bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2024–12–29
sixty-five papers selected by
Viktor Korolchuk, Newcastle University
  1. Cost-effective and simple flow cytometry quantification of receptor-mediated autophagy using fluorescent tagging.
  2. The Cullin3-Rbx1-KLHL9 E3 ubiquitin ligase complex ubiquitinates Rheb and supports amino acid-induced mTORC1 activation.
  3. Reconsidering the selectivity of bulk autophagy: cargo hitchhiking specifies cargo for degradation.
  4. Calmodulin enhances mTORC1 signaling by preventing TSC2-Rheb binding.
  5. Oscillatory autophagy induction is enabled by an updated AMPK-ULK1 regulatory wiring.
  6. V-ATPase in cancer: mechanistic insights and therapeutic potentials.
  7. Ubiquitin-mediated recruitment of the ATG9A-ATG2 lipid transfer complex drives clearance of phosphorylated p62 aggregates.
  8. Phosphatidic acid as a cofactor of mTORC1 in platinum-based chemoresistance: Mechanisms and therapeutic potential.
  9. Resveratrol promotes autophagosome elimination via SIRT1 in cardiomyocytes.
  10. Identification of the mammalian VPS4A as a selective lipophagy receptor.
  11. Preventing excessive autophagy protects from the pathology of mtDNA mutations in Drosophila melanogaster.
  12. Interaction Between Autophagy and the Inflammasome in Human Tumors: Implications for the Treatment of Human Cancers.
  13. The complex interplay between redox dysregulation and mTOR signaling pathway in cancer: A rationale for cancer treatment.
  14. SETD7 promotes LC3B methylation and degradation in ovarian cancer.
  15. Decoration of Autophagy Detecting Nanoparticle with an Anionic Fluorochrome Enhances Multispectral Characterization of Autophagosome Location and Flux.
  16. Autophagy protein Atg7 is essential for maintaining malaria parasite cellular homeostasis and organelle biogenesis.
  17. Novel exploitation of autophagy by tombusviruses.
  18. Pressure to evade cell-autonomous innate sensing reveals interplay between mitophagy, IFN signaling, and SARS-CoV-2 evolution.
  19. STAT1 Promotes PD-L1 Activation and Tumor Growth in Lymphangioleiomyomatosis.
  20. TFEB triggers a matrix degradation and invasion program in triple-negative breast cancer cells upon mTORC1 repression.
  21. Synthesis and structural modification of the natural product Ivesinol to discover novel autophagy activators.
  22. Cannabidiol induces autophagy via CB1 receptor and reduces α-synuclein cytosolic levels.
  23. Inositol phosphates dynamically enhance stability, solubility and catalytic activity of mTOR.
  24. The di-leucine motif in the host defense peptide LL-37 is essential for initiation of autophagy in human macrophages.
  25. The N-degron pathway mediates the autophagic degradation of cytosolic mitochondrial DNA during sterile innate immune responses.
  26. Autophagy deficiency protects against ocular hypertension and glaucoma.
  27. NOVEL APPROACHES IN TARGETING MEMBRANE AND SECRETED PROTEINS FOR LYSOSOMAL DEGRADATION.
  28. The steroid hormone 20-hydroxyecdysone inhibits RAPTOR expression by repressing Hox gene transcription to induce autophagy.
  29. Autophagy Modulates Glioblastoma Cell Sensitivity to Selinexor-mediated XPO1 inhibition.
  30. The pro-fibrotic role of autophagy in renal intrinsic cells: mechanisms and therapeutic potential in chronic kidney disease.
  31. Hyperaminoacidemia from interrupted glucagon signaling increases pancreatic acinar cell proliferation and size via mTORC1 and YAP pathways.
  32. Regulating the regulators: long non-coding RNAs as autophagic controllers in chronic disease management.
  33. Regulation of autophagy and cellular signaling through non-histone protein methylation.
  34. Autophagy Activated by Atg1 Interacts With Atg9 Promotes Biofilm Formation and Resistance of Candida albicans.
  35. HSP90 stabilizes visual cycle retinol dehydrogenase 5 in the endoplasmic reticulum by inhibiting its degradation during autophagy.
  36. Sanguinarine suppresses oral squamous cell carcinoma progression by targeting the PKM2/TFEB aix to inhibit autophagic flux.
  37. Regulation of N-Degron Recognin-Mediated Autophagy by the sars-cov-2 plpro ubiquitin deconjugase.
  38. Spns1-dependent endocardial lysosomal function drives valve morphogenesis through Notch1-signaling.
  39. Endosomal traffic disorders: a driving force behind neurodegenerative diseases.
  40. TANGO2-related rhabdomyolysis symptoms are associated with abnormal autophagy functioning.
  41. Temporal dissection of the roles of Atg4 and ESCRT in autophagosome formation in yeast.
  42. Impairment of lipid homeostasis causes lysosomal accumulation of endogenous protein aggregates through ESCRT disruption.
  43. Leucine Aminopeptidase LyLAP enables lysosomal degradation of membrane proteins.
  44. The effect of molecular chaperone mediated autophagy on ApoE expression in retinal pigment epithelial cells: Molecular structure and protein action mechanism.
  45. Antibody-mediated clearance of an ER-resident aggregate that causes glaucoma.
  46. TFEB Phase Separation Mediates the Amelioration Effect of Intermittent Fasting on Inflammatory Colitis.
  47. CHMP2B promotes CHMP7 mediated nuclear pore complex injury in sporadic ALS.
  48. Calcium level and autophagy defect in GNE mutants of rare neuromuscular disorder.
  49. mTOR pathway: A key player in diabetic nephropathy progression and therapeutic targets.
  50. The Vacuole Lipid Droplet Contact Site vCLIP.
  51. Urolithin A attenuates Doxorubicin-induced cardiotoxicity by enhancing PINK1-regulated mitophagy via Ambra1.
  52. Inhibition of autophagy attenuates cognitive decline and mitochondrial dysfunction in an Alzheimer's disease mouse model with chronic cerebral hypoperfusion.
  53. Comparative Analysis of Human Brain RNA-seq Reveals the Combined Effects of Ferroptosis and Autophagy on Alzheimer's Disease in Multiple Brain Regions.
