance for normal cellular and organismal metabolism. However, the underlying mechanism is not completely understood. Here we report that PGC-1α and nuclear respiratory factor 1 (NRF1), master regulators of mitochondrial biogenesis and metabolic adaptation, also transcriptionally upregulate the gene encoding FUNDC1, a previously characterized mitophagy receptor, in response to cold stress in brown fat tissue. NRF1 binds to the classic consensus site in the promoter of Fundc1 to upregulate its expression and to enhance mitophagy through its interaction with LC3. Specific knockout of Fundc1 in BAT results in reduced mitochondrial turnover and accumulation of functionally compromised mitochondria, leading to impaired adaptive thermogenesis. Our results demonstrate that FUNDC1-dependent mitophagy is directly coupled with mitochondrial biogenesis through the PGC-1α/NRF1 pathway, which dictates mitochondrial quantity, quality, and turnover and contributes to adaptive thermogenesis.
    Keywords:  adaptive thermogenesis; brown adipose tissue; mitochondrial biogenesis; mitophagy
    DOI:  https://doi.org/10.15252/embr.202050629
  23. Dev Cell. 2021 Feb 08. pii: S1534-5807(21)00038-1. [Epub ahead of print]56(3): 251-252
      Niemann-Pick type C is a neurological disorder caused by mutations in the lysosome cholesterol exporter NPC1. In this issue of Developmental Cell, Davis et al. dissect how NPC1 loss elevates mTORC1 signaling, and demonstrate that suppression of mTORC1 signaling can rescue disease pathology in NPC1-deficient cell models.
    DOI:  https://doi.org/10.1016/j.devcel.2021.01.007
  24. Biochim Biophys Acta Mol Cell Biol Lipids. 2021 Feb 09. pii: S1388-1981(21)00029-9. [Epub ahead of print] 158903
      Phosphoinositides are key lipids in eukaryotes, regulating organelles' identity and function. Their synthesis and turnover require specific phosphorylation/dephosphorylation events that are ensured by dedicated lipid kinases and phosphatases, which modulate the structure of the inositol ring by adding or removing phosphates on positions 3, 4 or 5. Beside their implication in intracellular signalization and cytoskeleton dynamics, phosphoinositides are essential for vesicular transport along intracellular trafficking routes, by providing molecular scaffolds to membrane related events such as budding, fission or fusion. Robust and detailed literature demonstrated that some members of the phosphoinositides family are crucial for the autophagy pathway, acting as fine tuners and regulators. In this review, we discuss the known functions of phosphoinositides in autophagy canonical processes, such as during autophagosome formation, as well as the importance of phosphoinositides in organelle-based processes directly connected to the autophagic machinery, such as endosomal dynamics, ciliogenesis and innate immunity.
    Keywords:  autophagy; membranes; phosphoinositides
    DOI:  https://doi.org/10.1016/j.bbalip.2021.158903
  25. Trends Cell Biol. 2021 Feb 08. pii: S0962-8924(21)00009-X. [Epub ahead of print]
      Autophagy and the ubiquitin-proteasome system (UPS) are two major pathways for protein degradation. The cullin-RING E3 ligases (CRLs) are the largest E3 ligase family and have key biological functions in maintaining protein homeostasis. We provide an updated review of the interactions between CRLs and autophagy, focusing on the regulatory effects of CRLs on the core autophagy machinery that consists of several autophagy-related protein (ATG) complexes and their key upstream signaling pathways. The involvement of such functional interactions in health and disease is also discussed. Understanding the role of CRLs in autophagy is helpful for the development of therapeutic strategies for diseases in which CRLs and autophagy are dysregulated, such as cancer and neurodegenerative conditions.
