bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2022–10–30
fifty papers selected by
Viktor Korolchuk, Newcastle University
  1. The mechanisms and roles of selective autophagy in mammals.
  2. Digest it all: the lysosomal turnover of cytoplasmic aggregates.
  3. Phospholipid imbalance impairs autophagosome completion.
  4. A method for the isolation and characterization of autophagic bodies from yeast provides a key tool to investigate cargos of autophagy.
  5. Autophagic perturbation caused by reduced lysosomal activity positively regulates cell competition.
  6. Autophagy controls Wolbachia infection upon bacterial damage and in aging Drosophila.
  7. Many roads lead to CASM: Diverse stimuli of noncanonical autophagy share a unifying molecular mechanism.
  8. Autophagy in Cancer: A Metabolic Perspective.
  9. PTP4A2 promotes lysophagy by dephosphorylation of VCP/p97 at Tyr805.
  10. Discovery of Mitophagy Inhibitors with Therapeutic Potential in Different Familial Amyotrophic Lateral Sclerosis Mutations.
  11. Targeting Deubiquitinating Enzymes (DUBs) That Regulate Mitophagy via Direct or Indirect Interaction with Parkin.
  12. mTORC1 beyond anabolic metabolism: Regulation of cell death.
  13. LC3-dependent EV loading and secretion (LDELS) promotes TFRC (transferrin receptor) secretion via extracellular vesicles.
  14. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS.
  15. Regulation of α-synuclein homeostasis and inflammasome activation by microglial autophagy.
  16. Mitochondrial proteotoxicity: implications and ubiquitin-dependent quality control mechanisms.
  17. Mitophagy in the aging nervous system.
  18. DEFECTS IN PINK1-PRKN-PARK7/DJ-1-DEPENDENT MITOPHAGY AND AUTOSOMAL RECESSIVE PARKINSON DISEASE.
  19. Acyl-CoA binding protein regulates nutrient-dependent autophagy.
  20. mTOR as a Potential Target for the Treatment of Microbial Infections, Inflammatory Bowel Diseases, and Colorectal Cancer.
  21. Insulin-induced mTOR signaling and gluconeogenesis in renal proximal tubules: A mini-review of current evidence and therapeutic potential.
  22. Inhibition of autophagy with chloroquine dysregulates mitochondrial quality control and energetics in adipocytes.
  23. Mitophagy-A New Target of Bone Disease.
  24. Beyond autophagy: LC3-associated phagocytosis and endocytosis.
  25. Mitochondrial Dysfunction, Mitophagy and Their Correlation with Perinatal Complications: Preeclampsia and Low Birth Weight.
  26. Editorial: Apoptosis, autophagy, and mitophagy dysfunction in Alzheimer's disease: Evolving emergence and mechanisms.
  27. Cryo-EM structure of the SEA complex.
  28. PINK1-PRKN mediated mitophagy: differences between in vitro and in vivo models.
  29. Autophagy: a game changer for plant development and crop improvement.
  30. A cell-based chemical-genetic screen for amino acid stress response inhibitors reveals torins reverse stress kinase GCN2 signaling.
  31. The autophagy inducer SMER28 attenuates microtubule dynamics mediating neuroprotection.
  32. Lysosomal positioning diseases: beyond substrate storage.
  33. The Emerging Role of Extracellular Vesicles and Autophagy Machinery in NASH-Future Horizons in NASH Management.
  34. TBK1 inhibitors enhance transfection efficiency by suppressing p62/SQSTM1 phosphorylation.
  35. GATOR2-dependent mTORC1 activity is a therapeutic vulnerability in FOXO1 fusion positive rhabdomyosarcoma.
  36. Adiponectin Protects Hypoxia/Reoxygenation-Induced Cardiomyocyte Injury by Suppressing Autophagy.
  37. TDP-43 Toxicity in Yeast Is Associated with a Reduction in Autophagy, and Deletions of TIP41 and PBP1 Counteract These Effects.
  38. Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis.
  39. Adipokines as Regulators of Autophagy in Obesity-Linked Cancer.
  40. PITTching in for lysosome repair.
  41. In human astrocytes neurotropic flaviviruses increase autophagy, yet their replication is autophagy-independent.
  42. The Relationship between DUGBE Virus Infection and Autophagy in Epithelial Cells.
  43. Autophagy in Hematological Malignancies.
  44. Akt Inhibition Promotes Autophagy and Clearance of Group B Streptococcus from the Alveolar Epithelium.
  45. Microglial autophagy in cerebrovascular diseases.
  46. The SAR and action mechanisms of autophagy inhibitors that eliminate drug resistance.
  47. mTOR Contributes to the Proteome Diversity through Transcriptome-Wide Alternative Splicing.
  48. The oncoprotein MUC1 facilitates breast cancer progression by promoting Pink1-dependent mitophagy via ATAD3A destabilization.
  49. Ablation of endothelial Atg7 inhibits ischemia-induced angiogenesis by upregulating Stat1 that suppresses Hif1a expression.
  50. Control of infection by LC3-associated phagocytosis, CASM, and detection of raised vacuolar pH by the V-ATPase-ATG16L1 axis.
  1. Nat Rev Mol Cell Biol. 2022 Oct 27.
    The mechanisms and roles of selective autophagy in mammals.
    Jose Norberto S Vargas, Maho Hamasaki, Tsuyoshi Kawabata, Richard J Youle, Tamotsu Yoshimori.
      Autophagy is a process that targets various intracellular elements for degradation. Autophagy can be non-selective - associated with the indiscriminate engulfment of cytosolic components - occurring in response to nutrient starvation and is commonly referred to as bulk autophagy. By contrast, selective autophagy degrades specific targets, such as damaged organelles (mitophagy, lysophagy, ER-phagy, ribophagy), aggregated proteins (aggrephagy) or invading bacteria (xenophagy), thereby being importantly involved in cellular quality control. Hence, not surprisingly, aberrant selective autophagy has been associated with various human pathologies, prominently including neurodegeneration and infection. In recent years, considerable progress has been made in understanding mechanisms governing selective cargo engulfment in mammals, including the identification of ubiquitin-dependent selective autophagy receptors such as p62, NBR1, OPTN and NDP52, which can bind cargo and ubiquitin simultaneously to initiate pathways leading to autophagy initiation and membrane recruitment. This progress opens the prospects for enhancing selective autophagy pathways to boost cellular quality control capabilities and alleviate pathology.
    DOI:  https://doi.org/10.1038/s41580-022-00542-2
  2. Trends Biochem Sci. 2022 Oct 21. pii: S0968-0004(22)00271-7. [Epub ahead of print]
    Digest it all: the lysosomal turnover of cytoplasmic aggregates.
    Mario Mauthe, Harm H Kampinga, Mark S Hipp, Fulvio Reggiori.
      Aggrephagy describes the selective lysosomal transport and turnover of cytoplasmic protein aggregates by macro-autophagy. In this process, protein aggregates and conglomerates are polyubiquitinated and then sequestered by autophagosomes. Soluble selective autophagy receptors (SARs) are central to aggrephagy and physically bind to both ubiquitin and the autophagy machinery, thus linking the cargo to the forming autophagosomal membrane. Because the accumulation of protein aggregates is associated with cytotoxicity in several diseases, a better molecular understanding of aggrephagy might provide a conceptual framework to develop therapeutic strategies aimed at delaying the onset of these pathologies by preventing the buildup of potentially toxic aggregates. We review recent advances in our knowledge about the mechanism of aggrephagy.
    Keywords:  cellular protein quality control; chaperone-mediated autophagy; macro-autophagy; micro-autophagy; p62 bodies; selective autophagy receptors
    DOI:  https://doi.org/10.1016/j.tibs.2022.09.012
  3. EMBO J. 2022 Oct 27. e110771
    Phospholipid imbalance impairs autophagosome completion.
    Alexandra Polyansky, Oren Shatz, Milana Fraiberg, Eyal Shimoni, Tali Dadosh, Muriel Mari, Fulvio M Reggiori, Chao Qin, Xianlin Han, Zvulun Elazar.
      Autophagy, a conserved eukaryotic intracellular catabolic pathway, maintains cell homeostasis by lysosomal degradation of cytosolic material engulfed in double membrane vesicles termed autophagosomes, which form upon sealing of single-membrane cisternae called phagophores. While the role of phosphatidylinositol 3-phosphate (PI3P) and phosphatidylethanolamine (PE) in autophagosome biogenesis is well-studied, the roles of other phospholipids in autophagy remain rather obscure. Here we utilized budding yeast to study the contribution of phosphatidylcholine (PC) to autophagy. We reveal for the first time that genetic loss of PC biosynthesis via the CDP-DAG pathway leads to changes in lipid composition of autophagic membranes, specifically replacement of PC by phosphatidylserine (PS). This impairs closure of the autophagic membrane and autophagic flux. Consequently, we show that choline-dependent recovery of de novo PC biosynthesis via the CDP-choline pathway restores autophagosome formation and autophagic flux in PC-deficient cells. Our findings therefore implicate phospholipid metabolism in autophagosome biogenesis.
    Keywords:  autophagosome biogenesis; autophagy; phagophore; phospholipids
    DOI:  https://doi.org/10.15252/embj.2022110771
  4. J Biol Chem. 2022 Oct 25. pii: S0021-9258(22)01084-5. [Epub ahead of print] 102641
    A method for the isolation and characterization of autophagic bodies from yeast provides a key tool to investigate cargos of autophagy.
    Tomoko Kawamata, Shiho Makino, Yoko Kagohashi, Michiko Sasaki, Yoshinori Ohsumi.
      Autophagy is a major cellular degradation pathway that is highly conserved among eukaryotes. The identification of cargos captured by autophagosomes is critical to our understanding of the physiological significance of autophagy in cells, but these studies can be challenging because autophagosomes disintegrate easily. In the yeast S. cerevisiae, cells deficient in the vacuolar lipase Atg15 accumulate autophagic bodies (ABs) within the vacuole following the induction of autophagy. As ABs contain cytosolic components including proteins, RNAs, and lipids, their purification allows the identification of material targeted by autophagy for degradation. In this study, we demonstrate a method to purify intact ABs using isolated vacuoles from atg15Δ cells. Taking advantage of the size discrepancy between the vacuoles and ABs, the vacuolar membrane was disrupted by filtration to release ABs. Filtered vacuolar lysates were subjected to density gradient centrifugation to obtain AB fractions. Purified ABs retain membrane integrity and contain autophagic cargos. This technique offers a valuable tool for the identification of the cargos of autophagy, examination of autophagic cargo selectivity, and biochemical characterization of autophagosome membranes.