  54. The glial UDP-glycosyltransferase Ugt35b regulates longevity by maintaining lipid homeostasis in Drosophila.
  55. Mechanism of starvation induced autophagy and apoptosis in the midgut of silkworm, Bombyx mori, based on calcium homeostasis.
  56. Tagless LysoIP for immunoaffinity enrichment of native lysosomes from clinical samples.
  57. Nuclear ESCRT is involved in intranuclear protein quality control by micronucleophagy.
  58. HMGB1 Promotes Accelerated Fracture Healing in Traumatic Brain Injury through PINK1/Parkin-Mediated Mitochondrial Autophagy.
  59. OTUD5 Protects Dopaminergic Neurons by Promoting the Degradation of α-Synuclein in Parkinson's Disease Model.
  60. SHIP-1 regulates the differentiation and function of Tregs via inhibiting mTORC1 activity.
  61. Cancer immunotherapeutic challenges from autophagy-immune checkpoint reciprocal regulation.
  62. Sleep deprivation activated AMPK/FOXO3a signaling mediates pineal autophagy impairment to reduce melatonin secretion in CUMS + SD rats leading to depression combined with insomnia.
  63. NRF-mediated autophagy and UPR: Exploring new avenues to overcome cancer chemo-resistance.
  64. Exploring the Impact of Apelin and Reactive Oxygen Species on Autophagy and Cell Senescence in Pre-eclampsia.
  65. The role of macroautophagy in substance use disorders.
  1. FEBS Open Bio. 2024 Dec 23.
    Cost-effective and simple flow cytometry quantification of receptor-mediated autophagy using fluorescent tagging.
    Mija Marinković, Ana Rožić, Denis Polančec, Ivana Novak.
      Mitophagy, a selective clearance of damaged or superfluous mitochondria via autophagy machinery and lysosomal degradation, is an evolutionarily conserved process essential for various physiological functions, including cellular differentiation and immune responses. Defects in mitophagy are implicated in numerous human diseases, such as neurodegenerative disorders, cancer, and metabolic conditions. Despite significant advancements in mitophagy research over recent decades, novel and robust methodologies are necessary to elucidate its molecular mechanisms comprehensively. In this study, we present a detailed protocol for quantitatively assessing mitophagy through flow cytometry using a mitochondria-targeted fluorescent mitophagy receptor, GFP-BNIP3L/NIX. This method offers a rapid alternative to conventional microscopy or immunoblotting techniques for analyzing mitophagy activity. Additionally, this approach can theoretically be adapted to utilize any fluorescent-tagged selective autophagy receptor, enabling the direct and rapid analysis of various types of receptor-mediated selective autophagy.
    Keywords:  BNIP3L/NIX; flow cytometry; fluorescent tagging; receptor‐mediated mitophagy
    DOI:  https://doi.org/10.1002/2211-5463.13958
  2. Cell Rep. 2024 Dec 20. pii: S2211-1247(24)01452-9. [Epub ahead of print]44(1): 115101
    The Cullin3-Rbx1-KLHL9 E3 ubiquitin ligase complex ubiquitinates Rheb and supports amino acid-induced mTORC1 activation.
    Yao Yao, Sungki Hong, Shota Yoshida, Vinamra Swaroop, Brady Curtin, Ken Inoki.
      Mechanistic target of rapamycin complex 1 (mTORC1) is recruited to the lysosomal membrane by the active Rag heterodimer, where mTORC1 interacts with active Rheb for its activation. It has been shown that polyubiquitination of Rheb is crucial for enhancing its interaction with mTORC1 on the lysosome. However, the specific ubiquitin ligases for Rheb, which promotes mTORC1 activation, remain elusive. We report that the CUL3-RBX1-KLHL9 E3 ubiquitin ligase complex is translocated to the lysosome and ubiquitinates Rheb in response to amino acid stimulation. KLHL9 serves as an essential adaptor for CUL3-RBX1 to target Rheb on the lysosome. Deleting either CUL3, RBX1, or KLHL9 diminishes Rheb ubiquitination and reduces amino acid-induced mTORC1 activation without impacting lysosomal mTORC1 localization or Akt activity. Thus, the CUL3-RBX1-KLHL9 complex functions as a mTORC1 activator by acting as an E3 ubiquitin ligase for Rheb and supports amino acid-induced mTORC1 activation.
    Keywords:  CP: Cell biology; CUL3; KLHL9; Rheb; lysosome; mTORC1; ubiquitination
    DOI:  https://doi.org/10.1016/j.celrep.2024.115101
  3. Autophagy. 2024 Dec 27.
    Reconsidering the selectivity of bulk autophagy: cargo hitchhiking specifies cargo for degradation.
    Eigo Takeda, Alexander I May, Yoshinori Ohsumi.
      Bulk macroautophagy/autophagy, typically induced by starvation, is generally thought to non-selectively isolate cytosolic components for degradation. However, a detailed analysis of bulk autophagy cargo has not been conducted. We recently employed mass spectrometry to analyze the contents of isolated autophagic bodies. In this process, we uncovered Hab1 (Highly enriched in Autophagic Bodies 1), a novel protein, that is preferentially delivered via autophagy. Hab1 is a receptor protein that binds Atg8-PE and ribosomes at its N- and C-termini, respectively. We found that ribosome-bound Hab1 is preferentially delivered to the vacuole by "'hitchhiking'" on phagophores/isolation membranes formed during bulk autophagy. This hitchhiking mechanism confers selectivity to bulk autophagy.
    Keywords:  Atg8; Hab1; Saccharomyces cerevisiae; hitchhiking; ribosome
    DOI:  https://doi.org/10.1080/15548627.2024.2447209
  4. J Biol Chem. 2024 Dec 21. pii: S0021-9258(24)02624-3. [Epub ahead of print] 108122
    Calmodulin enhances mTORC1 signaling by preventing TSC2-Rheb binding.
    Yuna Amemiya, Yuichiro Ioi, Makoto Araki, Kenji Kontani, Masatoshi Maki, Hideki Shibata, Terunao Takahara.
