bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2021–11–28
sixty-six papers selected by
Viktor Korolchuk, Newcastle University
  1. HYPK coordinates degradation of polyneddylated proteins by autophagy.
  2. The PINK1 advantage: recycling mitochondria in times of trouble?
  3. Lysosomal dysfunction impairs mitochondrial quality control and is associated with neurodegeneration in TBCK encephaloneuronopathy.
  4. The Emerging Roles of Autophagy in Human Diseases.
  5. Macroautophagy and Mitophagy in Neurodegenerative Disorders: Focus on Therapeutic Interventions.
  6. The Cell Wall Integrity Receptor Mtl1 Contributes to Articulate Autophagic Responses When Glucose Availability Is Compromised.
  7. Post-transcriptional regulation of ATG1 is a critical node that modulates autophagy during distinct nutrient stresses.
  8. Phosphate Restriction Promotes Longevity via Activation of Autophagy and the Multivesicular Body Pathway.
  9. Suppressor of Cytokine Signaling 2 Regulates Retinal Pigment Epithelium Metabolism by Enhancing Autophagy.
  10. Protein Kinase A and 5' AMP-Activated Protein Kinase Signaling Pathways Exert Opposite Effects on Induction of Autophagy in Luteal Cells.
  11. Conserved and Diversified Mechanism of Autophagy between Plants and Animals upon Various Stresses.
  12. Mitochondrial Defects in Fibroblasts of Pathogenic MAPT Patients.
  13. L-Arginine Ameliorates Defective Autophagy in GM2 Gangliosidoses by mTOR Modulation.
  14. Sestrin2 as a Potential Target for Regulating Metabolic-Related Diseases.
  15. Possible Involvement of the Nutrient and Energy Sensors mTORC1 and AMPK in Cell Fate Diversification in a Non-Metazoan Organism.
  16. Snazarus and its human ortholog SNX25 modulate autophagic flux.
  17. ALDOA maintains NLRP3 inflammasome activation by controlling AMPK activation.
  18. The Secrets of Alternative Autophagy.
  19. A novel role of KEAP1/PGAM5 complex: ROS sensor for inducing mitophagy.
  20. The mTOR Pathway in Pluripotent Stem Cells: Lessons for Understanding Cancer Cell Dormancy.
  21. α-synuclein suppresses microglial autophagy and promotes neurodegeneration in a mouse model of Parkinson's disease.
  22. Shining a light on autophagy in neurodegenerative diseases.
  23. Activation Mechanisms of the VPS34 Complexes.
  24. Direct Interaction of ATP7B and LC3B Proteins Suggests a Cooperative Role of Copper Transportation and Autophagy.
  25. A high-throughput protocol for monitoring starvation-induced autophagy in real time in mouse embryonic fibroblasts.
  26. Developing potent LC3-targeting AUTAC tools for protein degradation with selective autophagy.
  27. ERK5 Inhibition Induces Autophagy-Mediated Cancer Cell Death by Activating ER Stress.
  28. Innate host defense mechanisms SAC bacteria by regulating phosphoinositide kinases and phosphatases.
  29. The fission yeast FLCN/FNIP complex augments TORC1 repression or activation in response to amino acid (AA) availability.
  30. Disruption of Mitochondrial Homeostasis: The Role of PINK1 in Parkinson's Disease.
  31. Key Regulators of Autophagosome Closure.
  32. Autophagy regulates whitefly-symbiont metabolic interactions.
  33. Decanoic Acid Stimulates Autophagy in D. discoideum.
  34. Application of Metabolomics in the Study of Starvation-Induced Autophagy in Saccharomyces cerevisiae: A Scoping Review.
  35. Understanding the Role of Autophagy in Cancer Formation and Progression Is a Real Opportunity to Treat and Cure Human Cancers.
  36. The Cytotoxicity and Clearance of Mutant Huntingtin and Other Misfolded Proteins.
  37. Monomethyl branched-chain fatty acid mediates amino acid sensing upstream of mTORC1.
  38. Autophagy in α-Synucleinopathies-An Overstrained System.
  39. A neurodegeneration gene, WDR45, links impaired ferritinophagy to iron accumulation.
  40. An exploratory text analysis of the autophagy research field.
  41. MyD88 deficiency ameliorates weight loss caused by intestinal oxidative injury in an autophagy-dependent mechanism.
  42. Mitochondrial Quality Control in Cardiac-Conditioning Strategies against Ischemia-Reperfusion Injury.
  43. Dysregulation of Caveolin-1 Phosphorylation and Nuclear Translocation Is Associated with Senescence Onset.
  44. Homeostatic scaling is driven by a translation-dependent degradation axis that recruits miRISC remodeling.
  45. Sirtuins and Autophagy in Age-Associated Neurodegenerative Diseases: Lessons from the C. elegans Model.
  46. Over Fifty Years of Life, Death, and Cannibalism: A Historical Recollection of Apoptosis and Autophagy.
  47. ER-associated CTRP1 regulates mitochondrial fission via interaction with DRP1.
  48. Autophagy in Cisplatin Nephrotoxicity during Cancer Therapy.
  49. Thunbergia laurifolia Leaf Extract Inhibits Glutamate-Induced Neurotoxicity and Cell Death through Mitophagy Signaling.
  50. Rescue of thyroid cells from antibody induced cell death via induction of autophagy.
  51. Crosstalk Between ER Stress, Autophagy and Inflammation.
  52. Dual Role of SIRT1 in Autophagy and Lipid Metabolism Regulation in Osteoarthritic Chondrocytes.
  53. PINK1 deficiency impairs osteoblast differentiation through aberrant mitochondrial homeostasis.
  54. Autophagy Inhibits Intercellular Transport of Citrus Leaf Blotch Virus by Targeting Viral Movement Protein.
  55. Calcium Signaling Mediates Cell Death and Crosstalk with Autophagy in Kidney Disease.
  56. LAMP3 inhibits autophagy and contributes to cell death by lysosomal membrane permeabilization.
  57. Reactive oxygen species prevent lysosome coalescence during PIKfyve inhibition.
  58. Cellular Self-Digestion and Persistence in Bacteria.
  59. Exercise Ameliorates Diabetic Kidney Disease in Type 2 Diabetic Fatty Rats.
  60. Atg5 Regulates Selective Autophagy of the Parental Macronucleus during Tetrahymena Sexual Reproduction.
  61. Hsa_circRNA_103124 Upregulation in Crohn's Disease Promotes Cell Proliferation and Inhibits Autophagy by Regulating the Hsa-miR-650/AKT2 Signaling Pathway.
  62. Protein Misfolding and Aggregation: The Relatedness between Parkinson's Disease and Hepatic Endoplasmic Reticulum Storage Disorders.
  63. Mitochondrial Quality Control in the Maintenance of Cardiovascular Homeostasis: The Roles and Interregulation of UPS, Mitochondrial Dynamics and Mitophagy.
  64. Autophagy and disease: new insights and challenges ahead.
  65. Substrate stiffening promotes VEGF-A functions via the PI3K/Akt/mTOR pathway.
  66. MitoQ inhibits hepatic stellate cell activation and liver fibrosis by enhancing PINK1/parkin-mediated mitophagy.
  1. Autophagy. 2021 Nov 26. 1-22
    HYPK coordinates degradation of polyneddylated proteins by autophagy.
    Debasish Kumar Ghosh, Akash Ranjan.
      Selective degradation of protein aggregates by macroautophagy/autophagy is an essential homeostatic process of safeguarding cells from the effects of proteotoxicity. Among the ubiquitin-like proteins, NEDD8 conjugation to misfolded proteins is prominent in stress-induced protein aggregates, albeit the function of neddylation in autophagy is unclear. Here, we report that polyneddylation functions as a post-translational modification for autophagic degradation of proteotoxic-stress induced protein aggregates. We also show that HYPK functions as an autophagy receptor in the polyneddylation-dependent aggrephagy. The scaffolding function of HYPK is facilitated by its C-terminal ubiquitin-associated domain and N-terminal tyrosine-type LC3-interacting region which bind to NEDD8 and LC3 respectively. Both NEDD8 and HYPK are positive modulators of basal and proteotoxicity-induced autophagy, leading to protection of cells from protein aggregates, such as aggregates of mutant HTT exon 1. Thus, we propose an indispensable and additive role of neddylation and HYPK in clearance of protein aggregates by autophagy, resulting in cytoprotective effect during proteotoxic stress.Abbreviations: ATG5, autophagy related 5; ATG12, autophagy related 12; ATG14, autophagy related 14; BECN1, beclin 1; CBL, casitas B-lineage lymphoma; CBLB, Cbl proto-oncogene B; GABARAP, GABA type A receptor-associated protein; GABARAPL1, GABA type A receptor associated protein like 1; GABARAPL2, GABA type A receptor associated protein like 2; GFP, green fluorescent protein; HTT, huntingtin; HTT97Q exon 1, huntingtin 97-glutamine exon 1; HUWE1, HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1; HYPK, huntingtin interacting protein K; IgG, immunoglobulin G; IMR-32, Institute for Medical Research-32; KD, knockdown; Kd, dissociation constant; LAMP1, lysosomal associated membrane protein 1; LIR, LC3 interacting region; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MAP1LC3A/LC3A, microtubule associated protein 1 light chain 3 alpha; MAP1LC3B/LC3B, microtubule associated protein 1 light chain 3 beta; MARK1, microtubule affinity regulating kinase 1; MARK2, microtubule affinity regulating kinase 2; MARK3, microtubule affinity regulating kinase 3; MARK4, microtubule affinity regulating kinase 4; MCF7, Michigan Cancer Foundation-7; MTOR, mechanistic target of rapamycin kinase; NAE1, NEDD8 activating enzyme E1 subunit 1; NBR1, NBR1 autophagy cargo receptor; NEDD8, NEDD8 ubiquitin like modifier; Ni-NTA, nickel-nitrilotriacetic acid; NUB1, negative regulator of ubiquitin like proteins 1; PIK3C3, phosphatidylinositol 3-kinase catalytic subunit type 3; PolyQ, poly-glutamine; PSMD8, proteasome 26S subunit, non-ATPase 8; RAD23A, RAD23 homolog A, nucleotide excision repair protein; RAD23B, RAD23 homolog B, nucleotide excision repair protein; RFP, red fluorescent protein; RPS27A, ribosomal protein S27a; RSC1A1, regulator of solute carriers 1; SNCA, synuclein alpha; SIK1, salt inducible kinase 1; siRNA, small interfering ribonucleic acid; SOD1, superoxide dismutase 1; SPR, surface plasmon resonance; SQSTM1, sequestosome 1; SUMO1, small ubiquitin like modifier 1; TAX1BP1, Tax1 binding protein 1; TDRD3, tudor domain containing 3; TNRC6C, trinucleotide repeat containing adaptor 6C; TOLLIP, toll interacting protein; TUBA, tubulin alpha; TUBB, tubulin beta class I; UBA, ubiquitin-associated; UBA1, ubiquitin like modifier activating enzyme 1; UBA5, ubiquitin like modifier activating enzyme 5; UBAC1, UBA domain containing 1; UBAC2, UBA domain containing 2; UBAP1, ubiquitin associated protein 1; UBAP2, ubiquitin associated protein 2; UBASH3B, ubiquitin associated and SH3 domain containing B; UBD/FAT10, ubiquitin D; UBE2K, ubiquitin conjugating enzyme E2 K; UBLs, ubiquitin-like proteins; UBL7, ubiquitin like 7; UBQLN1, ubiquilin 1; UBQLN2, ubiquilin 2; UBQLN3, ubiquilin 3; UBQLN4, ubiquilin 4; UBXN1, UBX domain protein 1; ULK1, unc-51 like autophagy activating kinase 1; URM1, ubiquitin related modifier 1; USP5, ubiquitin specific peptidase 5; USP13, ubiquitin specific peptidase 13; VPS13D, vacuolar protein sorting 13 homolog D.
    Keywords:  Aggrephagy; HTT exon 1 aggregate; HYPK; NEDD8; autophagy flux; proteotoxic stress
    DOI:  https://doi.org/10.1080/15548627.2021.1997053
  2. Autophagy. 2021 Nov 23. 1-2
    The PINK1 advantage: recycling mitochondria in times of trouble?
    Zak Doric, Huihui Li, Ken Nakamura.
      Parkinson disease remains a debilitating neurodegenerative disorder, despite the discovery of multiple causative genes that account for familial forms. Prominent among these are PRKN/Parkin and PINK1, whose protein products participate in mitochondrial turnover, or mitophagy. But our poor understanding of the basic biological mechanisms driven by those genes in neurons limits our ability to target them therapeutically. Here, we summarize our recent findings enabled by a new platform to track individual mitochondria in neurons. Our analysis delineates the steps of PINK1- and PRKN-dependent mitochondrial turnover, including the unexplored fates of mitochondria after fusion with lysosomes. These studies reveal unexpected mechanisms of mitochondrial quality control, which may contribute to the reliance of neurons on PINK1 under conditions of stress.
    Keywords:  Mitophagy; PARKIN; PINK1; Parkinson’s disease; mitochondrial turnover
    DOI:  https://doi.org/10.1080/15548627.2021.1998872
  3. Brain Commun. 2021 ;3(4): fcab215
    Lysosomal dysfunction impairs mitochondrial quality control and is associated with neurodegeneration in TBCK encephaloneuronopathy.
    Jesus A Tintos-Hernández, Adrian Santana, Kierstin N Keller, Xilma R Ortiz-González.
      Biallelic variants in the TBCK gene cause intellectual disability with remarkable clinical variability, ranging from static encephalopathy to progressive neurodegeneration (TBCK-Encephaloneuronopathy). The biological factors underlying variable disease penetrance remain unknown. Since previous studies had suggested aberrant autophagy, we tested whether mitophagy and mitochondrial function are altered in TBCK -/- fibroblasts derived from patients exhibiting variable clinical severity. Our data show significant accumulation of mitophagosomes, reduced mitochondrial respiratory capacity and mitochondrial DNA content, suggesting impaired mitochondrial quality control. Furthermore, the degree of mitochondrial dysfunction correlates with a neurodegenerative clinical course. Since mitophagy ultimately depends on lysosomal degradation, we also examined lysosomal function. Our data show that lysosomal proteolytic function is significantly reduced in TBCK -/- fibroblasts. Moreover, acidifying lysosomal nanoparticles rescue the mitochondrial respiratory defects in fibroblasts, suggesting impaired mitochondrial quality control secondary to lysosomal dysfunction. Our data provide insight into the disease mechanisms of TBCK Encephaloneuronopathy and the potential relevance of mitochondrial function as a biomarker beyond primary mitochondrial disorders. It also supports the benefit of lysosomal acidification strategies for disorders of impaired lysosomal degradation affecting mitochondrial quality control.
    Keywords:  intellectual disability; lysosome; mitochondria; mitophagy; neurodegeneration
    DOI:  https://doi.org/10.1093/braincomms/fcab215
  4. Biomedicines. 2021 Nov 09. pii: 1651. [Epub ahead of print]9(11):
    The Emerging Roles of Autophagy in Human Diseases.
    Yuchen Lei, Daniel J Klionsky.