    Keywords:  autophagic bodies; autophagy; degradation; starvation; yeast
    DOI:  https://doi.org/10.1016/j.jbc.2022.102641
  5. Autophagy. 2022 Oct 26.
    Autophagic perturbation caused by reduced lysosomal activity positively regulates cell competition.
    Eilma Akter, Shunsuke Kon.
      Newly emerging transformed epithelial cells are recognized and apically removed by surrounding normal cells through a biological event termed "cell competition". However, little is known about the mechanisms underlying this process. In a recent study, we describe that RASG12V/RasV12-transformed cells surrounded by normal cells exhibit decreased lysosomal activity accompanied with accumulation of autophagosomes. Restoration of low lysosomal activity or inhibition of autophagosome formation significantly antagonizes apical extrusion of RASG12V cells, suggesting that non-degradable autophagosomes are required for cell competition. Notably, analysis of a cell competition mouse model demonstrates that macroautophagy/autophagy-ablated RASG12V cells are less readily eliminated by cell competition, and remaining transformed cells destroy ductal integrity, leading to chronic pancreatitis. Thus, our findings illuminate a critical role for non-degradable autophagosomes in cell competition and reveal a homeostasis-preserving role of autophagy upon emergence of transformed cells.
    Keywords:  cell competition; hindered autophagic flux; lysosomal dysfunction; non-degradable autophagosomes; pancreatic cancer
    DOI:  https://doi.org/10.1080/15548627.2022.2140559
  6. Front Cell Dev Biol. 2022 ;10 976882
    Autophagy controls Wolbachia infection upon bacterial damage and in aging Drosophila.
    Dávid Hargitai, Lili Kenéz, Muna Al-Lami, Győző Szenczi, Péter Lőrincz, Gábor Juhász.
      Autophagy is a conserved catabolic process in eukaryotic cells that degrades intracellular components in lysosomes, often in an organelle-specific selective manner (mitophagy, ERphagy, etc). Cells also use autophagy as a defense mechanism, eliminating intracellular pathogens via selective degradation known as xenophagy. Wolbachia pipientis is a Gram-negative intracellular bacterium, which is one of the most common parasites on Earth affecting approximately half of terrestrial arthropods. Interestingly, infection grants the host resistance against other pathogens and modulates lifespan, so this bacterium resembles an endosymbiont. Here we demonstrate that Drosophila somatic cells normally degrade a subset of these bacterial cells, and autophagy is required for selective elimination of Wolbachia upon antibiotic damage. In line with these, Wolbachia overpopulates in autophagy-compromised animals during aging while its presence fails to affect host lifespan unlike in case of control flies. The autophagic degradation of Wolbachia thus represents a novel antibacterial mechanism that controls the propagation of this unique bacterium, behaving both as parasite and endosymbiont at the same time.
    Keywords:  Drosophila; Wolbachia; autophagy; wolbophagy; xenophagy
    DOI:  https://doi.org/10.3389/fcell.2022.976882
  7. Sci Adv. 2022 Oct 28. 8(43): eabo1274
    Many roads lead to CASM: Diverse stimuli of noncanonical autophagy share a unifying molecular mechanism.
    Joanne Durgan, Oliver Florey.
      Autophagy is a fundamental catabolic process coordinated by a network of autophagy-related (ATG) proteins. These ATG proteins also perform an important parallel role in "noncanonical" autophagy, a lysosome-associated signaling pathway with key functions in immunity, inflammation, cancer, and neurodegeneration. While the noncanonical autophagy pathway shares the common ATG machinery, it bears key mechanistic and functional distinctions, and is characterized by conjugation of ATG8 to single membranes (CASM). Here, we review the diverse, and still expanding, collection of stimuli and processes now known to harness the noncanonical autophagy pathway, including engulfment processes, drug treatments, TRPML1 and STING signaling, viral infection, and other pathogenic factors. We discuss the multiple associated routes to CASM and assess their shared and distinctive molecular features. By integrating these findings, we propose an updated and unifying mechanism for noncanonical autophagy, centered on ATG16L1 and V-ATPase.
    DOI:  https://doi.org/10.1126/sciadv.abo1274
  8. Subcell Biochem. 2022 ;100 143-172
    Autophagy in Cancer: A Metabolic Perspective.
    Sweta Sikder, Atanu Mondal, Chandrima Das, Tapas K Kundu.
      Autophagy is an intracellular catabolic degradative process in which damaged cellular organelles, unwanted proteins and different cytoplasmic components get recycled to maintain cellular homeostasis or metabolic balance. During autophagy, a double membrane vesicle is formed to engulf these cytosolic materials and fuse to lysosomes wherein the entire cargo degrades to be used again. Because of this unique recycling ability of cells, autophagy is a universal stress response mechanism. Dysregulation of autophagy leads to several diseases, including cancer, neurodegeneration and microbial infection. Thus, autophagy machineries have become targets for therapeutics. This chapter provides an overview of the paradoxical role of autophagy in tumorigenesis in the perspective of metabolism.
    Keywords:  Autophagy; Cancer; Histone modifications; Metabolism
    DOI:  https://doi.org/10.1007/978-3-031-07634-3_5
  9. Autophagy. 2022 Oct 27.
    PTP4A2 promotes lysophagy by dephosphorylation of VCP/p97 at Tyr805.
    Yunpeng Bai, Guimei Yu, Hong-Ming Zhou, Ovini Amarasinghe, Yuan Zhou, Peipei Zhu, Qinglin Li, Lujuan Zhang, Frederick Nguele Meke, Yiming Miao, Eli Chapman, W Andy Tao, Zhong-Yin Zhang.
      Overexpression of PTP4A phosphatases are associated with advanced cancers, but their biological functions are far from fully understood due to limited knowledge about their physiological substrates. VCP is implicated in lysophagy via collaboration with specific cofactors in the ELDR complex. However, how the ELDR complex assembly is regulated has not been determined. Moreover, the functional significance of the penultimate and conserved Tyr805 phosphorylation in VCP has not been established. Here, we use an unbiased substrate trapping and mass spectrometry approach and identify VCP/p97 as a bona fide substrate of PTP4A2. Biochemical studies show that PTP4A2 dephosphorylates VCP at Tyr805, enabling the association of VCP with its C-terminal cofactors UBXN6/UBXD1 and PLAA, which are components of the ELDR complex responsible for lysophagy, the autophagic clearance of damaged lysosomes. Functionally, PTP4A2 is required for cellular homeostasis by promoting lysophagy through facilitating ELDR-mediated K48-linked ubiquitin conjugate removal and autophagosome formation on the damaged lysosomes. Deletion of Ptp4a2 in vivo compromises the recovery of glycerol-injection induced acute kidney injury due to impaired lysophagy and sustained lysosomal damage. Taken together, our data establish PTP4A2 as a critical regulator of VCP and uncover an important role for PTP4A2 in maintaining lysosomal homeostasis through dephosphorylation of VCP at Tyr805. Our study suggests that PTP4A2 targeting could be a potential therapeutic approach to treat cancers and other degenerative diseases by modulating lysosomal homeostasis and macroautophagy/autophagy.
    Keywords:  ELDR complex; PLAA; PRL phosphatase; PTP4A2; UBXN6; VCP; autophagy; dephosphorylation; lysosome
    DOI:  https://doi.org/10.1080/15548627.2022.2140558
  10. Int J Mol Sci. 2022 Oct 21. pii: 12676. [Epub ahead of print]23(20):
    Discovery of Mitophagy Inhibitors with Therapeutic Potential in Different Familial Amyotrophic Lateral Sclerosis Mutations.
    Ines Maestro, Laura R de la Ballina, Gracia Porras, Silvia Corrochano, Eva De Lago, Anne Simonsen, Patricia Boya, Ana Martinez.
      Mitophagy is the selective degradation of mitochondria by autophagy. It promotes the turnover of mitochondria and prevents the accumulation of dysfunctional mitochondria, which can lead to cellular degeneration. Mitophagy is known to be altered in several pathological conditions, especially in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). We recently demonstrated an increase in autophagy flux in lymphoblasts from ALS patients bearing a mutation in SOD1. Thus, the identification of mitophagy inhibitors may be a therapeutic option to recover mitochondrial homeostasis. Here, using a phenotypic mitophagy assay, we identified a new mitophagy inhibitor, the small molecule named IGS2.7 from the MBC library. Interestingly, the treatment of different cellular and in vivo models of ALS with mutations on SOD1 and TARDBP with this inhibitor restores autophagy to control levels. These results point mitophagy inhibitors, especially IGS2.7, to a new therapeutic approach for familial ALS patients.
    Keywords:  amyotrophic lateral sclerosis; drug discovery; mitophagy; phenotypic assay
    DOI:  https://doi.org/10.3390/ijms232012676
  11. Int J Mol Sci. 2022 Oct 11. pii: 12105. [Epub ahead of print]23(20):
    Targeting Deubiquitinating Enzymes (DUBs) That Regulate Mitophagy via Direct or Indirect Interaction with Parkin.
    Eliona Tsefou, Robin Ketteler.
      The quality control of mitochondria is critical for the survival of cells, and defects in the pathways required for this quality control can lead to severe disease. A key quality control mechanism in cells is mitophagy, which functions to remove damaged mitochondria under conditions of various stresses. Defective mitophagy can lead to a number of diseases including neurodegeneration. It has been proposed that an enhancement of mitophagy can improve cell survival, enhance neuronal function in neurodegeneration and extend health and lifespans. In this review, we highlight the role of deubiquitinating enzymes (DUBs) in the regulation of mitophagy. We summarise the current knowledge on DUBs that regulate mitophagy as drug targets and provide a list of small molecule inhibitors that are valuable tools for the further development of therapeutic strategies targeting the mitophagy pathway in neurodegeneration.
    Keywords:  DUB inhibitors; Parkin; Parkinson disease; deubiquitinating enzymes; mitophagy
    DOI:  https://doi.org/10.3390/ijms232012105
  12. J Cell Biol. 2022 Dec 05. pii: e202208103. [Epub ahead of print]221(12):
    mTORC1 beyond anabolic metabolism: Regulation of cell death.
    Jiajun Zhu, Hua Wang, Xuejun Jiang.