    Keywords:  MTORC1; autophagy; cancer; cullin-RING E3 ligases; neddylation; ubiquitination
    DOI:  https://doi.org/10.1016/j.tcb.2021.01.005
  26. J Drug Target. 2021 Feb 08. 1-16
      Mitophagy is a selective form of macroautophagy in which dysfunctional and damaged mitochondria can be efficiently degraded, removed and recycled through autophagy. Selective removal of damaged or fragmented mitochondria is critical to the functional integrity of the entire mitochondrial network and cells. In past decades, numerous studies have shown that mitophagy is involved in various diseases; however, since the dual role of mitophagy in tumour development, mitophagy role in tumour is controversial, and further elucidation is needed. That is, although mitophagy has been demonstrated to contribute to carcinogenesis, cell migration, ferroptosis inhibition, cancer stemness maintenance, tumour immune escape, drug resistance, etc. during cancer progression, many research also shows that to promote cancer cell death, mitophagy can be induced physiologically or pharmacologically to maintain normal cellular metabolism and prevent cell stress responses and genome damage by diminishing mitochondrial damage, thus suppressing tumour development accompanying these changes. Signalling pathway-specific molecular mechanisms are currently of great biological significance in the identification of potential therapeutic targets. Here, we review recent progress of molecular pathways mediating mitophagy including both canonical pathways (Parkin/PINK1- and FUNDC1-mediated mitophagy) and noncanonical pathways (FKBP8-, Nrf2-, and DRP1-mediated mitophagy); and the regulation of these pathways, and abovementioned pro-cancer and pro-death roles of mitophagy. Finally, we summarise the role of mitophagy in cancer therapy. Mitophagy can potentially be acted as the target for cancer therapy by promotion or inhibition.
    Keywords:  LC3; Mitophagy; PINK1; cancer; parkin
    DOI:  https://doi.org/10.1080/1061186X.2020.1867992
  27. Cell Biosci. 2021 Feb 08. 11(1): 35
      Autophagy is a conserved cellular degradation process in eukaryotes that facilitates the recycling and reutilization of damaged organelles and compartments. It plays a pivotal role in cellular homeostasis, pathophysiological processes, and diverse diseases in humans. Autophagy involves dynamic crosstalk between different stages associated with intracellular vesicle trafficking. Golgi apparatus is the central organelle involved in intracellular vesicle trafficking where Golgi-associated Rab GTPases function as important mediators. This review focuses on the recent findings that highlight Golgi-associated Rab GTPases as master regulators of autophagic flux. The scope for future research in elucidating the role and mechanism of Golgi-associated Rab GTPases in autophagy and autophagy-related diseases is discussed further.
    Keywords:  Autophagy; Golgi; Rab GTPase; Vesicle trafficking
    DOI:  https://doi.org/10.1186/s13578-021-00543-2
  28. Trends Biochem Sci. 2021 Feb 05. pii: S0968-0004(21)00006-2. [Epub ahead of print]
      The ATG8 family proteins are critical players in autophagy, a cytoprotective process that mediates degradation of cytosolic cargo. During autophagy, ATG8s conjugate to autophagosome membranes to facilitate cargo recruitment, autophagosome biogenesis, transport, and fusion with lysosomes, for cargo degradation. In addition to these canonical functions, recent reports demonstrate that ATG8s are also delivered to single-membrane organelles, which leads to highly divergent degradative or secretory fates, vesicle maturation, and cargo specification. The association of ATG8s with different vesicles involves complex regulatory mechanisms still to be fully elucidated. Whether individual ATG8 family members play unique canonical or non-canonical roles, also remains unclear. This review summarizes the many open molecular questions regarding ATG8s that are only beginning to be unraveled.
    Keywords:  GABARAP; LC3; LC3-associated phagocytosis; multivesicular bodies; non-canonical autophagy; unconventional secretion
    DOI:  https://doi.org/10.1016/j.tibs.2021.01.004
  29. Biomedicines. 2021 Jan 29. pii: 130. [Epub ahead of print]9(2):
      Enhanced oxidative stress is closely related to aging and impaired metabolic health and is influenced by diet-derived nutrients and energy. Recent studies have shown that methionine restriction (MetR) is related to longevity and metabolic health in organisms from yeast to rodents. The effect of MetR on lifespan extension and metabolic health is mediated partially through a reduction in oxidative stress. Methionine metabolism is involved in the supply of methyl donors such as S-adenosyl-methionine (SAM), glutathione synthesis and polyamine metabolism. SAM, a methionine metabolite, activates mechanistic target of rapamycin complex 1 and suppresses autophagy; therefore, MetR can induce autophagy. In the process of glutathione synthesis in methionine metabolism, hydrogen sulfide (H2S) is produced through cystathionine-β-synthase and cystathionine-γ-lyase; however, MetR can induce increased H2S production through this pathway. Similarly, MetR can increase the production of polyamines such as spermidine, which are involved in autophagy. In addition, MetR decreases oxidative stress by inhibiting reactive oxygen species production in mitochondria. Thus, MetR can attenuate oxidative stress through multiple mechanisms, consequently associating with lifespan extension and metabolic health. In this review, we summarize the current understanding of the effects of MetR on lifespan extension and metabolic health, focusing on the reduction in oxidative stress.