      Autophagy, a process of cellular self-digestion, delivers intracellular components including superfluous and dysfunctional proteins and organelles to the lysosome for degradation and recycling and is important to maintain cellular homeostasis. In recent decades, autophagy has been found to help fight against a variety of human diseases, but, at the same time, autophagy can also promote the procession of certain pathologies, which makes the connection between autophagy and diseases complex but interesting. In this review, we summarize the advances in understanding the roles of autophagy in human diseases and the therapeutic methods targeting autophagy and discuss some of the remaining questions in this field, focusing on cancer, neurodegenerative diseases, infectious diseases and metabolic disorders.
    Keywords:  autophagy; cancer; infection; metabolism; neurodegeneration
    DOI:  https://doi.org/10.3390/biomedicines9111651
  5. Biomedicines. 2021 Nov 05. pii: 1625. [Epub ahead of print]9(11):
    Macroautophagy and Mitophagy in Neurodegenerative Disorders: Focus on Therapeutic Interventions.
    João Duarte Magalhães, Lígia Fão, Rita Vilaça, Sandra Morais Cardoso, Ana Cristina Rego.
      Macroautophagy, a quality control mechanism, is an evolutionarily conserved pathway of lysosomal degradation of protein aggregates, pathogens, and damaged organelles. As part of its vital homeostatic role, macroautophagy deregulation is associated with various human disorders, including neurodegenerative diseases. There are several lines of evidence that associate protein misfolding and mitochondrial dysfunction in the etiology of Alzheimer's, Parkinson's, and Huntington's diseases. Macroautophagy has been implicated in the degradation of different protein aggregates such as Aβ, tau, alpha-synuclein (α-syn), and mutant huntingtin (mHtt) and in the clearance of dysfunctional mitochondria. Taking these into consideration, targeting autophagy might represent an effective therapeutic strategy to eliminate protein aggregates and to improve mitochondrial function in these disorders. The present review describes our current understanding on the role of macroautophagy in neurodegenerative disorders and focuses on possible strategies for its therapeutic modulation.
    Keywords:  autophagy; mitophagy mitochondrial dysfunction; mutant proteins; neurodegenerative disorders; therapeutic strategies
    DOI:  https://doi.org/10.3390/biomedicines9111625
  6. J Fungi (Basel). 2021 Oct 26. pii: 903. [Epub ahead of print]7(11):
    The Cell Wall Integrity Receptor Mtl1 Contributes to Articulate Autophagic Responses When Glucose Availability Is Compromised.
    Sandra Montella-Manuel, Nuria Pujol-Carrion, Maria Angeles de la Torre-Ruiz.
      Mtl1protein is a cell wall receptor belonging to the CWI pathway. Mtl1 function is related to glucose and oxidative stress signaling. In this report, we show data demonstrating that Mtl1 plays a critical role in the detection of a descent in glucose concentration, in order to activate bulk autophagy machinery as a response to nutrient deprivation and to maintain cell survival in starvation conditions. Autophagy is a tightly regulated mechanism involving several signaling pathways. The data here show that in Saccharomyces cerevisiae, Mtl1 signals glucose availability to either Ras2 or Sch9 proteins converging in Atg1 phosphorylation and autophagy induction. TORC1 complex function is not involved in autophagy induction during the diauxic shift when glucose is limited. In this context, the GCN2 gene is required to regulate autophagy activation upon amino acid starvation independent of the TORC1 complex. Mtl1 function is also involved in signaling the autophagic degradation of mitochondria during the stationary phase through both Ras2 and Sch9, in a manner dependent on either Atg33 and Atg11 proteins and independent of the Atg32 protein, the mitophagy receptor. All of the above suggest a pivotal signaling role for Mtl1 in maintaining correct cell homeostasis function in periods of glucose scarcity in budding yeast.
    Keywords:  Mtl1; Saccharomyces cerevisiae; autophagy; cell wall integrity (CWI); glucose; mitophagy
    DOI:  https://doi.org/10.3390/jof7110903
  7. Autophagy. 2021 Nov 26. 1-21
    Post-transcriptional regulation of ATG1 is a critical node that modulates autophagy during distinct nutrient stresses.
    Vikramjit Lahiri, Shree Padma Metur, Zehan Hu, Xinxin Song, Muriel Mari, Wayne D Hawkins, Janakraj Bhattarai, Elizabeth Delorme-Axford, Fulvio Reggiori, Daolin Tang, Joern Dengjel, Daniel J Klionsky.
      Macroautophagy/autophagy is a highly conserved nutrient-recycling pathway that eukaryotes utilize to combat diverse stresses including nutrient depletion. Dysregulation of autophagy disrupts cellular homeostasis leading to starvation susceptibility in yeast and disease development in humans. In yeast, the robust autophagy response to starvation is controlled by the upregulation of ATG genes, via regulatory processes involving multiple levels of gene expression. Despite the identification of several regulators through genetic studies, the predominant mechanism of regulation modulating the autophagy response to subtle differences in nutrient status remains undefined. Here, we report the unexpected finding that subtle changes in nutrient availability can cause large differences in autophagy flux, governed by hitherto unknown post-transcriptional regulatory mechanisms affecting the expression of the key autophagyinducing kinase Atg1 (ULK1/ULK2 in mammals). We have identified two novel post-transcriptional regulators of ATG1 expression, the kinase Rad53 and the RNA-binding protein Ded1 (DDX3 in mammals). Furthermore, we show that DDX3 regulates ULK1 expression post-transcriptionally, establishing mechanistic conservation and highlighting the power of yeast biology in uncovering regulatory mechanisms that can inform therapeutic approaches.
    Keywords:  ATG1; Amino acid starvation; DDX3; DED1; RAD53; ULK1; autophagosome; autophagy
    DOI:  https://doi.org/10.1080/15548627.2021.1997305
  8. Cells. 2021 Nov 13. pii: 3161. [Epub ahead of print]10(11):
    Phosphate Restriction Promotes Longevity via Activation of Autophagy and the Multivesicular Body Pathway.
    Mahsa Ebrahimi, Lukas Habernig, Filomena Broeskamp, Andreas Aufschnaiter, Jutta Diessl, Isabel Atienza, Steffen Matz, Felix A Ruiz, Sabrina Büttner.
      Nutrient limitation results in an activation of autophagy in organisms ranging from yeast, nematodes and flies to mammals. Several evolutionary conserved nutrient-sensing kinases are critical for efficient adaptation of yeast cells to glucose, nitrogen or phosphate depletion, subsequent cell-cycle exit and the regulation of autophagy. Here, we demonstrate that phosphate restriction results in a prominent extension of yeast lifespan that requires the coordinated activity of autophagy and the multivesicular body pathway, enabling efficient turnover of cytoplasmic and plasma membrane cargo. While the multivesicular body pathway was essential during the early days of aging, autophagy contributed to long-term survival at later days. The cyclin-dependent kinase Pho85 was critical for phosphate restriction-induced autophagy and full lifespan extension. In contrast, when cell-cycle exit was triggered by exhaustion of glucose instead of phosphate, Pho85 and its cyclin, Pho80, functioned as negative regulators of autophagy and lifespan. The storage of phosphate in form of polyphosphate was completely dispensable to in sustaining viability under phosphate restriction. Collectively, our results identify the multifunctional, nutrient-sensing kinase Pho85 as critical modulator of longevity that differentially coordinates the autophagic response to distinct kinds of starvation.
    Keywords:  Pho85; aging; autophagy; lifespan; nutrient limitation; polyphosphate; quiescence; vacuole fusion; yeast
    DOI:  https://doi.org/10.3390/cells10113161
  9. Front Neurosci. 2021 ;15 738022
    Suppressor of Cytokine Signaling 2 Regulates Retinal Pigment Epithelium Metabolism by Enhancing Autophagy.
    Xi-Yuan Liu, Rui Lu, Jing Chen, Jie Wang, Hong-Mei Qian, Gang Chen, Rong-Han Wu, Zai-Long Chi.
      Retinal pigment epithelium (RPE) serves critical functions in maintaining retinal homeostasis. An important function of RPE is to degrade the photoreceptor outer segment fragments daily to maintain photoreceptor function and longevity throughout life. An impairment of RPE functions such as metabolic regulation leads to the development of age-related macular degeneration (AMD) and inherited retinal degenerative diseases. As substrate recognition subunit of a ubiquitin ligase complex, suppressor of cytokine signaling 2 (SOCS2) specifically binds to the substrates for ubiquitination and negatively regulates growth hormone signaling. Herein, we explore the role of SOCS2 in the metabolic regulation of autophagy in the RPE cells. SOCS2 knockout mice exhibited the irregular morphological deposits between the RPE and Bruch's membrane. Both in vivo and in vitro experiments showed that RPE cells lacking SOCS2 displayed impaired autophagy, which could be recovered by re-expressing SOCS2. SOCS2 recognizes the ubiquitylated proteins and participates in the formation of autolysosome by binding with autophagy receptors and lysosome-associated membrane protein2 (LAMP-2), thereby regulating the phosphorylation of glycogen synthase kinase 3β (GSK3β) and mammalian target of rapamycin (mTOR) during the autophagy process. Our results imply that SOCS2 participates in ubiquitin-autophagy-lysosomal pathway and enhances autophagy by regulating GSK3β and mTOR. This study provides a potential therapeutic target for AMD.
    Keywords:  autophagy; glycogen synthase kinase (GSK)-3β; mammalian target of rapamycin (mTOR); retinal pigment epithelium; suppressor of cytokine signaling 2; ubiquitin
    DOI:  https://doi.org/10.3389/fnins.2021.738022
  10. Front Cell Dev Biol. 2021 ;9 723563
    Protein Kinase A and 5' AMP-Activated Protein Kinase Signaling Pathways Exert Opposite Effects on Induction of Autophagy in Luteal Cells.
    Emilia Przygrodzka, Corrine F Monaco, Michele R Plewes, Guojuan Li, Jennifer R Wood, Andrea S Cupp, John S Davis.
      In the absence of pregnancy the ovarian corpus luteum undergoes regression, a process characterized by decreased production of progesterone and structural luteolysis involving apoptosis. Autophagy has been observed in the corpus luteum during luteal regression. Autophagy is a self-degradative process important for balancing sources of cellular energy at critical times in development and in response to nutrient stress, but it can also lead to apoptosis. Mechanistic target of rapamycin (MTOR) and 5' AMP-activated protein kinase (AMPK), key players in autophagy, are known to inhibit or activate autophagy, respectively. Here, we analyzed the signaling pathways regulating the initiation of autophagy in bovine luteal cells. In vivo studies showed increased activating phosphorylation of AMPKα (Thr172) and elevated content of LC3B, a known marker of autophagy, in luteal tissue during PGF2α-induced luteolysis. In vitro, AMPK activators 1) stimulated phosphorylation of regulatory associated protein of MTOR (RPTOR) leading to decreased activity of MTOR, 2) increased phosphorylation of Unc-51-Like Kinase 1 (ULK1) and Beclin 1 (BECN1), at sites specific for AMPK and required for autophagy initiation, 3) increased levels of LC3B, and 4) enhanced colocalization of autophagosomes with lysosomes indicating elevated autophagy. In contrast, LH/PKA signaling in luteal cells 1) reduced activation of AMPKα and phosphorylation of RPTOR, 2) elevated MTOR activity, 3) stimulated phosphorylation of ULK1 at site required for ULK1 inactivation, and 4) inhibited autophagosome formation as reflected by reduced content of LC3B-II. Pretreatment with AICAR, a pharmacological activator of AMPK, inhibited LH-mediated effects on RPTOR, ULK1 and BECN1. Our results indicate that luteotrophic signaling via LH/PKA/MTOR inhibits, while luteolytic signaling via PGF2α/Ca2+/AMPK activates key signaling pathways involved in luteal cell autophagy.
    Keywords:  AMPK; LC3B; MTOR; PGF2α; PKA; Ulk1; corpus luteum; luteinizing hormone
    DOI:  https://doi.org/10.3389/fcell.2021.723563
  11. Antioxidants (Basel). 2021 Oct 29. pii: 1736. [Epub ahead of print]10(11):
    Conserved and Diversified Mechanism of Autophagy between Plants and Animals upon Various Stresses.
    Naveed Ur Rehman, Peichun Zeng, Zulong Mo, Shaoying Guo, Yunfeng Liu, Yifeng Huang, Qingjun Xie.
      Autophagy is a highly conserved degradation mechanism in eukaryotes, executing the breakdown of unwanted cell components and subsequent recycling of cellular material for stress relief through vacuole-dependence in plants and yeast while it is lysosome-dependent in animal manner. Upon stress, different types of autophagy are stimulated to operate certain biological processes by employing specific selective autophagy receptors (SARs), which hijack the cargo proteins or organelles to the autophagy machinery for subsequent destruction in the vacuole/lysosome. Despite recent advances in autophagy, the conserved and diversified mechanism of autophagy in response to various stresses between plants and animals still remain a mystery. In this review, we intend to summarize and discuss the characterization of the SARs and their corresponding processes, expectantly advancing the scope and perspective of the evolutionary fate of autophagy between plants and animals.
    Keywords:  autophagosomes; autophagy; autophagy-related protein; degradation; vacuole
    DOI:  https://doi.org/10.3390/antiox10111736
  12. Front Cell Dev Biol. 2021 ;9 765408
    Mitochondrial Defects in Fibroblasts of Pathogenic MAPT Patients.
    Vinita Bharat, Chung-Han Hsieh, Xinnan Wang.
      Mutations in MAPT gene cause multiple neurological disorders, including frontal temporal lobar degeneration and parkinsonism. Increasing evidence indicates impaired mitochondrial homeostasis and mitophagy in patients and disease models of pathogenic MAPT. Here, using MAPT patients' fibroblasts as a model, we report that disease-causing MAPT mutations compromise early events of mitophagy. By employing biochemical and mitochondrial assays we discover that upon mitochondrial depolarization, the recruitment of LRRK2 and Parkin to mitochondria and degradation of the outer mitochondrial membrane protein Miro1 are disrupted. Using high resolution electron microscopy, we reveal that the contact of mitochondrial membranes with ER and cytoskeleton tracks is dissociated following mitochondrial damage. This membrane dissociation is blocked by a pathogenic MAPT mutation. Furthermore, we provide evidence showing that tau protein, which is encoded by MAPT gene, interacts with Miro1 protein, and this interaction is abolished by pathogenic MAPT mutations. Lastly, treating fibroblasts of a MAPT patient with a small molecule promotes Miro1 degradation following depolarization. Altogether, our results show molecular defects in a peripheral tissue of patients and suggest that targeting mitochondrial quality control may have a broad application for future therapeutic intervention.
    Keywords:  ER; FTLD; MAPT; Miro; mitochondria; mitophagy; parkinsonism; tau
    DOI:  https://doi.org/10.3389/fcell.2021.765408
  13. Cells. 2021 Nov 11. pii: 3122. [Epub ahead of print]10(11):
    L-Arginine Ameliorates Defective Autophagy in GM2 Gangliosidoses by mTOR Modulation.
    Beatriz Castejón-Vega, Alejandro Rubio, Antonio J Pérez-Pulido, José L Quiles, Jon D Lane, Beatriz Fernández-Domínguez, María Begoña Cachón-González, Carmen Martín-Ruiz, Alberto Sanz, Timothy M Cox, Elísabet Alcocer-Gómez, Mario D Cordero.