      The mechanistic target of rapamycin complex 1 (mTORC1), a multi-subunit protein kinase complex, interrogates growth factor signaling with cellular nutrient and energy status to control metabolic homeostasis. Activation of mTORC1 promotes biosynthesis of macromolecules, including proteins, lipids, and nucleic acids, and simultaneously suppresses catabolic processes such as lysosomal degradation of self-constituents and extracellular components. Metabolic regulation has emerged as a critical determinant of various cellular death programs, including apoptosis, pyroptosis, and ferroptosis. In this article, we review the expanding knowledge on how mTORC1 coordinates metabolic pathways to impinge on cell death regulation. We focus on the current understanding on how nutrient status and cellular signaling pathways connect mTORC1 activity with ferroptosis, an iron-dependent cell death program that has been implicated in a plethora of human diseases. In-depth understanding of the principles governing the interaction between mTORC1 and cell death pathways can ultimately guide the development of novel therapies for the treatment of relevant pathological conditions.
    DOI:  https://doi.org/10.1083/jcb.202208103
  13. Autophagy. 2022 Oct 26.
    LC3-dependent EV loading and secretion (LDELS) promotes TFRC (transferrin receptor) secretion via extracellular vesicles.
    Jackson O Gardner, Andrew M Leidal, Tan A Nguyen, Jayanta Debnath.
      LC3-dependent EV loading and secretion (LDELS) is a secretory autophagy pathway in which the macroautophagy/autophagy machinery facilitates the packaging of cytosolic cargos, such as RNA-binding proteins, into extracellular vesicles (EVs) for secretion outside of the cell. Here, we identify TFRC (transferrin receptor), one of the first proteins found to be secreted via EVs, as a transmembrane cargo of the LDELS pathway. Similar to other LDELS targets, TFRC secretion via EVs genetically requires components of the MAP1LC3/LC3-conjugation machinery but is independent of other ATGs involved in classical autophagosome formation. Furthermore, the packaging and secretion of this transmembrane protein into EVs depends on multiple ESCRT pathway components and the small GTPase RAB27A. Based on these results, we propose that the LDELS pathway promotes TFRC incorporation into EVs and its secretion outside the cell.
    Keywords:  ATG7; ATG8; LC3-conjugation; extracellular vesicles; secretory autophagy; transferrin receptor
    DOI:  https://doi.org/10.1080/15548627.2022.2140557
  14. Cell Mol Life Sci. 2022 Oct 25. 79(11): 565
    Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS.
    Parsa Alan, Kurt R Vandevoorde, Bharat Joshi, Ben Cardoen, Guang Gao, Yahya Mohammadzadeh, Ghassan Hamarneh, Ivan R Nabi.
      Mitochondria are major sources of cytotoxic reactive oxygen species (ROS), such as superoxide and hydrogen peroxide, that when uncontrolled contribute to cancer progression. Maintaining a finely tuned, healthy mitochondrial population is essential for cellular homeostasis and survival. Mitophagy, the selective elimination of mitochondria by autophagy, monitors and maintains mitochondrial health and integrity, eliminating damaged ROS-producing mitochondria. However, mechanisms underlying mitophagic control of mitochondrial homeostasis under basal conditions remain poorly understood. E3 ubiquitin ligase Gp78 is an endoplasmic reticulum membrane protein that induces mitochondrial fission and mitophagy of depolarized mitochondria. Here, we report that CRISPR/Cas9 knockout of Gp78 in HT-1080 fibrosarcoma cells increased mitochondrial volume, elevated ROS production and rendered cells resistant to carbonyl cyanide m-chlorophenyl hydrazone (CCCP)-induced mitophagy. These effects were phenocopied by knockdown of the essential autophagy protein ATG5 in wild-type HT-1080 cells. Use of the mito-Keima mitophagy probe confirmed that Gp78 promoted both basal and damage-induced mitophagy. Application of a spot detection algorithm (SPECHT) to GFP-mRFP tandem fluorescent-tagged LC3 (tfLC3)-positive autophagosomes reported elevated autophagosomal maturation in wild-type HT-1080 cells relative to Gp78 knockout cells, predominantly in proximity to mitochondria. Mitophagy inhibition by either Gp78 knockout or ATG5 knockdown reduced mitochondrial potential and increased mitochondrial ROS. Live cell analysis of tfLC3 in HT-1080 cells showed the preferential association of autophagosomes with mitochondria of reduced potential. Xenograft tumors of HT-1080 knockout cells show increased labeling for mitochondria and the cell proliferation marker Ki67 and reduced labeling for the TUNEL cell death reporter. Basal Gp78-dependent mitophagic flux is, therefore, selectively associated with reduced potential mitochondria promoting maintenance of a healthy mitochondrial population, limiting ROS production and tumor cell proliferation.
    Keywords:  GFP-mRFP tandem fluorescent-tagged LC3; Gp78 ubiquitin ligase; Mitochondria; Mitophagy; Reactive oxygen species; SPECHT; Spot detection
    DOI:  https://doi.org/10.1007/s00018-022-04585-8
  15. Sci Adv. 2022 Oct 28. 8(43): eabn1298
    Regulation of α-synuclein homeostasis and inflammasome activation by microglial autophagy.
    Insup Choi, George R Heaton, You-Kyung Lee, Zhenyu Yue.
      Autophagy clears protein aggregates, damaged cellular organelles, and pathogens through the lysosome. Although autophagy is highly conserved across all cell types, its activity in each cell is specifically adapted to carry out distinct physiological functions. The role of autophagy in neurons has been well characterized; however, in glial cells, its function remains largely unknown. Microglia are brain-resident macrophages that survey the brain to remove injured neurons, excessive synapses, protein aggregates, and infectious agents. Current studies have demonstrated that dysfunctional microglia contribute to neurodegenerative diseases. In Alzheimer's disease animal models, microglia play a critical role in regulating amyloid plaque formation and neurotoxicity. However, how microglia are involved in Parkinson's disease (PD) remains poorly understood. Propagation of aggregated α-synuclein via cell-to-cell transmission and neuroinflammation have emerged as important mechanisms underlying neuropathologies in PD. Here, we review converging evidence that microglial autophagy maintains α-synuclein homeostasis, regulates neuroinflammation, and confers neuroprotection in PD experimental models.
    DOI:  https://doi.org/10.1126/sciadv.abn1298
  16. Cell Mol Life Sci. 2022 Oct 29. 79(11): 574
    Mitochondrial proteotoxicity: implications and ubiquitin-dependent quality control mechanisms.
    Mariusz Karbowski, Yumiko Oshima, Nicolas Verhoeven.
      Through their role in energy generation and regulation of several vital pathways, including apoptosis and inflammation, mitochondria are critical for the life of eukaryotic organisms. Mitochondrial dysfunction is a major problem implicated in the etiology of many pathologies, including neurodegenerative diseases, such as Parkinson's disease (PD), Alzheimer's disease (AD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS), diabetes, cardiovascular diseases, and many others. Proteotoxic stress, here defined as a reduction in bioenergetic activity induced by the accumulation of aberrant proteins in the mitochondria, is likely to be implicated in disease-linked mitochondrial and cellular decline. Various quality control pathways, such as mitochondrial unfolded protein response (mtUPR), the ubiquitin (Ub)-dependent degradation of aberrant mitochondrial proteins, and mitochondria-specific autophagy (mitophagy), respond to proteotoxic stress and eliminate defective proteins or dysfunctional mitochondria. This work provides a concise review of mechanisms by which disease-linked aberrant proteins affect mitochondrial function and an overview of mitochondrial quality control pathways that counteract mitochondrial proteotoxicity. We focus on mitochondrial quality control mechanisms relying on the Ub-mediated protein degradation, such as mitochondria-specific autophagy and the mitochondrial arm of the Ub proteasome system (UPS). We highlight the importance of a widening perspective of how these pathways protect mitochondria from proteotoxic stress to better understand mitochondrial proteotoxicity in overlapping pathophysiological pathways. Implications of these mechanisms in disease development are also briefly summarized.
    Keywords:  Mitochondria; Mitophagy; Proteotoxicity; Quality control; Ubiquitin
    DOI:  https://doi.org/10.1007/s00018-022-04604-8
  17. Front Cell Dev Biol. 2022 ;10 978142
    Mitophagy in the aging nervous system.
    Anna Rappe, Thomas G McWilliams.
      Aging is characterised by the progressive accumulation of cellular dysfunction, stress, and inflammation. A large body of evidence implicates mitochondrial dysfunction as a cause or consequence of age-related diseases including metabolic disorders, neuropathies, various forms of cancer and neurodegenerative diseases. Because neurons have high metabolic demands and cannot divide, they are especially vulnerable to mitochondrial dysfunction which promotes cell dysfunction and cytotoxicity. Mitophagy neutralises mitochondrial dysfunction, providing an adaptive quality control strategy that sustains metabolic homeostasis. Mitophagy has been extensively studied as an inducible stress response in cultured cells and short-lived model organisms. In contrast, our understanding of physiological mitophagy in mammalian aging remains extremely limited, particularly in the nervous system. The recent profiling of mitophagy reporter mice has revealed variegated vistas of steady-state mitochondrial destruction across different tissues. The discovery of patients with congenital autophagy deficiency provokes further intrigue into the mechanisms that underpin neural integrity. These dimensions have considerable implications for targeting mitophagy and other degradative pathways in age-related neurological disease.
    Keywords:  aging; autophagy; brain; disease; longevity; mitochondria; mitophagy
    DOI:  https://doi.org/10.3389/fcell.2022.978142
  18. Autophagy. 2022 Oct 25.
    DEFECTS IN PINK1-PRKN-PARK7/DJ-1-DEPENDENT MITOPHAGY AND AUTOSOMAL RECESSIVE PARKINSON DISEASE.
    Dorien Imberechts, Wim Vandenberghe.
      
    Keywords:  DJ-1; PARK7; PINK1; PRKN; Parkinson’s disease; mitochondria; mitophagy; neurons; optineurin; parkin
    DOI:  https://doi.org/10.1080/15548627.2022.2139129
  19. Metabolism. 2022 Oct 21. pii: S0026-0495(22)00216-5. [Epub ahead of print] 155338
    Acyl-CoA binding protein regulates nutrient-dependent autophagy.
    Prajna Udupa, Abhishek Kumar, Rahul Parit, Debasish Kumar Ghosh.
       BACKGROUND: Homeostasis of autophagy under normal conditions and nutrient stress is maintained by adaptive activation of regulatory proteins. However, the protein-lipid crosstalk that modulates the switch from suppression to activation of autophagy initiation is largely unknown.
