bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2021–07–04
fifty-six papers selected by
Viktor Korolchuk, Newcastle University
  1. Amino Acid-Mediated Intracellular Ca2+ Rise Modulates mTORC1 by Regulating the TSC2-Rheb Axis through Ca2+/Calmodulin.
  2. iCAL: a new pipeline to investigate autophagy selectivity and cancer.
  3. mTOR Driven Gene Transcription Is Required for Cholesterol Production in Neurons of the Developing Cerebral Cortex.
  4. Ubiquitination and receptor-mediated mitophagy converge to eliminate oxidation-damaged mitochondria during hypoxia.
  5. A natural small molecule induces MAPT clearance via mTOR-independent autophagy.
  6. Regulation of mTORC1 activity by the Golgi apparatus.
  7. Vacuolar accumulation and colocalization is not a proper criterion for cytoplasmic soluble proteins undergoing selective autophagy.
  8. The Pathways Underlying the Multiple Roles of p62 in Inflammation and Cancer.
  9. Atg12-Interacting Motif Is Crucial for E2-E3 Interaction in Plant Atg8 System.
  10. Autophagy activity contributes to the impairment of social recognition in Epac2-/- mice.
  11. Epigenetic Regulation of Autophagy Beyond the Cytoplasm: A Review.
  12. Vangl2 limits chaperone-mediated autophagy to balance osteogenic differentiation in mesenchymal stem cells.
  13. Autophagy deficiency modulates microglial lipid homeostasis and aggravates tau pathology and spreading.
  14. Chemical-Mediated Targeted Protein Degradation in Neurodegenerative Diseases.
  15. Genotoxic stress in constitutive trisomies induces autophagy and the innate immune response via the cGAS-STING pathway.
  16. Autophagy: A Friend or Foe in Allergic Asthma?
  17. Contextualizing Autophagy during Gametogenesis and Preimplantation Embryonic Development.
  18. Mammalian/mechanistic target of rapamycin (mTOR) complexes in neurodegeneration.
  19. V600EBRAF Inhibition Induces Cytoprotective Autophagy through AMPK in Thyroid Cancer Cells.
  20. Restructuring of the plasma membrane upon damage by LC3-associated macropinocytosis.
  21. Autophagy a Close Relative of AML Biology.
  22. Recent Advances in the Roles of Autophagy and Autophagy Proteins in Host Cells During Toxoplasma gondii Infection and Potential Therapeutic Implications.
  23. A Structural Approach into Drug Discovery Based on Autophagy.
  24. TM4SF5 knockout protects mice from diet-induced obesity partly by regulating autophagy in adipose tissue.
  25. AMPK hyperactivation promotes dendrite retraction, synaptic loss, and neuronal dysfunction in glaucoma.
  26. Fluorescent Protein-Based Autophagy Biosensors.
  27. Exploring the Role of Autophagy Dysfunction in Neurodegenerative Disorders.
  28. Wdfy3 regulates glycophagy, mitophagy, and synaptic plasticity.
  29. BECLIN1: Protein Structure, Function and Regulation.
  30. Loss of FYCO1 leads to cataract formation.
  31. Repurposing Niclosamide for Targeting Pancreatic Cancer by Inhibiting Hh/Gli Non-Canonical Axis of Gsk3β.
  32. Editorial: Autophagy and Mitophagy in Skeletal Muscle Health and Disease.
  33. The Role of Mitochondrial Quality Control in Cardiac Ischemia/Reperfusion Injury.
  34. In Silico and In Cell Hybrid Selection of Nonrapalog Ligands to Allosterically Inhibit the Kinase Activity of mTORC1.
  35. The Multifaceted Functions of Autophagy in Breast Cancer Development and Treatment.
  36. Revealing molecular pathways for cancer cell fitness through a genetic screen of the cancer translatome.
  37. Microtubule inhibitors identified through non-biased screening enhance DNA transfection efficiency by delaying p62-dependent ubiquitin recruitment.
  38. Tribbles homolog 3-mediated targeting the AKT/mTOR axis in mice with retinal degeneration.
  39. Dihydroartemisinin Inhibits mTORC1 Signaling by Activating the AMPK Pathway in Rhabdomyosarcoma Tumor Cells.
  40. Vascular Effects of Disrupting Endothelial mTORC1 (Mechanistic Target of Rapamycin Complex 1) Signaling in Obesity.
  41. EVA1A Plays an Important Role by Regulating Autophagy in Physiological and Pathological Processes.
  42. Friend or Foe: Paradoxical Roles of Autophagy in Gliomagenesis.
  43. The mTORC2 Regulator Homer1 Modulates Protein Levels and Sub-Cellular Localization of the CaSR in Osteoblast-Lineage Cells.
  44. The AMPK/p27Kip1 Pathway as a Novel Target to Promote Autophagy and Resilience in Aged Cells.
  45. TRIM44 mediated p62 deubiquitination enhances DNA damage repair by increasing nuclear FLNA and 53BP1 expression.
  46. MERTK-Mediated LC3-Associated Phagocytosis (LAP) of Apoptotic Substrates in Blood-Separated Tissues: Retina, Testis, Ovarian Follicles.
  47. Chemical and Structural Strategies to Selectively Target mTOR Kinase.
  48. Monitoring Mitophagy via the FRET Mechanism: Visualizing Mitochondria, Lysosomes, and Autolysosomes in Three Different Sets of Fluorescence Signals.
  49. Autophagy complements metalloprotease FtsH6 in degrading plastid heat shock protein HSP21 during heat stress recovery.
  50. The Roles of Oxidative Stress in Regulating Autophagy in Methylmercury-induced Neurotoxicity.
  51. The PINK1-Mediated Crosstalk between Neural Cells and the Underlying Link to Parkinson's Disease.
  52. Bcl-2-dependent autophagy disruption during aging impairs amino acid utilization that is restored by hochuekkito.
  53. Epigenetic Regulation of Autophagy in Cardiovascular Pathobiology.
  54. Effect of Chronic Stress Present in Fibroblasts Derived from Patients with a Sporadic Form of AD on Mitochondrial Function and Mitochondrial Turnover.
  55. Glycogen Synthase Kinase 3 Beta Regulates the Human Aryl Hydrocarbon Receptor Cellular Content and Activity.
  56. n-Butylidenephthalide Modulates Autophagy to Ameliorate Neuropathological Progress of Spinocerebellar Ataxia Type 3 through mTOR Pathway.
  1. Int J Mol Sci. 2021 Jun 27. pii: 6897. [Epub ahead of print]22(13):
    Amino Acid-Mediated Intracellular Ca2+ Rise Modulates mTORC1 by Regulating the TSC2-Rheb Axis through Ca2+/Calmodulin.
    Yuna Amemiya, Nao Nakamura, Nao Ikeda, Risa Sugiyama, Chiaki Ishii, Masatoshi Maki, Hideki Shibata, Terunao Takahara.
      Mechanistic target of rapamycin complex 1 (mTORC1) is a master growth regulator by controlling protein synthesis and autophagy in response to environmental cues. Amino acids, especially leucine and arginine, are known to be important activators of mTORC1 and to promote lysosomal translocation of mTORC1, where mTORC1 is thought to make contact with its activator Rheb GTPase. Although amino acids are believed to exclusively regulate lysosomal translocation of mTORC1 by Rag GTPases, how amino acids increase mTORC1 activity besides regulation of mTORC1 subcellular localization remains largely unclear. Here we report that amino acids also converge on regulation of the TSC2-Rheb GTPase axis via Ca2+/calmodulin (CaM). We showed that the amino acid-mediated increase of intracellular Ca2+ is important for mTORC1 activation and thereby contributes to the promotion of nascent protein synthesis. We found that Ca2+/CaM interacted with TSC2 at its GTPase activating protein (GAP) domain and that a CaM inhibitor reduced binding of CaM with TSC2. The inhibitory effect of a CaM inhibitor on mTORC1 activity was prevented by loss of TSC2 or by an active mutant of Rheb GTPase, suggesting that a CaM inhibitor acts through the TSC2-Rheb axis to inhibit mTORC1 activity. Taken together, in response to amino acids, Ca2+/CaM-mediated regulation of the TSC2-Rheb axis contributes to proper mTORC1 activation, in addition to the well-known lysosomal translocation of mTORC1 by Rag GTPases.
    Keywords:  Rheb GTPase; TSC; amino acid; calcium; calmodulin; mTOR
    DOI:  https://doi.org/10.3390/ijms22136897
  2. Autophagy. 2021 Jun 28. 1-3
    iCAL: a new pipeline to investigate autophagy selectivity and cancer.
    Weizhi Zhang, Zhu Han, Yu Xue, Da Jia.
      Macroautophagy/autophagy can selectively degrade misfolded proteins, damaged organelles and other cargoes. It is conceivable that alteration of the degradation processes could disrupt normal cellular signaling and contribute to human diseases such as cancer. To explore the link between aberrant autophagy selectivity and human cancer, we have developed a pipeline called "inference of cancer-associated LC3-interacting region-containing proteins" (iCAL), which integrates a sequence-based predictor, a model-based computational method, publicly available cancer mutations, and multiple experimental approaches. Using iCAL, we have identified 222 LIR motif-associated mutations (LAMs) in 148 LIR-containing proteins (LIRCPs), and validated that LAMs in ATG4B, STBD1, EHMT2 and BRAF impair their interactions with LC3 and/or autophagy activities. Moreover, we uncovered that STBD1, a previously poorly-characterized protein, inhibits tumor growth via metabolism reprogramming in cancer cells. A patient-derived mutation in STBD1 (W203C) disrupts the interaction with LC3 and promotes tumor growth. Taken together, iCAL provides an exciting new avenue to discover novel autophagy pathways that contribute to carcinogenesis.
    Keywords:  Autophagy; LIR; STBD1; cancer; cancer mutation; glycophagy; selective autophagy
    DOI:  https://doi.org/10.1080/15548627.2021.1939972
  3. Int J Mol Sci. 2021 Jun 03. pii: 6034. [Epub ahead of print]22(11):
    mTOR Driven Gene Transcription Is Required for Cholesterol Production in Neurons of the Developing Cerebral Cortex.
    Martin Schüle, Tamer Butto, Sri Dewi, Laura Schlichtholz, Susanne Strand, Susanne Gerber, Kristina Endres, Susann Schweiger, Jennifer Winter.
      Dysregulated mammalian target of rapamycin (mTOR) activity is associated with various neurodevelopmental disorders ranging from idiopathic autism spectrum disorders (ASD) to syndromes caused by single gene defects. This suggests that maintaining mTOR activity levels in a physiological range is essential for brain development and functioning. Upon activation, mTOR regulates a variety of cellular processes such as cell growth, autophagy, and metabolism. On a molecular level, however, the consequences of mTOR activation in the brain are not well understood. Low levels of cholesterol are associated with a wide variety of neurodevelopmental disorders. We here describe numerous genes of the sterol/cholesterol biosynthesis pathway to be transcriptionally regulated by mTOR complex 1 (mTORC1) signaling in vitro in primary neurons and in vivo in the developing cerebral cortex of the mouse. We find that these genes are shared targets of the transcription factors SREBP, SP1, and NF-Y. Prenatal as well as postnatal mTORC1 inhibition downregulated expression of these genes which directly translated into reduced cholesterol levels, pointing towards a substantial metabolic function of the mTORC1 signaling cascade. Altogether, our results indicate that mTORC1 is an essential transcriptional regulator of the expression of sterol/cholesterol biosynthesis genes in the developing brain. Altered expression of these genes may be an important factor contributing to the pathogenesis of neurodevelopmental disorders associated with dysregulated mTOR signaling.
    Keywords:  NF-Y; SP1; SREBP; cholesterol; mTOR; mTORC1; neurogenesis
    DOI:  https://doi.org/10.3390/ijms22116034
  4. Redox Biol. 2021 Jun 17. pii: S2213-2317(21)00206-8. [Epub ahead of print]45 102047
    Ubiquitination and receptor-mediated mitophagy converge to eliminate oxidation-damaged mitochondria during hypoxia.
    Prasad Sulkshane, Jonathan Ram, Anita Thakur, Noa Reis, Oded Kleifeld, Michael H Glickman.