       AIMS: Tay-Sachs and Sandhoff diseases (GM2 gangliosidosis) are autosomal recessive disorders of lysosomal function that cause progressive neurodegeneration in infants and young children. Impaired hydrolysis catalysed by β-hexosaminidase A (HexA) leads to the accumulation of GM2 ganglioside in neuronal lysosomes. Despite the storage phenotype, the role of autophagy and its regulation by mTOR has yet to be explored in the neuropathogenesis. Accordingly, we investigated the effects on autophagy and lysosomal integrity using skin fibroblasts obtained from patients with Tay-Sachs and Sandhoff diseases.
    RESULTS: Pathological autophagosomes with impaired autophagic flux, an abnormality confirmed by electron microscopy and biochemical studies revealing the accelerated release of mature cathepsins and HexA into the cytosol, indicating increased lysosomal permeability. GM2 fibroblasts showed diminished mTOR signalling with reduced basal mTOR activity. Accordingly, provision of a positive nutrient signal by L-arginine supplementation partially restored mTOR activity and ameliorated the cytopathological abnormalities.
    INNOVATION: Our data provide a novel molecular mechanism underlying GM2 gangliosidosis. Impaired autophagy caused by insufficient lysosomal function might represent a new therapeutic target for these diseases.
    CONCLUSIONS: We contend that the expression of autophagy/lysosome/mTOR-associated molecules may prove useful peripheral biomarkers for facile monitoring of treatment of GM2 gangliosidosis and neurodegenerative disorders that affect the lysosomal function and disrupt autophagy.
    Keywords:  GM2 gangliosidosis; L-arginine; autophagy; mTOR
    DOI:  https://doi.org/10.3390/cells10113122
  14. Front Endocrinol (Lausanne). 2021 ;12 751020
    Sestrin2 as a Potential Target for Regulating Metabolic-Related Diseases.
    Linan Gong, Zanzan Wang, Zhenggui Wang, Zhiguo Zhang.
      Sestrin2 is a highly conserved protein that can be induced under a variety of stress conditions, including DNA damage, oxidative stress, endoplasmic reticulum (ER) stress, and metabolic stress. Numerous studies have shown that the AMP-activated protein kinase (AMPK)/mammalian target of rapamycin (mTOR) signaling pathway has a crucial role in the regulation of metabolism. Sestrin2 regulates metabolism via a number of pathways, including activation of AMPK, inhibition of the mTOR complex 1 (mTORC1), activation of mTOR complex 2 (mTORC2), inhibition of ER stress, and promotion of autophagy. Therefore, modulation of Sestrin2 activity may provide a potential therapeutic target for the prevention of metabolic diseases such as insulin resistance, diabetes, obesity, non-alcoholic fatty liver disease, and myocardial ischemia/reperfusion injury. In this review, we examined the regulatory relationship between Sestrin2 and the AMPK/mTOR signaling pathway and the effects of Sestrin2 on energy metabolism.
    Keywords:  AMPK; Sestrin2; mTOR; metabolic diseases; metabolism
    DOI:  https://doi.org/10.3389/fendo.2021.751020
  15. Front Cell Dev Biol. 2021 ;9 758317
    Possible Involvement of the Nutrient and Energy Sensors mTORC1 and AMPK in Cell Fate Diversification in a Non-Metazoan Organism.
    Julian D Gross, Catherine J Pears.
      mTORC1 and AMPK are mutually antagonistic sensors of nutrient and energy status that have been implicated in many human diseases including cancer, Alzheimer's disease, obesity and type 2 diabetes. Starved cells of the social amoeba Dictyostelium discoideum aggregate and eventually form fruiting bodies consisting of stalk cells and spores. We focus on how this bifurcation of cell fate is achieved. During growth mTORC1 is highly active and AMPK relatively inactive. Upon starvation, AMPK is activated and mTORC1 inhibited; cell division is arrested and autophagy induced. After aggregation, a minority of the cells (prestalk cells) continue to express much the same set of developmental genes as during aggregation, but the majority (prespore cells) switch to the prespore program. We describe evidence suggesting that overexpressing AMPK increases the proportion of prestalk cells, as does inhibiting mTORC1. Furthermore, stimulating the acidification of intracellular acidic compartments likewise increases the proportion of prestalk cells, while inhibiting acidification favors the spore pathway. We conclude that the choice between the prestalk and the prespore pathways of cell differentiation may depend on the relative strength of the activities of AMPK and mTORC1, and that these may be controlled by the acidity of intracellular acidic compartments/lysosomes (pHv), cells with low pHv compartments having high AMPK activity/low mTORC1 activity, and those with high pHv compartments having high mTORC1/low AMPK activity. Increased insight into the regulation and downstream consequences of this switch should increase our understanding of its potential role in human diseases, and indicate possible therapeutic interventions.
    Keywords:  AMP-dependent protein kinase (AMPK); DIF-1; Dictyostelium discoideum; acidic vesicles; ammonia; cell fate decision; mechanistic target of rapamycin complex 1 (mTORC1)
    DOI:  https://doi.org/10.3389/fcell.2021.758317
  16. J Cell Sci. 2021 Nov 25. pii: jcs.258733. [Epub ahead of print]
    Snazarus and its human ortholog SNX25 modulate autophagic flux.
    Annie Lauzier, Marie-France Bossanyi, Raphaëlle Larcher, Sonya Nassari, Rupali Ugrankar, W Mike Henne, Steve Jean.
      Macroautophagy, the degradation and recycling of cytosolic components in the lysosome, is an important cellular mechanism. It is a membrane-mediated process that is linked to vesicular trafficking events. The sorting nexin (SNX) protein family controls the sorting of a large array of cargoes, and various SNXs impact autophagy. To improve our understanding of their functions in vivo, we screened all Drosophila SNXs using inducible RNA interference in the fat body. Significantly, depletion of snazarus (snz) led to decreased autophagic flux. Interestingly, we observed altered distribution of Vamp7-positive vesicles with snz depletion, and snz's roles were conserved in human cells. SNX25, the closest human ortholog to snz, regulates both VAMP8 endocytosis and lipid metabolism. Through knockout-rescue experiments, we demonstrate that these activities are dependent on specific SNX25 domains and that the autophagic defects upon SNX25 loss can be rescued by ethanolamine addition. We also demonstrate the presence of differentially spliced forms of SNX14 and SNX25 in cancer cells. This work identifies a conserved role for snz/SNX25 as regulators of autophagic flux and reveals differential isoform expression between paralogs.
    Keywords:  Autophagy; Endocytosis; Lipid metabolism; Snazarus; Sorting nexin 25; Trafficking; VAMP8
    DOI:  https://doi.org/10.1242/jcs.258733
  17. Autophagy. 2021 Nov 25. 1-21
    ALDOA maintains NLRP3 inflammasome activation by controlling AMPK activation.
    Dongsheng Bai, Jiaying Du, Xiumin Bu, Wangjia Cao, Tifan Sun, Jiawei Zhao, Yue Zhao, Na Lu.
       ABBREVIATIONS: ALDOA: aldolase A; AMPK: AMP-activated protein kinase; ATG: autophagy related; ATG5: autophagy related 5; ATP: adenosine triphosphate; BMDMs: bone marrow-derived macrophages; CALCOCO2: calcium binding and coiled-coil domain 2; CASP1: caspase 1; CQ: chloroquine; FOXO3: forkhead box O3; IL1B: interleukin 1 beta; LPS: lipopolysaccharide; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MT: mutant; mtDNA: mitochondrial DNA; MTORC1: mechanistic target of rapamycin kinase complex 1; mtROS: mitochondrial reactive oxygen species; NLRP3: NLR family, pyrin domain containing 3; OPTN: optineurin; PBS: phosphate-buffered saline; PRKN/Parkin: parkin RBR E3 ubiquitin protein ligase; SN: supernatant; SQSTM1/p62: sequestosome 1; STK11/LKB1: serine/threonine kinase 11; TOMM20: translocase of outer mitochondrial membrane 20; ULK1: unc-51 like autophagy activating kinase 1; v-ATPase: vacuolar type H+-ATPase; WT: wild-type.
    Keywords:  ALDOA; AMPK; LYG-202; NLRP3 inflammasome; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2021.1997051
  18. Cells. 2021 Nov 19. pii: 3241. [Epub ahead of print]10(11):
    The Secrets of Alternative Autophagy.
    Kaja Urbańska, Arkadiusz Orzechowski.
      For many years, it was thought that ATG5 and ATG7 played a pivotal role in autophagy, and that the knockdown of one of these genes would result in its inhibition. However, cells with ATG5 or ATG7 depletion still generate autophagic vacuoles with mainly trans-Golgi-originated isolation membranes and do not die. This indicates that autophagy can occur via ATG5/ATG7-independent alternative autophagy. Its molecular mechanism differs from that of the canonical pathway, including inter alia the phosphorylation of ULK1, and lack of LC3 modifications. As the alternative autophagy pathway has only recently been described, little is known of its precise role; however, a considerable body of evidence suggests that alternative autophagy participates in mitochondrion removal. This review summarizes the latest progress made in research on alternative autophagy and describes its possible molecular mechanism, roles and methods of detection, and possible modulators. There is a need for further research focused on types of autophagy, as this can elucidate the functioning of various cell types and the pathogenesis of human and animal diseases.
    Keywords:  ATG5; ATG7; Golgi apparatus; RAB9; ULK1; alternative autophagy; lysosome
    DOI:  https://doi.org/10.3390/cells10113241
  19. Redox Biol. 2021 Nov 11. pii: S2213-2317(21)00346-3. [Epub ahead of print]48 102186
    A novel role of KEAP1/PGAM5 complex: ROS sensor for inducing mitophagy.
    Akbar Zeb, Vinay Choubey, Ruby Gupta, Malle Kuum, Dzhamilja Safiulina, Annika Vaarmann, Nana Gogichaishvili, Mailis Liiv, Ivar Ilves, Kaido Tämm, Vladimir Veksler, Allen Kaasik.
      When ROS production exceeds the cellular antioxidant capacity, the cell needs to eliminate the defective mitochondria responsible for excessive ROS production. It has been proposed that the removal of these defective mitochondria involves mitophagy, but the mechanism of this regulation remains unclear. Here, we demonstrate that moderate mitochondrial superoxide and hydrogen peroxide production oxidates KEAP1, thus breaking the interaction between this protein and PGAM5, leading to the inhibition of its proteasomal degradation. Accumulated PGAM5 interferes with the processing of the PINK1 in the mitochondria leading to the accumulation of PINK1 on the outer mitochondrial membrane. In turn, PINK1 promotes Parkin recruitment to mitochondria and sensitizes mitochondria for autophagic removal. We also demonstrate that inhibitors of the KEAP1-PGAM5 protein-protein interaction (including CPUY192018) mimic the effect of mitochondrial ROS and sensitize mitophagy machinery, suggesting that these inhibitors could be used as pharmacological regulators of mitophagy. Together, our results show that KEAP1/PGAM5 complex senses mitochondrially generated superoxide/hydrogen peroxide to induce mitophagy.
    Keywords:  Mitophagy; NRF2/KEAP1 pathway; Neurodegenerative diseases; Oxidative stress; PINK1/Parkin pathway
    DOI:  https://doi.org/10.1016/j.redox.2021.102186
  20. Membranes (Basel). 2021 Nov 07. pii: 858. [Epub ahead of print]11(11):
    The mTOR Pathway in Pluripotent Stem Cells: Lessons for Understanding Cancer Cell Dormancy.
    Bashar A Alhasan, Sergei A Gordeev, Aleksandra R Knyazeva, Kseniia V Aleksandrova, Boris A Margulis, Irina V Guzhova, Irina I Suvorova.
      Currently, the success of targeted anticancer therapies largely depends on the correct understanding of the dormant state of cancer cells, since it is increasingly regarded to fuel tumor recurrence. The concept of cancer cell dormancy is often considered as an adaptive response of cancer cells to stress, and, therefore, is limited. It is possible that the cancer dormant state is not a privilege of cancer cells but the same reproductive survival strategy as diapause used by embryonic stem cells (ESCs). Recent advances reveal that high autophagy and mTOR pathway reduction are key mechanisms contributing to dormancy and diapause. ESCs, sharing their main features with cancer stem cells, have a delicate balance between the mTOR pathway and autophagy activity permissive for diapause induction. In this review, we discuss the functioning of the mTOR signaling and autophagy in ESCs in detail that allows us to deepen our understanding of the biology of cancer cell dormancy.
    Keywords:  autophagy; cancer cell dormancy; embryonic diapause; embryonic stem cells; mTOR; pluripotency; pluripotent stem cells
    DOI:  https://doi.org/10.3390/membranes11110858
  21. Aging Cell. 2021 Nov 22. e13522
    α-synuclein suppresses microglial autophagy and promotes neurodegeneration in a mouse model of Parkinson's disease.
    Hai-Yue Tu, Bao-Shi Yuan, Xiao-Ou Hou, Xiao-Jun Zhang, Chong-Shuang Pei, Ya-Ting Ma, Ya-Ping Yang, Yi Fan, Zheng-Hong Qin, Chun-Feng Liu, Li-Fang Hu.
      The cell-to-cell transfer of α-synuclein (α-Syn) greatly contributes to Parkinson's disease (PD) pathogenesis and underlies the spread of α-Syn pathology. During this process, extracellular α-Syn can activate microglia and neuroinflammation, which plays an important role in PD. However, the effect of extracellular α-Syn on microglia autophagy is poorly understood. In the present study, we reported that extracellular α-Syn inhibited the autophagy initiation, as indicated by LC3-II reduction and p62 protein elevation in BV2 and cultured primary microglia. The in vitro findings were verified in microglia-enriched population isolated from α-Syn-overexpressing mice induced by adeno-associated virus (AAV2/9)-encoded wildtype human α-Syn injection into the substantia nigra (SN). Mechanistically, α-Syn led to microglial autophagic impairment through activating toll-like receptor 4 (Tlr4) and its downstream p38 and Akt-mTOR signaling because Tlr4 knockout and inhibition of p38, Akt as well as mTOR prevented α-Syn-induced autophagy inhibition. Moreover, inhibition of Akt reversed the mTOR activation but failed to affect p38 phosphorylation triggered by α-Syn. Functionally, the in vivo evidence showed that lysozyme 2 Cre (Lyz2cre )-mediated depletion of autophagy-related gene 5 (Atg5) in microglia aggravated the neuroinflammation and dopaminergic neuron losses in the SN and exacerbated the locomotor deficit in α-Syn-overexpressing mice. Taken together, the results suggest that extracellular α-Syn, via Tlr4-dependent p38 and Akt-mTOR signaling cascades, disrupts microglial autophagy activity which synergistically contributes to neuroinflammation and PD development.
    Keywords:  Parkinson's disease; autophagy; microglia; neuroinflammation; α-synuclein
    DOI:  https://doi.org/10.1111/acel.13522
  22. J Biol Chem. 2021 Nov 18. pii: S0021-9258(21)01246-1. [Epub ahead of print] 101437
    Shining a light on autophagy in neurodegenerative diseases.
    Aswathy Chandran, Jean-Christophe Rochet.