      The mechanistic target of rapamycin complex 1 (mTORC1) functions as a master regulator of cell growth and proliferation. We previously demonstrated that intracellular calcium ion (Ca2+) concentration modulates the mTORC1 pathway via binding of the Ca2+ sensor protein calmodulin (CaM) to tuberous sclerosis complex 2 (TSC2), a critical negative regulator of mTORC1. However, the precise molecular mechanism by which Ca2+/CaM modulates mTORC1 activity remains unclear. Here, we performed a binding assay based on nano-luciferase reconstitution, a method for detecting weak interactions between TSC2 and its target, Ras homolog enriched in brain (Rheb), an activator of mTORC1. CaM inhibited the binding of TSC2 to Rheb in a Ca2+-dependent manner. Live-cell imaging analysis indicated increased interaction between the CaM-binding region of TSC2 and CaM in response to elevated intracellular Ca2+ levels. Furthermore, treatment with carbachol, an acetylcholine analog, elevated intracellular Ca2+ levels, and activated mTORC1. Notably, carbachol-induced activation of mTORC1 was inhibited by CaM inhibitors, corroborating the role of Ca2+/CaM in promoting the mTORC1 pathway. Consistent with the effect of Ca2+/CaM on the TSC2-Rheb interaction, increased intracellular Ca2+ concentration promoted the dissociation of TSC2 from lysosomes without affecting Akt-dependent phosphorylation of TSC2, suggesting that the regulatory mechanism of TSC2 by Ca2+/CaM is distinct from the previously established action mechanism of TSC2. Collectively, our findings offer mechanistic insights into TSC2-Rheb regulation mediated by Ca2+/CaM, which links Ca2+ signaling to mTORC1 activation.
    Keywords:  Rheb; calcium; calmodulin; mechanistic target of rapamycin complex 1; tuberous sclerosis complex
    DOI:  https://doi.org/10.1016/j.jbc.2024.108122
  5. PLoS One. 2024 ;19(12): e0313302
    Oscillatory autophagy induction is enabled by an updated AMPK-ULK1 regulatory wiring.
    Orsolya Kapuy, Marianna Holczer, Luca Csabai, Tamás Korcsmáros.
      Autophagy-dependent survival relies on a crucial oscillatory response during cellular stress. Although oscillatory behaviour is typically associated with processes like the cell cycle or circadian rhythm, emerging experimental and theoretical evidence suggests that such periodic dynamics may explain conflicting experimental results in autophagy research. In this study, we demonstrate that oscillatory behaviour in the regulation of the non-selective, stress-induced macroautophagy arises from a series of interlinked negative and positive feedback loops within the mTORC1-AMPK-ULK1 regulatory triangle. While many of these interactions have been known for decades, recent discoveries have revealed how mTORC1, AMPK, and ULK1 are truly interconnected. Although these new findings initially appeared contradictory to established models, additional experiments and our systems biology analysis clarify the updated regulatory structure. Through computational modelling of the autophagy oscillatory response, we show how this regulatory network governs autophagy induction. Our results not only reconcile previous conflicting experimental observations but also offer insights for refining autophagy regulation and advancing understanding of its mechanisms of action.
    DOI:  https://doi.org/10.1371/journal.pone.0313302
  6. Cell Commun Signal. 2024 Dec 20. 22(1): 613
    V-ATPase in cancer: mechanistic insights and therapeutic potentials.
    Tingting Chen, Xiaotan Lin, Shuo Lu, Bo Li.
      Vacuolar-type H+-ATPase (V-ATPase) is a crucial proton pump that plays an essential role in maintaining intracellular pH homeostasis and a variety of physiological processes. This review provides an in-depth exploration of the structural components, functional mechanisms, and regulatory modes of V-ATPase in cancer cells. Comprising two main domains, V1 and V0, V-ATPase drives the proton pump through ATP hydrolysis, sustaining the pH balance within the cell and organelles. In cancer cells, the enhanced activity of V-ATPase is closely associated with the proliferation and metastasis of tumor cells, and it promotes the growth and invasion of tumor cells by regulating pH values in the tumor microenvironment. Moreover, the interaction between V-ATPase and key metabolic regulatory factors, the mechanistic target of rapamycin complex 1 (mTORC1) and AMP-activated protein kinase (AMPK), impacts the metabolic state of cancer cells. The role of V-ATPase in tumor drug resistance and its regulatory mechanism in non-canonical autophagy offer new perspectives and potential targets for cancer therapy. Future research directions will focus on the specific mechanisms of action of V-ATPase in the tumor microenvironment and how to translate its inhibitors into clinical applications, providing significant scientific evidence for the development of new therapeutic strategies.
    Keywords:  Proton pump; Therapeutic targets; V-ATPase; pH homeostasis
    DOI:  https://doi.org/10.1186/s12964-024-01998-9
  7. Mol Biol Cell. 2024 Dec 24. mbcE24030101
    Ubiquitin-mediated recruitment of the ATG9A-ATG2 lipid transfer complex drives clearance of phosphorylated p62 aggregates.
    D G Broadbent, C M McEwan, D Jayatunge, E G Kaminsky, T M Tsang, D M Poole, B C Naylor, J C Price, J C Schmidt, J L Andersen.
      Autophagy is an essential cellular recycling process that maintains protein and organelle homeostasis. ATG9A vesicle recruitment is a critical early step in autophagy to initiate autophagosome biogenesis. The mechanisms of ATG9A vesicle recruitment are best understood in the context of starvation-induced non-selective autophagy, whereas less is known about the signals driving ATG9A vesicle recruitment to autophagy initiation sites in the absence of nutrient stress. Here we demonstrate that loss of ATG9A, or the lipid transfer protein ATG2, leads to the accumulation of phosphorylated p62 aggregates in nutrient replete conditions. Furthermore, we show that p62 degradation requires the lipid scramblase activity of ATG9A. Lastly, we present evidence that poly-ubiquitin is an essential signal that recruits ATG9A and mediates autophagy foci assembly in nutrient replete cells. Together, our data support a ubiquitin-driven model of ATG9A recruitment and autophagosome formation during basal autophagy. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E24-03-0101
  8. Eur J Pharmacol. 2024 Dec 21. pii: S0014-2999(24)00910-5. [Epub ahead of print]988 177220
    Phosphatidic acid as a cofactor of mTORC1 in platinum-based chemoresistance: Mechanisms and therapeutic potential.