    RESULTS: Here, we show that human diazepam-binding inhibitor (DBI), also known as acyl-CoA binding protein (ACBP), binds to phosphatidylethanolamine of the phagophore membrane under nutrient-rich growth conditions, leading to inhibition of LC3 lipidation and suppression of autophagy initiation. Specific residues, including the conserved tyrosine residues of DBI, interact with phosphatidylethanolamine to stabilize the later molecule in the acyl-CoA binding cavity of the protein. Under starvation, phosphorylation of serine-21 of DBI mediated by the AMP-activated protein kinase results in a drastic reduction in the affinity of the protein for phosphatidylethanolamine. The release of serine-21 phosphorylated DBI from the phagophore upon nutrient starvation restores the high LC3 lipidation flux and maturation of the phagophore to autophagosome.
    CONCLUSION: DBI acts as a strategic barrier against overactivation of phagophore maturation under nutrient-rich conditions, while triggering autophagy under nutrient-deficient conditions.
    Keywords:  Autophagy; Diazepam-binding inhibitor; Nutrient stress; Phosphorylation; Protein-lipid binding
    DOI:  https://doi.org/10.1016/j.metabol.2022.155338
  20. Int J Mol Sci. 2022 Oct 18. pii: 12470. [Epub ahead of print]23(20):
    mTOR as a Potential Target for the Treatment of Microbial Infections, Inflammatory Bowel Diseases, and Colorectal Cancer.
    Obaid Afzal, Abdulmalik S A Altamimi, Bismillah Mubeen, Sami I Alzarea, Waleed Hassan Almalki, Salwa D Al-Qahtani, Eman M Atiya, Fahad A Al-Abbasi, Fatima Ali, Inam Ullah, Muhammad Shahid Nadeem, Imran Kazmi.
      The mammalian target of rapamycin (mTOR) is the major controller of a number of important cellular activities, including protein synthesis, cell expansion, multiplication, autophagy, lysosomal function, and cellular metabolism. When mTOR interacts with specific adaptor proteins, it forms two complexes, mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2). The mTOR signaling system regulates gene transcription and protein manufacturing to control proliferation of cell, differentiation of immune cell, and tumor metabolism. Due to its vital role in case of microbial infections, inflammations and cancer development and progression, mTOR has been considered as a key therapeutic target for the development of targeted medication. As autophagy dysfunction is linked to changes in both innate and adaptive immune responses, bacterial clearance defects, and goblet and Paneth cell malfunction, all of these changes are linked to inflammatory bowel diseases (IBD) and colorectal cancer (CRC) pathogenesis. Preclinical and clinical data have shown that the inhibition and induction of autophagy have significant potential to be translated into the clinical applications. In IBD and several CRC models, mTORC1 inhibitors have been found effective. In the recent years, a number of novel mTOR inhibitors have been investigated in clinical trials, and a number of drugs have shown considerably enhanced efficacy when combined with mTOR inhibitors. The future developments in the mTOR targeting medications can benefit patients in individualized therapy. Advanced and innovative medicines that are more effective and have lower drug resistance are still in high demand. New findings could be relevant in medicine development, pharmacological modification, or future mTOR inhibitor research. Therefore, the goal of this review is to present a comprehensive account of current developments on the mTOR pathway and its inhibitors, with an emphasis on the management of microbial infections, the treatment of inflammatory bowel disease, and the management of colon cancer.
    Keywords:  colorectal cancer (CRC); inflammatory bowel diseases (IBD); mammalian target of rapamycin (mTOR)
    DOI:  https://doi.org/10.3390/ijms232012470
  21. Front Pharmacol. 2022 ;13 1015204
    Insulin-induced mTOR signaling and gluconeogenesis in renal proximal tubules: A mini-review of current evidence and therapeutic potential.
    Motonobu Nakamura, Nobuhiko Satoh, Shoko Horita, Masaomi Nangaku.
      Energy is continuously expended in the body, and gluconeogenesis maintains glucose homeostasis during starvation. Gluconeogenesis occurs in the liver and kidneys. The proximal tubule is the primary location for renal gluconeogenesis, accounting for up to 25% and 60% of endogenous glucose production during fasting and after a meal, respectively. The mechanistic target of rapamycin (mTOR), which exists downstream of the insulin pathway, plays an important role in regulating proximal tubular gluconeogenesis. mTOR is an atypical serine/threonine kinase present in two complexes. mTORC1 phosphorylates substrates that enhance anabolic processes such as mRNA translation and lipid synthesis and catabolic processes such as autophagy. mTORC2 regulates cytoskeletal dynamics and controls ion transport and proliferation via phosphorylation of SGK1. Therefore, mTOR signaling defects have been implicated in various pathological conditions, including cancer, cardiovascular disease, and diabetes. However, concrete elucidations of the associated mechanisms are still unclear. This review provides an overview of mTOR and describes the relationship between mTOR and renal.
    Keywords:  diabetes; gluconeogenesis; insulin resistance; mTOR; proximal tubules
    DOI:  https://doi.org/10.3389/fphar.2022.1015204
  22. Arch Pharm Res. 2022 Oct 28.
    Inhibition of autophagy with chloroquine dysregulates mitochondrial quality control and energetics in adipocytes.
    Hafiz Muhammad Ahmad Javaid, Hwayeon Lim, Sooim Shin, Joo Young Huh.
      Autophagy is a complex degradation pathway through which damaged or dysfunctional proteins and organelles are removed. Its pharmacological modulators have been extensively used in a wide range of basic research and preclinical studies. However, the effects of these inhibitors on metabolism, in addition to autophagy inhibition, are not fully elucidated. Chloroquine is a clinically relevant compound that inhibits autophagy by preventing the fusion of autophagosomes with lysosomes. In this study, we aimed to examine the effect of chloroquine on mitochondrial quality control and respiratory function by utilizing 3T3-L1 mouse adipocytes treated with chloroquine at various time points. We found that chloroquine could disturb genes related to mitochondrial fission, biogenesis, and mitophagy, leading to mitochondrial DNA damage. Although the inhibition of autophagy by chloroquine resulted in an increased prohibitin expression, respiratory function was downregulated in a time-dependent manner. Moreover, chloroquine treatment induced oxidative stress, apoptosis, and metabolic dysregulation. These data demonstrated that chloroquine significantly affected mitochondrial respiratory function and metabolism, which was consistent with impaired mitochondrial quality associated with autophagy inhibition.
    Keywords:  Adipocytes; Autophagy; Chloroquine; Mitochondria; Obesity
    DOI:  https://doi.org/10.1007/s12272-022-01412-3
  23. Biomolecules. 2022 Oct 04. pii: 1420. [Epub ahead of print]12(10):
    Mitophagy-A New Target of Bone Disease.
    Zhipeng Zeng, Xuchang Zhou, Yan Wang, Hong Cao, Jianmin Guo, Ping Wang, Yajing Yang, Yan Wang.
      Bone diseases are usually caused by abnormal metabolism and death of cells in bones, including osteoblasts, osteoclasts, osteocytes, chondrocytes, and bone marrow mesenchymal stem cells. Mitochondrial dysfunction, as an important cause of abnormal cell metabolism, is widely involved in the occurrence and progression of multiple bone diseases, including osteoarthritis, intervertebral disc degeneration, osteoporosis, and osteosarcoma. As selective mitochondrial autophagy for damaged or dysfunctional mitochondria, mitophagy is closely related to mitochondrial quality control and homeostasis. Accumulating evidence suggests that mitophagy plays an important regulatory role in bone disease, indicating that regulating the level of mitophagy may be a new strategy for bone-related diseases. Therefore, by reviewing the relevant literature in recent years, this paper reviews the potential mechanism of mitophagy in bone-related diseases, including osteoarthritis, intervertebral disc degeneration, osteoporosis, and osteosarcoma, to provide a theoretical basis for the related research of mitophagy in bone diseases.
    Keywords:  intervertebral disc degeneration; mitophagy; osteoarthritis; osteoporosis; osteosarcoma
    DOI:  https://doi.org/10.3390/biom12101420
  24. Sci Adv. 2022 Oct 28. 8(43): eabn1702
    Beyond autophagy: LC3-associated phagocytosis and endocytosis.
    Carolina Peña-Martinez, Alexis D Rickman, Bradlee L Heckmann.
      Noncanonical functions of the autophagy machinery in pathways including LC3-associated phagocytosis and LC3-associated endocytosis have garnered increasing interest in both normal physiology and pathobiology. New discoveries over the past decade of noncanonical uses of the autophagy machinery in these distinct molecular mechanisms have led to robust investigation into the roles of single-membrane LC3 lipidation. Noncanonical autophagy pathways have now been implicated in the regulation of multiple processes ranging from debris clearance, cellular signaling, and immune regulation and inflammation. Accumulating evidence is demonstrating roles in a variety of disease states including host-pathogen responses, autoimmunity, cancer, and neurological and neurodegenerative pathologies. Here, we broadly summarize the differences in the mechanistic regulation between autophagy and LAP and LANDO and highlight some of the key roles of LAP and LANDO in innate immune function, inflammation, and disease pathology.
    DOI:  https://doi.org/10.1126/sciadv.abn1702
  25. Biomedicines. 2022 Oct 12. pii: 2539. [Epub ahead of print]10(10):
    Mitochondrial Dysfunction, Mitophagy and Their Correlation with Perinatal Complications: Preeclampsia and Low Birth Weight.
    Raziye Melike Yildirim, Yagmur Ergun, Murat Basar.
      Mitochondria are essential organelles and crucial for cellular survival. Mitochondrial biogenesis and mitophagy are dynamic features that are essential for both maintaining the health of the mitochondrial network and cellular demands. The accumulation of damaged mitochondria has been shown to be related to a wide range of pathologies ranging from neurological to musculoskeletal. Mitophagy is the selective autophagy of mitochondria, eliminating dysfunctional mitochondria in cells by engulfment within double-membraned vesicles. Preeclampsia and low birth weight constitute prenatal complications during pregnancy and are leading causes of maternal and fetal mortality and morbidity. Both placental implantation and fetal growth require a large amount of energy, and a defect in the mitochondrial quality control mechanism may be responsible for the pathophysiology of these diseases. In this review, we compiled current studies investigating the role of BNIP3, DRAM1, and FUNDC1, mediators of receptor-mediated mitophagy, in the progression of preeclampsia and the role of mitophagy pathways in the pathophysiology of low birth weight. Recent studies have indicated that mitochondrial dysfunction and accumulation of reactive oxygen species are related to preeclampsia and low birth weight. However, due to the lack of studies in this field, the results are controversial. Therefore, mitophagy-related pathways associated with these pathologies still need to be elucidated. Mitophagy-related pathways are among the promising study targets that can reveal the pathophysiology behind preeclampsia and low birth weight.