    Keywords:  autophagy; lifespan extension; metabolic health; methionine restriction; oxidative stress
    DOI:  https://doi.org/10.3390/biomedicines9020130
  30. Biomedicines. 2021 Feb 04. pii: 149. [Epub ahead of print]9(2):
      During the past few decades, considerable efforts have been made to discover and validate new molecular mechanisms and biomarkers of neurodegenerative diseases. Recent discoveries have demonstrated how autophagy and its specialized form mitophagy are extensively associated with the development, maintenance, and progression of several neurodegenerative diseases. These mechanisms play a pivotal role in the homeostasis of neural cells and are responsible for the clearance of intracellular aggregates and misfolded proteins and the turnover of organelles, in particular, mitochondria. In this review, we summarize recent advances describing the importance of autophagy and mitophagy in neurodegenerative diseases, with particular attention given to multiple sclerosis, Parkinson's disease, and Alzheimer's disease. We also review how elements involved in autophagy and mitophagy may represent potential biomarkers for these common neurodegenerative diseases. Finally, we examine the possibility that the modulation of autophagic and mitophagic mechanisms may be an innovative strategy for overcoming neurodegenerative conditions. A deeper knowledge of autophagic and mitophagic mechanisms could facilitate diagnosis and prognostication as well as accelerate the development of therapeutic strategies for neurodegenerative diseases.
    Keywords:  Alzheimer’s disease; Parkinson’s disease; autophagy; biomarker; mitophagy; multiple sclerosis; neurodegeneration; therapy
    DOI:  https://doi.org/10.3390/biomedicines9020149
  31. Neuroscience. 2021 Feb 09. pii: S0306-4522(21)00071-3. [Epub ahead of print]
      Ubiquitin specific protease (USP)-13 is a de-ubiquitinase member of the cysteine-dependent protease superfamily that cleaves ubiquitin off protein substrates to reverse ubiquitin-mediated protein degradation. Several findings implicate USPs in neurodegeneration. Ubiquitin targets proteins to major degradation pathways, including the proteasome and the lysosome. In melanoma cells, USP13 regulates the degradation of several proteins primarily via ubiquitination and de-ubiquitination. However, the significance of USP13 in regulating protein clearance in neurodegeneration is largely unknown. This mini-review summarizes the most recent evidence pertaining to the role of USP13 in protein clearance via autophagy and the proteasome in neurodegenerative diseases.
    Keywords:  USP13; autophagy; neurodegenerative diseases; ubiquitin
    DOI:  https://doi.org/10.1016/j.neuroscience.2021.02.004
  32. Biochem Biophys Res Commun. 2021 Feb 06. pii: S0006-291X(21)00121-2. [Epub ahead of print]545 183-188
      The mechanistic target of rapamycin complex 1 (mTORC1) signaling is the prototypical pathway regulating protein synthesis and cell proliferation. The level of mTORC1 activity is high in intestinal stem cells located at the base of the crypts and thought to gradually decrease as transit-amplifying cells migrate out of the crypts and differentiate into enterocytes, goblet cells or enteroendocrine cells along the epithelium. The unknown mechanism responsible for the silencing of intestinal epithelium mTORC1 during cell differentiation was investigated in Caco-2 cells, which spontaneously differentiate into enterocytes in standard growth medium. The results show that TSC2, an upstream negative regulator of mTORC1 was central to mTORC1 silencing in differentiated Caco-2 cells. AMPK-mediated activation of TSC2 (Ser1387) and repression of Raptor (Ser792), an essential component of mTORC1, were stimulated in differentiated Caco-2 cells. ERK1/2-mediated repression of TSC2 (Ser664) seen in undifferentiated Caco-2 cells was lifted in differentiated cells. IRS-1-mediated activation of AKT (Thr308) phosphorylation was stimulated in differentiated Caco-2 cells and may be involved in cross-pathway repression of ERK1/2. Additionally, PRAS40 (Thr246) phosphorylation was decreased in differentiated Caco-2 cells compared to undifferentiated cells allowing dephosphorylated PRAS40 to displace Raptor thereby repressing mTORC1 kinase activity.