    Hadi Alizadeh, Sana Kerachian, Keyvan Jabbari, Bahram Mohammad Soltani.
      Platinum-based chemotherapeutics, such as cisplatin and carboplatin, are widely used to treat various malignancies. However, the development of chemoresistance remains a significant challenge, limiting their efficacy. This review explores the multifaceted mechanisms of platinum-based chemoresistance, with a particular focus on the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway, which plays a critical role in promoting tumor survival and resistance to platinum compounds. Additionally, we examined the role of phosphatidic acid (PA) and its synthesizing enzymes, phospholipase D (PLD) and lysophosphatidic acid acyltransferase (LPAAT), in the regulation of mTORC1 activity. Given the involvement of mTORC1 in chemoresistance, we evaluated the potential of mTOR inhibitors as a therapeutic strategy to overcome platinum resistance. Finally, we discuss combination therapies targeting the mTOR pathway alongside conventional chemotherapy to improve treatment outcomes. This review highlights the potential of targeting mTORC1 and related pathways to improve therapeutic strategies for chemoresistant cancers.
    Keywords:  Phosphatidic acid; Platinum-based chemoresistance; mTOR inhibitors; mTORC1
    DOI:  https://doi.org/10.1016/j.ejphar.2024.177220
  9. J Pharmacol Sci. 2025 Jan;pii: S1347-8613(24)00076-8. [Epub ahead of print]157(1): 25-34
    Resveratrol promotes autophagosome elimination via SIRT1 in cardiomyocytes.
    Atsushi Kuno, Ryusuke Hosoda, Yukika Saga, Naotoshi Iwahara, Yuki Tatekoshi, Ryo Numazawa, Yoshiyuki Horio.
      The processes of autophagy, including autophagosome formation, fusion of autophagosomes with lysosomes, and degradation of autophagosomes by lysosomes, are regulated by various mechanisms. We recently found that treatment with resveratrol, an activator of the NAD+-dependent protein deacetylase Sirtuin-1 (SIRT1), in a mouse model prevented autophagosome accumulation in the heart with high mTORC1 activity. In this study, we investigated whether SIRT1 mediates the effects of resveratrol on autophagosome elimination using a cardiomyocyte model. In H9c2 cardiomyocytes, treatment with the mTORC1 activator MHY1485 induced autophagosome accumulation accompanied by increases in fragmented mitochondria within the autophagosomes and levels of intracellular reactive oxygen species (ROS), indicative of impaired autophagy-mediated elimination of mitochondria and resultant oxidative stress. MHY1485 suppressed the fusion of autophagosomes with lysosomes. Co-treatment with resveratrol attenuated the MHY1485-induced increases in autophagosomes, mitochondria within autophagosomes, and levels of ROS. Knockdown of Sirt1 reversed the reductions in autophagosomes and ROS levels induced by resveratrol under the condition of MHY1485 treatment. Neither resveratrol treatment nor Sirt1 knockdown modulated the phosphorylation levels of UVRAG, a target of mTORC1 for suppression of autophagosome-lysosome fusion. Our findings suggest that SIRT1 mediates the resveratrol-induced promotion of autophagosome elimination in cells with high mTORC1 activity.
    Keywords:  Autophagosome elimination; Reactive oxygen species; Resveratrol; SIRT1; mTORC1
    DOI:  https://doi.org/10.1016/j.jphs.2024.11.006
  10. Autophagy. 2024 Dec 26.
    Identification of the mammalian VPS4A as a selective lipophagy receptor.
    Dimitra Dialynaki, Daniel J Klionsky.
      Lipophagy is a selective type of autophagy where lipid droplets are targeted to the lysosome/vacuole for degradation. Even though lipophagy has been reported in various species, many questions remain unaddressed. How are the lipid droplets sequestered to the lysosome? What is the lipophagy receptor(s)? How is this receptor(s) regulated at a posttranslational level? A new collaborative study among several universities conducted on mouse and human hepatocytes sheds light on these questions, deciphering the lipophagy mechanism in the liver. In a recent paper, Das and colleagues identified VPS4A (vacuolar protein sorting 4 homolog A) as a selective receptor, providing new insights into the mechanistic pathway of lipophagy in mammals and its inverse association with steatotic liver diseases.
    Keywords:  Autophagy; LD homeostasis; VPS4A; lipophagy; lipophagy receptor
    DOI:  https://doi.org/10.1080/15548627.2024.2441535
  11. Nat Commun. 2024 Dec 23. 15(1): 10719
    Preventing excessive autophagy protects from the pathology of mtDNA mutations in Drosophila melanogaster.
    Najla El Fissi, Florian A Rosenberger, Kai Chang, Alissa Wilhalm, Tom Barton-Owen, Fynn M Hansen, Zoe Golder, David Alsina, Anna Wedell, Matthias Mann, Patrick F Chinnery, Christoph Freyer, Anna Wredenberg.
      Aberration of mitochondrial function is a shared feature of many human pathologies, characterised by changes in metabolic flux, cellular energetics, morphology, composition, and dynamics of the mitochondrial network. While some of these changes serve as compensatory mechanisms to maintain cellular homeostasis, their chronic activation can permanently affect cellular metabolism and signalling, ultimately impairing cell function. Here, we use a Drosophila melanogaster model expressing a proofreading-deficient mtDNA polymerase (POLγexo-) in a genetic screen to find genes that mitigate the harmful accumulation of mtDNA mutations. We identify critical pathways associated with nutrient sensing, insulin signalling, mitochondrial protein import, and autophagy that can rescue the lethal phenotype of the POLγexo- flies. Rescued flies, hemizygous for dilp1, atg2, tim14 or melted, normalise their autophagic flux and proteasome function and adapt their metabolism. Mutation frequencies remain high with the exception of melted-rescued flies, suggesting that melted may act early in development. Treating POLγexo- larvae with the autophagy activator rapamycin aggravates their lethal phenotype, highlighting that excessive autophagy can significantly contribute to the pathophysiology of mitochondrial diseases. Moreover, we show that the nucleation process of autophagy is a critical target for intervention.