    Keywords:  fetal growth restriction; low birth weight; mitochondria; mitophagy; perinatal complications; preeclampsia
    DOI:  https://doi.org/10.3390/biomedicines10102539
  26. Front Mol Neurosci. 2022 ;15 1049914
    Editorial: Apoptosis, autophagy, and mitophagy dysfunction in Alzheimer's disease: Evolving emergence and mechanisms.
    Rajkumar Singh Kalra, Ramesh Kandimalla, Binukumar Bk.
      
    Keywords:  Alzheimer's disease; amyloid-β plaques; apoptosis; autophagy; mitophagy; neuro-fibrillary tangles; neurodegeneration; neuroinflammation
    DOI:  https://doi.org/10.3389/fnmol.2022.1049914
  27. Nature. 2022 Oct 26.
    Cryo-EM structure of the SEA complex.
    Lucas Tafur, Kerstin Hinterndorfer, Caroline Gabus, Chiara Lamanna, Ariane Bergmann, Yashar Sadian, Farzad Hamdi, Fotis L Kyrilis, Panagiotis L Kastritis, Robbie Loewith.
      The SEA complex (SEAC) is a growth regulator that acts as a GTPase-activating protein (GAP) towards Gtr1, a Rag GTPase that relays nutrient status to the Target of Rapamycin Complex 1 (TORC1) in yeast1. Functionally, the SEAC has been divided into two subcomplexes: SEACIT, which has GAP activity and inhibits TORC1, and SEACAT, which regulates SEACIT2. This system is conserved in mammals: the GATOR complex, consisting of GATOR1 (SEACIT) and GATOR2 (SEACAT), transmits amino acid3 and glucose4 signals to mTORC1. Despite its importance, the structure of SEAC/GATOR, and thus molecular understanding of its function, is lacking. Here, we solve the cryo-EM structure of the native eight-subunit SEAC. The SEAC has a modular structure in which a COPII-like cage corresponding to SEACAT binds two flexible wings, which correspond to SEACIT. The wings are tethered to the core via Sea3, which forms part of both modules. The GAP mechanism of GATOR1 is conserved in SEACIT, and GAP activity is unaffected by SEACAT in vitro. In vivo, the wings are essential for recruitment of the SEAC to the vacuole, primarily via the EGO complex. Our results indicate that rather than being a direct inhibitor of SEACIT, SEACAT acts as a scaffold for the binding of TORC1 regulators.
    DOI:  https://doi.org/10.1038/s41586-022-05370-0
  28. Autophagy. 2022 Oct 25.
    PINK1-PRKN mediated mitophagy: differences between in vitro and in vivo models.
    Rui Han, Yanting Liu, Shihua Li, Xiao-Jiang Li, Weili Yang.
      Mitophagy is a key intracellular process that selectively removes damaged mitochondria to prevent their accumulation that can cause neuronal degeneration. During mitophagy, PINK1 (PTEN induced kinase 1), a serine/threonine kinase, works with PRKN/parkin, an E3 ubiquitin ligase, to target damaged mitochondria to the lysosome for degradation. Mutations in the PINK1 and PRKN genes cause early-onset Parkinson disease that is also associated with mitochondrial dysfunction. There are a large number of reports indicating the critical role of PINK1 in mitophagy. However, most of these findings were obtained from in vitro experiments with exogenous PINK1 expression and acute damage of mitochondria by toxins. Recent studies using novel animal models suggest that PINK1-PRKN can also function independent of mitochondria. In this review, we highlight the major differences between in vitro and in vivo models for investigating PINK1 and discuss the potential mechanisms underlying these differences with the aim of understanding how PINK1 functions under different circumstances.
    Keywords:  Mitochondria dysfunction; PINK1; PRKN; Parkinson disease; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2022.2139080
  29. Planta. 2022 Oct 28. 256(6): 103
    Autophagy: a game changer for plant development and crop improvement.
    Isha Sharma, Pulugurtha Bharadwaja Kirti, Pratap Kumar Pati.
       MAIN CONCLUSION: Manipulation of autophagic pathway represents a tremendous opportunity for designing climate-smart crops with improved yield and better adaptability to changing environment. For exploiting autophagy to its full potential, identification and comprehensive characterization of adapters/receptor complex and elucidation of its regulatory network in crop plants is highly warranted.  Autophagy is a major intracellular trafficking pathway in eukaryotes involved in vacuolar degradation of cytoplasmic constituents, mis-folded proteins, and defective organelles. Under optimum conditions, autophagy operates at a basal level to maintain cellular homeostasis, but under stressed conditions, it is induced further to provide temporal stress relief. Our understanding of this highly dynamic process has evolved exponentially in the past few years with special reference to several plant-specific roles of autophagy. Here, we review the most recent advances in the field of autophagy in plants and discuss its potential implications in designing crops with improved stress and disease-tolerance, enhanced yield potential, and improved capabilities for producing metabolites of high economic value. We also assess the current knowledge gaps and the possible strategies to develop a robust module for biotechnological application of autophagy to enhance bioeconomy and sustainability of agriculture.
    Keywords:  Autophagy; Chlorophagy; Crop improvement; Endosomal trafficking; Growth and development; Lipophagy; Stress tolerance
    DOI:  https://doi.org/10.1007/s00425-022-04004-z
  30. J Biol Chem. 2022 Oct 20. pii: S0021-9258(22)01072-9. [Epub ahead of print] 102629
    A cell-based chemical-genetic screen for amino acid stress response inhibitors reveals torins reverse stress kinase GCN2 signaling.
    Johanna B Brüggenthies, Alessandra Fiore, Marion Russier, Christina Bitsina, Julian Brötzmann, Susanne Kordes, Sascha Menninger, Alexander Wolf, Elena Conti, Jan E Eickhoff, Peter J Murray.
      mTORC1 and GCN2 are serine/threonine kinases that control how cells adapt to amino acid availability. mTORC1 responds to amino acids to promote translation and cell growth while GCN2 senses limiting amino acids to hinder translation via eIF2α phosphorylation. GCN2 is an appealing target for cancer therapies because malignant cells can harness the GCN2 pathway to temper the rate of translation during rapid amino acid consumption. To isolate new GCN2 inhibitors, we created cell-based, amino acid limitation reporters via genetic manipulation of Ddit3 (encoding the transcription factor CHOP). CHOP is strongly induced by limiting amino acids and in this context, GCN2-dependent. Using leucine starvation as a model for essential amino acid sensing, we unexpectedly discovered ATP-competitive PI3 kinase-related kinase inhibitors, including ATR and mTOR inhibitors like torins, completely reversed GCN2 activation in a time-dependent way. Mechanistically, via inhibiting mTORC1-dependent translation, torins increased intracellular leucine, which was sufficient to reverse GCN2 activation and the downstream integrated stress response including stress-induced transcriptional factor ATF4 expression. Strikingly, we found that general translation inhibitors mirrored the effects of torins. Therefore, we propose that mTOR kinase inhibitors concurrently inhibit different branches of amino acid sensing by a dual mechanism involving direct inhibition of mTOR and indirect suppression of GCN2 that are connected by effects on the translation machinery. Collectively, our results highlight distinct ways of regulating GCN2 activity.
    Keywords:  GCN2; amino acid starvation; integrated stress response; mTORC1; torins
    DOI:  https://doi.org/10.1016/j.jbc.2022.102629
  31. Sci Rep. 2022 Oct 25. 12(1): 17805
    The autophagy inducer SMER28 attenuates microtubule dynamics mediating neuroprotection.
    Marco Kirchenwitz, Stephanie Stahnke, Kyra Grunau, Lars Melcher, Marco van Ham, Klemens Rottner, Anika Steffen, Theresia E B Stradal.
      SMER28 originated from a screen for small molecules that act as modulators of autophagy. SMER28 enhanced the clearance of autophagic substrates such as mutant huntingtin, which was additive to rapamycin-induced autophagy. Thus, SMER28 was established as a positive regulator of autophagy acting independently of the mTOR pathway, increasing autophagosome biosynthesis and attenuating mutant huntingtin-fragment toxicity in cellular- and fruit fly disease models, suggesting therapeutic potential. Despite many previous studies, molecular mechanisms mediating SMER28 activities and its direct targets have remained elusive. Here we analyzed the effects of SMER28 on cells and found that aside from autophagy induction, it significantly stabilizes microtubules and decelerates microtubule dynamics. Moreover, we report that SMER28 displays neurotrophic and neuroprotective effects at the cellular level by inducing neurite outgrowth and protecting from excitotoxin-induced axon degeneration. Finally, we compare the effects of SMER28 with other autophagy-inducing or microtubule-stabilizing drugs: whereas SMER28 and rapamycin both induce autophagy, the latter does not stabilize microtubules, and whereas both SMER28 and epothilone B stabilize microtubules, epothilone B does not stimulate autophagy. Thus, the effect of SMER28 on cells in general and neurons in particular is based on its unique spectrum of bioactivities distinct from other known microtubule-stabilizing or autophagy-inducing drugs.
    DOI:  https://doi.org/10.1038/s41598-022-20563-3
  32. Open Biol. 2022 Oct;12(10): 220155
    Lysosomal positioning diseases: beyond substrate storage.
    Gianluca Scerra, Valeria De Pasquale, Melania Scarcella, Maria Gabriella Caporaso, Luigi Michele Pavone, Massimo D'Agostino.
      Lysosomal storage diseases (LSDs) comprise a group of inherited monogenic disorders characterized by lysosomal dysfunctions due to undegraded substrate accumulation. They are caused by a deficiency in specific lysosomal hydrolases involved in cellular catabolism, or non-enzymatic proteins essential for normal lysosomal functions. In LSDs, the lack of degradation of the accumulated substrate and its lysosomal storage impairs lysosome functions resulting in the perturbation of cellular homeostasis and, in turn, the damage of multiple organ systems. A substantial number of studies on the pathogenesis of LSDs has highlighted how the accumulation of lysosomal substrates is only the first event of a cascade of processes including the accumulation of secondary metabolites and the impairment of cellular trafficking, cell signalling, autophagic flux, mitochondria functionality and calcium homeostasis, that significantly contribute to the onset and progression of these diseases. Emerging studies on lysosomal biology have described the fundamental roles of these organelles in a variety of physiological functions and pathological conditions beyond their canonical activity in cellular waste clearance. Here, we discuss recent advances in the knowledge of cellular and molecular mechanisms linking lysosomal positioning and trafficking to LSDs.