      The contribution of the Ubiquitin-Proteasome System (UPS) to mitophagy has been largely attributed to the E3 ubiquitin ligase Parkin. Here we show that in response to the oxidative stress associated with hypoxia or the hypoxia mimic CoCl2, the damaged and fragmented mitochondria are removed by Parkin-independent mitophagy. Mitochondria isolated from hypoxia or CoCl2-treated cells exhibited extensive ubiquitination, predominantly Lysine 48-linked and involves the degradation of key mitochondrial proteins such as the mitofusins MFN1/2, or the import channel component TOM20. Reflecting the critical role of mitochondrial protein degradation, proteasome inhibition blocked CoCl2-induced mitophagy. The five conserved ubiquitin-binding autophagy receptors (p62, NDP52, Optineurin, NBR1, TAX1BP1) were dispensable for the ensuing mitophagy, suggesting that the mitophagy step itself was independent of ubiquitination. Instead, the expression of two ubiquitin-independent mitophagy receptor proteins BNIP3 and NIX was induced by hypoxia or CoCl2-treatment followed by their recruitment to the oxidation-damaged mitochondria. By employing BNIP3/NIX double knockout and DRP1-null cell lines, we confirmed that mitochondrial clearance relies on DRP1-dependent mitochondrial fragmentation and BNIP3/NIX-mediated mitophagy. General antioxidants such as N-Acetyl Cysteine (NAC) or the mitochondria-specific Mitoquinone prevented HIF-1α stabilization, ameliorated hypoxia-related mitochondrial oxidative stress, and suppressed mitophagy. We conclude that the UPS and receptor-mediated autophagy converge to eliminate oxidation-damaged mitochondria.
    Keywords:  HIF-1α; Hypoxia; Mitochondria; Mitophagy; Oxidative stress; Proteasome; Ubiquitin
    DOI:  https://doi.org/10.1016/j.redox.2021.102047
  5. Biochem Biophys Res Commun. 2021 Jun 23. pii: S0006-291X(21)00981-5. [Epub ahead of print]568 30-36
    A natural small molecule induces MAPT clearance via mTOR-independent autophagy.
    Dasol Kim, Hui-Yun Hwang, Ho Jeong Kwon.
      Autophagy, the process of lysosomal degradation of biological materials within cells, is often halted abnormally in proteopathies, such as tauopathy and amyloidopathy. Thus, autophagy regulators that rescue dysregulated autophagy have great potential to treat proteopathies. We previously reported that the natural small molecule kaempferide (Kaem) induces autophagy without perturbing mTOR signaling. Here, we report that Kaem promotes lysosomal degradation of microtubule-associated protein tau (MAPT) in inducible MAPT cells. Kaem enhanced autophagy flux by mitigating microtubule-associated protein 1 light chain 3 (LC3) accumulation when MAPT expression was induced. Kaem also promoted activation of transcription factor EB (TFEB) without inhibiting mTOR and without mTOR inhibition-mediated cytotoxicity. In addition, Kaem-induced MAPT degradation was abolished in the absence of mitochondrial elongation factor Tu (TUFM), which was previously shown to be a direct binding partner of Kaem. Collectively, these results demonstrate that Kaem could be a potential therapeutic for tauopathy and reveal that TUFM can be a drug target for autophagy-driven disorders.
    Keywords:  Autophagy; Kaempferide; MAPT; Tauopathy; mTOR
    DOI:  https://doi.org/10.1016/j.bbrc.2021.06.060
  6. Fac Rev. 2021 ;10 50
    Regulation of mTORC1 activity by the Golgi apparatus.
    Christian Makhoul, Paul A Gleeson.
      Mechanistic (or mammalian) target of rapamycin complex 1 (mTORC1) is a major signalling kinase in cells that regulates proliferation and metabolism and is controlled by extrinsic and intrinsic signals. The lysosome has received considerable attention as a major hub of mTORC1 activation. However, mTOR has also been located to a variety of other intracellular sites, indicating the possibility of spatial regulation of mTORC1 signalling within cells. In particular, there have been numerous recent reports of mTORC1 activation associated with the Golgi apparatus. Here, we review the evidence for the regulation of mTORC1 signalling at the Golgi in mammalian cells. mTORC1 signalling is closely linked to the morphology of the Golgi architecture; a number of Golgi membrane tethers/scaffolds that influence Golgi architecture in mammalian cells that directly or indirectly regulate mTORC1 activation have been identified. Perturbation of the Golgi mTORC1 pathway arising from fragmentation of the Golgi has been shown to promote oncogenesis. Here, we highlight the potential mechanisms for the activation mTORC1 at the Golgi, which is emerging as a major site for mTORC1 signalling.
    Keywords:  Arf1; GAT4; GCC88; GOLPH3; Golgi architecture; Rab1A; actin; mTORC1; signalling; trans-Golgi network
    DOI:  https://doi.org/10.12703/r/10-50
  7. Plant Signal Behav. 2021 Jun 27. 1932319
    Vacuolar accumulation and colocalization is not a proper criterion for cytoplasmic soluble proteins undergoing selective autophagy.
    Jingfang Yu, Jun Zhou.
      Autophagy is an important cytoprotective process that mediates degradation of dysfunctional or unnecessary cellular components. In the process of autophagy, a double-membrane organelle termed the autophagosome is formed to sequestrate portions of cytoplasm and subsequently delivered into lysosome or vacuole for degradation. The accumulation of autophagic bodies in the vacuoles after treatment with concanamycin A (ConcA) is a widely used protocol for monitoring the occurrence of autophagy in plants. Here, it was found that the cytoplasmic soluble GFP was accumulated in vacuoles upon ConcA treatment. Importantly, the GFP signal showed good colocalization with the autophagic marker mCherry-ATG8f in vacuoles based on two commonly used methods, the Pearson-Spearman correlation colocalization analysis and the plot profile analysis. Further results showed that the free GFP did not interact with ATG8s. Thus, analysis of accumulation and colocalization only in vacuoles is not a trustworthy way to judge whether degradation of cytoplasmic protein is dependent on the selective autophagy pathway in plants. In this short perspective, we propose several primary steps to distinguish that the cytoplasmic proteins are degraded by selective or bulk autophagy, hoping they could contribute to identify and clarify the selective autophagic cargos and receptors in plants.
    Keywords:  Autophagy; cargos; colocalization analysis; concanamycin A; cytoplasmic soluble protein; receptors
    DOI:  https://doi.org/10.1080/15592324.2021.1932319
  8. Biomedicines. 2021 Jun 22. pii: 707. [Epub ahead of print]9(7):
    The Pathways Underlying the Multiple Roles of p62 in Inflammation and Cancer.
    Paulina Hennig, Gabriele Fenini, Michela Di Filippo, Tugay Karakaya, Hans-Dietmar Beer.
      p62 is a highly conserved, multi-domain, and multi-functional adaptor protein critically involved in several important cellular processes. Via its pronounced domain architecture, p62 binds to numerous interaction partners, thereby influencing key pathways that regulate tissue homeostasis, inflammation, and several common diseases including cancer. Via binding of ubiquitin chains, p62 acts in an anti-inflammatory manner as an adaptor for the auto-, xeno-, and mitophagy-dependent degradation of proteins, pathogens, and mitochondria. Furthermore, p62 is a negative regulator of inflammasome complexes. The transcription factor Nrf2 regulates expression of a bundle of ROS detoxifying genes. p62 activates Nrf2 by interaction with and autophagosomal degradation of the Nrf2 inhibitor Keap1. Moreover, p62 activates mTOR, the central kinase of the mTORC1 sensor complex that controls cell proliferation and differentiation. Through different mechanisms, p62 acts as a positive regulator of the transcription factor NF-κB, a central player in inflammation and cancer development. Therefore, p62 represents not only a cargo receptor for autophagy, but also a central signaling hub, linking several important pro- and anti-inflammatory pathways. This review aims to summarize knowledge about the molecular mechanisms underlying the roles of p62 in health and disease. In particular, different types of tumors are characterized by deregulated levels of p62. The elucidation of how p62 contributes to inflammation and cancer progression at the molecular level might promote the development of novel therapeutic strategies.
    Keywords:  NF-κB; Nrf2/Keap1; autophagy; cancer; inflammasomes; inflammation; mTORC1; p62
    DOI:  https://doi.org/10.3390/biomedicines9070707
  9. Biol Pharm Bull. 2021 Jul 01.
    Atg12-Interacting Motif Is Crucial for E2-E3 Interaction in Plant Atg8 System.
    Kazuaki Matoba, Nobuo N Noda.
      Autophagy is an intracellular degradation system regulating cellular homeostasis. The two ubiquitin-like modification systems named the Atg8 system and the Atg12 system are essential for autophagy. Atg8 and Atg12 are ubiquitin-like proteins covalently conjugated with a phosphatidylethanolamine (PE) and Atg5, respectively, via enzymatic reactions. The Atg8-PE conjugate binds to autophagic membranes and recruits various proteins through direct interaction, whereas the Atg12-Atg5 conjugate recognizes Atg3, the E2 enzyme for Atg8, and facilitates Atg8-PE conjugation by functioning as the E3 enzyme. Although structural and biochemical analyses have well established the Atg8-family interacting motif (AIM), studies on the interacting sequence for Atg12 are rare (only one example for human ATG12-ATG3), thereby making it challenging to define a binding motif. Here we determined the crystal structure of the plant ATG12b as a complex with the ATG12b-binding region of ATG3 and revealed that ATG12b recognizes the Asp-Met motif in ATG3 via a hydrophobic pocket and a basic residue, which we confirmed critical for the complex formation by mutational analysis. This recognition mode is similar to that reported between human ATG12 and ATG3, suggesting that the Asp-Met sequence is a conserved Atg12-interacting motif (AIM12). These data suggest that AIM12 mediates E2-E3 interaction during Atg8 lipidation and provide structural basis for developing chemicals that regulate autophagy by targeting Atg12-family proteins.
    Keywords:  Atg12-interacting motif; Atg8 system; autophagy; crystal structure
    DOI:  https://doi.org/10.1248/bpb.b21-00439
  10. Mol Brain. 2021 Jun 28. 14(1): 100
    Autophagy activity contributes to the impairment of social recognition in Epac2-/- mice.
    Ji-Hye Kwak, You-Kyung Lee, Mi-Hee Jun, Mootaek Roh, Hyunhyo Seo, Juhyun Lee, Kyungmin Lee, Jin-A Lee.
      Autophagy is a lysosomal degradation pathway that regulates cellular homeostasis. It is constitutively active in neurons and controls the essential steps of neuronal development, leading to its dysfunction in neurodevelopmental disorders. Although mTOR-associated impaired autophagy has previously been reported in neurodevelopmental disorders, there is lack of information about the dysregulation of mTOR-independent autophagy in neurodevelopmental disorders. In this study, we investigated whether the loss of Epac2, involved in the mTOR-independent pathway, affects autophagy activity and whether the activity of autophagy is associated with social-behavioral phenotypes in mice with Epac2 deficiencies. We observed an accumulation of autophagosomes and a significant increase in autophagic flux in Epac2-deficient neurons, which had no effect on mTOR activity. Next, we examined whether an increase in autophagic activity contributed to the social behavior exhibited in Epac2-/- mice. The social recognition deficit observed in Epac2-/- mice recovered in double transgenic Epac2-/-: Atg5+/- mice. Our study suggests that excessive autophagy due to Epac2 deficiencies may contribute to social recognition defects through an mTOR-independent pathway.
    Keywords:  Autophagy; Epac2; Neurodevelopmental disorders; Social recognition
    DOI:  https://doi.org/10.1186/s13041-021-00814-6
  11. Front Cell Dev Biol. 2021 ;9 675599
    Epigenetic Regulation of Autophagy Beyond the Cytoplasm: A Review.
    Yin Shi, Han-Ming Shen, Vidya Gopalakrishnan, Nancy Gordon.
      Autophagy is a highly conserved catabolic process induced under various stress conditions to protect the cell from harm and allow survival in the face of nutrient- or energy-deficient states. Regulation of autophagy is complex, as cells need to adapt to a continuously changing microenvironment. It is well recognized that the AMPK and mTOR signaling pathways are the main regulators of autophagy. However, various other signaling pathways have also been described to regulate the autophagic process. A better understanding of these complex autophagy regulatory mechanisms will allow the discovery of new potential therapeutic targets. Here, we present a brief overview of autophagy and its regulatory pathways with emphasis on the epigenetic control mechanisms.