    DOI:  https://doi.org/10.1038/s41467-024-55559-2
  12. Cell Biochem Funct. 2025 Jan;43(1): e70035
    Interaction Between Autophagy and the Inflammasome in Human Tumors: Implications for the Treatment of Human Cancers.
    Qing Xia, Jingzhou Zhang.
      Autophagy is a physiologically regulated cellular process orchestrated by autophagy-related genes (ATGs) that, depending on the tumor type and stage, can either promote or suppress tumor growth and progression. It can also modulate cancer stem cell maintenance and immune responses. Therefore, targeted manipulation of autophagy may inhibit tumor development by overcoming tumor-promoting mechanisms. The inflammasome is another multifunctional bioprocess that induces a form of pro-inflammatory programmed cell death, called pyroptosis. Dysregulation or overactivation of the inflammasome has been implicated in tumor pathogenesis and development. Additionally, autophagy can inhibit the NLRP3 inflammasome by removing inflammatory drivers. Recent research suggests that the NLRP3 inflammasome, in turn, affects autophagy. Understanding the complex interplay between autophagy and inflammasomes could lead to more precise and effective strategies for cancer treatments. In this review, we summarize the impact of autophagy and inflammasome dysregulation on tumor progression or suppression. We then highlight their targeting for cancer treatment as monotherapy or in combination with other therapies. Furthermore, we discuss the interaction between autophagy and tumor-promoting inflammation or the NLRP3 inflammasome. Finally, based on recent findings, we review the potential of this interaction for cancer treatment.
    Keywords:  cancer stem cell; combination therapy; drug resistance; immunogenicity; inflammation; mitophagy
    DOI:  https://doi.org/10.1002/cbf.70035
  13. Biochem Pharmacol. 2024 Dec 19. pii: S0006-2952(24)00730-5. [Epub ahead of print]232 116729
    The complex interplay between redox dysregulation and mTOR signaling pathway in cancer: A rationale for cancer treatment.
    Christophe Glorieux, Cinthya Enríquez, Pedro Buc Calderon.
      The mechanistic target of rapamycin (mTOR) is a highly conserved serine/threonine kinase that plays a critical role in regulating cellular processes such as growth, proliferation, and metabolism in healthy cells. Dysregulation of mTOR signaling and oxidative stress have been implicated in various diseases including cancer. This review aims to provide an overview of the current understanding of mTOR and its involvement in cell survival and the regulation of cancer cell metabolism as well as its complex interplay with reactive oxygen species (ROS). On the one hand, ROS can inhibit or activate mTOR pathway in cancer cells through various mechanisms. Conversely, mTOR signaling can induce oxidative stress in tumor cells notably due to the inhibition in the expression of antioxidant enzyme genes. Since mTOR is often activated and plays crucial role in cancer cell survival, the use of mTOR inhibitors, which often induce ROS accumulation, could be an interesting approach for cancer treatment. This review will address the advantages, disadvantages, combination strategies, and limitations associated with therapeutic modulation of mTOR signaling pathway in cancer treatment.
    Keywords:  Cancer; Cell survival; Metabolism; Oxidative stress; ROS; mTOR; mTOR inhibitors
    DOI:  https://doi.org/10.1016/j.bcp.2024.116729
  14. J Biol Chem. 2024 Dec 24. pii: S0021-9258(24)02636-X. [Epub ahead of print] 108134
    SETD7 promotes LC3B methylation and degradation in ovarian cancer.
    Ziwei Zhang, Mingyang Li, Yanan Hou, Ting Huang, Bowen Zhang, Qiong Lin, Genbao Shao.
      Microtubule-associated protein 1 light chain 3 (LC3) is a key autophagy-related protein involved in regulating autophagosome formation and autophagy activity. Post-translational modifications of LC3 are necessary to modulate its function. However, LC3 protein methylation and its physiological significance have not yet been elucidated. Here, we show that SET domain containing lysine methyltransferase 7 (SETD7) interacts with LC3B, a common isoform of LC3, and methylates LC3B at lysine 51 (K51). SETD7-mediated methylation of LC3B promotes ubiquitination and degradation of LC3B, resulting in reduced autophagosome formation. Furthermore, SETD7 exerts a tumor-promotive function in ovarian cancer (OC) cells in a K51 methylation-dependent manner. Collectively, our data define a novel modification of LC3B and highlight the oncogenic effect of SETD7 via mediating LC3B methylation and degradation.
    Keywords:  Autophagy; LC3B; Ovarian cancer; Posttranslational modification; SETD7
    DOI:  https://doi.org/10.1016/j.jbc.2024.108134
  15. Small. 2024 Dec 26. e2407915
    Decoration of Autophagy Detecting Nanoparticle with an Anionic Fluorochrome Enhances Multispectral Characterization of Autophagosome Location and Flux.
    Eman Akam-Baxter, Howard H Chen, Asma Boukhalfa, Ada Yu, Lauren A Ling, Andrew H Kung, Susana Bulnes Rodriguez, Hushan Yuan, Lee Josephson, David E Sosnovik.
      Autophagy is a key biological process that has proven extremely difficult to detect noninvasively. To address this, an autophagy detecting nanoparticle (ADN) was recently developed, consisting of an iron oxide nanoparticle decorated with cathepsin-cleavable arginine-rich peptides bound to the near-infrared fluorochrome Cy5.5. Activation of the probe in autophagolysosomes results in the emission of Cy5.5 fluorescence and provides a measure of autophagosome flux. However, in the early autophagosome ADN fluorescence is silent due to fluorochrome stacking. Here, we introduce to ADN a second non-cleavable fluorophore that allows the probe to be tracked through all stages of autophagy. The nature of the secondary/tracking fluorophore has a profound effect on the activation of ADN and the emission of Cy5.5 fluorescence. The lead candidate, ADN2 (featuring AZDye546 as the secondary fluorophore) has the highest activation rate and change in Cy5.5 fluorescence. Absorbance and fluorescence spectrophotometry methods show that the negatively charged AZDye546 interacts with the positively charged polyarginine motifs of the Cy5.5-polyArg activatable fluorophore, resulting in enhanced baseline quenching of the Cy5.5 signal in the nanoprobe. Flow cytometry shows that the activation of ADN2 remains specific for autophagy and is strongly modulated by classical regulators of autophagy (starvation, bafilomycin) and genetic deletion of key autophagy proteins (ATG5, ATG7). ADN2 co-localized strongly with LC3-GFP positive autophagosomes and provided readouts of in vivo probe delivery and activation in the hearts of fed/starved mice. ADN2 enhances the ability to image autophagy without genetic transfection of cells/animals and underscores the possible effects for unanticipated interactions between fluorochromes and other moieties on the surface of decorated nanoparticles.