    Keywords:  lysosomal storage diseases; lysosome; membrane contact sites; microtubule tracks; positioning; trafficking
    DOI:  https://doi.org/10.1098/rsob.220155
  33. Int J Mol Sci. 2022 Oct 12. pii: 12185. [Epub ahead of print]23(20):
    The Emerging Role of Extracellular Vesicles and Autophagy Machinery in NASH-Future Horizons in NASH Management.
    Eleni-Myrto Trifylli, Anastasios G Kriebardis, Evangelos Koustas, Nikolaos Papadopoulos, Melanie Deutsch, Georgios Aloizos, Sotirios P Fortis, Effie G Papageorgiou, Ariadne Tsagarakis, Spilios Manolakopoulos.
      Non-alcoholic fatty liver disease (NAFLD) is considered the most frequent chronic hepatic disease in the general population, while it is the first cause of liver transplantation in the US. NAFLD patients will subsequently develop non-alcoholic steatohepatitis (NASH), which is characterized by aberrant hepatocellular inflammation with or without the presence of fibrosis. The lack of specific biomarkers and therapeutic strategies makes non-alcoholic steatohepatitis (NASH) management a difficult task for clinicians. Extracellular vesicles (EVs) constitute a heterogenic population of vesicles produced by inward or outward plasma-membrane budding. There is an emerging connection between autophagy EVs production, via an unconventional non-degradative procedure. Alterations in the amount of the secreted EVs and the cargo they carry are also involved in the disease progression and development of NASH. Autophagy constitutes a multistep lysosomal degradative pathway that reassures cell homeostasis and survival under stressful conditions, such as oxygen and energy deprivation. It prevents cellular damage by eliminating defected proteins or nοn-functional intracellular organelles. At the same time, it reassures the optimal conditions for the cells via a different mechanism that includes the removal of cargo via the secretion of EVs. Similarly, autophagy machinery is also associated with the pathogenetic mechanism of NAFLD, while it has a significant implication for the progression of the disease and the development of NASH. In this review, we will shed light on the interplay between autophagy and EVs in NASH, the emerging connection of EVs production with the autophagy pathway, and their possible manipulation for developing future therapeutic strategies for NASH.
    Keywords:  autophagy; extracellular vesicles; liver injury; non-alcoholic fatty liver disease; non-alcoholic steatohepatitis; steatosis
    DOI:  https://doi.org/10.3390/ijms232012185
  34. Genes Cells. 2022 Oct 25.
    TBK1 inhibitors enhance transfection efficiency by suppressing p62/SQSTM1 phosphorylation.
    Megumi Tsuchiya, Weixia Kong, Yasushi Hiraoka, Tokuko Haraguchi, Hidesato Ogawa.
      DNA transfection is an essential technique in life sciences. Non-viral transfection reagents are widely used for transfection in basic science. However, low transfection efficiency is a problem in some cell types. This low efficiency can be primarily attributed to the intracellular degradation of transfected DNA by p62-dependent selective autophagy, specifically by p62 phosphorylated at the S403 residue (p62-S403-P). To achieve efficient DNA transfection, we focused on a phosphorylation process that generates p62-S403-P and investigated whether inhibition of this process affects transfection efficiency. One of the kinases that phosphorylate p62 is TBK1. The TBK1 gene depletion in murine embryonic fibroblast (MEF) cells by genome editing caused a significant reduction or loss of p62-S405-P (equivalent to human S403-P) and enhanced transfection efficiency, suggesting that TBK1 is a major kinase that phosphorylates p62 at S403. Therefore, TBK1 is a viable target for drug treatment to increase transfection efficiency. Transfection efficiency was enhanced when cells were treated with one of the following TBK1 inhibitors, BX795, MRT67307, or amlexanox. This effect was synergistically improved when the two inhibitors were used in combination. Our results indicate that TBK1 inhibitors enhanced transfection efficiency by suppressing p62 phosphorylation.
    Keywords:  TBK1; TBK1 inhibitor; gene delivery; p62, p62 phosphorylation; selective autophagy
    DOI:  https://doi.org/10.1111/gtc.12987
  35. JCI Insight. 2022 Oct 25. pii: e162207. [Epub ahead of print]
    GATOR2-dependent mTORC1 activity is a therapeutic vulnerability in FOXO1 fusion positive rhabdomyosarcoma.
    Jacqueline Morales, David V Allegakoen, José A Garcia, Kristen Kwong, Pushpendra K Sahu, Drew A Fajardo, Yue Pan, Max A Horlbeck, Jonathan S Weissman, W Clay Gustafson, Trever G Bivona, Amit J Sabnis.
      Oncogenic FOXO1 gene fusions drive a subset of rhabdomyosarcoma (RMS) with poor survival and to date these cancer drivers are therapeutically intractable. To identify new therapies for this disease, we undertook an isogenic CRISPR-interference screen to define PAX3-FOXO1 specific genetic dependencies and identified genes in the GATOR2 complex. GATOR2 loss in RMS abrogated amino acid-induced lysosomal localization of mTORC1 and consequent downstream signaling, slowing G1-S cell cycle transition. In vivo suppression of GATOR2 impaired the growth of tumor xenografts and favored the outgrowth of cells lacking PAX3-FOXO1. Loss of a subset of GATOR2 members can be compensated by direct genetic activation of mTORC1. RAS mutations are also sufficient to decouple mTORC1 activation from GATOR2, and indeed fusion negative RMS harboring such mutations exhibit amino acid-independent mTORC1 activity. A bi-steric, mTORC1-selective small molecule induced tumor regressions in fusion positive patient-derived tumor xenografts. These findings highlight a vulnerability in FOXO1 fusion positive RMS and provide rationale for the clinical evaluation of bi-steric mTORC1 inhibitors, currently in phase 1 testing, to treat this disease. Isogenic genetic screens can thus identify potentially exploitable vulnerabilities in fusion driven pediatric cancers which otherwise remain mostly undruggable.
    Keywords:  Cancer; Drug therapy; Genetics; Oncology; Signal transduction
    DOI:  https://doi.org/10.1172/jci.insight.162207
  36. J Immunol Res. 2022 ;2022 8433464
    Adiponectin Protects Hypoxia/Reoxygenation-Induced Cardiomyocyte Injury by Suppressing Autophagy.
    Jia Guo, Kaiyi Zhu, Zhidong Li, Chuanshi Xiao.
      Adiponectin is a cytokine produced by adipocytes and acts as a potential cardioprotective agent and plays an important role in myocardial ischemia/reperfusion injury. In a myocardial hypoxia/reoxygenation model using neonatal rat ventricular myocytes, we investigated the contribution of adiponectin-mediated autophagy to its cardioprotective effects. Cardiomyocytes were exposed to hypoxia/reoxygenation pretreated with or without adiponectin in the presence of absence of rapamycin. Cell viability was analyzed using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide method. Western blotting assay was used to determine the expression levels of microtubule-associated proteins 1A/1B light chain 3B (LC3B), adenosine monophosphate-activated protein kinase (AMPK), mammalian target of rapamycin (mTOR), p62/sequestosome 1, unc-51 like autophagy activating kinase 1 (ULK1), and Beclin-1. Autophagosome formation was detected by monodansylcadaverine staining. We found that hypoxia induced a time dependent decline in cardiomyocyte viability, and increase in autophagy and reoxygenation further augmented hypoxia-induced autophagy induction and consequently reduced cell viability. Adiponectin treatment alleviated hypoxia/reoxygenation-induced cellular damage and autophagy in cardiomyocytes. Adiponectin treatment also attenuated hypoxia/reoxygenation-promoted cardiomyocyte autophagy even in the presence of another autophagy stimulator rapamycin in part by inhibiting vacuolar hydron-adenosine triphosphatase. Additionally, autophagy suppression by adiponectin during hypoxia/reoxygenation was associated with the attenuated phosphorylation of AMPK and ULK1, augmented phosphorylation of mTOR, and the reduced protein expression levels of Beclin-1 in cardiomyocytes. Taken together, these results suggest that adiponectin protects ischemia/reperfusion-induced cardiomyocytes by suppressing autophagy in part through AMPK/mTOR/ULK1/Beclin-1 signaling pathway.
    DOI:  https://doi.org/10.1155/2022/8433464
  37. Viruses. 2022 Oct 15. pii: 2264. [Epub ahead of print]14(10):
    TDP-43 Toxicity in Yeast Is Associated with a Reduction in Autophagy, and Deletions of TIP41 and PBP1 Counteract These Effects.
    Sei-Kyoung Park, Sangeun Park, Susan W Liebman.
      When human TDP-43 is overexpressed in yeast it is toxic and forms cytoplasmic aggregates. The mechanism of this toxicity is unknown. Genetic screens for TDP-43 toxicity modifiers in the yeast system previously identified proteins, including PBP1, that enhance TDP-43 toxicity. The determination in yeast that deletion of PBP1 reduces TDP-43 toxicity while overexpression enhances toxicity, led to the discovery that its human homolog, ATXN2, is associated with ALS risk. Thus, the yeast system has relevance to human disease. We now show that deletion of a new yeast gene, tip41Δ, likewise suppresses TDP-43 toxicity. We also found that TDP-43 overexpression and toxicity is associated with reduced autophagy. This is consistent with findings in other systems that increasing autophagy reduces TDP-43 toxicity and is in contrast to a report of enhanced autophagy when TDP-43 was overexpressed in yeast. Interestingly, we found that deletions of PBP1 and TIP41, which reduced TDP-43 toxicity, eliminated TDP-43's inhibition of autophagy. This suggests that toxicity of TDP-43 expressed in yeast is in part due to its inhibition of autophagy and that deletions of PBP1 and TIP41 may reduce TDP-43 toxicity by preventing TDP-43 from inhibiting autophagy.
    Keywords:  PBP1; TDP-43; TIP41; autophagy; yeast
    DOI:  https://doi.org/10.3390/v14102264
  38. Commun Biol. 2022 Oct 27. 5(1): 1141
    Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis.
    Marco S Kaiser, Giulia Milan, Daniel J Ham, Shuo Lin, Filippo Oliveri, Kathrin Chojnowska, Lionel A Tintignac, Nitish Mittal, Christian E Zimmerli, David J Glass, Mihaela Zavolan, Markus A Rüegg.