    Keywords:  autophagy; chromatin; epigenetic; histone deacetylases; methyltransferases
    DOI:  https://doi.org/10.3389/fcell.2021.675599
  12. Dev Cell. 2021 Jun 29. pii: S1534-5807(21)00518-9. [Epub ahead of print]
    Vangl2 limits chaperone-mediated autophagy to balance osteogenic differentiation in mesenchymal stem cells.
    Yan Gong, Ziqi Li, Shitian Zou, Daizhao Deng, Pinglin Lai, Hongling Hu, Yongzhou Yao, Le Hu, Sheng Zhang, Kai Li, Tiantian Wei, Xiaoyang Zhao, Guozhi Xiao, Zifeng Chen, Yu Jiang, Xiaochun Bai, Zhipeng Zou.
      Lysosomes are the recycling center and nutrient signaling hub of the cell. Here, we show that lysosomes also control mesenchymal stem cell (MSC) differentiation by proteomic reprogramming. The chaperone-mediated autophagy (CMA) lysosome subgroup promotes osteogenesis, while suppressing adipogenesis, by selectively removing osteogenesis-deterring factors, especially master transcriptional factors, such as adipogenic TLE3, ZNF423, and chondrogenic SOX9. The activity of the CMA-committed lysosomes in MSCs are controlled by Van-Gogh-like 2 (Vangl2) at lysosomes. Vangl2 directly binds to lysosome-associated membrane protein 2A (LAMP-2A) and targets it for degradation. MSC-specific Vangl2 ablation in mice increases LAMP-2A expression and CMA-lysosome numbers, promoting bone formation while reducing marrow fat. The Vangl2:LAMP-2A ratio in MSCs correlates inversely with the capacity of the cells for osteoblastic differentiation in humans and mice. These findings demonstrate a critical role for lysosomes in MSC lineage acquisition and establish Vangl2-LAMP-2A signaling as a critical control mechanism.
    Keywords:  LAMP-2A; MSC; Vangl2; autophagy; lysosome; osteoblast; osteogenesis
    DOI:  https://doi.org/10.1016/j.devcel.2021.06.011
  13. Proc Natl Acad Sci U S A. 2021 Jul 06. pii: e2023418118. [Epub ahead of print]118(27):
    Autophagy deficiency modulates microglial lipid homeostasis and aggravates tau pathology and spreading.
    Yin Xu, Nicholas E Propson, Shuqi Du, Wen Xiong, Hui Zheng.
      The autophagy-lysosomal pathway plays a critical role in intracellular clearance and metabolic homeostasis. While neuronal autophagy is known to participate in the degradation of neurofibrillary tangles composed of hyperphosphorylated and misfolded tau protein in Alzheimer's disease and other tauopathies, how microglial-specific autophagy regulates microglial intrinsic properties and neuronal tau pathology is not well understood. We report here that Atg7, a key mediator of autophagosome biogenesis, plays an essential role in the regulation of microglial lipid metabolism and neuroinflammation. Microglia-specific deletion of Atg7 leads to the transition of microglia to a proinflammatory status in vivo and to inflammasome activation in vitro. Activation of ApoE and lipid efflux attenuates the lipid droplets accumulation and inhibits cytokine production in microglial cells with Atg7 deficiency. Functionally, we show that the absence of microglial Atg7 enhances intraneuronal tau pathology and its spreading. Our results reveal an essential role for microglial autophagy in regulating lipid homeostasis, neuroinflammation, and tau pathology.
    Keywords:  Alzheimer's disease; autophagy; lipid metabolism; microglia; tau
    DOI:  https://doi.org/10.1073/pnas.2023418118
  14. Life (Basel). 2021 Jun 24. pii: 607. [Epub ahead of print]11(7):
    Chemical-Mediated Targeted Protein Degradation in Neurodegenerative Diseases.
    Soonsil Hyun, Dongyun Shin.
      Neurodegenerative diseases, including Alzheimer's disease, Huntington's disease, and Parkinson's disease, are a class of diseases that lead to dysfunction of cognition and mobility. Aggregates of misfolded proteins such as β-amyloid, tau, α-synuclein, and polyglutamates are known to be among the main causes of neurodegenerative diseases; however, they are considered to be some of the most challenging drug targets because they cannot be modulated by conventional small-molecule agents. Recently, the degradation of target proteins by small molecules has emerged as a new therapeutic modality and has garnered the interest of the researchers in the pharmaceutical industry. Bifunctional molecules that recruit target proteins to a cellular protein degradation machinery, such as the ubiquitin-proteasome system and autophagy-lysosome pathway, have been designed. The representative targeted protein degradation technologies include molecular glues, proteolysis-targeting chimeras, hydrophobic tagging, autophagy-targeting chimeras, and autophagosome-tethering compounds. Although these modalities have been shown to degrade many disease-related proteins, such technologies are expected to be potentially important for neurogenerative diseases caused by protein aggregation. Herein, we review the recent progress in chemical-mediated targeted protein degradation toward the discovery of drugs for neurogenerative diseases.
    Keywords:  autophagy; drug design; neurodegenerative disease; protac; protein degradation; ubiquitin-proteasome system
    DOI:  https://doi.org/10.3390/life11070607
  15. Commun Biol. 2021 Jul 02. 4(1): 831
    Genotoxic stress in constitutive trisomies induces autophagy and the innate immune response via the cGAS-STING pathway.
    Maria Krivega, Clara M Stiefel, Sahar Karbassi, Line L Andersen, Narendra K Chunduri, Neysan Donnelly, Andreas Pichlmair, Zuzana Storchová.
      Gain of even a single chromosome leads to changes in human cell physiology and uniform perturbations of specific cellular processes, including downregulation of DNA replication pathway, upregulation of autophagy and lysosomal degradation, and constitutive activation of the type I interferon response. Little is known about the molecular mechanisms underlying these changes. We show that the constitutive nuclear localization of TFEB, a transcription factor that activates the expression of autophagy and lysosomal genes, is characteristic of human trisomic cells. Constitutive nuclear localization of TFEB in trisomic cells is independent of mTORC1 signaling, but depends on the cGAS-STING activation. Trisomic cells accumulate cytoplasmic dsDNA, which activates the cGAS-STING signaling cascade, thereby triggering nuclear accumulation of the transcription factor IRF3 and, consequently, upregulation of interferon-stimulated genes. cGAS depletion interferes with TFEB-dependent upregulation of autophagy in model trisomic cells. Importantly, activation of both the innate immune response and autophagy occurs also in primary trisomic embryonic fibroblasts, independent of the identity of the additional chromosome. Our research identifies the cGAS-STING pathway as an upstream regulator responsible for activation of autophagy and inflammatory response in human cells with extra chromosomes, such as in Down syndrome or other aneuploidy-associated pathologies.
    DOI:  https://doi.org/10.1038/s42003-021-02278-9
  16. Int J Mol Sci. 2021 Jun 12. pii: 6314. [Epub ahead of print]22(12):
    Autophagy: A Friend or Foe in Allergic Asthma?
    Efthymia Theofani, Georgina Xanthou.
      Autophagy is a major self-degradative process through which cytoplasmic material, including damaged organelles and proteins, are delivered and degraded in the lysosome. Autophagy represents a dynamic recycling system that produces new building blocks and energy, essential for cellular renovation, physiology, and homeostasis. Principal autophagy triggers include starvation, pathogens, and stress. Autophagy plays also a pivotal role in immune response regulation, including immune cell differentiation, antigen presentation and the generation of T effector responses, the development of protective immunity against pathogens, and the coordination of immunometabolic signals. A plethora of studies propose that both impaired and overactive autophagic processes contribute to the pathogenesis of human disorders, including infections, cancer, atherosclerosis, autoimmune and neurodegenerative diseases. Autophagy has been also implicated in the development and progression of allergen-driven airway inflammation and remodeling. Here, we provide an overview of recent studies pertinent to the biology of autophagy and molecular pathways controlling its activation, we discuss autophagy-mediated beneficial and detrimental effects in animal models of allergic diseases and illuminate new advances on the role of autophagy in the pathogenesis of human asthma. We conclude contemplating the potential of targeting autophagy as a novel therapeutic approach for the management of allergic responses and linked asthmatic disease.
    Keywords:  airway inflammation; asthma; autophagy
    DOI:  https://doi.org/10.3390/ijms22126314
  17. Int J Mol Sci. 2021 Jun 12. pii: 6313. [Epub ahead of print]22(12):
    Contextualizing Autophagy during Gametogenesis and Preimplantation Embryonic Development.
    Marcelo T Moura, Laís B Latorraca, Fabíola F Paula-Lopes.
      Mammals face environmental stressors throughout their lifespan, which may jeopardize cellular homeostasis. Hence, these organisms have acquired mechanisms to cope with stressors by sensing, repairing the damage, and reallocating resources to increase the odds of long-term survival. Autophagy is a pro-survival lysosome-mediated cytoplasm degradation pathway for organelle and macromolecule recycling. Furthermore, autophagy efflux increases, and this pathway becomes idiosyncratic depending upon developmental and environmental contexts. Mammalian germ cells and preimplantation embryos are attractive models for dissecting autophagy due to their metastable phenotypes during differentiation and exposure to varying environmental cues. The aim of this review is to explore autophagy during mammalian gametogenesis, fertilization and preimplantation embryonic development by contemplating its physiological role during development, under key stressors, and within the scope of assisted reproduction technologies.
    Keywords:  ART; autophagic; cloning; embryogenesis; oogenesis; reproduction; reprogramming; spermatozoa
    DOI:  https://doi.org/10.3390/ijms22126313
  18. Mol Neurodegener. 2021 Jul 02. 16(1): 44
    Mammalian/mechanistic target of rapamycin (mTOR) complexes in neurodegeneration.
    Henry Querfurth, Han-Kyu Lee.
      Novel targets to arrest neurodegeneration in several dementing conditions involving misfolded protein accumulations may be found in the diverse signaling pathways of the Mammalian/mechanistic target of rapamycin (mTOR). As a nutrient sensor, mTOR has important homeostatic functions to regulate energy metabolism and support neuronal growth and plasticity. However, in Alzheimer's disease (AD), mTOR alternately plays important pathogenic roles by inhibiting both insulin signaling and autophagic removal of β-amyloid (Aβ) and phospho-tau (ptau) aggregates. It also plays a role in the cerebrovascular dysfunction of AD. mTOR is a serine/threonine kinase residing at the core in either of two multiprotein complexes termed mTORC1 and mTORC2. Recent data suggest that their balanced actions also have implications for Parkinson's disease (PD) and Huntington's disease (HD), Frontotemporal dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS). Beyond rapamycin; an mTOR inhibitor, there are rapalogs having greater tolerability and micro delivery modes, that hold promise in arresting these age dependent conditions.
    Keywords:  Akt; Alzheimer’s; Insulin signaling; Parkinson’s; Rapamycin; mTOR
    DOI:  https://doi.org/10.1186/s13024-021-00428-5
  19. Int J Mol Sci. 2021 Jun 03. pii: 6033. [Epub ahead of print]22(11):
    V600EBRAF Inhibition Induces Cytoprotective Autophagy through AMPK in Thyroid Cancer Cells.
    Eva Jiménez-Mora, Beatriz Gallego, Sergio Díaz-Gago, Marina Lasa, Pablo Baquero, Antonio Chiloeches.
      The dysregulation of autophagy is important in the development of many cancers, including thyroid cancer, where V600EBRAF is a main oncogene. Here, we analyse the effect of V600EBRAF inhibition on autophagy, the mechanisms involved in this regulation and the role of autophagy in cell survival of thyroid cancer cells. We reveal that the inhibition of V600EBRAF activity with its specific inhibitor PLX4720 or the depletion of its expression by siRNA induces autophagy in thyroid tumour cells. We show that V600EBRAF downregulation increases LKB1-AMPK signalling and decreases mTOR activity through a MEK/ERK-dependent mechanism. Moreover, we demonstrate that PLX4720 activates ULK1 and increases autophagy through the activation of the AMPK-ULK1 pathway, but not by the inhibition of mTOR. In addition, we find that autophagy blockade decreases cell viability and sensitize thyroid cancer cells to V600EBRAF inhibition by PLX4720 treatment. Finally, we generate a thyroid xenograft model to demonstrate that autophagy inhibition synergistically enhances the anti-proliferative and pro-apoptotic effects of V600EBRAF inhibition in vivo. Collectively, we uncover a new role of AMPK in mediating the induction of cytoprotective autophagy by V600EBRAF inhibition. In addition, these data establish a rationale for designing an integrated therapy targeting V600EBRAF and the LKB1-AMPK-ULK1-autophagy axis for the treatment of V600EBRAF-positive thyroid tumours.