      Small-molecule modulators of autophagy have been widely investigated as potential therapies for neurodegenerative diseases. In a recent issue of JBC, Safren et al. described a novel assay that uses a photoconvertible fusion protein to identify compounds that alter autophagic flux. Autophagy inducers identified using this assay were found to either alleviate or exacerbate neurotoxicity in different cellular models of amyotrophic lateral sclerosis, challenging the notion that autophagy stimulation can be used as a one-size-fits-all therapy for neurodegenerative disease.
    DOI:  https://doi.org/10.1016/j.jbc.2021.101437
  23. Cells. 2021 Nov 11. pii: 3124. [Epub ahead of print]10(11):
    Activation Mechanisms of the VPS34 Complexes.
    Yohei Ohashi.
      Phosphatidylinositol-3-phosphate (PtdIns(3)P) is essential for cell survival, and its intracellular synthesis is spatially and temporally regulated. It has major roles in two distinctive cellular pathways, namely, the autophagy and endocytic pathways. PtdIns(3)P is synthesized from phosphatidylinositol (PtdIns) by PIK3C3C/VPS34 in mammals or Vps34 in yeast. Pathway-specific VPS34/Vps34 activity is the consequence of the enzyme being incorporated into two mutually exclusive complexes: complex I for autophagy, composed of VPS34/Vps34-Vps15/Vps15-Beclin 1/Vps30-ATG14L/Atg14 (mammals/yeast), and complex II for endocytic pathways, in which ATG14L/Atg14 is replaced with UVRAG/Vps38 (mammals/yeast). Because of its involvement in autophagy, defects in which are closely associated with human diseases such as cancer and neurodegenerative diseases, developing highly selective drugs that target specific VPS34/Vps34 complexes is an essential goal in the autophagy field. Recent studies on the activation mechanisms of VPS34/Vps34 complexes have revealed that a variety of factors, including conformational changes, lipid physicochemical parameters, upstream regulators, and downstream effectors, greatly influence the activity of these complexes. This review summarizes and highlights each of these influences as well as clarifying key questions remaining in the field and outlining future perspectives.
    Keywords:  ATG14L; Beclin 1; PtdIns(3)P; UVRAG; VPS15; VPS34; autophagy; endocytic pathway; lipids; membranes
    DOI:  https://doi.org/10.3390/cells10113124
  24. Cells. 2021 Nov 10. pii: 3118. [Epub ahead of print]10(11):
    Direct Interaction of ATP7B and LC3B Proteins Suggests a Cooperative Role of Copper Transportation and Autophagy.
    Supansa Pantoom, Adam Pomorski, Katharina Huth, Christina Hund, Janine Petters, Artur Krężel, Andreas Hermann, Jan Lukas.
      Macroautophagy/autophagy plays an important role in cellular copper clearance. The means by which the copper metabolism and autophagy pathways interact mechanistically is vastly unexplored. Dysfunctional ATP7B, a copper-transporting ATPase, is involved in the development of monogenic Wilson disease, a disorder characterized by disturbed copper transport. Using in silico prediction, we found that ATP7B contains a number of potential binding sites for LC3, a central protein in the autophagy pathway, the so-called LC3 interaction regions (LIRs). The conserved LIR3, located at the C-terminal end of ATP7B, was found to directly interact with LC3B in vitro. Replacing the two conserved hydrophobic residues W1452 and L1455 of LIR3 significantly reduced interaction. Furthermore, autophagy was induced in normal human hepatocellular carcinoma cells (HepG2) leading to enhanced colocalization of ATP7B and LC3B on the autophagosome membranes. By contrast, HepG2 cells deficient of ATP7B (HepG2 ATP7B-/-) showed autophagy deficiency at elevated copper condition. This phenotype was complemented by heterologous ATP7B expression. These findings suggest a cooperative role of ATP7B and LC3B in autophagy-mediated copper clearance.
    Keywords:  ATPase copper transporting beta; HepG2; LC3 interaction region; Wilson disease; autophagosome-lysosome fusion
    DOI:  https://doi.org/10.3390/cells10113118
  25. STAR Protoc. 2021 Dec 17. 2(4): 100966
    A high-throughput protocol for monitoring starvation-induced autophagy in real time in mouse embryonic fibroblasts.
    Ada Nowosad, Arnaud Besson.
      Autophagy measurement has been challenging due to the transient nature of autophagy vesicles, in which degradation of cargo occurs. Here, we present a protocol to monitor starvation-induced autophagy using a live high-throughput microscopy system in a fast and automated manner without the need for sample preparation. We provide a detailed protocol describing the generation of turboGFP-LC3B expressing mouse embryonic fibroblasts (MEFs), the measurement of autophagy over time and the analysis of data. For complete details on the use and execution of this protocol, please refer to Nowosad et al. (2020, 2021).
    Keywords:  Cell Biology; Cell-based Assays; High Throughput Screening; Microscopy
    DOI:  https://doi.org/10.1016/j.xpro.2021.100966
  26. Chem Commun (Camb). 2021 Nov 24.
    Developing potent LC3-targeting AUTAC tools for protein degradation with selective autophagy.
    Junping Pei, Xiaoli Pan, Aoxue Wang, Wen Shuai, Faqian Bu, Pan Tang, Shuai Zhang, Yiwen Zhang, Guan Wang, Liang Ouyang.
      Autophagy-based protein degradation is emerging as a promising technology for anti-diseases and innovative drug discovery. Here, we demonstrate a novel type of autophagy-targeting chimera (AUTAC) to degrade protein by targeting autophagy key protein LC3. The best compound 10f powerfully degraded BRD4 protein through the autophagy pathway and exhibited good anti-proliferative activity in multiple tumor cells, providing a powerful toolbox for medicinal chemists to study disease-related targets with autophagy-based degradation.
    DOI:  https://doi.org/10.1039/d1cc04661f
  27. Front Cell Dev Biol. 2021 ;9 742049
    ERK5 Inhibition Induces Autophagy-Mediated Cancer Cell Death by Activating ER Stress.
    Andrés Gámez-García, Idoia Bolinaga-Ayala, Guillermo Yoldi, Sergio Espinosa-Gil, Nora Diéguez-Martínez, Elisabet Megías-Roda, Pau Muñoz-Guardiola, Jose M Lizcano.
      Autophagy is a highly conserved intracellular process that preserves cellular homeostasis by mediating the lysosomal degradation of virtually any component of the cytoplasm. Autophagy is a key instrument of cellular response to several stresses, including endoplasmic reticulum (ER) stress. Cancer cells have developed high dependency on autophagy to overcome the hostile tumor microenvironment. Thus, pharmacological activation or inhibition of autophagy is emerging as a novel antitumor strategy. ERK5 is a novel member of the MAP kinase family that is activated in response to growth factors and different forms of stress. Recent work has pointed ERK5 as a major player controlling cancer cell proliferation and survival. Therefore small-molecule inhibitors of ERK5 have shown promising therapeutic potential in different cancer models. Here, we report for the first time ERK5 as a negative regulator of autophagy. Thus, ERK5 inhibition or silencing induced autophagy in a panel of human cancer cell lines with different mutation patterns. As reported previously, ERK5 inhibitors (ERK5i) induced apoptotic cancer cell death. Importantly, we found that autophagy mediates the cytotoxic effect of ERK5i, since ATG5-/- autophagy-deficient cells viability was not affected by these compounds. Mechanistically, ERK5i stimulated autophagic flux independently of the canonical regulators AMPK or mTORC1. Moreover, ERK5 inhibition resulted in ER stress and activation of the Unfolded Protein Response (UPR) pathways. Specifically, ERK5i induced expression of the ER luminal chaperone BiP (a hallmark of ER stress), the UPR markers CHOP and ATF4, and the spliced form of XBP1. Pharmacological inhibition of UPR with chemical chaperone TUDC, or ATF4 silencing, resulted in impaired ERK5i-mediated UPR, autophagy and cytotoxicity. Overall, our results suggest that ERK5 inhibition induces autophagy-mediated cancer cell death by activating ER stress. Since ERK5 inhibition sensitizes cancer cells and tumors to chemotherapy, future work will determine the relevance of UPR and autophagy in the combined use of chemotherapy and ERK5i to tackle Cancer.
    Keywords:  ERK5 kinase; MAPK signal pathway; UPR – unfolded protein response; antitumor drug; apoptosis; autopaghy; cancer cell survival; endoplamic reticulum stress
    DOI:  https://doi.org/10.3389/fcell.2021.742049
  28. Autophagy. 2021 Nov 23. 1-3
    Innate host defense mechanisms SAC bacteria by regulating phosphoinositide kinases and phosphatases.
    Kimberly L Carey, Kai Liu, Ramnik J Xavier.
      Human genetics and loss-of-function studies revealed a critical role for macroautophagy/autophagy in host defense. The autophagic delivery of intracellular pathogens to lysosomes is a central mechanism of innate immunity; thus, augmentation of host xenophagy represents a promising and powerful approach to combat infections. The precise mechanisms required for autophagosome biogenesis and maturation, however, remain unclear. Using a targeted genetic screen against phosphoinositide kinases and phosphatases, our recent work identified an essential role for the phosphoinositide phosphatase SACM1L/SAC1 in xenophagy. Re-expression of wild-type or catalytically-dead SACM1L in CRISPR knockout cells confirmed that SACM1L enzymatic activity is required to suppress replication of intracellular Salmonella. Time-dependent, quantitative and live confocal imaging demonstrated that SACM1L-deficient cells accumulate phosphatidylinositol-4-phosphate (PtdIns4P) on bacteria-containing autophagosomes, resulting in delayed fusion with degradative lysosomes and reduced bacterial killing. We further discovered that the secreted Salmonella effector protein SteA, which specifically binds PtdIns4P, exacerbates the SACM1L-dependent delay in autophagosomal maturation. These findings reveal a relationship in which the balance between host defense and bacterial survival depends upon autophagosomal membrane composition.
    Keywords:  Autophagosome; PtdIns4P; SAC1; SACM1L; Salmonella; SteA; phosphatidylinositol-4-phosphate; phosphoinositide phosphatase; selective autophagy; xenophagy
    DOI:  https://doi.org/10.1080/15548627.2021.2002102
  29. iScience. 2021 Nov 19. 24(11): 103338
    The fission yeast FLCN/FNIP complex augments TORC1 repression or activation in response to amino acid (AA) availability.
    Isabel A Calvo, Shalini Sharma, Joao A Paulo, Alexander O D Gulka, Andras Boeszoermenyi, Jingyu Zhang, Jose M Lombana, Christina M Palmieri, Laura A Laviolette, Haribabu Arthanari, Othon Iliopoulos, Steven P Gygi, Mo Motamedi.
      The target of Rapamycin complex1 (TORC1) senses and integrates several environmental signals, including amino acid (AA) availability, to regulate cell growth. Folliculin (FLCN) is a tumor suppressor (TS) protein in renal cell carcinoma, which paradoxically activates TORC1 in response to AA supplementation. Few tractable systems for modeling FLCN as a TS are available. Here, we characterize the FLCN-containing complex in Schizosaccharomyces pombe (called BFC) and show that BFC augments TORC1 repression and activation in response to AA starvation and supplementation, respectively. BFC co-immunoprecipitates V-ATPase, a TORC1 modulator, and regulates its activity in an AA-dependent manner. BFC genetic and proteomic networks identify the conserved peptide transmembrane transporter Ptr2 and the phosphoribosylformylglycinamidine synthase Ade3 as new AA-dependent regulators of TORC1. Overall, these data ascribe an additional repressive function to Folliculin in TORC1 regulation and reveal S. pombe as an excellent system for modeling the AA-dependent, FLCN-mediated repression of TORC1 in eukaryotes.
    Keywords:  Cell biology; Cellular physiology; Functional aspects of cell biology
    DOI:  https://doi.org/10.1016/j.isci.2021.103338
  30. Cells. 2021 Nov 04. pii: 3022. [Epub ahead of print]10(11):
    Disruption of Mitochondrial Homeostasis: The Role of PINK1 in Parkinson's Disease.
    Maria Vizziello, Linda Borellini, Giulia Franco, Gianluca Ardolino.
      The progressive reduction of the dopaminergic neurons of the substantia nigra is the fundamental process underlying Parkinson's disease (PD), while the mechanism of susceptibility of this specific neuronal population is largely unclear. Disturbances in mitochondrial function have been recognized as one of the main pathways in sporadic PD since the finding of respiratory chain impairment in animal models of PD. Studies on genetic forms of PD have provided new insight on the role of mitochondrial bioenergetics, homeostasis, and autophagy. PINK1 (PTEN-induced putative kinase 1) gene mutations, although rare, are the second most common cause of recessively inherited early-onset PD, after Parkin gene mutations. Our knowledge of PINK1 and Parkin function has increased dramatically in the last years, with the discovery that a process called mitophagy, which plays a key role in the maintenance of mitochondrial health, is mediated by the PINK1/Parkin pathway. In vitro and in vivo models have been developed, supporting the role of PINK1 in synaptic transmission, particularly affecting dopaminergic neurons. It is of paramount importance to further define the role of PINK1 in mitophagy and mitochondrial homeostasis in PD pathogenesis in order to delineate novel therapeutic targets.
    Keywords:  PINK1; Parkin; Parkinson’s disease; mitochondrial quality control; mitophagy
    DOI:  https://doi.org/10.3390/cells10113022
  31. Cells. 2021 Oct 20. pii: 2814. [Epub ahead of print]10(11):
    Key Regulators of Autophagosome Closure.
    Wenyan Jiang, Xuechai Chen, Cuicui Ji, Wenting Zhang, Jianing Song, Jie Li, Juan Wang.
      Autophagy is an evolutionarily conserved pathway, in which cytoplasmic components are sequestered within double-membrane vesicles called autophagosomes and then transported into lysosomes or vacuoles for degradation. Over 40 conserved autophagy-related (ATG) genes define the core machinery for the five processes of autophagy: initiation, nucleation, elongation, closure, and fusion. In this review, we focus on one of the least well-characterized events in autophagy, namely the closure of the isolation membrane/phagophore to form the sealed autophagosome. This process is tightly regulated by ESCRT machinery, ATG proteins, Rab GTPase and Rab-related proteins, SNAREs, sphingomyelin, and calcium. We summarize recent progress in the regulation of autophagosome closure and discuss the key questions remaining to be addressed.
    Keywords:  autophagosome; autophagy; closure; isolation membrane
    DOI:  https://doi.org/10.3390/cells10112814
  32. Appl Environ Microbiol. 2021 Nov 24. AEM0208921
    Autophagy regulates whitefly-symbiont metabolic interactions.
    Yan-Bin Wang, Ce Li, Jin-Yang Yan, Tian-Yu Wang, Ya-Lin Yao, Fei-Rong Ren, Jun-Bo Luan.