    Keywords:  autophagy; ferumoxytol; fluorescence; quenching; surface decoration
    DOI:  https://doi.org/10.1002/smll.202407915
  16. mBio. 2024 Dec 23. e0273524
    Autophagy protein Atg7 is essential for maintaining malaria parasite cellular homeostasis and organelle biogenesis.
    Akancha Mishra, Suryansh Rajput, Pratik Narain Srivastava, H Shabeer Ali, Satish Mishra.
      Plasmodium parasites have a complex life cycle that transitions between mosquito and mammalian hosts, and undergo continuous cellular remodeling to adapt to various drastic environments. Following hepatocyte invasion, the parasite discards superfluous organelles for intracellular replication, and the remnant organelles undergo extensive branching and mature into hepatic merozoites. Autophagy is a ubiquitous eukaryotic process that permits the recycling of intracellular components. Here, we show that the Plasmodium berghei autophagy-related E1-like enzyme Atg7 is expressed in the blood, sporozoites, and liver stages, localized to the parasite cytosol, and is essential for the localization of Atg8 on the membrane and the development of parasite blood and liver forms. We found that depleting Atg7 abolishes Atg8 lipidation, exocytosis of micronemes, organelle biogenesis, and the formation of merozoites during liver-stage development. Overall, this study establishes the essential functions of Atg7 in Plasmodium blood and liver stages, and highlights its role in maintaining the parasite's cellular homeostasis and organelle biogenesis.IMPORTANCEThe malaria life cycle involves two hosts, mosquitoes and vertebrates. Plasmodium parasites undergo complex intracellular and extracellular stages during this transition. Here, we report that an autophagy-related E1-like enzyme Atg7 is required to conjugate Atg8 on the apicoplast membrane. Atg7 depletion in Plasmodium berghei resulted in the loss of Atg8 lipidation and multiple defects like clearance of micronemes, organelle biogenesis, and maturation of hepatic schizonts during liver-stage development. The essentiality of Plasmodium Atg7 in blood and liver stages suggests it is a prospective target for developing autophagy-specific inhibitors. These results highlight the importance of autophagy in malaria parasite development.
    Keywords:  Atg7; Atg8; ER; Plasmodium; apicoplast; autophagy; liver stage; malaria; sporozoites
    DOI:  https://doi.org/10.1128/mbio.02735-24
  17. Virology. 2024 Dec 17. pii: S0042-6822(24)00387-8. [Epub ahead of print]603 110363
    Novel exploitation of autophagy by tombusviruses.
    Peter D Nagy, Judit Pogany, Yuanrong Kang.
      Positive-strand (+)RNA viruses are major pathogens of humans, animals and plants. This review summarizes the complex interplay between the host autophagy pathway and Tomato bushy stunt virus (TBSV) replication. Recent discoveries with TBSV have revealed virus-driven exploitation of autophagy in multiple ways that contributes to the unique phospholipid composition of viral replication organellar (VROs) membranes. Viral replication protein-driven subversion of phagophore membranes, recruitment of ATG2 bulk lipid transfer protein to enrich phosphatidylethanolamine and phosphatidylserine in VROs, recruitment of VPS34 PI3K to produce PI(3)P; and ATG11-facilitated formation of stable viral membrane contact sites contributes to VRO membrane proliferation. Recruitment of autophagy core proteins to vir-NBR1 bodies within vir-condensates associated with VROs results in dampened antiviral degradation by autophagy. Overall, TBSV intricate interplay with the autophagy machinery highlights the importance of lipid dynamics in viral life cycles and points toward potential directions for therapeutic intervention.
    Keywords:  Dependency factor; Host factor; Lipid transfer protein; Nicotiana benthamiana; Phospholipids; Replication; Tomato bushy stunt virus; Virus-host interaction; Yeast
    DOI:  https://doi.org/10.1016/j.virol.2024.110363
  18. Cell Rep. 2024 Dec 20. pii: S2211-1247(24)01466-9. [Epub ahead of print]44(1): 115115
    Pressure to evade cell-autonomous innate sensing reveals interplay between mitophagy, IFN signaling, and SARS-CoV-2 evolution.
    Jae Seung Lee, Mark Dittmar, Jesse Miller, Minghua Li, Kasirajan Ayyanathan, Max Ferretti, Jesse Hulahan, Kanupriya Whig, Zienab Etwebi, Trevor Griesman, David C Schultz, Sara Cherry.
      SARS-CoV-2 emerged, and continues to evolve, to efficiently infect humans worldwide. SARS-CoV-2 evades early innate recognition, interferon signaling occurring only in bystander cells. How the virus continues to evolve in the face of innate responses has important consequences, but the pathways involved are incompletely understood. Here, we find that autophagy genes regulate innate immune signaling, impacting the basal set point of interferons and, thus, permissivity to infection. Mechanistically, autophagy (mitophagy) genes negatively regulate MAVS, and this low basal level of MAVS is efficiently antagonized by SARS-CoV-2 ORF9b, blocking interferon activation in infected cells. However, loss of autophagy increased MAVS and overcomes ORF9b-mediated antagonism. This has driven the evolution of SARS-CoV-2 to express more ORF9b, allowing SARS-CoV-2 to replicate under conditions of increased MAVS signaling. Altogether, we find a critical role of mitophagy in the regulation of innate immunity and uncover an evolutionary trajectory of SARS-CoV-2 ORF9b to overcome host defenses.
    Keywords:  CP: Immunology; CP: Microbiology; ORF9b; SARS-CoV-2; autophagy; cell-autonomous interferon response; coronavirus; innate immune signaling; mitophagy; viral evolution
    DOI:  https://doi.org/10.1016/j.celrep.2024.115115
  19. bioRxiv. 2024 Dec 12. pii: 2024.12.11.627871. [Epub ahead of print]
    STAT1 Promotes PD-L1 Activation and Tumor Growth in Lymphangioleiomyomatosis.