    Keywords:  AMPK; LKB1; ULK1; V600EBRAF; autophagy; survival; thyroid cancer
    DOI:  https://doi.org/10.3390/ijms22116033
  20. Sci Adv. 2021 Jul;pii: eabg1969. [Epub ahead of print]7(27):
    Restructuring of the plasma membrane upon damage by LC3-associated macropinocytosis.
    Stine Lauritzen Sønder, Swantje Christin Häger, Anne Sofie Busk Heitmann, Lisa B Frankel, Catarina Dias, Adam Cohen Simonsen, Jesper Nylandsted.
      The plasma membrane shapes and protects the eukaryotic cell from its surroundings and is crucial for cell life. Although initial repair mechanisms to reseal injured membranes are well established, less is known about how cells restructure damaged membranes in the aftermath to restore homeostasis. Here, we show that cells respond to plasma membrane injury by activating proteins associated with macropinocytosis specifically at the damaged membrane. Subsequent to membrane resealing, cells form large macropinosomes originating from the repair site, which eventually become positive for autophagy-related LC3B protein. This process occurs independent of ULK1, ATG13, and WIPI2 but dependent on ATG7, p62, and Rubicon. Internalized macropinosomes shrink in the cytoplasm, likely by osmotic draining, and eventually fuse with lysosomes. We propose that a form of macropinocytosis coupled to noncanonical autophagy, which we term LC3-associated macropinocytosis (LAM) functions to remove damaged material from the plasma membrane and restore membrane integrity upon injury.
    DOI:  https://doi.org/10.1126/sciadv.abg1969
  21. Biology (Basel). 2021 Jun 18. pii: 552. [Epub ahead of print]10(6):
    Autophagy a Close Relative of AML Biology.
    Carine Joffre, Charlotte Ducau, Laura Poillet-Perez, Charly Courdy, Véronique Mansat-De Mas.
      Autophagy, which literally means "eat yourself", is more than just a lysosomal degradation pathway. It is a well-known regulator of cellular metabolism and a mechanism implicated in tumor initiation/progression and therapeutic resistance in many cancers. However, whether autophagy acts as a tumor suppressor or promoter is still a matter of debate. In acute myeloid leukemia (AML), it is now proven that autophagy supports cell proliferation in vitro and leukemic progression in vivo. Mitophagy, the specific degradation of mitochondria through autophagy, was recently shown to be required for leukemic stem cell functions and survival, highlighting the prominent role of this selective autophagy in leukemia initiation and progression. Moreover, autophagy in AML sustains fatty acid oxidation through lipophagy to support mitochondrial oxidative phosphorylation (OxPHOS), a hallmark of chemotherapy-resistant cells. Nevertheless, in the context of therapy, in AML, as well as in other cancers, autophagy could be either cytoprotective or cytotoxic, depending on the drugs used. This review summarizes the recent findings that mechanistically show how autophagy favors leukemic transformation of normal hematopoietic stem cells, as well as AML progression and also recapitulates its ambivalent role in resistance to chemotherapies and targeted therapies.
    Keywords:  AML; autophagy; hematopoiesis; mitophagy; therapy
    DOI:  https://doi.org/10.3390/biology10060552
  22. Front Cell Dev Biol. 2021 ;9 673813
    Recent Advances in the Roles of Autophagy and Autophagy Proteins in Host Cells During Toxoplasma gondii Infection and Potential Therapeutic Implications.
    Carlos S Subauste.
      Toxoplasma gondii is an obligate intracellular protozoan that can cause encephalitis and retinitis in humans. The success of T. gondii as a pathogen depends in part on its ability to form an intracellular niche (parasitophorous vacuole) that allows protection from lysosomal degradation and parasite replication. The parasitophorous vacuole can be targeted by autophagy or by autophagosome-independent processes triggered by autophagy proteins. However, T. gondii has developed many strategies to preserve the integrity of the parasitophorous vacuole. Here, we review the interaction between T. gondii, autophagy, and autophagy proteins and expand on recent advances in the field, including the importance of autophagy in the regulation of invasion of the brain and retina by the parasite. We discuss studies that have begun to explore the potential therapeutic applications of the knowledge gained thus far.
    Keywords:  CD40; IFN-γ; cell signaling; endothelial; epithelial; macrophage
    DOI:  https://doi.org/10.3389/fcell.2021.673813
  23. Life (Basel). 2021 Jun 04. pii: 526. [Epub ahead of print]11(6):
    A Structural Approach into Drug Discovery Based on Autophagy.
    Sung-Min Kang, Do-Hee Kim.
      Autophagy is a lysosome-dependent intracellular degradation machinery that plays an essential role in the regulation of cellular homeostasis. As many studies have revealed that autophagy is related to cancer, neurodegenerative diseases, metabolic diseases, and so on, and it is considered as a promising drug target. Recent advances in structural determination and computational technologies provide important structural information on essential autophagy-related proteins. Combined with high-throughput screening methods, structure-activity relationship studies have led to the discovery of molecules that modulate autophagy. In this review, we summarize the recent structural studies on autophagy-related proteins and the discovery of modulators, indicating that targeting autophagy can be utilized as an effective strategy for novel drug development.
    Keywords:  autophagy; drug discovery; protein structure
    DOI:  https://doi.org/10.3390/life11060526
  24. Diabetes. 2021 Jun 29. pii: db210145. [Epub ahead of print]
    TM4SF5 knockout protects mice from diet-induced obesity partly by regulating autophagy in adipose tissue.
    Cheoljun Choi, Yeonho Son, Jinyoung Kim, Yoon Keun Cho, Abhirup Saha, Minsu Kim, Hyeonyeong Im, Kyungmin Kim, Juhyeong Han, Jung Weon Lee, Je Kyung Seong, Yun-Hee Lee.
      Transmembrane 4 L six family member 5 (TM4SF5) functions as a sensor for lysosomal arginine levels and activates the mammalian target of rapamycin complex 1 (mTORC1). While the mTORC1 signaling pathway plays a key role in adipose tissue metabolism, the regulatory function of TM4SF5 in adipocytes remains unclear. This study aimed to establish a TM4SF5 knockout (KO) mouse model and investigated the effects of TM4SF5 KO on mTORC1 signaling-mediated autophagy and mitochondrial metabolism in adipose tissue. TM4SF5 expression was higher in inguinal white adipose tissue (iWAT) than in brown adipose tissue and significantly upregulated by a high-fat diet (HFD). TM4SF5 KO reduced mTORC1 activation and enhanced autophagy and lipolysis in adipocytes. RNAseq analysis of TM4SF5 KO mouse iWAT showed that the expression of genes involved in peroxisome proliferator-activated receptor alpha signaling pathways and mitochondrial oxidative metabolism were upregulated. Consequently, TM4SF5 KO reduced adiposity and increased energy expenditure and mitochondrial oxidative metabolism. TM4SF5 KO prevented HFD-induced glucose intolerance and inflammation in adipose tissue. Collectively, our study demonstrated that TM4SF5 can regulate autophagy and lipid catabolism in adipose tissue and suggested that TM4SF5 could be therapeutically targeted for the treatment of obesity-related metabolic diseases.
    DOI:  https://doi.org/10.2337/db21-0145
  25. Mol Neurodegener. 2021 Jun 29. 16(1): 43
    AMPK hyperactivation promotes dendrite retraction, synaptic loss, and neuronal dysfunction in glaucoma.
    Nicolas Belforte, Jessica Agostinone, Luis Alarcon-Martinez, Deborah Villafranca-Baughman, Florence Dotigny, Jorge L Cueva Vargas, Adriana Di Polo.
       BACKGROUND: The maintenance of complex dendritic arbors and synaptic transmission are processes that require a substantial amount of energy. Bioenergetic decline is a prominent feature of chronic neurodegenerative diseases, yet the signaling mechanisms that link energy stress with neuronal dysfunction are poorly understood. Recent work has implicated energy deficits in glaucoma, and retinal ganglion cell (RGC) dendritic pathology and synapse disassembly are key features of ocular hypertension damage.
    RESULTS: We show that adenosine monophosphate-activated protein kinase (AMPK), a conserved energy biosensor, is strongly activated in RGC from mice with ocular hypertension and patients with primary open angle glaucoma. Our data demonstrate that AMPK triggers RGC dendrite retraction and synapse elimination. We show that the harmful effect of AMPK is exerted through inhibition of the mammalian target of rapamycin complex 1 (mTORC1). Attenuation of AMPK activity restores mTORC1 function and rescues dendrites and synaptic contacts. Strikingly, AMPK depletion promotes recovery of light-evoked retinal responses, improves axonal transport, and extends RGC survival.
    CONCLUSIONS: This study identifies AMPK as a critical nexus between bioenergetic decline and RGC dysfunction during pressure-induced stress, and highlights the importance of targeting energy homeostasis in glaucoma and other neurodegenerative diseases.
    Keywords:  Adenosine monophosphate-activated protein kinase; Glaucoma; Mammalian target of rapamycin; Metabolic stress; Neurodegeneration
    DOI:  https://doi.org/10.1186/s13024-021-00466-z
  26. Materials (Basel). 2021 Jun 02. pii: 3019. [Epub ahead of print]14(11):
    Fluorescent Protein-Based Autophagy Biosensors.
    Heejung Kim, Jihye Seong.
      Autophagy is an essential cellular process of self-degradation for dysfunctional or unnecessary cytosolic constituents and organelles. Dysregulation of autophagy is thus involved in various diseases such as neurodegenerative diseases. To investigate the complex process of autophagy, various biochemical, chemical assays, and imaging methods have been developed. Here we introduce various methods to study autophagy, in particular focusing on the review of designs, principles, and limitations of the fluorescent protein (FP)-based autophagy biosensors. Different physicochemical properties of FPs, such as pH-sensitivity, stability, brightness, spectral profile, and fluorescence resonance energy transfer (FRET), are considered to design autophagy biosensors. These FP-based biosensors allow for sensitive detection and real-time monitoring of autophagy progression in live cells with high spatiotemporal resolution. We also discuss future directions utilizing an optobiochemical strategy to investigate the in-depth mechanisms of autophagy. These cutting-edge technologies will further help us to develop the treatment strategies of autophagy-related diseases.
    Keywords:  autophagy; biosensors; fluorescence imaging; fluorescent protein; neurodegenerative diseases
    DOI:  https://doi.org/10.3390/ma14113019
  27. Mol Neurobiol. 2021 Jul 02.
    Exploring the Role of Autophagy Dysfunction in Neurodegenerative Disorders.
    Tarapati Rana, Tapan Behl, Aayush Sehgal, Vineet Mehta, Sukhbir Singh, Saurabh Bhatia, Ahmed Al-Harrasi, Simona Bungau.
      Autophagy is a catabolic pathway by which misfolded proteins or damaged organelles are engulfed by autophagosomes and then transported to lysosomes for degradation. Recently, a great improvement has been done to explain the molecular mechanisms and roles of autophagy in several important cellular metabolic processes. Besides being a vital clearance pathway or a cell survival pathway in response to different stresses, autophagy dysfunction, either upregulated or down-regulated, has been suggested to be linked with numerous neurodegenerative disorders like Alzheimer's disease, Parkinson's disease, Huntington's disease, and Amyotrophic lateral sclerosis. Impairment at different stages of autophagy results in the formation of large protein aggregates and damaged organelles, which leads to the onset and progression of different neurodegenerative disorders. This article elucidates the recent progress about the role of autophagy in neurodegenerative disorders and explains how autophagy dysfunction is linked with the pathogenesis of such disorders as well as the novel potential autophagy-associated therapies for treating them.
    Keywords:  Autophagosome; Autophagy; Dysfunction; Neurodegenerative disorders; Pathophysiology
    DOI:  https://doi.org/10.1007/s12035-021-02472-0
  28. J Cereb Blood Flow Metab. 2021 Jun 29. 271678X211027384
    Wdfy3 regulates glycophagy, mitophagy, and synaptic plasticity.