      Nutritional symbionts are restricted to specialized host cells called bacteriocytes in various insect orders. These symbionts can provide essential nutrients to the host. However, the cellular mechanisms underlying the regulation of these insect-symbiont metabolic associations remain largely unclear. The whitefly, Bemisia tabaci MEAM1, hosts Portiera and Hamiltonella bacteria in the same bacteriocyte. In this study, the induction of autophagy by chemical treatment and gene silencing decreased symbiont titers, and essential amino acid (EAA) and B vitamin contents. In contrast, the repression of autophagy in bacteriocytes via Atg8 silencing increased symbiont titers, and amino acid and B vitamin contents. Furthermore, dietary supplementation with non-EAAs or B vitamins alleviated autophagy in whitefly bacteriocytes, elevated TOR (target of rapamycin) expression and increased symbiont titers. TOR silencing restored symbiont titers in whiteflies after dietary supplementation with B vitamins. These data suggest that Portiera and Hamiltonella evade autophagy of the whitefly bacteriocytes by activating the TOR pathway via providing essential nutrients. Taken together, we demonstrated that autophagy plays a critical role in regulating the metabolic interactions between the whitefly and two intracellular symbionts. Therefore, this study reveals that autophagy is an important cellular basis for bacteriocyte evolution and symbiosis persistence in whiteflies. The whitefly symbiosis unravels the interactions between cellular and metabolic functions of bacteriocytes. Importance Nutritional symbionts, which are restricted to specialized host cells called bacteriocytes, can provide essential nutrients for many hosts. However, the cellular mechanisms of regulation of animal-symbiont metabolic associations have been largely unexplored. Here, using the whitefly-Portiera/Hamiltonella endosymbiosis, we demonstrate autophagy regulates the symbiont titers, and thereby alters the essential amino acid and B vitamin contents. For persistence in the whitefly bacteriocytes, Portiera and Hamiltonella alleviate autophagy by activating the TOR (target of rapamycin) pathway through providing essential nutrients. Therefore, we demonstrate that autophagy plays a critical role in regulating the metabolic interactions between the whitefly and two intracellular symbionts. This study also provides insight into the cellular basis of bacteriocyte evolution and symbiosis persistence in the whitefly. The mechanisms underlying the role of autophagy in whitefly symbiosis could be widespread in many insect nutritional symbioses. These findings provide new avenue for whitefly control via regulating autophagy in the future.
    DOI:  https://doi.org/10.1128/AEM.02089-21
  33. Cells. 2021 Oct 29. pii: 2946. [Epub ahead of print]10(11):
    Decanoic Acid Stimulates Autophagy in D. discoideum.
    Eleanor C Warren, Pavol Kramár, Katie Lloyd-Jones, Robin S B Williams.
      Ketogenic diets, used in epilepsy treatment, are considered to work through reduced glucose and ketone generation to regulate a range of cellular process including autophagy induction. Recent studies into the medium-chain triglyceride (MCT) ketogenic diet have suggested that medium-chain fatty acids (MCFAs) provided in the diet, decanoic acid and octanoic acid, cause specific therapeutic effects independent of glucose reduction, although a role in autophagy has not been investigated. Both autophagy and MCFAs have been widely studied in Dictyostelium, with findings providing important advances in the study of autophagy-related pathologies such as neurodegenerative diseases. Here, we utilize this model to analyze a role for MCFAs in regulating autophagy. We show that treatment with decanoic acid but not octanoic acid induces autophagosome formation and modulates autophagic flux in high glucose conditions. To investigate this effect, decanoic acid, but not octanoic acid, was found to induce the expression of autophagy-inducing proteins (Atg1 and Atg8), providing a mechanism for this effect. Finally, we demonstrate a range of related fatty acid derivatives with seizure control activity, 4BCCA, 4EOA, and Epilim (valproic acid), also function to induce autophagosome formation in this model. Thus, our data suggest that decanoic acid and related compounds may provide a less-restrictive therapeutic approach to activate autophagy.
    Keywords:  4BCCA; 4EOA; Dictyostelium; autophagy; cancer; decanoic acid; epilepsy; medium-chain triglycerides
    DOI:  https://doi.org/10.3390/cells10112946
  34. J Fungi (Basel). 2021 Nov 19. pii: 987. [Epub ahead of print]7(11):
    Application of Metabolomics in the Study of Starvation-Induced Autophagy in Saccharomyces cerevisiae: A Scoping Review.
    Muhammad Luqman Nasaruddin, Khaizurin Tajul Arifin.
      This scoping review is aimed at the application of the metabolomics platform to dissect key metabolites and their intermediates to observe the regulatory mechanisms of starvation-induced autophagy in Saccharomyces cerevisiae. Four research papers were shortlisted in this review following the inclusion and exclusion criteria. We observed a commonly shared pathway undertaken by S. cerevisiae under nutritional stress. Targeted and untargeted metabolomics was applied in either of these studies using varying platforms resulting in the annotation of several different observable metabolites. We saw a commonly shared pathway undertaken by S. cerevisiae under nutritional stress. Following nitrogen starvation, the concentration of cellular nucleosides was altered as a result of autophagic RNA degradation. Additionally, it is also found that autophagy replenishes amino acid pools to sustain macromolecule synthesis. Furthermore, in glucose starvation, nucleosides were broken down into carbonaceous metabolites that are being funneled into the non-oxidative pentose phosphate pathway. The ribose salvage allows for the survival of starved yeast. Moreover, acute glucose starvation showed autophagy to be involved in maintaining ATP/energy levels. We highlighted the practicality of metabolomics as a tool to better understand the underlying mechanisms involved to maintain homeostasis by recycling degradative products to ensure the survival of S. cerevisiae under starvation. The application of metabolomics has extended the scope of autophagy and provided newer intervention targets against cancer as well as neurodegenerative diseases in which autophagy is implicated.
    Keywords:  Saccharomyces cerevisiae; autophagy; glucose starvation; metabolites; metabolomic; nitrogen starvation; nutritional stress; self-degradation; starvation; yeast
    DOI:  https://doi.org/10.3390/jof7110987
  35. Cancers (Basel). 2021 Nov 10. pii: 5622. [Epub ahead of print]13(22):
    Understanding the Role of Autophagy in Cancer Formation and Progression Is a Real Opportunity to Treat and Cure Human Cancers.
    Simone Patergnani, Sonia Missiroli, Giampaolo Morciano, Mariasole Perrone, Cristina M Mantovani, Gabriele Anania, Francesco Fiorica, Paolo Pinton, Carlotta Giorgi.
      The malignant transformation of a cell produces the accumulation of several cellular adaptions. These changes determine variations in biological processes that are necessary for a cancerous cell to survive during stressful conditions. Autophagy is the main nutrient recycling and metabolic adaptor mechanism in eukaryotic cells, represents a continuous source of energy and biomolecules, and is fundamental to preserve the correct cellular homeostasis during unfavorable conditions. In recent decades, several findings demonstrate a close relationship between autophagy, malignant transformation, and cancer progression. The evidence suggests that autophagy in the cancer context has a bipolar role (it may act as a tumor suppressor and as a mechanism of cell survival for established tumors) and demonstrates that the targeting of autophagy may represent novel therapeutic opportunities. Accordingly, the modulation of autophagy has important clinical benefits in patients affected by diverse cancer types. Currently, about 30 clinical trials are actively investigating the efficacy of autophagy modulators to enhance the efficacy of cytotoxic chemotherapy treatments. A deeper understanding of the molecular pathways regulating autophagy in the cancer context will provide new ways to target autophagy for improving the therapeutic benefits. Herein, we describe how autophagy participates during malignant transformation and cancer progression, and we report the ultimate efforts to translate this knowledge into specific therapeutic approaches to treat and cure human cancers.
    Keywords:  autophagy; cancer; clinical trials; therapy; tumor suppression
    DOI:  https://doi.org/10.3390/cancers13225622
  36. Cells. 2021 Oct 21. pii: 2835. [Epub ahead of print]10(11):
    The Cytotoxicity and Clearance of Mutant Huntingtin and Other Misfolded Proteins.
    Austin Folger, Yanchang Wang.
      Protein misfolding and aggregation are implicated in many neurodegenerative diseases. One of these diseases is Huntington's, which is caused by increased glutamine-encoding trinucleotide repeats within the Huntingtin gene. Like other misfolded proteins, mutated Huntingtin proteins with polyglutamine expansions are prone to aggregation. Misfolded proteins exist as soluble monomers, small aggregates, or as large insoluble inclusion bodies. Misfolded protein aggregates are believed to be cytotoxic by stressing the protein degradation machinery, disrupting membrane structure, or sequestering other proteins. We recently showed that expression of misfolded proteins lowers cellular free ubiquitin levels, which compromises the protein degradation machinery. Therefore, the efficient degradation of misfolded proteins is critical to preserve cell health. Cells employ two major mechanisms to degrade misfolded proteins. The first is the ubiquitin-proteasome system (UPS), which ubiquitinates and degrades misfolded proteins with the assistance of segregase Cdc48/p97. The UPS pathway is mainly responsible for the clearance of misfolded proteins present as monomers or smaller aggregates. The second pathway is macroautophagy/autophagy, in which protein aggregates or inclusion bodies are recruited into an autophagosome before transport to the vacuole/lysosome for degradation. This review is focused on the current understanding of the cytotoxicity of misfolded proteins as well as their clearance pathways, with a particular emphasis on mutant Huntingtin.
    Keywords:  Cdc48; autophagy; mutated Huntingtin; protein misfolding; ubiquitin-proteasome system (UPS)
    DOI:  https://doi.org/10.3390/cells10112835
  37. Dev Cell. 2021 Nov 22. pii: S1534-5807(21)00890-X. [Epub ahead of print]56(22): 3171
    Monomethyl branched-chain fatty acid mediates amino acid sensing upstream of mTORC1.
    Mengnan Zhu, Fukang Teng, Na Li, Li Zhang, Shuxian Zhang, Fan Xu, Jing Shao, Haipeng Sun, Huanhu Zhu.
      
    DOI:  https://doi.org/10.1016/j.devcel.2021.11.005
  38. Cells. 2021 Nov 12. pii: 3143. [Epub ahead of print]10(11):
    Autophagy in α-Synucleinopathies-An Overstrained System.
    Lisa Fellner, Elisa Gabassi, Johannes Haybaeck, Frank Edenhofer.
      Alpha-synucleinopathies comprise progressive neurodegenerative diseases, including Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA). They all exhibit the same pathological hallmark, which is the formation of α-synuclein positive deposits in neuronal or glial cells. The aggregation of α-synuclein in the cell body of neurons, giving rise to the so-called Lewy bodies (LBs), is the major characteristic for PD and DLB, whereas the accumulation of α-synuclein in oligodendroglial cells, so-called glial cytoplasmic inclusions (GCIs), is the hallmark for MSA. The mechanisms involved in the intracytoplasmic inclusion formation in neuronal and oligodendroglial cells are not fully understood to date. A possible mechanism could be an impaired autophagic machinery that cannot cope with the high intracellular amount of α-synuclein. In fact, different studies showed that reduced autophagy is involved in α-synuclein aggregation. Furthermore, altered levels of different autophagy markers were reported in PD, DLB, and MSA brains. To date, the trigger point in disease initiation is not entirely clear; that is, whether autophagy dysfunction alone suffices to increase α-synuclein or whether α-synuclein is the pathogenic driver. In the current review, we discuss the involvement of defective autophagy machinery in the formation of α-synuclein aggregates, propagation of α-synuclein, and the resulting neurodegenerative processes in α-synucleinopathies.
    Keywords:  Parkinson’s disease; alpha-synuclein; autophagy; multiple system atrophy; neurons; oligodendroglia
    DOI:  https://doi.org/10.3390/cells10113143
  39. J Neurochem. 2021 Nov 27.
    A neurodegeneration gene, WDR45, links impaired ferritinophagy to iron accumulation.
    Luisa Aring, Eun-Kyung Choi, Huira Kopera, Thomas Lanigan, Shigeki Iwase, Daniel J Klionsky, Young Ah Seo.
      Neurodegeneration with brain iron accumulation (NBIA) is a clinically and genetically heterogeneous group of neurodegenerative diseases characterized by the abnormal accumulation of brain iron and the progressive degeneration of the nervous system. One of the recently identified subtypes of NBIA is β-propeller protein-associated neurodegeneration (BPAN). BPAN is caused by de novo mutations in the WDR45/WIPI4 (WD repeat domain 45) gene. WDR45 is one of the four mammalian homologs of yeast Atg18, a regulator of autophagy. WDR45 deficiency in BPAN patients and animal models may result in defects in autophagic flux. However, how WDR45 deficiency leads to brain iron overload remains unclear. To elucidate the role of WDR45, we generated a WDR45-knockout (KO) SH-SY5Y neuroblastoma cell line using CRISPR-Cas9-mediated genome editing. Using these cells, we demonstrated that the non-TF (transferrin)-bound iron pathway dominantly mediated the accumulation of iron. Moreover, the loss of WDR45 led to defects in ferritinophagy, a form of autophagy that degrades the iron storage protein ferritin. We showed that impaired ferritinophagy contributes to iron accumulation in WDR45-KO cells. Iron accumulation was also detected in the mitochondria, which was accompanied by impaired mitochondrial respiration, elevated reactive oxygen species, and increased cell death. Thus, our study links WDR45 to specific iron acquisition pathways and ferritinophagy.
    Keywords:  BPAN; NBIA; ferritinophagy; iron; neurodegeneration
    DOI:  https://doi.org/10.1111/jnc.15548
  40. Autophagy. 2021 Nov 23. 1-14
    An exploratory text analysis of the autophagy research field.
    Willa Wen-You Yim, Yoshitaka Kurikawa, Noboru Mizushima.
      After its discovery in the 1950 s, the autophagy research field has seen its annual number of publications climb from tens to thousands. The ever-growing number of autophagy publications is a wealth of information but presents a challenge to researchers, especially those new to the field, who are looking for a general overview of the field to, for example, determine current topics of the field or formulate new hypotheses. Here, we employed text mining tools to extract research trends in the autophagy field, including those of genes, terms, and topics. The publication trend of the field can be separated into three phases. The exponential rise in publication number began in the last phase and is most likely spurred by a series of highly cited research papers published in previous phases. The exponential increase in papers has resulted in a larger variety of research topics, with the majority involving those that are directly physiologically relevant, such as disease and modulating autophagy. Our findings provide researchers a summary of the history of the autophagy research field and perhaps hints of what is to come.Abbreviations: 5Y-IF: 5-year impact factor; AIS: article influence score; EM: electron microscopy; HGNC: HUGO gene nomenclature committee; LDA: latent Dirichlet allocation; MeSH: medical subject headings; ncRNA: non-coding RNA.
    Keywords:  Autophagy; text analysis; text analytics; text mining; topic modeling
    DOI:  https://doi.org/10.1080/15548627.2021.1995151
  41. J Cachexia Sarcopenia Muscle. 2021 Nov 22.
    MyD88 deficiency ameliorates weight loss caused by intestinal oxidative injury in an autophagy-dependent mechanism.
    Ming Qi, Simeng Liao, Jing Wang, Yuankun Deng, Andong Zha, Yirui Shao, Zhijuan Cui, Tongxing Song, Yulong Tang, Bie Tan, Yulong Yin.
       BACKGROUND: Gut health plays a vital role in the overall health and disease control of human and animals. Intestinal oxidative stress is a critical player in the induction and progression of cachexia which is conventionally diagnosed and classified by weight loss. Therefore, reduction of intestinal oxidative injury is a common and highly effective strategy for the maintenance of human and animal health. Here we identify intestinal myeloid differentiation primary response gene 88 (MyD88) as a novel target for intestinal oxidative stress using canonical oxidative stress model induced by paraquat (PQ) in vitro and in vivo.