    Keywords:  AKT; ERK; Enterocyte; PRAS40; Raptor; Tight junction protein
    DOI:  https://doi.org/10.1016/j.bbrc.2021.01.070
  33. Front Cell Dev Biol. 2020 ;8 620409
      The skeletal muscle tissue in the adult is relatively stable under normal conditions but retains a striking ability to regenerate by its resident stem cells (satellite cells). Satellite cells exist in a quiescent (G0) state; however, in response to an injury, they reenter the cell cycle and start proliferating to provide sufficient progeny to form new myofibers or undergo self-renewal and returning to quiescence. Maintenance of satellite cell quiescence and entry of satellite cells into the activation state requires autophagy, a fundamental degradative and recycling process that preserves cellular proteostasis. With aging, satellite cell regenerative capacity declines, correlating with loss of autophagy. Enhancing autophagy in aged satellite cells restores their regenerative functions, underscoring this proteostatic activity's relevance for tissue regeneration. Here we describe two strategies for assessing autophagic activity in satellite cells from GFP-LC3 reporter mice, which allows direct autophagosome labeling, or from non-transgenic (wild-type) mice, where autophagosomes can be immunostained. Treatment of GFP-LC3 or WT satellite cells with compounds that interfere with autophagosome-lysosome fusion enables measurement of autophagic activity by flow cytometry and immunofluorescence. Thus, the methods presented permit a relatively rapid assessment of autophagy in stem cells from skeletal muscle in homeostasis and in different pathological scenarios such as regeneration, aging or disease.
    Keywords:  autophagy; flow cytometry; immunofluorescence; quiescence; regeneration; satellite cell; skeletal muscle; stem cell
    DOI:  https://doi.org/10.3389/fcell.2020.620409
  34. Biochim Biophys Acta Mol Cell Res. 2021 Feb 04. pii: S0167-4889(21)00038-0. [Epub ahead of print] 118984
      Protein aggregation is a hallmark of neurodegenerative diseases. However, the mechanism that induces pathogenic aggregation is not well understood. Recently, it has emerged that several of the pathological proteins found in an aggregated or mislocalized state in neurodegenerative diseases are also able to undergo liquid-liquid phase separation under physiological conditions. Although these phase transitions are important for various physiological functions, neurodegenerative disease-related mutations and conditions can alter the LLPS behavior of these proteins, which can elicit toxicity. Therefore, therapeutics that antagonize aberrant LLPS may be able to mitigate toxicity and aggregation that is ubiquitous in neurodegenerative disease. Here, we discuss the mechanisms by which aberrant protein phase transitions may contribute to neurodegenerative disease. We also outline potential therapeutic strategies to counter deleterious phases.
    Keywords:  FUS; RNA-binding proteins; TDP-43; intrinsically disordered proteins; liquid-liquid phase separation; tau; α-synuclein
    DOI:  https://doi.org/10.1016/j.bbamcr.2021.118984
  35. J Cell Biol. 2021 Apr 05. pii: e201912060. [Epub ahead of print]220(4):
      The target of rapamycin complex 1 (TORC1) is mainly localized to the vacuolar membrane and regulates eukaryotic cell growth in response to nutrient availability. To obtain deeper insights into the functional roles of TORC1, we performed a genome-wide analysis of the TORC1 interactome in yeast using the bimolecular fluorescence complementation (BiFC) assay. We found that while most of the BiFC signals are observed at the vacuolar membrane, a fraction of them are detected at cytoplasmic messenger ribonucleoprotein (mRNP) granules. Moreover, mRNA-binding proteins are enriched in the TORC1 interactome, suggesting a functional relationship between TORC1 and mRNA metabolism. We show that a portion of TORC1 is consistently associated with mRNP complexes and interacts with a specific subset of mRNAs. We also demonstrate that TORC1 directly targets a translational repressor Scd6 and that the activity of Scd6 is inhibited by TORC1-dependent phosphorylation. Collectively, our data suggest that TORC1 plays a novel role in posttranscriptional regulation by controlling the activity of Scd6.