    Eleonora Napoli, Alexios A Panoutsopoulos, Patricia Kysar, Nathaniel Satriya, Kira Sterling, Bradley Shibata, Denise Imai, David N Ruskin, Konstantinos S Zarbalis, Cecilia Giulivi.
      Autophagy is essential to cell function, as it enables the recycling of intracellular constituents during starvation and in addition functions as a quality control mechanism by eliminating spent organelles and proteins that could cause cellular damage if not properly removed. Recently, we reported on Wdfy3's role in mitophagy, a clinically relevant macroautophagic scaffold protein that is linked to intellectual disability, neurodevelopmental delay, and autism spectrum disorder. In this study, we confirm our previous report that Wdfy3 haploinsufficiency in mice results in decreased mitophagy with accumulation of mitochondria with altered morphology, but expanding on that observation, we also note decreased mitochondrial localization at synaptic terminals and decreased synaptic density, which may contribute to altered synaptic plasticity. These changes are accompanied by defective elimination of glycogen particles and a shift to increased glycogen synthesis over glycogenolysis and glycophagy. This imbalance leads to an age-dependent higher incidence of brain glycogen deposits with cerebellar hypoplasia. Our results support and further extend Wdfy3's role in modulating both brain bioenergetics and synaptic plasticity by including glycogen as a target of macroautophagic degradation.
    Keywords:  Glycogen; brain; electron microscopy; mitochondria; synapses
    DOI:  https://doi.org/10.1177/0271678X211027384
  29. Cells. 2021 Jun 17. pii: 1522. [Epub ahead of print]10(6):
    BECLIN1: Protein Structure, Function and Regulation.
    Sharon Tran, W Douglas Fairlie, Erinna F Lee.
      BECLIN1 is a well-established regulator of autophagy, a process essential for mammalian survival. It functions in conjunction with other proteins to form Class III Phosphoinositide 3-Kinase (PI3K) complexes to generate phosphorylated phosphatidylinositol (PtdIns), lipids essential for not only autophagy but other membrane trafficking processes. Over the years, studies have elucidated the structural, biophysical, and biochemical properties of BECLIN1, which have shed light on how this protein functions to allosterically regulate these critical processes of autophagy and membrane trafficking. Here, we review these findings and how BECLIN1's diverse protein interactome regulates it, as well as its impact on organismal physiology.
    Keywords:  BCL-2; BECLIN1; PI3K Class III complexes; autophagy
    DOI:  https://doi.org/10.3390/cells10061522
  30. Sci Rep. 2021 Jul 02. 11(1): 13771
    Loss of FYCO1 leads to cataract formation.
    Kiyotoshi Satoh, Yukitoshi Takemura, Motohiko Satoh, Kiyokazu Ozaki, Shunichiro Kubota.
      Autophagy is a degradation process of cytoplasmic proteins and organelles trafficked to degradation vesicles known as autophagosomes. The conversion of LC3-I to LC3-II is an essential step of autophagosome formation, and FYCO1 is a LC3-binding protein that mediates autophagosome transport. The p62 protein also directly binds to LC3 and is degraded by autophagy. In the present study, we demonstrated that disrupting the FYCO1 gene in mice resulted in cataract formation. LC3 conversion decreased in eyes from FYCO1 knockout mice. Further, FYCO1 interacted with αA- and αB-crystallin, as demonstrated by yeast two-hybrid screening and immunoprecipitation analyses. In eyes from knockout mice, the soluble forms of αA- and αB-crystallin, the lens's major protein components, decreased. In addition, p62 accumulated in eyes from FYCO1 knockout mice. Collectively, these findings suggested that FYCO1 recruited damaged α-crystallin into autophagosomes to protect lens cells from cataract formation.
    DOI:  https://doi.org/10.1038/s41598-021-93110-1
  31. Cancers (Basel). 2021 Jun 22. pii: 3105. [Epub ahead of print]13(13):
    Repurposing Niclosamide for Targeting Pancreatic Cancer by Inhibiting Hh/Gli Non-Canonical Axis of Gsk3β.
    Jyoti B Kaushal, Rakesh Bhatia, Ranjana K Kanchan, Pratima Raut, Surya Mallapragada, Quan P Ly, Surinder K Batra, Satyanarayana Rachagani.
      Niclosamide (Nic), an FDA-approved anthelmintic drug, is reported to have anti-cancer efficacy and is being assessed in clinical trials for various solid tumors. Based on its ability to target multiple signaling pathways, in the present study, we evaluated the therapeutic efficacy of Nic on pancreatic cancer (PC) in vitro. We observed an anti-cancerous effect of this drug as shown by the G0/G1 phase cell cycle arrest, inhibition of PC cell viability, colony formation, and migration. Our results revealed the involvement of mitochondrial stress and mTORC1-dependent autophagy as the predominant players of Nic-induced PC cell death. Significant reduction of Nic-induced reactive oxygen species (ROS) and cell death in the presence of a selective autophagy inhibitor spautin-1 demonstrated autophagy as a major contributor to Nic-mediated cell death. Mechanistically, Nic inhibited the interaction between BCL2 and Beclin-1 that supported the crosstalk of autophagy and apoptosis. Further, Nic treatment resulted in Gsk3β inactivation by phosphorylating its Ser-9 residue leading to upregulation of Sufu and Gli3, thereby negatively impacting hedgehog signaling and cell survival. Nic induced autophagic cell death, and p-Gsk3b mediated Sufu/Gli3 cascade was further confirmed by Gsk3β activator, LY-294002, by rescuing inactivation of Hh signaling upon Nic treatment. These results suggested the involvement of a non-canonical mechanism of Hh signaling, where p-Gsk3β acts as a negative regulator of Hh/Gli1 cascade and a positive regulator of autophagy-mediated cell death. Overall, this study established the therapeutic efficacy of Nic for PC by targeting p-Gsk3β mediated non-canonical Hh signaling and promoting mTORC1-dependent autophagy and cell death.
    Keywords:  Gsk3β; Hh signaling; apoptosis; autophagy; niclosamide; pancreatic cancer
    DOI:  https://doi.org/10.3390/cancers13133105
  32. Front Physiol. 2021 ;12 703458
    Editorial: Autophagy and Mitophagy in Skeletal Muscle Health and Disease.
    Sabah N A Hussain, Marco Sandri, Gilles Gouspillou.
      
    Keywords:  atrophy; autophagy; mitophagy; proteolysis; skeletal muscles; sympathethic nervous system
    DOI:  https://doi.org/10.3389/fphys.2021.703458
  33. Oxid Med Cell Longev. 2021 ;2021 5543452
    The Role of Mitochondrial Quality Control in Cardiac Ischemia/Reperfusion Injury.
    Jia Huang, Ruibing Li, Chengbin Wang.
      A healthy mitochondrial network produces a large amount of ATP and biosynthetic intermediates to provide sufficient energy for myocardium and maintain normal cell metabolism. Mitochondria form a dynamic and interconnected network involved in various cellular metabolic signaling pathways. As mitochondria are damaged, controlling mitochondrial quantity and quality is activated by changing their morphology and tube network structure, mitophagy, and biogenesis to replenish a healthy mitochondrial network to preserve cell function. There is no doubt that mitochondrial dysfunction has become a key factor in many diseases. Ischemia/reperfusion (IR) injury is a pathological manifestation of various heart diseases. Cardiac ischemia causes temporary tissue and organelle damage. Although reperfusion is essential to compensate for nutrient deficiency, blood flow restoration inconsequently further kills the previously ischemic cardiomyocytes. To date, dysfunctional mitochondria and disturbed mitochondrial quality control have been identified as critical IR injury mechanisms. Many researchers have detected abnormal mitochondrial morphology and mitophagy, as well as aberrant levels and activity of mitochondrial biogenesis factors in the IR injury model. Although mitochondrial damage is well-known in myocardial IR injury, the causal relationship between abnormal mitochondrial quality control and IR injury has not been established. This review briefly describes the molecular mechanisms of mitochondrial quality control, summarizes our current understanding of the complex role of mitochondrial quality control in IR injury, and finally speculates on the possibility of targeted control of mitochondria and the methods available to mitigate IR injury.
    DOI:  https://doi.org/10.1155/2021/5543452
  34. J Med Chem. 2021 Jun 30.
    In Silico and In Cell Hybrid Selection of Nonrapalog Ligands to Allosterically Inhibit the Kinase Activity of mTORC1.
    Raef Shams, Akihiro Matsukawa, Yukari Ochi, Yoshihiro Ito, Hideyuki Miyatake.
      Cancer-specific metabolic alterations hyperactivate the kinase activity of the mammalian/mechanistic target of rapamycin (mTOR) for overcoming stressful environments. Rapalogs, which allosterically inhibit mTOR complex 1 (mTORC1), have been approved as anticancer agents. However, the immunosuppressive side effect of these compounds results in the promotion of tumor metastasis, thereby limiting their therapeutic efficacy. We first report a nonrapalog inhibitor, WRX606, identified by a hybrid strategy of in silico and in cell selections. Our studies showed that WRX606 formed a ternary complex with FK506-binding protein-12 (FKBP12) and FKBP-rapamycin-binding (FRB) domain of mTOR, resulting in the allosteric inhibition of mTORC1. WRX606 inhibited the phosphorylation of not only the ribosomal protein S6 kinase 1 (S6K1) but also eIF4E-binding protein-1 (4E-BP1). Hence, WRX606 efficiently suppressed tumor growth in mice without promotion of metastasis. These results suggest that WRX606 is a potent lead compound for developing anticancer drugs discovered by in silico and in cell methods.
    DOI:  https://doi.org/10.1021/acs.jmedchem.1c00536
  35. Cells. 2021 Jun 09. pii: 1447. [Epub ahead of print]10(6):
    The Multifaceted Functions of Autophagy in Breast Cancer Development and Treatment.
    Nicolas J Niklaus, Igor Tokarchuk, Mara Zbinden, Anna M Schläfli, Paola Maycotte, Mario P Tschan.
      Macroautophagy (herein referred to as autophagy) is a complex catabolic process characterized by the formation of double-membrane vesicles called autophagosomes. During this process, autophagosomes engulf and deliver their intracellular content to lysosomes, where they are degraded by hydrolytic enzymes. Thereby, autophagy provides energy and building blocks to maintain cellular homeostasis and represents a dynamic recycling mechanism. Importantly, the clearance of damaged organelles and aggregated molecules by autophagy in normal cells contributes to cancer prevention. Therefore, the dysfunction of autophagy has a major impact on the cell fate and can contribute to tumorigenesis. Breast cancer is the most common cancer in women and has the highest mortality rate among all cancers in women worldwide. Breast cancer patients often have a good short-term prognosis, but long-term survivors often experience aggressive recurrence. This phenomenon might be explained by the high heterogeneity of breast cancer tumors rendering mammary tumors difficult to target. This review focuses on the mechanisms of autophagy during breast carcinogenesis and sheds light on the role of autophagy in the traits of aggressive breast cancer cells such as migration, invasion, and therapeutic resistance.
    Keywords:  EMT; aggressiveness; autophagy; breast cancer subtypes; differentiation; metastasis; stem cells; therapy resistance; tumor dormancy
    DOI:  https://doi.org/10.3390/cells10061447
  36. Cell Rep. 2021 Jun 29. pii: S2211-1247(21)00697-5. [Epub ahead of print]35(13): 109321
    Revealing molecular pathways for cancer cell fitness through a genetic screen of the cancer translatome.
    Duygu Kuzuoglu-Ozturk, Zhiqiang Hu, Martina Rama, Emily Devericks, Jacob Weiss, Gary G Chiang, Stephen T Worland, Steven E Brenner, Hani Goodarzi, Luke A Gilbert, Davide Ruggero.
      The major cap-binding protein eukaryotic translation initiation factor 4E (eIF4E), an ancient protein required for translation of all eukaryotic genomes, is a surprising yet potent oncogenic driver. The genetic interactions that maintain the oncogenic activity of this key translation factor remain unknown. In this study, we carry out a genome-wide CRISPRi screen wherein we identify more than 600 genetic interactions that sustain eIF4E oncogenic activity. Our data show that eIF4E controls the translation of Tfeb, a key executer of the autophagy response. This autophagy survival response is triggered by mitochondrial proteotoxic stress, which allows cancer cell survival. Our screen also reveals a functional interaction between eIF4E and a single anti-apoptotic factor, Bcl-xL, in tumor growth. Furthermore, we show that eIF4E and the exon-junction complex (EJC), which is involved in many steps of RNA metabolism, interact to control the migratory properties of cancer cells. Overall, we uncover several cancer-specific vulnerabilities that provide further resolution of the cancer translatome.