    Tasnim Olatoke, Erik Y Zhang, Andrew Wagner, Quan He, Siru Li, Aristotelis Astreinidis, Francis X McCormack, Yan Xu, Jane J Yu.
      Lymphangioleiomyomatosis (LAM) is a cystic lung disease that primarily affects women. LAM is caused by the invasion of metastatic smooth muscle-like cells into the lung parenchyma, leading to abnormal cell proliferation, lung remodeling and progressive respiratory failure. LAM cells have TSC gene mutations, which occur sporadically or in people with Tuberous Sclerosis Complex. Although it is known that hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1) due to TSC2 gene mutations contributes to aberrant cell growth in LAM lung, tumor origin and invasive mechanism remain unclear. To determine molecular drivers responsible for aberrant LAM cell growth, we performed integrative single-cell transcriptomic analysis and predicted that STAT1 interacts with Pre-B cell leukemia transcription factor (PBX1) to regulate LAM cell survival. Here, we show activation of STAT1 and STAT3 proteins in TSC2-deficient LAM models. Fludarabine, a potent STAT1 inhibitor, induced the death of TSC2-deficient cells, increased caspase-3 cleavage, and phosphorylation of necroptosis marker RIP1. Fludarabine treatment impeded lung colonization of TSC2-deficient cells and uterine tumor progression, associated with reduced percentage of PCNA-positive cells in vivo. Interestingly, IFN-γ treatment increased STAT1 phosphorylation and PD-L1 expression, indicating that STAT1 aids TSC2-deficient tumor cells in evading immune surveillance in LAM. Our findings indicate that STAT1 signaling is critical for LAM cell survival and could be targeted to treat LAM and other mTORC1 hyperactive tumors.
    DOI:  https://doi.org/10.1101/2024.12.11.627871
  20. Dev Cell. 2024 Dec 21. pii: S1534-5807(24)00727-5. [Epub ahead of print]
    TFEB triggers a matrix degradation and invasion program in triple-negative breast cancer cells upon mTORC1 repression.
    David Remy, Sandra Antoine-Bally, Sophie de Toqueville, Célia Jolly, Anne-Sophie Macé, Gabriel Champenois, Fariba Nemati, Isabel Brito, Virginie Raynal, Amulya Priya, Adèle Berlioz, Ahmed Dahmani, André Nicolas, Didier Meseure, Elisabetta Marangoni, Philippe Chavrier.
      The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway is frequently hyperactivated in triple-negative breast cancers (TNBCs) associated with poor prognosis and is a therapeutic target in breast cancer management. Here, we describe the effects of repression of mTOR-containing complex 1 (mTORC1) through knockdown of several key mTORC1 components or with mTOR inhibitors used in cancer therapy. mTORC1 repression results in an ∼10-fold increase in extracellular matrix proteolytic degradation. Repression in several TNBC models, including in patient-derived xenografts (PDXs), induces nuclear translocation of transcription factor EB (TFEB), which drives a transcriptional program that controls endolysosome function and exocytosis. This response triggers a surge in endolysosomal recycling and the surface exposure of membrane type 1 matrix metalloproteinase (MT1-MMP) associated with invadopodia hyperfunctionality. Furthermore, repression of mTORC1 results in a basal-like breast cancer cell phenotype and disruption of ductal carcinoma in situ (DCIS)-like organization in a tumor xenograft model. Altogether, our data call for revaluation of mTOR inhibitors in breast cancer therapy.
    Keywords:  MT1-MMP; TFEB; extracellular matrix; invadopodia; mTOR inhibitors; mTORC1; patient-derived xenograft; triple-negative breast cancer; tumor invasion
    DOI:  https://doi.org/10.1016/j.devcel.2024.12.005
  21. Eur J Med Chem. 2024 Dec 17. pii: S0223-5234(24)01062-6. [Epub ahead of print]284 117180
    Synthesis and structural modification of the natural product Ivesinol to discover novel autophagy activators.
    Zhi-Peng Wang, Wenxin You, Jie Peng, Biao Xu, Xiaohong Yang, Wanyan Tang, Yun He, Aimin Yang, Chao Yu, Weiqi Nian.
      Autophagy is a lysosome-dependent cellular degradation pathway that responds to a variety of environmental and cellular stresses, which is defective in aging and age-related diseases, therefore, targeting autophagy with small-molecule activators has potential therapeutic benefits. In this study, we successfully completed the first total synthesis of Ivesinol, an identified antibacterial natural product, and efficiently constructed a library of its analogs. To measure the effect of Ivesinol analogs on autophagic activity, we performed cell imaging-based screening approach, and observed that several Ivesinol analogs exhibited potent autophagy-regulating activity. Specifically, the derivative B2 significantly activated autophagy activity in concentration- and time-dependent manners, and even outperformed the commonly used activator Torin1 in activating autophagy in MCF-7 cells at 0.5 μM. Bioinformatics analysis showed that B2 treatment significantly impacted ubiquitin mediated proteolysis and AMPK signaling pathway, with functionally related gene sets displaying strong correlations. Based on these findings, we proposed that B2 activates autophagy by mechanisms involved in downregulation of key HSP70 family members, activation of the UPR, and ultimately leading to autophagy. In conclusion, we suggest that B2 could be a promising and valuable autophagy activator with significant potential for further development.
    Keywords:  Autophagy activator; Ivesinol; Natural product; Total synthesis
    DOI:  https://doi.org/10.1016/j.ejmech.2024.117180
  22. Brain Res. 2024 Dec 20. pii: S0006-8993(24)00669-3. [Epub ahead of print]1850 149414
    Cannabidiol induces autophagy via CB1 receptor and reduces α-synuclein cytosolic levels.
    Adolfo G Erustes, Vanessa C Abílio, Claudia Bincoletto, Mauro Piacentini, Gustavo J S Pereira, Soraya S Smaili.