    DOI:  https://doi.org/10.1083/jcb.201912060
  36. Drug Discov Today. 2021 Feb 04. pii: S1359-6446(21)00064-7. [Epub ahead of print]
      Obesity is positively correlated with a variety of metabolic disorders. Autophagy is the major recycling process in adipocytes, dynamically regulating adipogenesis, lipid mobilization, and browning. miRNAs, a class of endogenous small noncoding RNAs, participate in each step of autophagy. Autophagy-regulating miRNAs are crucial for lipid homeostasis and proper adipocyte functioning. Herein, we summarize our current understanding of autophagy-regulating miRNAs related to obesity, as well as their specific targets. Autophagy-regulating miRNAs might fill crucial gaps in our understanding of the nature of obesity and provide promising targets for the diagnosis and treatment of obesity-related metabolic disorders.
    DOI:  https://doi.org/10.1016/j.drudis.2021.01.033
  37. Biochim Biophys Acta Gen Subj. 2021 Feb 08. pii: S0304-4165(21)00030-1. [Epub ahead of print] 129871
      PINK1, a serine/threonine ubiquitin kinase, and Parkin, an E3 ubiquitin ligase, work in coordination to target damaged mitochondria to the lysosome in a process called mitophagy. This review will cover what we have learned from PINK1 and Parkin knockout (KO) mice. Systemic PINK1 and Parkin KO mouse models haven't faithfully recapitulated early onset forms of Parkinson's disease found in humans with recessive mutations in these genes. However, the utilization of these mouse models has given us insight into how PINK1 and Parkin contribute to mitochondrial quality control and function in different tissues beyond the brain such as in heart and adipose tissue. Although PINK1 and Parkin KO mice have been generated over a decade ago, these models are still being used today to creatively elucidate cell-type specific functions. Recently, these mouse models have uncovered that these proteins contribute to innate immunity and cancer phenotypes.
    Keywords:  PINK1; Parkin; knockout mouse; mitophagy
    DOI:  https://doi.org/10.1016/j.bbagen.2021.129871
  38. Cells. 2021 Jan 31. pii: 283. [Epub ahead of print]10(2):
      Parkin and α-synuclein are two key proteins involved in the pathophysiology of Parkinson's disease (PD). Neurotoxic alterations of α-synuclein that lead to the formation of toxic oligomers and fibrils contribute to PD through synaptic dysfunction, mitochondrial impairment, defective endoplasmic reticulum and Golgi function, and nuclear dysfunction. In half of the cases, the recessively inherited early-onset PD is caused by loss of function mutations in the PARK2 gene that encodes the E3-ubiquitin ligase, parkin. Parkin is involved in the clearance of misfolded and aggregated proteins by the ubiquitin-proteasome system and regulates mitophagy and mitochondrial biogenesis. PARK2-related PD is generally thought not to be associated with Lewy body formation although it is a neuropathological hallmark of PD. In this review article, we provide an overview of post-mortem neuropathological examinations of PARK2 patients and present the current knowledge of a functional interaction between parkin and α-synuclein in the regulation of protein aggregates including Lewy bodies. Furthermore, we describe prevailing hypotheses about the formation of intracellular micro-aggregates (synuclein inclusions) that might be more likely than Lewy bodies to occur in PARK2-related PD. This information may inform future studies aiming to unveil primary signaling processes involved in PD and related neurodegenerative disorders.
    Keywords:  Lewy bodies; PARK2; familial Parkinson’s disease; parkin; α-synuclein
    DOI:  https://doi.org/10.3390/cells10020283