    Keywords:  Bcl-xL; CRISPRi; EJC; Tfeb; UPR(mt)-like stress response; autophagy; cancer; eIF4E; mitochondria; translation control
    DOI:  https://doi.org/10.1016/j.celrep.2021.109321
  37. Genes Cells. 2021 Jul 01.
    Microtubule inhibitors identified through non-biased screening enhance DNA transfection efficiency by delaying p62-dependent ubiquitin recruitment.
    Megumi Tsuchiya, Hidesato Ogawa, Kento Watanabe, Takako Koujin, Chie Mori, Kazuto Nunomura, Bangzhong Lin, Akiyoshi Tani, Yasushi Hiraoka, Tokuko Haraguchi.
      Ectopic gene expression is an indispensable tool in biology and medicine, but is often limited by the low efficiency of DNA transfection. We previously reported that depletion of the autophagy receptor p62/SQSTM1 enhances DNA transfection efficiency by preventing the degradation of transfected DNA. Therefore, p62 is a potential target for drugs to increase transfection efficiency. To identify such drugs, a non-biased high-throughput screening was applied to over 4,000 compounds from the Osaka University compound library, and their p62-dependency was evaluated. The top-scoring drugs were mostly microtubule inhibitors, such as colchicine and vinblastine, and all of them showed positive effects only in the presence of p62. To understand the p62-dependent mechanisms, the time required for p62-dependent ubiquitination, which is required for autophagosome formation, was examined using polystyrene beads that were introduced into cells as materials that mimicked transfected DNA. Microtubule inhibitors caused a delay in ubiquitination. Furthermore, the level of phosphorylated p62 at S405 was markedly decreased in the drug-treated cells. These results suggest that microtubule inhibitors inhibit p62-dependent autophagosome formation. Our findings demonstrate for the first time that microtubule inhibitors suppress p62 activation as a mechanism for increasing DNA transfection efficiency and provide solutions to increase efficiency.
    Keywords:  autophagy; gene delivery; high-throughput screening; p62; phosphorylation; transfection efficiency; ubiquitination
    DOI:  https://doi.org/10.1111/gtc.12881
  38. Cell Death Dis. 2021 Jul 02. 12(7): 664
    Tribbles homolog 3-mediated targeting the AKT/mTOR axis in mice with retinal degeneration.
    Irina V Saltykova, Asif Elahi, Priyam M Pitale, Oleg S Gorbatyuk, Mohammad Athar, Marina S Gorbatyuk.
      Various retinal degenerative disorders manifest in alterations of the AKT/mTOR axis. Despite this, consensus on the therapeutic targeting of mTOR in degenerating retinas has not yet been achieved. Therefore, we investigated the role of AKT/mTOR signaling in rd16 retinas, in which we restored the AKT/mTOR axis by genetic ablation of pseudokinase TRB3, known to inhibit phosphorylation of AKT and mTOR. First, we found that TRB3 ablation resulted in preservation of photoreceptor function in degenerating retinas. Then, we learned that the mTOR downstream cellular pathways involved in the homeostasis of photoreceptors were also reprogrammed in rd16 TRB3-/- retinas. Thus, the level of inactivated translational repressor p-4E-BP1 was significantly increased in these mice along with the restoration of translational rate. Moreover, in rd16 mice manifesting decline in p-mTOR at P15, we found elevated expression of Beclin-1 and ATG5 autophagy genes. Thus, these mice showed impaired autophagy flux measured as an increase in LC3 conversion and p62 accumulation. In addition, the RFP-EGFP-LC3 transgene expression in rd16 retinas resulted in statistically fewer numbers of red puncta in photoreceptors, suggesting impaired late autophagic vacuoles. In contrast, TRIB3 ablation in these mice resulted in improved autophagy flux. The restoration of translation rate and the boost in autophagosome formation occurred concomitantly with an increase in total Ub and rhodopsin protein levels and the elevation of E3 ligase Parkin1. We propose that TRB3 may retard retinal degeneration and be a promising therapeutic target to treat various retinal degenerative disorders.
    DOI:  https://doi.org/10.1038/s41419-021-03944-w
  39. Cells. 2021 Jun 01. pii: 1363. [Epub ahead of print]10(6):
    Dihydroartemisinin Inhibits mTORC1 Signaling by Activating the AMPK Pathway in Rhabdomyosarcoma Tumor Cells.
    Jun Luo, Yoshinobu Odaka, Zhu Huang, Bing Cheng, Wang Liu, Lin Li, Chaowei Shang, Chao Zhang, Yang Wu, Yan Luo, Shengyong Yang, Peter J Houghton, Xiaofeng Guo, Shile Huang.
      Dihydroartemisinin (DHA), an anti-malarial drug, has been shown to possess potent anticancer activity, partly by inhibiting the mammalian target of rapamycin (mTOR) complex 1 (mTORC1) signaling. However, how DHA inhibits mTORC1 is still unknown. Here, using rhabdomyosarcoma (RMS) as a model, we found that DHA reduced cell proliferation and viability in RMS cells, but not those in normal cells, which was associated with inhibition of mTORC1. Mechanistically, DHA did not bind to mTOR or FK506 binding protein 12 (FKBP12). In addition, DHA neither inhibited insulin-like growth factor-1 receptor (IGF-1R), phosphoinositide 3-kinase (PI3K), and extracellular signal-regulated kinase ½ (Erk1/2), nor activated phosphatase and tensin homolog (PTEN) in the cells. Rather, DHA activated AMP-activated protein kinase (AMPK). Pharmacological inhibition of AMPK, ectopic expression dominant negative or kinase-dead AMPK, or knockdown of AMPKa attenuated the inhibitory effect of DHA on mTORC1 in the cells. Additionally, DHA was able to induce dissociation of regulatory-associated protein of mTOR (raptor) from mTOR and inhibit mTORC1 activity. Moreover, treatment with artesunate, a prodrug of DHA, dose-dependently inhibited tumor growth and concurrently activated AMPK and suppressed mTORC1 in RMS xenografts. The results indicated that DHA inhibits mTORC1 by activating AMPK in tumor cells. Our finding supports that DHA or artesunate has a great potential to be repositioned for treatment of RMS.
    Keywords:  AMPK; PTEN; dihydroartemisinin; mTOR; raptor; rhabdomyosarcoma
    DOI:  https://doi.org/10.3390/cells10061363
  40. Am J Physiol Regul Integr Comp Physiol. 2021 06 30.
    Vascular Effects of Disrupting Endothelial mTORC1 (Mechanistic Target of Rapamycin Complex 1) Signaling in Obesity.
    John J Reho, Deng-Fu Guo, Andreas M Beyer, Lauren Wegman-Points, Gary L Pierce, Kamal Rahmouni.
      The mechanistic target of rapamycin complex 1 (mTORC1) signaling complex is emerging as a critical regulator of cardiovascular function with alterations in this pathway implicated in cardiovascular diseases. In this study, we utilized animal models and human tissues to examine the role of vascular mTORC1 signaling in the endothelial dysfunction associated with obesity. In mice, obesity induced by high fat/high sucrose diet feeding for ~2 months resulted in aortic endothelial dysfunction without appreciable changes in vascular mTORC1 signaling. On the other hand, chronic high fat diet feeding (45% or 60% kcal: ~9 months) in mice resulted in endothelial dysfunction associated with elevated vascular mTORC1 signaling. Endothelial cells and visceral adipose vessels isolated from obese humans display a trend toward elevated mTORC1 signaling. Surprisingly, genetic disruption of endothelial mTORC1 signaling through constitutive or tamoxifen inducible deletion of endothelial Raptor (critical subunit of mTORC1) did not prevent or rescue the endothelial dysfunction associated with high fat diet feeding in mice. Endothelial mTORC1 deficiency also failed to reverse the endothelial dysfunction evoked by a high fat/high sucrose diet in mice. Taken together, these data show increased vascular mTORC1 signaling in obesity, but this vascular mTORC1 activation appears not to be required for the development of endothelial impairment in obesity.
    Keywords:  endothelial dysfunction; high fat diet; mTORC1; obesity
    DOI:  https://doi.org/10.1152/ajpregu.00113.2021
  41. Int J Mol Sci. 2021 Jun 08. pii: 6181. [Epub ahead of print]22(12):
    EVA1A Plays an Important Role by Regulating Autophagy in Physiological and Pathological Processes.
    Shizhen Zhao, Honggang Wang.
      Eva-1 homolog A (EVA1A) is regarded as TMEM166 (transmembrane protein 166) or FAM176A (family with sequence similarity 176) and a lysosome and endoplasmic reticulum-associated protein involved in regulating autophagy and apoptosis. EVA1A regulates embryonic neurogenesis, cardiac remodeling, islet alpha-cell functions, acute liver failure, and hepatitis B virus replication. However, the related mechanisms are not fully clear. Autophagy is a process in which cells transfer pathogens, abnormal proteins and organelles to lysosomes for degradation. It plays an important role in various physiological and pathological processes, including cancer, aging, neurodegeneration, infection, heart disease, development, cell differentiation and nutritional starvation. Recently, there are many studies on the important role of EVA1A in many physiological and pathological processes by regulating autophagy. However, the related molecular mechanisms need further study. Therefore, we summarize the above-mentioned researches about the role of EVA1A in physiological and pathological processes through regulating autophagy in order to provide theoretical basis for future researches.
    Keywords:  EVA1A; apoptosis; autophagy; liver injury; tumor
    DOI:  https://doi.org/10.3390/ijms22126181
  42. Cells. 2021 Jun 06. pii: 1411. [Epub ahead of print]10(6):
    Friend or Foe: Paradoxical Roles of Autophagy in Gliomagenesis.
    Don Carlo Ramos Batara, Moon-Chang Choi, Hyeon-Uk Shin, Hyunggee Kim, Sung-Hak Kim.
      Glioblastoma multiforme (GBM) is the most common and aggressive type of primary brain tumor in adults, with a poor median survival of approximately 15 months after diagnosis. Despite several decades of intensive research on its cancer biology, treatment for GBM remains a challenge. Autophagy, a fundamental homeostatic mechanism, is responsible for degrading and recycling damaged or defective cellular components. It plays a paradoxical role in GBM by either promoting or suppressing tumor growth depending on the cellular context. A thorough understanding of autophagy's pleiotropic roles is needed to develop potential therapeutic strategies for GBM. In this paper, we discussed molecular mechanisms and biphasic functions of autophagy in gliomagenesis. We also provided a summary of treatments for GBM, emphasizing the importance of autophagy as a promising molecular target for treating GBM.
    Keywords:  autophagy; glioblastoma multiforme; treatment
    DOI:  https://doi.org/10.3390/cells10061411
  43. Int J Mol Sci. 2021 Jun 17. pii: 6509. [Epub ahead of print]22(12):
    The mTORC2 Regulator Homer1 Modulates Protein Levels and Sub-Cellular Localization of the CaSR in Osteoblast-Lineage Cells.
    Mark S Rybchyn, Tara Clare Brennan-Speranza, David Mor, Zhiqiang Cheng, Wenhan Chang, Arthur D Conigrave, Rebecca S Mason.
      We recently found that, in human osteoblasts, Homer1 complexes to Calcium-sensing receptor (CaSR) and mediates AKT initiation via mechanistic target of rapamycin complex (mTOR) complex 2 (mTORC2) leading to beneficial effects in osteoblasts including β-catenin stabilization and mTOR complex 1 (mTORC1) activation. Herein we further investigated the relationship between Homer1 and CaSR and demonstrate a link between the protein levels of CaSR and Homer1 in human osteoblasts in primary culture. Thus, when siRNA was used to suppress the CaSR, we observed upregulated Homer1 levels, and when siRNA was used to suppress Homer1 we observed downregulated CaSR protein levels using immunofluorescence staining of cultured osteoblasts as well as Western blot analyses of cell protein extracts. This finding was confirmed in vivo as the bone cells from osteoblast specific CaSR-/- mice showed increased Homer1 expression compared to wild-type (wt). CaSR and Homer1 protein were both expressed in osteocytes embedded in the long bones of wt mice, and immunofluorescent studies of these cells revealed that Homer1 protein sub-cellular localization was markedly altered in the osteocytes of CaSR-/- mice compared to wt. The study identifies additional roles for Homer1 in the control of the protein level and subcellular localization of CaSR in cells of the osteoblast lineage, in addition to its established role of mTORC2 activation downstream of the receptor.