      Muscle size is controlled by the PI3K-PKB/Akt-mTORC1-FoxO pathway, which integrates signals from growth factors, energy and amino acids to activate protein synthesis and inhibit protein breakdown. While mTORC1 activity is necessary for PKB/Akt-induced muscle hypertrophy, its constant activation alone induces muscle atrophy. Here we show that this paradox is based on mTORC1 activity promoting protein breakdown through the ubiquitin-proteasome system (UPS) by simultaneously inducing ubiquitin E3 ligase expression via feedback inhibition of PKB/Akt and proteasome biogenesis via Nuclear Factor Erythroid 2-Like 1 (Nrf1). Muscle growth was restored by reactivation of PKB/Akt, but not by Nrf1 knockdown, implicating ubiquitination as the limiting step. However, both PKB/Akt activation and proteasome depletion by Nrf1 knockdown led to an immediate disruption of proteome integrity with rapid accumulation of damaged material. These data highlight the physiological importance of mTORC1-mediated PKB/Akt inhibition and point to juxtaposed roles of the UPS in atrophy and proteome integrity.
    DOI:  https://doi.org/10.1038/s42003-022-04097-y
  39. Cells. 2022 Oct 14. pii: 3230. [Epub ahead of print]11(20):
    Adipokines as Regulators of Autophagy in Obesity-Linked Cancer.
    Alin García-Miranda, Alejandra Garcia-Hernandez, Eduardo Castañeda-Saucedo, Napoleon Navarro-Tito, Paola Maycotte.
      Excess body weight and obesity have become significant risk factors for cancer development. During obesity, adipose tissue alters its biological function, deregulating the secretion of bioactive factors such as hormones, cytokines, and adipokines that promote an inflammatory microenvironment conducive to carcinogenesis and tumor progression. Adipokines regulate tumor processes such as apoptosis, proliferation, migration, angiogenesis, and invasion. Additionally, it has been found that they can modulate autophagy, a process implicated in tumor suppression in healthy tissue and cancer progression in established tumors. Since the tumor-promoting role of autophagy has been well described, the process has been suggested as a therapeutic target in cancer. However, the effects of targeting autophagy might depend on the tumor type and microenvironmental conditions, where circulating adipokines could influence the role of autophagy in cancer. Here, we review recent evidence related to the role of adipokines in cancer cell autophagy in an effort to understand the tumor response in the context of obesity under the assumption of an autophagy-targeting treatment.
    Keywords:  adipokines; adiponectin; apelin; autophagy; cancer; leptin; obesity; resistin; visfatin
    DOI:  https://doi.org/10.3390/cells11203230
  40. Dev Cell. 2022 Oct 24. pii: S1534-5807(22)00684-0. [Epub ahead of print]57(20): 2347-2349
    PITTching in for lysosome repair.
    Claire S Goul, Roberto Zoncu.
      Lysosomes, guardians of cell health, can sustain physical damage from biological, mechanical, and chemical stressors, necessitating dedicated mechanisms for their upkeep. In a recent issue of Nature, Tan and Finkel report the discovery of a lysosomal repair pathway controlled by phosphoinositides, which operates via bulk transport of lipids across ER-lysosome contacts.
    DOI:  https://doi.org/10.1016/j.devcel.2022.09.014
  41. Cell Mol Life Sci. 2022 Oct 25. 79(11): 566
    In human astrocytes neurotropic flaviviruses increase autophagy, yet their replication is autophagy-independent.
    Petra Tavčar Verdev, Maja Potokar, Miša Korva, Katarina Resman Rus, Marko Kolenc, Tatjana Avšič Županc, Robert Zorec, Jernej Jorgačevski.
      Astrocytes, an abundant type of glial cells, are the key cells providing homeostasis in the central nervous system. Due to their susceptibility to infection, combined with high resilience to virus-induced cell death, astrocytes are now considered one of the principal types of cells, responsible for virus retention and dissemination within the brain. Autophagy plays an important role in elimination of intracellular components and in maintaining cellular homeostasis and is also intertwined with the life cycle of viruses. The physiological significance of autophagy in astrocytes, in connection with the life cycle and transmission of viruses, remains poorly investigated. In the present study, we investigated flavivirus-induced modulation of autophagy in human astrocytes by monitoring a tandem fluorescent-tagged LC3 probe (mRFP-EGFP-LC3) with confocal and super-resolution fluorescence microscopy. Astrocytes were infected with tick-borne encephalitis virus (TBEV) or West Nile virus (WNV), both pathogenic flaviviruses, and with mosquito-only flavivirus (MOF), which is considered non-pathogenic. The results revealed that human astrocytes are susceptible to infection with TBEV, WNV and to a much lower extent also to MOF. Infection and replication rates of TBEV and WNV are paralleled by increased rate of autophagy, whereas autophagosome maturation and the size of autophagic compartments are not affected. Modulation of autophagy by rapamycin and wortmannin does not influence TBEV and WNV replication rate, whereas bafilomycin A1 attenuates their replication and infectivity. In human astrocytes infected with MOF, the low infectivity and the lack of efficient replication of this flavivirus are mirrored by the absence of an autophagic response.
    Keywords:  Astrocyte; Autolysosome; Autophagosome; Flavivirus; Infection; LC3
    DOI:  https://doi.org/10.1007/s00018-022-04578-7
  42. Viruses. 2022 Oct 11. pii: 2230. [Epub ahead of print]14(10):
    The Relationship between DUGBE Virus Infection and Autophagy in Epithelial Cells.
    Marie Moroso, Aurore Rozières, Pauline Verlhac, Florence Komurian-Pradel, Olivier Ferraris, Christophe N Peyrefitte, Glaucia Paranhos-Baccalà, Christophe Viret, Mathias Faure.
      Dugbe orthonairovirus (DUGV) is a tick-borne arbovirus within the order Bunyavirales. Although displaying mild pathogenic potential, DUGV is genetically related to the Crimean-Congo hemorrhagic fever virus (CCHFV), another orthonairovirus that causes severe liver dysfunction and hemorrhagic fever with a high mortality rate in humans. As we previously observed that CCHFV infection could massively recruit and lipidate MAP1LC3 (LC3), a core factor involved in the autophagic degradation of cytosolic components, we asked whether DUGV infection also substantially impacts the autophagy machinery in epithelial cells. We observed that DUGV infection does impose LC3 lipidation in cultured hepatocytes. DUGV infection also caused an upregulation of the MAP1LC3 and SQSTM1/p62 transcript levels, which were, however, more moderate than those seen during CCHFV infection. In contrast, unlike during CCHFV infection, the modulation of core autophagy factors could influence both LC3 lipidation and viral particle production: the silencing of ATG5 and/or ATG7 diminished the induction of LC3 lipidation and slightly upregulated the level of infectious DUGV particle production. Overall, the results are compatible with the notion that in epithelial cells infected with DUGV in vitro, the autophagy machinery may be recruited to exert a certain level of restriction on viral replication. Thus, the relationship between DUGV infection and autophagy in epithelial cells appears to present both similarities and distinctions with that seen during CCHFV infection.
    Keywords:  Crimean–Congo hemorrhagic fever orthonairovirus; Dugbe orthonairovirus; MAP1LC3 lipidation; autophagy; epithelial cells; viral infection
    DOI:  https://doi.org/10.3390/v14102230
  43. Cancers (Basel). 2022 Oct 17. pii: 5072. [Epub ahead of print]14(20):
    Autophagy in Hematological Malignancies.
    Olga García Ruiz, José Manuel Sánchez-Maldonado, Miguel Ángel López-Nevot, Paloma García, Angelica Macauda, Francisca Hernández-Mohedo, Pedro Antonio González-Sierra, Manuel Martínez-Bueno, Eva Pérez, Fernando Jesús Reyes-Zurita, Daniele Campa, Federico Canzian, Manuel Jurado, Juan José Rodríguez-Sevilla, Juan Sainz.
      Autophagy is a highly conserved metabolic pathway via which unwanted intracellular materials, such as unfolded proteins or damaged organelles, are digested. It is activated in response to conditions of oxidative stress or starvation, and is essential for the maintenance of cellular homeostasis and other vital functions, such as differentiation, cell death, and the cell cycle. Therefore, autophagy plays an important role in the initiation and progression of tumors, including hematological malignancies, where damaged autophagy during hematopoiesis can cause malignant transformation and increase cell proliferation. Over the last decade, the importance of autophagy in response to standard pharmacological treatment of hematological tumors has been observed, revealing completely opposite roles depending on the tumor type and stage. Thus, autophagy can promote tumor survival by attenuating the cellular damage caused by drugs and/or stabilizing oncogenic proteins, but can also have an antitumoral effect due to autophagic cell death. Therefore, autophagy-based strategies must depend on the context to create specific and safe combination therapies that could contribute to improved clinical outcomes. In this review, we describe the process of autophagy and its role on hematopoiesis, and we highlight recent research investigating its role as a potential therapeutic target in hematological malignancies. The findings suggest that genetic variants within autophagy-related genes modulate the risk of developing hemopathies, as well as patient survival.
    Keywords:  autophagy; autophagy-related variants; clinical outcomes; disease progression; hematological malignancies; hematopoiesis; patient survival; therapeutic target
    DOI:  https://doi.org/10.3390/cancers14205072
  44. Pathogens. 2022 Sep 30. pii: 1134. [Epub ahead of print]11(10):
    Akt Inhibition Promotes Autophagy and Clearance of Group B Streptococcus from the Alveolar Epithelium.
    Ioanna Pantazi, Iosif Papafragkos, Ourania Kolliniati, Ioanna Lapi, Christos Tsatsanis, Eleni Vergadi.