    METHODS: Intestinal oxidative stress was induced by administration of PQ in intestinal epithelial cells (IECs) and mouse model. Cell proliferation, apoptosis, DNA damage, mitochondrial function, oxidative status, and autophagy process were measured in wild-type and MyD88-deficient IECs during PQ exposure. Autophagy inhibitor (3-methyladenine) and activator (rapamycin) were employed to assess the role of autophagy in MyD88-deficient IECs during PQ exposure. MyD88 specific inhibitor, ST2825, was used to verify function of MyD88 during PQ exposure in mouse model.
    RESULTS: MyD88 protein levels and apoptotic rate of IECs are increased in response to PQ exposure (P < 0.001). Intestinal deletion of MyD88 blocks PQ-induced apoptosis (~42% reduction) and DNA damage (~86% reduction), and improves mitochondrial fission (~37% reduction) and function including mitochondrial membrane potential (~23% increment) and respiratory metabolism capacity (~26% increment) (P < 0.01). Notably, there is a marked decrease in reactive oxygen species in MyD88-deficient IECs during PQ exposure (~70% reduction), which are consistent with high activity of antioxidative enzymes (~83% increment) (P < 0.001). Intestinal ablation of MyD88 inhibits mTOR signalling, and further phosphorylates p53 proteins during PQ exposure, which eventually promotes intestinal autophagy (~74% increment) (P < 0.01). Activation of autophagy (rapamycin) promotes IECs growth as compared with 3-methyladenine-treatment during PQ exposure (~173% increment), while inhibition of autophagy (3-methyladenine) exacerbates oxidative stress in MyD88-deficient IECs (P < 0.001). In mouse model, inhibition of MyD88 using specific inhibitor ST2825 followed by PQ treatment effectively ameliorates weight loss (~4% increment), decreased food intake (~92% increment), gastrocnemius and soleus loss (~24% and ~20% increment, respectively), and intestinal oxidative stress in an autophagy dependent manner (P < 0.01).
    CONCLUSIONS: MyD88 modulates intestinal oxidative stress in an autophagy-dependent mechanism, which suggests that reducing MyD88 level may constitute a putative therapeutic target for intestinal oxidative injury-induced weight loss.
    Keywords:  Autophagy; Cachexia; DNA damage repair; Intestinal epithelial cells; Mitochondrial fission; Weight loss
    DOI:  https://doi.org/10.1002/jcsm.12858
  42. Life (Basel). 2021 Oct 21. pii: 1123. [Epub ahead of print]11(11):
    Mitochondrial Quality Control in Cardiac-Conditioning Strategies against Ischemia-Reperfusion Injury.
    Wylly Ramsés García-Niño, Cecilia Zazueta, Mabel Buelna-Chontal, Alejandro Silva-Palacios.
      Mitochondria are the central target of ischemic preconditioning and postconditioning cardioprotective strategies, which consist of either the application of brief intermittent ischemia/reperfusion (I/R) cycles or the administration of pharmacological agents. Such strategies reduce cardiac I/R injury by activating protective signaling pathways that prevent the exacerbated production of reactive oxygen/nitrogen species, inhibit opening of mitochondrial permeability transition pore and reduce apoptosis, maintaining normal mitochondrial function. Cardioprotection also involves the activation of mitochondrial quality control (MQC) processes, which replace defective mitochondria or eliminate mitochondrial debris, preserving the structure and function of the network of these organelles, and consequently ensuring homeostasis and survival of cardiomyocytes. Such processes include mitochondrial biogenesis, fission, fusion, mitophagy and mitochondrial-controlled cell death. This review updates recent advances in MQC mechanisms that are activated in the protection conferred by different cardiac conditioning interventions. Furthermore, the role of extracellular vesicles in mitochondrial protection and turnover of these organelles will be discussed. It is concluded that modulation of MQC mechanisms and recognition of mitochondrial targets could provide a potential and selective therapeutic approach for I/R-induced mitochondrial dysfunction.
    Keywords:  apoptosis; autophagy; cardioprotection; exosomes; ischemic postconditioning; ischemic preconditioning; mitochondrial biogenesis; mitochondrial dynamics; mitophagy; myocardial infarction
    DOI:  https://doi.org/10.3390/life11111123
  43. Cells. 2021 Oct 28. pii: 2939. [Epub ahead of print]10(11):
    Dysregulation of Caveolin-1 Phosphorylation and Nuclear Translocation Is Associated with Senescence Onset.
    Andreas Goutas, Zozo Outskouni, Ioanna Papathanasiou, Maria Satra, George Koliakos, Varvara Trachana.
      We recently reported that the inability of osteoarthritic (OA) chondrocytes to repair oxidative stress (OS) induced DNA damage is linked to Cav-1 overexpression/improper localization. We speculated that the senescent status of OA cells was responsible for this Cav-1 dysregulation. Here, to further investigate this hypothesis, we used Wharton Jelly derived mesenchymal stem cells (WJ-MSCs) and investigated Cav-1 function as cells reached replicative senescence or upon stress induced senescence (SIPS). We showed that Cav-1 is upregulated, phosphorylated and translocated to the nucleus in young WJ-MSCs upon acute exogenous OS, and that it returns back to basal/nonphosphorylated levels and exports the nucleus in the recovery phase. However, as cells reach senescence, this regulation is lost. OS did not induce any Cav-1-mediated response, which is concomitant with the inability of older cells to restore DNA damage. Furthermore, downregulation of Cav-1 resulted in persistent OS-induced DNA damage and subsequent onset of senescence. We also report that the establishment of senescence is mediated by autophagy stimulation, since downregulation of autophagy key molecule Atg5, simultaneously with Cav-1 downregulation, was found to inhibit SIPS. Basically, we propose that Cav-1 involvement in DNA damage response can lead to senescence, either because the damage is extensive or because Cav-1 is absent/unable to perform its homeostatic role.
    Keywords:  DNA damage; caveolin-1; mesenchymal stem cells; oxidative stress; senescence
    DOI:  https://doi.org/10.3390/cells10112939
  44. PLoS Biol. 2021 Nov;19(11): e3001432
    Homeostatic scaling is driven by a translation-dependent degradation axis that recruits miRISC remodeling.
    Balakumar Srinivasan, Sarbani Samaddar, Sivaram V S Mylavarapu, James P Clement, Sourav Banerjee.
      Homeostatic scaling in neurons has been attributed to the individual contribution of either translation or degradation; however, there remains limited insight toward understanding how the interplay between the two processes effectuates synaptic homeostasis. Here, we report that a codependence between protein synthesis and degradation mechanisms drives synaptic homeostasis, whereas abrogation of either prevents it. Coordination between the two processes is achieved through the formation of a tripartite complex between translation regulators, the 26S proteasome, and the miRNA-induced silencing complex (miRISC) components such as Argonaute, MOV10, and Trim32 on actively translating transcripts or polysomes. The components of this ternary complex directly interact with each other in an RNA-dependent manner. Disruption of polysomes abolishes this ternary interaction, suggesting that translating RNAs facilitate the combinatorial action of the proteasome and the translational apparatus. We identify that synaptic downscaling involves miRISC remodeling, which entails the mTORC1-dependent translation of Trim32, an E3 ligase, and the subsequent degradation of its target, MOV10 via the phosphorylation of p70 S6 kinase. We find that the E3 ligase Trim32 specifically polyubiquitinates MOV10 for its degradation during synaptic downscaling. MOV10 degradation alone is sufficient to invoke downscaling by enhancing Arc translation through its 3' UTR and causing the subsequent removal of postsynaptic AMPA receptors. Synaptic scaling was occluded when we depleted Trim32 and overexpressed MOV10 in neurons, suggesting that the Trim32-MOV10 axis is necessary for synaptic downscaling. We propose a mechanism that exploits a translation-driven protein degradation paradigm to invoke miRISC remodeling and induce homeostatic scaling during chronic network activity.
    DOI:  https://doi.org/10.1371/journal.pbio.3001432
  45. Int J Mol Sci. 2021 Nov 12. pii: 12263. [Epub ahead of print]22(22):
    Sirtuins and Autophagy in Age-Associated Neurodegenerative Diseases: Lessons from the C. elegans Model.
    Anam Naseer, Snober Shabnam Mir, Krisztina Takacs-Vellai, Aamir Nazir.
      Age-associated neurodegenerative diseases are known to have "impaired protein clearance" as one of the key features causing their onset and progression. Hence, homeostasis is the key to maintaining balance throughout the cellular system as an organism ages. Any imbalance in the protein clearance machinery is responsible for accumulation of unwanted proteins, leading to pathological consequences-manifesting in neurodegeneration and associated debilitating outcomes. Multiple processes are involved in regulating this phenomenon; however, failure to regulate the autophagic machinery is a critical process that hampers the protein clearing pathway, leading to neurodegeneration. Another important and widely known component that plays a role in modulating neurodegeneration is a class of proteins called sirtuins. These are class III histone deacetylases (HDACs) that are known to regulate various vital processes such as longevity, genomic stability, transcription and DNA repair. These enzymes are also known to modulate neurodegeneration in an autophagy-dependent manner. Considering its genetic relevance and ease of studying disease-related endpoints in neurodegeneration, the model system Caenorhabditis elegans has been successfully employed in deciphering various functional outcomes related to critical protein molecules, cell death pathways and their association with ageing. This review summarizes the vital role of sirtuins and autophagy in ageing and neurodegeneration, in particular highlighting the knowledge obtained using the C. elegans model system.
    Keywords:  C. elegans; autophagy; neurodegenerative diseases; sirtuins
    DOI:  https://doi.org/10.3390/ijms222212263
  46. Int J Mol Sci. 2021 Nov 18. pii: 12466. [Epub ahead of print]22(22):
    Over Fifty Years of Life, Death, and Cannibalism: A Historical Recollection of Apoptosis and Autophagy.
    Mahmoud Izadi, Tayyiba Akbar Ali, Ehsan Pourkarimi.
      Research in biomedical sciences has changed dramatically over the past fifty years. There is no doubt that the discovery of apoptosis and autophagy as two highly synchronized and regulated mechanisms in cellular homeostasis are among the most important discoveries in these decades. Along with the advancement in molecular biology, identifying the genetic players in apoptosis and autophagy has shed light on our understanding of their function in physiological and pathological conditions. In this review, we first describe the history of key discoveries in apoptosis with a molecular insight and continue with apoptosis pathways and their regulation. We touch upon the role of apoptosis in human health and its malfunction in several diseases. We discuss the path to the morphological and molecular discovery of autophagy. Moreover, we dive deep into the precise regulation of autophagy and recent findings from basic research to clinical applications of autophagy modulation in human health and illnesses and the available therapies for many diseases caused by impaired autophagy. We conclude with the exciting crosstalk between apoptosis and autophagy, from the early discoveries to recent findings.
    Keywords:  Apaf1; Bcl-2; C. elegans; apoptosis; autophagy; caspase; electron microscopy
    DOI:  https://doi.org/10.3390/ijms222212466
  47. Exp Mol Med. 2021 Nov 26.
    ER-associated CTRP1 regulates mitochondrial fission via interaction with DRP1.
    Seong Keun Sonn, Seungwoon Seo, Jaemoon Yang, Ki Sook Oh, Hsiuchen Chen, David C Chan, Kunsoo Rhee, Kyung S Lee, Young Yang, Goo Taeg Oh.
      C1q/TNF-related protein 1 (CTRP1) is a CTRP family member that has collagenous and globular C1q-like domains. The secreted form of CTRP1 is known to be associated with cardiovascular and metabolic diseases, but its cellular roles have not yet been elucidated. Here, we showed that cytosolic CTRP1 localizes to the endoplasmic reticulum (ER) membrane and that knockout or depletion of CTRP1 leads to mitochondrial fission defects, as demonstrated by mitochondrial elongation. Mitochondrial fission events are known to occur through an interaction between mitochondria and the ER, but we do not know whether the ER and/or its associated proteins participate directly in the entire mitochondrial fission event. Interestingly, we herein showed that ablation of CTRP1 suppresses the recruitment of DRP1 to mitochondria and provided evidence suggesting that the ER-mitochondrion interaction is required for the proper regulation of mitochondrial morphology. We further report that CTRP1 inactivation-induced mitochondrial fission defects induce apoptotic resistance and neuronal degeneration, which are also associated with ablation of DRP1. These results demonstrate for the first time that cytosolic CTRP1 is an ER transmembrane protein that acts as a key regulator of mitochondrial fission, providing new insight into the etiology of metabolic and neurodegenerative disorders.
    DOI:  https://doi.org/10.1038/s12276-021-00701-z
  48. Cancers (Basel). 2021 Nov 10. pii: 5618. [Epub ahead of print]13(22):
    Autophagy in Cisplatin Nephrotoxicity during Cancer Therapy.
    Xiaoru Hu, Zhengwei Ma, Lu Wen, Siyao Li, Zheng Dong.
      Cisplatin is a widely used chemotherapeutic agent but its clinical use is often limited by nephrotoxicity. Autophagy is a lysosomal degradation pathway that removes protein aggregates and damaged or dysfunctional cellular organelles for maintaining cell homeostasis. Upon cisplatin exposure, autophagy is rapidly activated in renal tubule cells to protect against acute cisplatin nephrotoxicity. Mechanistically, the protective effect is mainly related to the clearance of damaged mitochondria via mitophagy. The role and regulation of autophagy in chronic kidney problems after cisplatin treatment are currently unclear, despite the significance of research in this area. In cancers, autophagy may prevent tumorigenesis, but autophagy may reduce the efficacy of chemotherapy by protecting cancer cells. Future research should focus on developing drugs that enhance the anti-tumor effects of cisplatin while protecting kidneys during cisplatin chemotherapy.
    Keywords:  acute kidney injury; autophagy; cancer therapy; chronic kidney disease; cisplatin; nephrotoxicity
    DOI:  https://doi.org/10.3390/cancers13225618
  49. Antioxidants (Basel). 2021 Oct 25. pii: 1678. [Epub ahead of print]10(11):
    Thunbergia laurifolia Leaf Extract Inhibits Glutamate-Induced Neurotoxicity and Cell Death through Mitophagy Signaling.
    Wudtipong Vongthip, Chanin Sillapachaiyaporn, Kyu-Won Kim, Monruedee Sukprasansap, Tewin Tencomnao.
      Oxidative stress plays a crucial role in neurodegeneration. Therefore, reducing oxidative stress in the brain is an important strategy to prevent neurodegenerative disorders. Thunbergia laurifolia (Rang-jued) is well known as an herbal tea in Thailand. Here, we aimed to determine the protective effects of T. laurifolia leaf extract (TLE) on glutamate-induced oxidative stress toxicity and mitophagy-mediated cell death in mouse hippocampal cells (HT-22). Our results reveal that TLE possesses a high level of bioactive antioxidants by LC-MS technique. We found that the pre-treatment of cells with TLE prevented glutamate-induced neuronal death in a concentration-dependent manner. TLE reduced the intracellular ROS and maintained the mitochondrial membrane potential caused by glutamate. Moreover, TLE upregulated the gene expression of antioxidant enzymes (SOD1, SOD2, CAT, and GPx). Interestingly, glutamate also induced the activation of the mitophagy process. However, TLE could reverse this activity by inhibiting autophagic protein (LC3B-II/LC3B-I) activation and increasing a specific mitochondrial protein (TOM20). Our results suggest that excessive glutamate can cause neuronal death through mitophagy-mediated cell death signaling in HT-22 cells. Our findings indicate that TLE protects cells from neuronal death by stimulating the endogenous antioxidant enzymes and inhibiting glutamate-induced oxidative toxicity via the mitophagy-autophagy pathway. TLE might have potential as an alternative or therapeutic approach in neurodegenerative diseases.