    Keywords:  AKT; CaSR; Homer1; chaperone function; mTOR; osteoblast; osteocyte
    DOI:  https://doi.org/10.3390/ijms22126509
  44. Cells. 2021 Jun 08. pii: 1430. [Epub ahead of print]10(6):
    The AMPK/p27Kip1 Pathway as a Novel Target to Promote Autophagy and Resilience in Aged Cells.
    Lauren K McKay, James P White.
      Once believed to solely function as a cyclin-dependent kinase inhibitor, p27Kip1 is now emerging as a critical mediator of autophagy, cytoskeletal dynamics, cell migration and apoptosis. During periods of metabolic stress, the subcellular location of p27Kip1 largely dictates its function. Cytoplasmic p27Kip1 has been found to be promote cellular resilience through autophagy and anti-apoptotic mechanisms. Nuclear p27Kip1, however, inhibits cell cycle progression and makes the cell susceptible to quiescence, apoptosis, and/or senescence. Cellular location of p27Kip1 is regulated, in part, by phosphorylation by various kinases, including Akt and AMPK. Aging promotes nuclear localization of p27Kip1 and a predisposition to senescence or apoptosis. Here, we will review the role of p27Kip1 in healthy and aging cells with a particular emphasis on the interplay between autophagy and apoptosis.
    Keywords:  AMPK; Akt; aging; apoptosis; autophagy; p27; senescence
    DOI:  https://doi.org/10.3390/cells10061430
  45. Oncogene. 2021 Jul 01.
    TRIM44 mediated p62 deubiquitination enhances DNA damage repair by increasing nuclear FLNA and 53BP1 expression.
    Lin Lyu, Tsung-Chin Lin, Nami McCarty.
      Cancer cells show increases in protein degradation pathways, including autophagy, during progression to meet the increased protein degradation demand and support cell survival. On the other hand, reduced autophagy activity during aging is associated with a reduced DNA damage response and increased genomic instability. Therefore, it is a puzzling how DNA repair can be increased in cancer cells that are resistant to chemotherapies or during progression when autophagy activity is intact or increased. We discovered that tripartite motif containing 44 (TRIM44) is a pivotal element regulating the DNA damage response in cancer cells with intact autophagy. TRIM44 deubiquitinates p62, an autophagy substrate, which leads to its oligomerization. This prevents p62 localization to the nucleus upon irradiation. Increased cytoplasmic retention of p62 by TRIM44 prevents the degradation of FLNA and 53BP1, which increases DNA damage repair. Together, our data support TRIM44 a potential therapeutic target for therapy-resistant tumor cells with intact autophagy.
    DOI:  https://doi.org/10.1038/s41388-021-01890-7
  46. Cells. 2021 Jun 09. pii: 1443. [Epub ahead of print]10(6):
    MERTK-Mediated LC3-Associated Phagocytosis (LAP) of Apoptotic Substrates in Blood-Separated Tissues: Retina, Testis, Ovarian Follicles.
    Marina G Yefimova, Celia Ravel, Antoine D Rolland, Nicolas Bourmeyster, Bernard Jégou.
      Timely and efficient elimination of apoptotic substrates, continuously produced during one's lifespan, is a vital need for all tissues of the body. This task is achieved by cells endowed with phagocytic activity. In blood-separated tissues such as the retina, the testis and the ovaries, the resident cells of epithelial origin as retinal pigmented epithelial cells (RPE), testis Sertoli cells and ovarian granulosa cells (GC) provide phagocytic cleaning of apoptotic cells and cell membranes. Disruption of this process leads to functional ablation as blindness in the retina and compromised fertility in males and females. To ensure the efficient elimination of apoptotic substrates, RPE, Sertoli cells and GC combine various mechanisms allowing maintenance of tissue homeostasis and avoiding acute inflammation, tissue disorganization and functional ablation. In tight cooperation with other phagocytosis receptors, MERTK-a member of the TAM family of receptor tyrosine kinases (RTK)-plays a pivotal role in apoptotic substrate cleaning from the retina, the testis and the ovaries through unconventional autophagy-assisted phagocytosis process LAP (LC3-associated phagocytosis). In this review, we focus on the interplay between TAM RTKs, autophagy-related proteins, LAP, and Toll-like receptors (TLR), as well as the regulatory mechanisms allowing these components to sustain tissue homeostasis and prevent functional ablation of the retina, the testis and the ovaries.
    Keywords:  LAP; Mer tyrosine kinase; autophagy; ovaries; phagocytosis; retina; testis
    DOI:  https://doi.org/10.3390/cells10061443
  47. ChemMedChem. 2021 Jun 11.
    Chemical and Structural Strategies to Selectively Target mTOR Kinase.
    Chiara Borsari, Martina De Pascale, Matthias P Wymann.
      Dysregulation of the mechanistic target of rapamycin (mTOR) pathway is implicated in cancer and neurological disorder, which identifies mTOR inhibition as promising strategy for the treatment of a variety of human disorders. First-generation mTOR inhibitors include rapamycin and its analogues (rapalogs) which act as allosteric inhibitors of TORC1. Structurally unrelated, ATP-competitive inhibitors that directly target the mTOR catalytic site inhibit both TORC1 and TORC2. Here, we review investigations of chemical scaffolds explored for the development of highly selective ATP-competitive mTOR kinase inhibitors (TORKi). Extensive medicinal chemistry campaigns allowed to overcome challenges related to structural similarity between mTOR and the phosphoinositide 3-kinase (PI3K) family. A broad region of chemical space is covered by TORKi. Here, the investigation of chemical substitutions and physicochemical properties has shed light on the compounds' ability to cross the blood brain barrier (BBB). This work provides insights supporting the optimization of TORKi for the treatment of cancer and central nervous system disorders.
    Keywords:  BBB permeability; binding modes; chemical scaffolds; mTOR inhibitors; physicochemical properties
    DOI:  https://doi.org/10.1002/cmdc.202100332
  48. Anal Chem. 2021 Jun 28.
    Monitoring Mitophagy via the FRET Mechanism: Visualizing Mitochondria, Lysosomes, and Autolysosomes in Three Different Sets of Fluorescence Signals.
    Qingqing Lu, Wenpeng Li, Kaiyuan Chen, Minggang Tian.
      Mitophagy is a vital biological process playing central roles in the regulation of metabolic activity and quality control of mitochondria. The presented dual-color fluorescent probes to directly monitor mitophagy were based on the optical response to pH change during mitophagy, but pH fluctuation may lead to interference. To overcome this, herein, two fluorescent probes (G-Mito, R-Lyso) were rationally designed to visualize mitophagy directly in a dual-color manner, relying on the Förster resonance energy transfer (FRET) process for the first time. Green emissive G-Mito targeted and anchored the mitochondria via reaction with protein thiols. Red-emissive R-Lyso exclusively targeted lysosomes. Live cells loaded with the two probes demonstrated strong fluorescence in only the green channel with excitation at 405 nm. After mitophagy, G-Mito in mitochondria was delivered into the lysosomes, and red fluorescence evidently increased due to the FRET process. With the probes, mitochondria, lysosomes, and autolysosomes could be discriminatively visualized in three different sets of signals. Mitophagy induced by starvation and in normal physiological status were successfully observed. The probes revealed that a certain amount of H2O2 could induce mitophagy. We expect that the two probes can serve as molecular tools for validation of mitophagy and promote the development of related areas.
    DOI:  https://doi.org/10.1021/acs.analchem.1c01237
  49. J Exp Bot. 2021 Jun 29. pii: erab304. [Epub ahead of print]
    Autophagy complements metalloprotease FtsH6 in degrading plastid heat shock protein HSP21 during heat stress recovery.
    Mastoureh Sedaghatmehr, Venkatesh P Thirumalaikumar, Iman Kamranfar, Karina Schulz, Bernd Mueller-Roeber, Arun Sampathkumar, Salma Balazadeh.
      Moderate and temporary heat stresses (HS) prime plants to tolerate, and survive, a subsequent severe HS. Such acquired thermotolerance can be maintained for several days under normal growth conditions, and create a HS memory. We recently demonstrated that plastid-localized small heat shock protein HSP21 is a key component of HS memory in Arabidopsis thaliana. A sustained high abundance of HSP21 during the HS recovery phase extends HS memory. The level of HSP21 is negatively controlled by plastid-localized metalloprotease FtsH6 during HS recovery. Here, we demonstrate that autophagy, a cellular recycling mechanism, exerts additional control over HSP21 degradation. Genetic and chemical disruption of both, metalloprotease activity and autophagy trigger superior HSP21 accumulation, thereby improving memory. Furthermore, we provide evidence that autophagy cargo receptor ATG8-INTERACTING PROTEIN1 (ATI1) is associated with HS memory. ATI1 bodies colocalize with both autophagosomes and HSP21, and their abundance and transport to the vacuole increase during HS recovery. Together, our results provide new insights into the control module for the regulation of HS memory, in which two distinct protein degradation pathways act in concert to degrade HSP21, thereby enabling cells to recover from the HS effect at the cost of reducing the HS memory.
    Keywords:  ATI1; Arabidopsis thaliana; FtsH6; HSP21; heat stress; plastid; selective autophagy; stress memory; stress recovery
    DOI:  https://doi.org/10.1093/jxb/erab304
  50. Neuroscience. 2021 Jun 23. pii: S0306-4522(21)00325-0. [Epub ahead of print]
    The Roles of Oxidative Stress in Regulating Autophagy in Methylmercury-induced Neurotoxicity.
    Yanfeng Wei, Linlin Ni, Jingjing Pan, Xiaoyang Li, Bin Xu, Yu Deng, Tianyao Yang, Wei Liu.
      Methylmercury (MeHg) is a potential neurotoxin that is highly toxic to the human central nervous system. Although MeHg neurotoxicity has been widely studied, the mechanism of MeHg neurotoxicity has not yet been fully elucidated. Some research evidence suggests that oxidative stress and autophagy are important molecular mechanisms of MeHg-induced neurotoxicity. Researchers have widely accepted that oxidative stress regulates the autophagy pathway. The current study reviews the activation of Nuclear factor-erythroid-2-related factor (Nrf2)-related oxidative stress pathways and autophagy signaling pathways in the case of MeHg neurotoxicity. In addition, autophagy mainly plays a role in the neurotoxicity of MeHg through mTOR-dependent and mTOR-independent autophagy signaling pathways. Finally, the regulation of autophagy by reactive oxygen species (ROS) and Nrf2 in MeHg neurotoxicity was explored in this review, providing a new concept for the study of the neurotoxicity mechanism of MeHg. peroxidase; GR, glutathione reductase; GST, glutathione S-transferase; CAT, catalase; SOD, superoxide dismutase; MDA, malondialdehyde; xCT, cystine-glutamate transporter; hNPCs, hippocampal neural progenitor cells; TEM, transmission electron microscopy; GCs, germ cells; PI3K, phosphoinositide 3-kinase; Akt, protein kinase B; mTOR, mammalian target of rapamycin; BBB, blood-brain barrier; p70s6k, p70 ribosomal protein S6 kinase; NSCs , neural stem cells; ERK, extracellular signal-regulated kinase; rPT, rat proximal tubular cells; AMPK, AMP-activated protein kinase; ALS, amyotrophic lateral sclerosis; GCs, germ cells; Cyt c, cytochrome c; MOMP, mitochondrial outer membrane permeabilization; MPT, mitochondrial permeability transition; -SH, sulfhydryl; Cd, cadmium; 3-MA, 3-Methyladenine; IKKβ, inhibitor of kappa B kinase beta; JNK, C-Jun N-terminal kinase; Vps34, vacuolar protein sorting 34; FOXO, forkhead transcription factors of the O class; GSK3β, glycogen synthase kinase; ULK1, the unc-51-like autophagy activating kinase 1; CaMKKβ, calmodulin-dependent kinase; HMGB1, high mobility group box 1; ASK, apoptosis signal-regulating kinase; LC3, Microtubule-associated protein II/I-light chain 3; Pb, lead; AS, arsenic; Mn, Manganese; PC12, the adrenal phaeochromocytoma cell line; Bcl-2, B‑cell lymphoma 2; NUPR1, Nuclear protein 1; Sb, Antimony; Nrf2, Nuclear factor-erythroid-2-related factor; Rheb, Ras homolog enriched in brain; RPTOR, regulatory-associated protein of mTOR; FIP 200, focal adhesion kinase (FAK) family interacting protein of 200 kDa; Bnip3, Bcl-2/adenovirus E1B 19 kDa-interacting protein 3; LKB1, Liver kinase B1; TSC, tuberous sclerosis complex; sMaf, small molecule Maf protein; AREs/EpREs, antioxidant/electrophilic response elements; GCL, glutamic cysteine ligase; HO-1, heme oxygenase-1; Keap1, kelch-like ECH-related protein 1; β-TRCP, β-transducin repeat-containing protein; NQO-1, NADPH quinone oxido-reductase-1; EGCG, epigallocatechin-3-gallate; GFP, green fluorescent protein; SQSTM 1, sequestosome 1; MAPKs, Mitogen-activated protein kinases; MSCs, mesenchymal stem cells; SGK1, serum- and glucocorticoid-responsive kinase-1; Sesn, sestrin; 6-OHDA, 6-hydroxydopamine; NiO-NPs, nickel oxide nanoparticles; HDACi, histone deacetylase inhibitor; DMCMP, diabetic-related cardiomyopathy; CsA, Cyclosporine A; NDP52, nuclear dot protein 52; UBA, ubiquitin association domain; LIR, LC3-interaction region; KIR, Keap1 interacting region; Rbx1, RING box protein 1; Ψm, mitochondrial membrane potential; O2•-, superoxide anion; •OH, hydroxyl radicals; PbNO3, lead nitrate; RagD, Rag small GTPases D; GSTs, glutethione-S-transferases; Neh6, Nrf2-ECH Homology 6 Domain of Nrf2 ; Gsta4, glutathione S-transferase A4; Gclc, glutamate-cysteine ligase catalytic subunit.