      Group B Streptococcus (GBS) is a gram-positive bacterium that is harmless for healthy individuals but may provoke invasive disease in young infants and immunocompromised hosts. GBS invades the epithelial barriers to enter the bloodstream, and thus strategies that enhance epithelial cell responses may hamper GBS invasion. In the present study, we sought to investigate whether the inhibition of Akt, a kinase that regulates host inflammatory responses and autophagy via suppression of mTOR, can enhance the response of non-phagocytic alveolar epithelial cells against GBS. Treatment of the alveolar epithelial cell line A549 with the Akt inhibitor MK-2206 resulted in the enhanced production of reactive oxygen species and inflammatory mediators in response to GBS. Additionally, Akt inhibition via MK-2206 resulted in elevated LC3II/I ratios and increased autophagic flux in alveolar epithelial cells. Importantly, the inhibition of Akt promoted GBS clearance both in alveolar epithelial cells in vitro and in lung tissue in vivo in a murine model of GBS pneumonia. The induction of autophagy was essential for GBS clearance in MK-2206 treated cells, as knockdown of ATG5, a critical component of autophagy, abrogated the effect of Akt inhibition on GBS clearance. Our findings highlight the role of Akt kinase inhibition in promoting autophagy and GBS clearance in the alveolar epithelium. The inhibition of Akt may serve as a promising measure to strengthen epithelial barriers and prevent GBS invasion in susceptible hosts.
    Keywords:  Akt; Group B Streptococcus; alveolar; autophagy; epithelial cells; lung; mTOR; neonate
    DOI:  https://doi.org/10.3390/pathogens11101134
  45. Front Aging Neurosci. 2022 ;14 1023679
    Microglial autophagy in cerebrovascular diseases.
    Man Chen, Hang Zhang, Yun-Hui Chu, Yue Tang, Xiao-Wei Pang, Chuan Qin, Dai-Shi Tian.
      Microglia are considered core regulators for monitoring homeostasis in the brain and primary responders to central nervous system (CNS) injuries. Autophagy affects the innate immune functions of microglia. Recently some evidence suggests that microglial autophagy is closely associated with brain function in both ischemic stroke and hemorrhagic stroke. Herein, we will discuss the interaction between autophagy and other biological processes in microglia under physiological and pathological conditions and highlight the interaction between microglial metabolism and autophagy. In the end, we focus on the effect of microglial autophagy in cerebrovascular diseases.
    Keywords:  autophagy; cerebrovascular diseases; inflammation; metabolism; microglia
    DOI:  https://doi.org/10.3389/fnagi.2022.1023679
  46. Eur J Med Chem. 2022 Oct 13. pii: S0223-5234(22)00748-6. [Epub ahead of print]244 114846
    The SAR and action mechanisms of autophagy inhibitors that eliminate drug resistance.
    Wenchong Ye, Chuangchuang Fan, Kaishou Fu, Xiaoyang Wang, Jingchao Lin, Sihui Nian, Chunhui Liu, Wen Zhou.
      Autophagy is an essential homeostatic and catabolic process crucial for the degradation or recycling of proteins and cellular components. Drug resistance has been demonstrated to be closely implicated in increased autophagy. Autophagy inhibition to reverse drug resistance involves in the five stages of autophagy, including phagophore initiation, vesicle nucleation, vesicle elongation, vesicle fusion and cargo degradation. Herein, emphases were placed on discussions on the targets responsible for the upstream phagophore initiation and nucleation of autophagosome, as well as the ones mediating the downstream autophagosome and lysosome fusion and cargo degradation. The structure-activity relationships (SARs) and action mechanisms of the corresponding target-based small molecule autophagy inhibitors were analyzed and delineated. This review will provide a promising guidance for the design and optimization of drug-like scaffolds in the discovery of autophagy inhibitors able to eliminate drug resistance.
    Keywords:  Action mechanisms; Autophagy; Autophagy inhibitors; Drug resistance; Structure-activity relationships (SARs)
    DOI:  https://doi.org/10.1016/j.ejmech.2022.114846
  47. Int J Mol Sci. 2022 Oct 17. pii: 12416. [Epub ahead of print]23(20):
    mTOR Contributes to the Proteome Diversity through Transcriptome-Wide Alternative Splicing.
    Sze Cheng, Naima Ahmed Fahmi, Meeyeon Park, Jiao Sun, Kaitlyn Thao, Hsin-Sung Yeh, Wei Zhang, Jeongsik Yong.
      The mammalian target of rapamycin (mTOR) pathway is crucial in energy metabolism and cell proliferation. Previously, we reported transcriptome-wide 3'-untranslated region (UTR) shortening by alternative polyadenylation upon mTOR activation and its impact on the proteome. Here, we further interrogated the mTOR-activated transcriptome and found that hyperactivation of mTOR promotes transcriptome-wide exon skipping/exclusion, producing short isoform transcripts from genes. This widespread exon skipping confers multifarious regulations in the mTOR-controlled functional proteomics: AS in coding regions widely affects the protein length and functional domains. They also alter the half-life of proteins and affect the regulatory post-translational modifications. Among the RNA processing factors differentially regulated by mTOR signaling, we found that SRSF3 mechanistically facilitates exon skipping in the mTOR-activated transcriptome. This study reveals a role of mTOR in AS regulation and demonstrates that widespread AS is a multifaceted modulator of the mTOR-regulated functional proteome.
    Keywords:  alternative splicing; functional proteome; mTOR signaling; post-transcriptional gene regulation
    DOI:  https://doi.org/10.3390/ijms232012416
  48. Cell Death Dis. 2022 Oct 26. 13(10): 899
    The oncoprotein MUC1 facilitates breast cancer progression by promoting Pink1-dependent mitophagy via ATAD3A destabilization.
    Quanfu Li, Yunkai Chu, Shengze Li, Liping Yu, Huayun Deng, Chunhua Liao, Xiaodong Liao, Chihyu Yang, Min Qi, Jinke Cheng, Guoqiang Chen, Lei Huang.
      Mitophagy is a vital process that controls mitochondria quality, dysregulation of which can promote cancer. Oncoprotein mucin 1 (MUC1) targets mitochondria to attenuate drug-induced apoptosis. However, little is known about whether and how MUC1 contributes to mitochondrial homeostasis in cancer cells. We identified a novel role of MUC1 in promoting mitophagy. Increased mitophagy is coupled with the translocation of MUC1 to mitochondria, where MUC1 interacts with and induces degradation of ATPase family AAA domain-containing 3A (ATAD3A), resulting in protection of PTEN-induced kinase 1 (Pink1) from ATAD3A-mediated cleavage. Interestingly, MUC1-induced mitophagy is associated with increased oncogenicity of cancer cells. Similarly, inhibition of mitophagy significantly suppresses MUC1-induced cancer cell activity in vitro and in vivo. Consistently, MUC1 and ATAD3A protein levels present an inverse relationship in tumor tissues of breast cancer patients. Our data validate that MUC1/ATAD3A/Pink1 axis-mediated mitophagy constitutes a novel mechanism for maintaining the malignancy of cancer cells, providing a novel therapeutic approach for MUC1-positive cancers.
    DOI:  https://doi.org/10.1038/s41419-022-05345-z
  49. Autophagy. 2022 Oct 27.
    Ablation of endothelial Atg7 inhibits ischemia-induced angiogenesis by upregulating Stat1 that suppresses Hif1a expression.
    Hongmin Yao, Jian Li, Zhixue Liu, Changhan Ouyang, Yu Qiu, Xiaoxu Zheng, Jing Mu, Zhonglin Xie.
      Ischemia-induced angiogenesis is critical for blood flow restoration and tissue regeneration, but the underlying molecular mechanism is not fully understood. ATG7 (autophagy related 7) is essential for classical degradative macroautophagy/autophagy and cell cycle regulation. However, whether and how ATG7 influences endothelial cell (EC) function and regulates post-ischemic angiogenesis remain unknown. Here, we showed that in mice subjected to femoral artery ligation, EC-specific deletion of Atg7 significantly impaired angiogenesis, delayed the recovery of blood flow reperfusion, and displayed reduction in HIF1A (hypoxia inducible factor 1 subunit alpha) expression. In addition, in cultured human umbilical vein endothelial cells (HUVECs), overexpression of HIF1A prevented ATG7 deficiency-reduced tube formation. Mechanistically, we identified STAT1 (signal transducer and activator of transcription 1) as a transcription suppressor of HIF1A and demonstrated that ablation of Atg7 upregulated STAT1 in an autophagy independent pathway, increased STAT1 binding to HIF1A promoter, and suppressed HIF1A expression. Moreover, lack of ATG7 in the cytoplasm disrupted the association between ATG7 and the transcription factor ZNF148/ZFP148/ZBP-89 (zinc finger protein 148) that is required for STAT1 constitutive expression, increased the binding between ZNF148/ZFP148/ZBP-89 and KPNB1 (karyopherin subunit beta 1), which promoted ZNF148/ZFP148/ZBP-89 nuclear translocation, and increased STAT1 expression. Finally, inhibition of STAT1 by fludarabine prevented the inhibition of HIF1A expression, angiogenesis, and blood flow recovery in atg7 KO mice. Our work reveals that lack of ATG7 inhibits angiogenesis by suppression of HIF1A expression through upregulation of STAT1 independently of autophagy under ischemic conditions, and suggest new therapeutic strategies for cancer and cardiovascular diseases.
    Keywords:  ATG7; Angiogenesis; HIF1A; STAT1; ZNF148/ZFP148/ZBP-89; endothelial cell; ischemia
    DOI:  https://doi.org/10.1080/15548627.2022.2139920
  50. Sci Adv. 2022 Oct 28. 8(43): eabn3298
    Control of infection by LC3-associated phagocytosis, CASM, and detection of raised vacuolar pH by the V-ATPase-ATG16L1 axis.
    Yingxue Wang, Maria Ramos, Matthew Jefferson, Weijiao Zhang, Naiara Beraza, Simon Carding, Penny P Powell, James P Stewart, Ulrike Mayer, Thomas Wileman.
      The delivery of pathogens to lysosomes for degradation provides an important defense against infection. Degradation is enhanced when LC3 is conjugated to endosomes and phagosomes containing pathogens to facilitate fusion with lysosomes. In phagocytic cells, TLR signaling and Rubicon activate LC3-associated phagocytosis (LAP) where stabilization of the NADPH oxidase leads to sustained ROS production and raised vacuolar pH. Raised pH triggers the assembly of the vacuolar ATPase on the vacuole membrane where it binds ATG16L1 to recruit the core LC3 conjugation complex (ATG16L1:ATG5-12). This V-ATPase-ATG16L1 axis is also activated in nonphagocytic cells to conjugate LC3 to endosomes containing extracellular microbes. Pathogens provide additional signals for recruitment of LC3 when they raise vacuolar pH with pore-forming toxins and proteins, phospholipases, or specialized secretion systems. Many microbes secrete virulence factors to inhibit ROS production and/or the V-ATPase-ATG16L1 axis to slow LC3 recruitment and avoid degradation in lysosomes.
    DOI:  https://doi.org/10.1126/sciadv.abn3298
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