    Keywords:  Thunbergia laurifolia; autophagy; glutamate; mitophagy; neurodegenerative diseases; oxidative stress
    DOI:  https://doi.org/10.3390/antiox10111678
  50. J Autoimmun. 2021 Nov 18. pii: S0896-8411(21)00154-2. [Epub ahead of print]126 102746
    Rescue of thyroid cells from antibody induced cell death via induction of autophagy.
    Syed Morshed, Rauf Latif, Terry F Davies.
       BACKGROUND: Graves' disease (GD) is associated with thyroid stimulating hormone (TSH) receptor (TSHR) antibodies of variable bioactivity. We have previously characterized "neutral" TSHR antibodies (N-TSHR-Abs) that bind to the hinge region of the TSHR ectodomain. We showed that an N-TSHR monoclonal antibody (mAb) failed to induce any G proteins to sustain survival signaling and lead to excessive stress and apoptosis. Furthermore, the addition of TSH, or the antioxidant N-acetyl-l-cysteine (NAC), rescued N-TSHR-mAb-induced apoptotic death. However, the detailed mechanisms of this rescue remained unclear.
    METHODS: Autophagy is activated in response to diverse stress related stimuli so we have, therefore, studied the autophagy response in rat thyroid cells (FRTL-5) during N-TSHR-mAb induced thyrocyte stress and apoptosis using the In Cell Western technique for quantitation along with immunocytochemistry.
    RESULTS: Under starvation conditions with N-TSHR-mAb the addition of TSH or NAC prevented thyroid cell death by enhancing autophagy. This was evidenced by elevated levels of autophagy related proteins including beclin 1, LC3A, LC3B, ULK1, p62, and also activated pink and perkin mitophagy related proteins. The phenomenon was further confirmed by image analyses using Cyto-ID and Mito-ID autophagy detection systems. We also found that either TSH or NAC enhanced PKA, Akt, mTORC, AMPK, Sirtuins, PGC1α, NRF-2, mitofusin-2, TFAM and catalase in the N-TSHR-mAb stressed cells. Thus TSH or NAC restored cell survival signaling which reduced cell stress and enhanced mitochondrial biogenesis. The N-TSHR-mAb also activated cytochrome-C, Bax, caspase-9, caspase-3A, and had less effect on FADD or caspase-8 indicating activation of the intrinsic pathway for apoptosis.
    CONCLUSIONS: These findings indicated that TSH or antioxidant can rescue thyroid cells from N-TSHR-mAb induced apoptosis via enhanced autophagy. These observations signify that N-TSHR-mAb in GD under low TSH conditions caused by the hyperthyroidism could be detrimental for thyrocyte survival which would be another factor able to precipitate ongoing autoinflammation.
    Keywords:  Apoptosis; Autophagy; Cell signaling; Graves' disease; TSH receptor antibodies
    DOI:  https://doi.org/10.1016/j.jaut.2021.102746
  51. Front Med (Lausanne). 2021 ;8 758311
    Crosstalk Between ER Stress, Autophagy and Inflammation.
    Sandhya Chipurupalli, Unni Samavedam, Nirmal Robinson.
      The endoplasmic reticulum (ER) is not only responsible for protein synthesis and folding but also plays a critical role in sensing cellular stress and maintaining cellular homeostasis. Upon sensing the accumulation of unfolded proteins due to perturbation in protein synthesis or folding, specific intracellular signaling pathways are activated, which are collectively termed as unfolded protein response (UPR). UPR expands the capacity of the protein folding machinery, decreases protein synthesis and enhances ER-associated protein degradation (ERAD) which degrades misfolded proteins through the proteasomes. More recent evidences suggest that UPR also amplifies cytokines-mediated inflammatory responses leading to pathogenesis of inflammatory diseases. UPR signaling also activates autophagy; a lysosome-dependent degradative pathwaythat has an extended capacity to degrade misfolded proteins and damaged ER. Thus, activation of autophagy limits inflammatory response and provides cyto-protection by attenuating ER-stress. Here we review the mechanisms that couple UPR, autophagy and cytokine-induced inflammation that can facilitate the development of novel therapeutic strategies to mitigate cellular stress and inflammation associated with various pathologies.
    Keywords:  ER-stress; autophagy; cytokines; inflammation; unfolded protein response
    DOI:  https://doi.org/10.3389/fmed.2021.758311
  52. Medicina (Kaunas). 2021 Nov 04. pii: 1203. [Epub ahead of print]57(11):
    Dual Role of SIRT1 in Autophagy and Lipid Metabolism Regulation in Osteoarthritic Chondrocytes.
    Aliki-Alexandra Papageorgiou, Andreas Goutas, Varvara Trachana, Aspasia Tsezou.
      Background and Objectives: Osteoarthritis (OA) is one of the most common and highly prevalent types of arthritis, also considered a multiphenotypic disease with a strong metabolic component. Ageing is the primary risk factor for OA, while the age-related decline in autophagic activity affects cell function and chondrocyte homeostasis. The aim of this study was to investigate the role of sirtuin 1 (SIRT1) in autophagy dysregulation and lipid metabolism in human OA chondrocytes. Materials and Methods: OA chondrocytes were treated with Resveratrol, Hydroxycloroquine (HCQ) or 3-Methyladenine (3-MA) and HCQ or 3-MA followed by siRNA against SIRT1 (siSIRT1). Then, SIRT1, AcNF-κBp65, LOX-1 and autophagy-related proteins ATG5, ATG13, PI3K class III, Beclin-1, LC3 and ULK protein levels were evaluated using Western blot. Normal articular chondrocytes were treated under serum starvation and/or siSIRT1, and the protein expression levels of the above autophagy-related proteins were evaluated. The staining patterns of LC3/p62 and LOX-1 were analyzed microscopically by immunofluorescence. SIRT1/LC3 complex formation was analyzed by immunoprecipitation. Results: SIRT1 and LOX-1 protein expression were negatively correlated in OA chondrocytes. SIRT1 regulated LOX-1 expression via NF-κΒ deacetylation, while treatment with Resveratrol enhanced SIRT1 enzymatic activity, resulting in LOX-1 downregulation and autophagy induction. In OA chondrocytes, SIRT1 was recognized as an autophagy substrate, formed a complex with LC3 and was consequently subjected to cytoplasmic autophagosome-lysosome degradation. Moreover, siSIRT1-treated normal chondrocytes showed decreased autophagic activity, while double-treated (siSIRT1 and serum starvation) cells showed no induction of autophagy. Conclusions: Our results suggest that SIRT1 regulates lipid homeostasis through LOX-1 expression regulation. Additionally, we indicate that the necessity of SIRT1 for autophagy induction in normal chondrocytes, together with its selective autophagic degradation in OA chondrocytes, could contribute to autophagy dysregulation in OA. We, therefore, suggest a novel regulatory scheme that functionally connects lipid metabolism and autophagy in late-stage OA.
    Keywords:  autophagy; lipid metabolism; osteoarthritis; sirtuin 1
    DOI:  https://doi.org/10.3390/medicina57111203
  53. Stem Cell Res Ther. 2021 Nov 25. 12(1): 589
    PINK1 deficiency impairs osteoblast differentiation through aberrant mitochondrial homeostasis.
    So-Young Lee, Hyun-Ju An, Jin Man Kim, Min-Ji Sung, Do Kyung Kim, Hyung Kyung Kim, Jongbeom Oh, Hye Yun Jeong, Yu Ho Lee, Taeyoung Yang, Jun Han Kim, Ha Jeong Lim, Soonchul Lee.
       BACKGROUND: PTEN-induced kinase 1 (PINK1) is a serine/threonine-protein kinase in mitochondria that is critical for mitochondrial quality control. PINK1 triggers mitophagy, a selective autophagy of mitochondria, and is involved in mitochondrial regeneration. Although increments of mitochondrial biogenesis and activity are known to be crucial during differentiation, data regarding the specific role of PINK1 in osteogenic maturation and bone remodeling are limited.
    METHODS: We adopted an ovariectomy model in female wildtype and Pink1-/- mice. Ovariectomized mice were analyzed using micro-CT, H&E staining, Masson's trichrome staining. RT-PCR, western blot, immunofluorescence, alkaline phosphatase, and alizarin red staining were performed to assess the expression of PINK1 and osteogenic markers in silencing of PINK1 MC3T3-E1 cells. Clinical relevance of PINK1 expression levels was determined via qRT-PCR analysis in normal and osteoporosis patients.
    RESULTS: A significant decrease in bone mass and collagen deposition was observed in the femurs of Pink1-/- mice after ovariectomy. Ex vivo, differentiation of osteoblasts was inhibited upon Pink1 downregulation, accompanied by impaired mitochondrial homeostasis, increased mitochondrial reactive oxygen species production, and defects in mitochondrial calcium handling. Furthermore, PINK1 expression was reduced in bones from patients with osteoporosis, which supports the practical role of PINK1 in human bone disease.
    CONCLUSIONS: In this study, we demonstrated that activation of PINK1 is a requisite in osteoblasts during differentiation, which is related to mitochondrial quality control and low reactive oxygen species production. Enhancing PINK1 activity might be a possible treatment target in bone diseases as it can promote a healthy pool of functional mitochondria in osteoblasts.
    Keywords:  Mitochondria; Osteogenesis; Osteoporosis; PINK1
    DOI:  https://doi.org/10.1186/s13287-021-02656-4
  54. Viruses. 2021 Oct 30. pii: 2189. [Epub ahead of print]13(11):
    Autophagy Inhibits Intercellular Transport of Citrus Leaf Blotch Virus by Targeting Viral Movement Protein.
    Erbo Niu, Huan Liu, Hongsheng Zhou, Lian Luo, Yunfeng Wu, Ida Bagus Andika, Liying Sun.
      Autophagy is an evolutionarily conserved cellular-degradation mechanism implicated in antiviral defense in plants. Studies have shown that autophagy suppresses virus accumulation in cells; however, it has not been reported to specifically inhibit viral spread in plants. This study demonstrated that infection with citrus leaf blotch virus (CLBV; genus Citrivirus, family Betaflexiviridae) activated autophagy in Nicotiana benthamiana plants as indicated by the increase of autophagosome formation. Impairment of autophagy through silencing of N. benthamiana autophagy-related gene 5 (NbATG5) and NbATG7 enhanced cell-to-cell and systemic movement of CLBV; however, it did not affect CLBV accumulation when the systemic infection had been fully established. Treatment using an autophagy inhibitor or silencing of NbATG5 and NbATG7 revealed that transiently expressed movement protein (MP), but not coat protein, of CLBV was targeted by selective autophagy for degradation. Moreover, we identified that CLBV MP directly interacted with NbATG8C1 and NbATG8i, the isoforms of autophagy-related protein 8 (ATG8), which are key factors that usually bind cargo receptors for selective autophagy. Our results present a novel example in which autophagy specifically targets a viral MP to limit the intercellular spread of the virus in plants.
    Keywords:  antiviral machinery; autophagy; citrus leaf blotch virus; protein degradation; virus movement
    DOI:  https://doi.org/10.3390/v13112189
  55. Cells. 2021 Nov 17. pii: 3204. [Epub ahead of print]10(11):
    Calcium Signaling Mediates Cell Death and Crosstalk with Autophagy in Kidney Disease.
    Bo Ning, Chuanzhi Guo, Anqi Kong, Kongdong Li, Yimin Xie, Haifeng Shi, Jie Gu.
      The kidney is an important organ for the maintenance of Ca2+ homeostasis in the body. However, disruption of Ca2+ homeostasis will cause a series of kidney diseases, such as acute kidney injury (AKI), chronic kidney disease (CKD), renal ischemia/reperfusion (I/R) injury, autosomal dominant polycystic kidney disease (ADPKD), podocytopathy, and diabetic nephropathy. During the progression of kidney disease, Ca2+ signaling plays key roles in various cell activities such as necrosis, apoptosis, eryptosis and autophagy. Importantly, there are complex Ca2+ flux networks between the endoplasmic reticulum (ER), mitochondria and lysosomes which regulate intracellular Ca2+ signaling in renal cells and contribute to kidney disease. In addition, Ca2+ signaling also links the crosstalk between various cell deaths and autophagy under the stress of heavy metals or high glucose. In this regard, we present a review of Ca2+ signaling in cell death and crosstalk with autophagy and its potential as a therapeutic target for the development of new and efficient drugs against kidney diseases.
    Keywords:  Ca2+ signaling; autophagy; cell death; kidney diseases
    DOI:  https://doi.org/10.3390/cells10113204
  56. Autophagy. 2021 Nov 22. 1-19
    LAMP3 inhibits autophagy and contributes to cell death by lysosomal membrane permeabilization.
    Tsutomu Tanaka, Blake M Warner, Drew G Michael, Hiroyuki Nakamura, Toshio Odani, Hongen Yin, Tatsuya Atsumi, Masayuki Noguchi, John A Chiorini.
      Sjögren syndrome (SS) is a chronic and progressive autoimmune disease characterized by dry mouth and dry eyes, and characteristic autoantibodies. Evidence of altered macroautophagy/autophagy and apoptosis has been associated with SS, but a mechanistic understanding of the gene expression changes associated with these abnormal processes has not been realized. Recently, increased LAMP3 (lysosomal associated membrane protein 3) expression was found in a subset of SS patients and was associated with increased apoptosis and autoantigen accumulation and release. To better understand how LAMP3 expression might modulate apoptosis, cell biology, and biochemical studies were used to examine the effect of LAMP3 expression in minor salivary gland cells. LAMP3 expression resulted in degradation of LAMP1 increasing lysosomal membrane permeabilization and relocalization of cathepsins to the cytoplasm, resulting in destabilizing autophagic flux and caspase activation. These findings highlight the central role of LAMP3 expression in the pathogenesis of SS.
    Keywords:  Apoptosis; Sjögren syndrome; autophagy; lysosomal membrane permeabilization; lysosome-associated membrane protein 3; salivary gland
    DOI:  https://doi.org/10.1080/15548627.2021.1995150
  57. PLoS One. 2021 ;16(11): e0259313
    Reactive oxygen species prevent lysosome coalescence during PIKfyve inhibition.
    Golam T Saffi, Evan Tang, Sami Mamand, Subothan Inpanathan, Aaron Fountain, Leonardo Salmena, Roberto J Botelho.