    Keywords:  Methylmercury; Nrf2; autophagy; mTOR; oxidative stress
    DOI:  https://doi.org/10.1016/j.neuroscience.2021.06.026
  51. Cells. 2021 Jun 05. pii: 1395. [Epub ahead of print]10(6):
    The PINK1-Mediated Crosstalk between Neural Cells and the Underlying Link to Parkinson's Disease.
    Elvira Pequeno Leites, Vanessa Alexandra Morais.
      Mitochondrial dysfunction has a fundamental role in the development of idiopathic and familiar forms of Parkinson's disease (PD). The nuclear-encoded mitochondrial kinase PINK1, linked to familial PD, is responsible for diverse mechanisms of mitochondrial quality control, ATP production, mitochondrial-mediated apoptosis and neuroinflammation. The main pathological hallmark of PD is the loss of dopaminergic neurons. However, novel discoveries have brought forward the concept that a disruption in overall brain homeostasis may be the underlying cause of this neurodegeneration disease. To sustain this, astrocytes and microglia cells lacking PINK1 have revealed increased neuroinflammation and deficits in physiological roles, such as decreased wound healing capacity and ATP production, which clearly indicate involvement of these cells in the physiopathology of PD. PINK1 executes vital functions within mitochondrial regulation that have a detrimental impact on the development and progression of PD. Hence, in this review, we aim to broaden the horizon of PINK1-mediated phenotypes occurring in neurons, astrocytes and microglia and, ultimately, highlight the importance of the crosstalk between these neural cells that is crucial for brain homeostasis.
    Keywords:  PINK1; Parkinson’s disease; astrocytes; microglia; mitochondrial dysfunction; neurons
    DOI:  https://doi.org/10.3390/cells10061395
  52. NPJ Aging Mech Dis. 2021 Jul 01. 7(1): 13
    Bcl-2-dependent autophagy disruption during aging impairs amino acid utilization that is restored by hochuekkito.
    Miwa Nahata, Sachiko Mogami, Hitomi Sekine, Seiichi Iizuka, Naoto Okubo, Naoki Fujitsuka, Hiroshi Takeda.
      Chronic undernutrition contributes to the increase in frailty observed among elderly adults, which is a pressing issue in the sector of health care for older people worldwide. Autophagy, an intracellular recycling system, is closely associated with age-related pathologies. Therefore, decreased autophagy in aging could be involved in the disruption of energy homeostasis that occurs during undernutrition; however, the physiological mechanisms underlying this process remain unknown. Here, we showed that 70% daily food restriction (FR) induced fatal hypoglycemia in 23-26-month-old (aged) mice, which exhibited significantly lower hepatic autophagy than 9-week-old (young) mice. The liver expressions of Bcl-2, an autophagy-negative regulator, and Beclin1-Bcl-2 binding, were increased in aged mice compared with young mice. The autophagy inducer Tat-Beclin1 D11, not the mTOR inhibitor rapamycin, decreased the plasma levels of the glucogenic amino acid and restored the blood glucose levels in aged FR mice. Decreased liver gluconeogenesis, body temperature, physical activity, amino acid metabolism, and hepatic mitochondrial dynamics were observed in the aged FR mice. These changes were restored by treatment with hochuekkito that is a herbal formula containing several autophagy-activating ingredients. Our results indicate that Bcl-2 upregulation in the liver during the aging process disturbs autophagy activation, which increases the vulnerability to undernutrition. The promotion of liver autophagy may offer clinical therapeutic benefits to frail elderly patients.
    DOI:  https://doi.org/10.1038/s41514-021-00065-8
  53. Int J Mol Sci. 2021 Jun 18. pii: 6544. [Epub ahead of print]22(12):
    Epigenetic Regulation of Autophagy in Cardiovascular Pathobiology.
    Shuhan Bu, Krishna K Singh.
      Cardiovascular diseases (CVDs) are the number one cause of debilitation and mortality worldwide, with a need for cost-effective therapeutics. Autophagy is a highly conserved catabolic recycling pathway triggered by various intra- or extracellular stimuli to play an essential role in development and pathologies, including CVDs. Accordingly, there is great interest in identifying mechanisms that govern autophagic regulation. Autophagic regulation is very complex and multifactorial that includes epigenetic pathways, such as histone modifications to regulate autophagy-related gene expression, decapping-associated mRNA degradation, microRNAs, and long non-coding RNAs; pathways are also known to play roles in CVDs. Molecular understanding of epigenetic-based pathways involved in autophagy and CVDs not only will enhance the understanding of CVDs, but may also provide novel therapeutic targets and biomarkers for CVDs.
    Keywords:  atherosclerosis; autophagy; cardiovascular diseases; epigenetics
    DOI:  https://doi.org/10.3390/ijms22126544
  54. Antioxidants (Basel). 2021 Jun 10. pii: 938. [Epub ahead of print]10(6):
    Effect of Chronic Stress Present in Fibroblasts Derived from Patients with a Sporadic Form of AD on Mitochondrial Function and Mitochondrial Turnover.
    Karolina Drabik, Dominika Malińska, Karolina Piecyk, Grażyna Dębska-Vielhaber, Stefan Vielhaber, Jerzy Duszyński, Joanna Szczepanowska.
      Although the sporadic form of Alzheimer's disease (AD) is the prevalent form, the cellular events underlying the disease pathogenesis have not been fully characterized. Accumulating evidence points to mitochondrial dysfunction as one of the events responsible for AD progression. We investigated mitochondrial function in fibroblasts collected from patients diagnosed with the sporadic form of AD (sAD), placing a particular focus on mitochondrial turnover. We measured mitochondrial biogenesis and autophagic clearance, and evaluated the presence of bioenergetic stress in sAD cells. The mitochondrial turnover was clearly lower in the fibroblasts from sAD patients than in the fibroblasts from the control subjects, and the levels of many proteins regulating mitochondrial biogenesis, autophagy and mitophagy were decreased in patient cells. Additionally, the sAD fibroblasts had slightly higher mitochondrial superoxide levels and impaired antioxidant defense. Mitochondrial turnover undergoes feedback regulation through mitochondrial retrograde signaling, which is responsible for the maintenance of optimal mitochondrial functioning, and mitochondria-derived ROS participate as signaling molecules in this process. Our results showed that in sAD patients cells, there is a shift in the balance of mitochondrial function, possibly in response to the presence of cellular stress related to disease development.
    Keywords:  Alzheimer’s disease; mitochondria; mitochondrial biogenesis; mitochondrial retrograde signaling; mitophagy; reactive oxygen species
    DOI:  https://doi.org/10.3390/antiox10060938
  55. Int J Mol Sci. 2021 Jun 05. pii: 6097. [Epub ahead of print]22(11):
    Glycogen Synthase Kinase 3 Beta Regulates the Human Aryl Hydrocarbon Receptor Cellular Content and Activity.
    Yujie Yang, William K Chan.
      The aryl hydrocarbon receptor (AHR) is a cytosolic receptor which is involved in diverse cellular events in humans. The most well-characterized function of AHR is its ability to upregulate gene transcription after exposure to its ligands, such as environmental toxicants, dietary antioxidants, drugs, and endogenous ligands. The cellular content of AHR is partly controlled by its degradation via the ubiquitin-proteasome system and the lysosome-dependent autophagy. We used human cervical cancer (HeLa) cells to investigate how AHR undergoes protein degradation and how its activity is modulated. Since the glycogen synthase kinase 3 beta (GSK3β)-mediated phosphorylation can trigger protein degradation and substrates of GSK3β contain stretches of serine/threonine residues which can be found in AHR, we examined whether degradation and activity of AHR can be controlled by GSK3β. We observed that AHR undergoes the GSK3β-dependent, LC3-mediated lysosomal degradation without ligand treatment. The AHR can be phosphorylated in a GSK3β-dependent manner at three putative sites (S436/S440/S444, S689/S693/T697, and S723/S727/T731), which leads to lysosomal degradation of the AHR protein. Inhibition of the GSK3β activity suppresses the ligand-activated transcription of an AHR target gene in HeLa, human liver cancer (Hep3B), and human breast cancer (MCF-7) cells. Collectively, our findings support that phosphorylation of AHR by GSK3β is essential for the optimal activation of its target gene transcription and this phosphorylation may partake as an "off" switch by subjecting the receptor to lysosomal degradation.
    Keywords:  GSK3β; LC3; aryl hydrocarbon receptor; autophagy; lysosomal degradation; p23
    DOI:  https://doi.org/10.3390/ijms22116097
  56. Int J Mol Sci. 2021 Jun 13. pii: 6339. [Epub ahead of print]22(12):
    n-Butylidenephthalide Modulates Autophagy to Ameliorate Neuropathological Progress of Spinocerebellar Ataxia Type 3 through mTOR Pathway.
    Jui-Hao Lee, Si-Yin Lin, Jen-Wei Liu, Shinn-Zong Lin, Horng-Jyh Harn, Tzyy-Wen Chiou.
      Spinocerebellar ataxia type 3 (SCA3), a hereditary and lethal neurodegenerative disease, is attributed to the abnormal accumulation of undegradable polyglutamine (polyQ), which is encoded by mutated ataxin-3 gene (ATXN3). The toxic fragments processed from mutant ATXN3 can induce neuronal death, leading to the muscular incoordination of the human body. Some treatment strategies of SCA3 are preferentially focused on depleting the abnormal aggregates, which led to the discovery of small molecule n-butylidenephthalide (n-BP). n-BP-promoted autophagy protected the loss of Purkinje cell in the cerebellum that regulates the network associated with motor functions. We report that the n-BP treatment may be effective in treating SCA3 disease. n-BP treatment led to the depletion of mutant ATXN3 with the expanded polyQ chain and the toxic fragments resulting in increased metabolic activity and alleviated atrophy of SCA3 murine cerebellum. Furthermore, n-BP treated animal and HEK-293GFP-ATXN3-84Q cell models could consistently show the depletion of aggregates through mTOR inhibition. With its unique mechanism, the two autophagic inhibitors Bafilomycin A1 and wortmannin could halt the n-BP-induced elimination of aggregates. Collectively, n-BP shows promising results for the treatment of SCA3.
    Keywords:  MJD; PolyQ; Purkinje cell; SCA3; atxain-3; autophagy; mTOR; toxic fragment
    DOI:  https://doi.org/10.3390/ijms22126339
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