      Lysosomes are terminal, degradative organelles of the endosomal pathway that undergo repeated fusion-fission cycles with themselves, endosomes, phagosomes, and autophagosomes. Lysosome number and size depends on balanced fusion and fission rates. Thus, conditions that favour fusion over fission can reduce lysosome numbers while enlarging their size. Conversely, favouring fission over fusion may cause lysosome fragmentation and increase their numbers. PIKfyve is a phosphoinositide kinase that generates phosphatidylinositol-3,5-bisphosphate to modulate lysosomal functions. PIKfyve inhibition causes an increase in lysosome size and reduction in lysosome number, consistent with lysosome coalescence. This is thought to proceed through reduced lysosome reformation and/or fission after fusion with endosomes or other lysosomes. Previously, we observed that photo-damage during live-cell imaging prevented lysosome coalescence during PIKfyve inhibition. Thus, we postulated that lysosome fusion and/or fission dynamics are affected by reactive oxygen species (ROS). Here, we show that ROS generated by various independent mechanisms all impaired lysosome coalescence during PIKfyve inhibition and promoted lysosome fragmentation during PIKfyve re-activation. However, depending on the ROS species or mode of production, lysosome dynamics were affected distinctly. H2O2 impaired lysosome motility and reduced lysosome fusion with phagosomes, suggesting that H2O2 reduces lysosome fusogenecity. In comparison, inhibitors of oxidative phosphorylation, thiol groups, glutathione, or thioredoxin, did not impair lysosome motility but instead promoted clearance of actin puncta on lysosomes formed during PIKfyve inhibition. Additionally, actin depolymerizing agents prevented lysosome coalescence during PIKfyve inhibition. Thus, we discovered that ROS can generally prevent lysosome coalescence during PIKfyve inhibition using distinct mechanisms depending on the type of ROS.
    DOI:  https://doi.org/10.1371/journal.pone.0259313
  58. Microorganisms. 2021 Oct 31. pii: 2269. [Epub ahead of print]9(11):
    Cellular Self-Digestion and Persistence in Bacteria.
    Sayed Golam Mohiuddin, Sreyashi Ghosh, Han G Ngo, Shayne Sensenbach, Prashant Karki, Narendra K Dewangan, Vahideh Angardi, Mehmet A Orman.
      Cellular self-digestion is an evolutionarily conserved process occurring in prokaryotic cells that enables survival under stressful conditions by recycling essential energy molecules. Self-digestion, which is triggered by extracellular stress conditions, such as nutrient depletion and overpopulation, induces degradation of intracellular components. This self-inflicted damage renders the bacterium less fit to produce building blocks and resume growth upon exposure to fresh nutrients. However, self-digestion may also provide temporary protection from antibiotics until the self-digestion-mediated damage is repaired. In fact, many persistence mechanisms identified to date may be directly or indirectly related to self-digestion, as these processes are also mediated by many degradative enzymes, including proteases and ribonucleases (RNases). In this review article, we will discuss the potential roles of self-digestion in bacterial persistence.
    Keywords:  RNA degradation; autophagy; bacterial persisters; intracellular degradation; lipid degradation; protein degradation; self-digestion; stationary-phase metabolism; viable but non-culturable cells
    DOI:  https://doi.org/10.3390/microorganisms9112269
  59. Antioxidants (Basel). 2021 Nov 03. pii: 1754. [Epub ahead of print]10(11):
    Exercise Ameliorates Diabetic Kidney Disease in Type 2 Diabetic Fatty Rats.
    Itaru Monno, Yoshio Ogura, Jing Xu, Daisuke Koya, Munehiro Kitada.
      Lifestyle improvement, including through exercise, has been recognized as an important mode of therapy for the suppression of diabetic kidney disease (DKD). However, the detailed molecular mechanisms by which exercise exerts beneficial effects in the suppression of DKD have not yet been fully elucidated. In this study, we investigate the effects of treadmill exercise training (TET) for 8 weeks (13 m/min, 30 min/day, 5 days/week) on kidney injuries of type 2 diabetic male rats with obesity (Wistar fatty (fa/fa) rats: WFRs) at 36 weeks of age. TET significantly suppressed the levels of albuminuria and urinary liver-type fatty-acid-binding protein (L-FABP), tubulointerstitial fibrosis, inflammation, and oxidative stress in the kidneys of WFRs. In addition, TET mitigated excessive apoptosis and restored autophagy in the renal cortex, as well as suppressed the development of morphological abnormalities in the mitochondria of proximal tubular cells, which were also accompanied by the restoration of AMP-activated kinase (AMPK) activity and suppression of the mechanistic target of rapamycin complex 1 (mTORC1). In conclusion, TET ameliorates diabetes-induced kidney injury in type 2 diabetic fatty rats.
    Keywords:  AMP-activated kinase; autophagy; diabetic kidney disease; exercise; inflammation; mechanistic target of rapamycin complex 1; oxidative stress
    DOI:  https://doi.org/10.3390/antiox10111754
  60. Cells. 2021 Nov 08. pii: 3071. [Epub ahead of print]10(11):
    Atg5 Regulates Selective Autophagy of the Parental Macronucleus during Tetrahymena Sexual Reproduction.
    Tao Bo, Yu Kang, Ya Liu, Jing Xu, Wei Wang.
      Nuclear autophagy is an important selective autophagy process. The selective autophagy of sexual development micronuclei (MICs) and the programmed nuclear degradation of parental macronucleus (paMAC) occur during sexual reproduction in Tetrahymena thermophila. The molecular regulatory mechanism of nuclear selective autophagy is unclear. In this study, the autophagy-related protein Atg5 was identified from T. thermophila. Atg5 was localized in the cytoplasm in the early sexual-development stage and was localized in the paMAC in the late sexual-development stage. During this stage, the degradation of meiotic products of MIC was delayed in atg5i mutants. Furthermore, paMAC was abnormally enlarged and delayed or failed to degrade. The expression level and lipidation of Atg8.2 significantly decreased in the mutants. All these results indicated that Atg5 was involved in the regulation of the selective autophagy of paMAC by regulating Atg8.2 in Tetrahymena.
    Keywords:  Tetrahymena thermophila; autophagy-related protein 5; parental macronucleus; programmed nuclear degradation
    DOI:  https://doi.org/10.3390/cells10113071
  61. Front Genet. 2021 ;12 753161
    Hsa_circRNA_103124 Upregulation in Crohn's Disease Promotes Cell Proliferation and Inhibits Autophagy by Regulating the Hsa-miR-650/AKT2 Signaling Pathway.
    Juan Yin, Fuyi Tong, Yulan Ye, Tong Hu, Lijuan Xu, Liping Zhang, Jianyun Zhu, Zhi Pang.
      Circular RNAs (circRNAs) play important roles in the pathogenesis of Crohn's disease (CD). We discovered that hsa_circRNA_103124 was upregulated in CD patients in our previous study. Nonetheless, the function of hsa_circRNA_103124 is unclear. In this study, hsa_circRNA_103124 was predicted to interact with hsa-miR-650. Gene Ontology (GO) and pathway analyses identified AKT serine/threonine kinase 2 (AKT2) as the downstream target protein of hsa-miR-650. Activated AKT2 inhibits autophagy, but promotes cell proliferation. Recent studies suggest that the inhibition of autophagy is one of the mechanisms of CD pathogenesis. Therefore, we inferred that hsa_circRNA_103124 might regulate autophagy and proliferation by targeting AKT2 as a sponge for hsa-miR-650. Here, quantitative reverse transcription PCR (RT-QPCR) results revealed that upregulated hsa_circRNA_103124 expression in patients with CD was negatively correlated with hsa-miR-650 expression but positively correlated with the white blood cell count and calprotectin levels. TSC complex subunit 1 (TSC1), one of the proteins upstream of autophagy was downregulated in patients with CD. Consisting with the bioinformatics prediction, it was verified that hsa_circRNA_103124 targeted to hsa-miR650 by fluorescence in situ hybridization (FISH) and luciferase reporter assays. A hsa-miR-650 inhibitor reversed the promotion of rapamycin-induced autophagy and the inhibition of cell proliferation by the hsa_circRNA_103124 siRNA. However, hsa-miR-650 mimics reversed the inhibition of rapamycin-induced autophagy and the promotion of cell proliferation through hsa_circRNA_103124 overexpression. These results indicate that hsa_circRNA_103124 upregulation in patients with CD promotes cell proliferation and inhibits autophagy by regulating the hsa-miR-650/AKT2 signaling pathway.
    Keywords:  AKT2; Cohn’s disease; autophagy; hsa-miR-650; hsa_circRNA_103124
    DOI:  https://doi.org/10.3389/fgene.2021.753161
  62. Int J Mol Sci. 2021 Nov 18. pii: 12467. [Epub ahead of print]22(22):
    Protein Misfolding and Aggregation: The Relatedness between Parkinson's Disease and Hepatic Endoplasmic Reticulum Storage Disorders.
    Francisco J Padilla-Godínez, Rodrigo Ramos-Acevedo, Hilda Angélica Martínez-Becerril, Luis D Bernal-Conde, Jerónimo F Garrido-Figueroa, Marcia Hiriart, Adriana Hernández-López, Rubén Argüero-Sánchez, Francesco Callea, Magdalena Guerra-Crespo.
      Dysfunction of cellular homeostasis can lead to misfolding of proteins thus acquiring conformations prone to polymerization into pathological aggregates. This process is associated with several disorders, including neurodegenerative diseases, such as Parkinson's disease (PD), and endoplasmic reticulum storage disorders (ERSDs), like alpha-1-antitrypsin deficiency (AATD) and hereditary hypofibrinogenemia with hepatic storage (HHHS). Given the shared pathophysiological mechanisms involved in such conditions, it is necessary to deepen our understanding of the basic principles of misfolding and aggregation akin to these diseases which, although heterogeneous in symptomatology, present similarities that could lead to potential mutual treatments. Here, we review: (i) the pathological bases leading to misfolding and aggregation of proteins involved in PD, AATD, and HHHS: alpha-synuclein, alpha-1-antitrypsin, and fibrinogen, respectively, (ii) the evidence linking each protein aggregation to the stress mechanisms occurring in the endoplasmic reticulum (ER) of each pathology, (iii) a comparison of the mechanisms related to dysfunction of proteostasis and regulation of homeostasis between the diseases (such as the unfolded protein response and/or autophagy), (iv) and clinical perspectives regarding possible common treatments focused on improving the defensive responses to protein aggregation for diseases as different as PD, and ERSDs.
    Keywords:  Parkinson’s disease; alpha-1-antitrypsin; alpha-1-antitrypsin deficiency; alpha-synuclein; endoplasmic reticulum storage disease; fibrinogen; hereditary hypofibrinogenemia with hepatic storage; protein aggregation; protein misfolding
    DOI:  https://doi.org/10.3390/ijms222212467
  63. Oxid Med Cell Longev. 2021 ;2021 3960773
    Mitochondrial Quality Control in the Maintenance of Cardiovascular Homeostasis: The Roles and Interregulation of UPS, Mitochondrial Dynamics and Mitophagy.
    Yujie Song, Yuerong Xu, Yingying Liu, Jie Gao, Lele Feng, Yuxi Zhang, Lei Shi, Miao Zhang, Dong Guo, Bingchao Qi, Mingming Zhang.
      Maintenance of normal function of mitochondria is vital to the fate and health of cardiomyocytes. Mitochondrial quality control (MQC) mechanisms are essential in governing mitochondrial integrity and function. The ubiquitin-proteasome system (UPS), mitochondrial dynamics, and mitophagy are three major components of MQC. With the progress of research, our understanding of MQC mechanisms continues to deepen. Gradually, we realize that the three MQC mechanisms are not independent of each other. To the contrary, there are crosstalk among the mechanisms, which can make them interact with each other and cooperate well, forming a triangle interplay. Briefly, the UPS system can regulate the level of mitochondrial dynamic proteins and mitophagy receptors. In the process of Parkin-dependent mitophagy, the UPS is also widely activated, performing critical roles. Mitochondrial dynamics have a profound influence on mitophagy. In this review, we provide new processes of the three major MQC mechanisms in the background of cardiomyocytes and delve into the relationship between them.
    DOI:  https://doi.org/10.1155/2021/3960773
  64. Mol Aspects Med. 2021 Nov 23. pii: S0098-2997(21)00107-2. [Epub ahead of print] 101047
    Autophagy and disease: new insights and challenges ahead.
    Patricia Boya.
      
    DOI:  https://doi.org/10.1016/j.mam.2021.101047
  65. Biochem Biophys Res Commun. 2021 Nov 13. pii: S0006-291X(21)01541-2. [Epub ahead of print]586 27-33
    Substrate stiffening promotes VEGF-A functions via the PI3K/Akt/mTOR pathway.
    Amjad Husain, Arogya Khadka, Allen Ehrlicher, Magali Saint-Geniez, Ramaswamy Krishnan.
      While it is now well-established that substrate stiffness regulates vascular endothelial growth factor-A (VEGF-A) mediated signaling and functions, causal mechanisms remain poorly understood. Here, we report an underlying role for the PI3K/Akt/mTOR signaling pathway. This pathway is activated on stiffer substrates, is amplified by VEGF-A stimulation, and correlates with enhanced endothelial cell (EC) proliferation, contraction, pro-angiogenic secretion, and capillary-like tube formation. In the settings of advanced age-related macular degeneration, characterized by EC and retinal pigment epithelial (RPE)-mediated angiogenesis, these data implicate substrate stiffness as a novel causative mechanism and Akt/mTOR inhibition as a novel therapeutic pathway.
    Keywords:  AMD; Angiogenesis; Contraction; Endothelial cell; Proliferation; RPE; Rigidity
    DOI:  https://doi.org/10.1016/j.bbrc.2021.11.030
  66. Open Med (Wars). 2021 ;16(1): 1718-1727
    MitoQ inhibits hepatic stellate cell activation and liver fibrosis by enhancing PINK1/parkin-mediated mitophagy.
    Shi-Ding Dou, Jiu-Na Zhang, Xiao-Li Xie, Ting Liu, Jun-Li Hu, Xiao-Yu Jiang, Miao-Miao Wang, Hui-Ding Jiang.
      Mitophagy affects the activation of hepatic stellate cells (HSCs). Mitochondria-targeted ubiquinone (MitoQ) is a mitochondria-targeted antioxidant that reduces the production of intracellular reactive oxygen species (ROS). However, its relationship with mitophagy remains unclear. This study evaluated mitophagy during HSC activation and the effects of MitoQ on mitophagy in cell culture and in an animal model of the activation of HSCs. We found that MitoQ reduced the activation of HSCs and alleviated hepatic fibrosis. PINK1 (PTEN-induced putative kinase 1) is a putative serine/threonine kinase located in the mitochondria's outer membrane. While the activation of primary HSCs or LX-2 cells was associated with reduced PINK1/parkin-mediated mitophagy, MitoQ reduced intracellular ROS levels, enhanced PINK1/parkin-mediated mitophagy, and inhibited the activation of HSCs. After knocking down the key mitophagy-related protein, PINK1, in LX-2 cells to block mitophagy, MitoQ intervention failed to inhibit HSC activation. Our results showed that MitoQ inhibited the activation of HSCs and alleviated hepatic fibrosis by enhancing PINK1/parkin-mediated mitophagy.
    Keywords:  PINK1 mitophagy; hepatic stellate cell; liver fibrosis; ubiquinone
    DOI:  https://doi.org/10.1515/med-2021-0394
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