      Numerous studies have explored the role of cannabinoids in neurological conditions, chronic pain and neurodegenerative diseases. Restoring autophagy has been proposed as a potential target for the treatment of neurodegenerative diseases. In our study, we used a neuroblastoma cell line that overexpresses wild-type α-synuclein to investigate the effects of cannabidiol on autophagy modulation and reduction in the level of cytosolic α-synuclein. Our results demonstrated that cannabidiol enhances the accumulation of LC3-II- and GFP-LC3-positive vesicles, which indicates an increase in autophagic flux. In addition, cannabidiol-treated cells showed a reduction in cytosolic α-synuclein levels. These effects were inhibited when the cells were treated with a CB1 receptor-selective antagonist, which indicates that the biological effects of cannabidiol are mediated via its interaction with CB1 receptor. Additionally, we also observed that cannabinoid compounds induce autophagy and α-synuclein degradation after they interact with the CB1 receptor. In summary, our data suggest that cannabidiol induces autophagy and reduces cytosolic α-synuclein levels. These biological effects are mediated preferentially through the interaction of cannabidiol with CB1 receptors, and therefore, cannabinoid compounds that act selectively on this receptor could represent a new approach for autophagy modulation and degradation of protein aggregates.
    Keywords:  Autophagy; Cannabidiol; Cannabinoid receptors; Cannabis sp.; α-synuclein, Parkinson’s disease
    DOI:  https://doi.org/10.1016/j.brainres.2024.149414
  23. J Biol Chem. 2024 Dec 18. pii: S0021-9258(24)02597-3. [Epub ahead of print] 108095
    Inositol phosphates dynamically enhance stability, solubility and catalytic activity of mTOR.
    Lucia E Rameh, John D York, Raymond D Blind.
      Mechanistic Target of Rapamycin (mTOR) binds the small metabolite inositol hexakisphosphate (IP6) as shown in structures of mTOR, however it remains unclear if IP6, or any other inositol phosphate species, function as an integral structural element(s) or catalytic regulator(s) of mTOR. Here, we show that multiple, exogenously added inositol phosphate species can enhance the ability of mTOR and mTORC1 to phosphorylate itself and peptide substrates in in vitro kinase reactions, with the higher order phosphorylated species being more potent (IP6=IP5>IP4>>IP3). IP6 increased the VMAX and decreased the apparent KM of mTOR for ATP. Although IP6 did not affect the apparent KM of mTORC1 for ATP, monitoring kinase activity over longer reaction times showed increased product formation, suggesting inositol phosphates stabilize an active form of mTORC1 in vitro. The effects of IP6 on mTOR were reversible, suggesting IP6 bound to mTOR can be exchanged dynamically with the free solvent. Interestingly, we also observed that IP6 could alter mTOR electrophoretic mobility under denaturing conditions and its solubility in the presence of manganese. Together, these data suggest for the first time that multiple inositol phosphate species (IP6, IP5, IP4 and to a lesser extent IP3) can dynamically regulate mTOR and mTORC1 by promoting a stable, more soluble active-state of the kinase. Our data suggest that studies of the dynamics of inositol phosphate regulation of mTOR in cells are well justified.
    Keywords:  enzyme kinetics; inositol hexakisphosphate; inositol phosphates; kinase; kinetics; mTOR; mTOR complex; signaling
    DOI:  https://doi.org/10.1016/j.jbc.2024.108095
  24. Cell Rep. 2024 Dec 20. pii: S2211-1247(24)01382-2. [Epub ahead of print]44(1): 115031
    The di-leucine motif in the host defense peptide LL-37 is essential for initiation of autophagy in human macrophages.
    Rokeya Sultana Rekha, Avinash Padhi, Nicolai Frengen, Julia Hauenstein, Ákos Végvári, Birgitta Agerberth, Robert Månsson, Guðmundur H Guðmundsson, Peter Bergman.
      The human cathelicidin peptide LL-37 induces autophagy in human macrophages. Different post-translational modifications (PTMs) such as citrullination, acetylation, and formylation impact LL-37, yet their effect on autophagy remains unknown. Thus, we set out to study how the cellular source could impact PTM of LL-37 and subsequent effects on autophagy initiation. Neutrophil-released LL-37 failed to induce autophagy, unlike macrophage-released LL-37. Mass spectrometry analysis revealed modifications on neutrophil-derived LL-37, especially at the N terminus, while macrophage-derived LL-37 remained mostly native. Native LL-37 initiated autophagy, while formylated and acetylated versions did not. Truncated peptides lacking the N-terminal di-leucine motif or substituted with di-alanine did not initiate autophagy. Native LL-37 failed to initiate autophagy in macrophages with genetic inactivation of dipeptidyl peptidase-1. An intact N-terminal di-leucine motif in LL-37 was crucial for autophagy initiation, and modifications abrogated the effects. This pathway presents a novel way to regulate the effects of LL-37 in infection or inflammation.
    Keywords:  CP: Immunology; LL-37; Papillon Lefevre syndrome; cathelicidin; dipeptidyl peptidase 1; lysosomal damage; macrophages; post-translational modification
    DOI:  https://doi.org/10.1016/j.celrep.2024.115031
  25. Cell Rep. 2024 Dec 21. pii: S2211-1247(24)01445-1. [Epub ahead of print]44(1): 115094
    The N-degron pathway mediates the autophagic degradation of cytosolic mitochondrial DNA during sterile innate immune responses.
    Chan Hoon Jung, Yoon Jee Lee, Eun Hye Cho, Gee Eun Lee, Sung Tae Kim, Ki Sa Sung, Daeho Kim, Dong Hyun Kim, Yeon Sung Son, Jin-Hyun Ahn, Dohyun Han, Yong Tae Kwon.
      The human body reacts to tissue damage by generating damage-associated molecular patterns (DAMPs) that activate sterile immune responses. To date, little is known about how DAMPs are removed to avoid excessive immune responses. Here, we show that proteasomal dysfunction induces the release of mitochondrial DNA (mtDNA) as a DAMP that activates the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon gene (STING) pathway and is subsequently degraded through the N-degron pathway. In the resolution phase of sterile immune responses, DNA-dependent protein kinase (DNA-PK) senses cytosolic mtDNA and activates N-terminal (Nt-) arginylation by ATE1 R-transferases. The substrates of Nt-arginylation include the molecular chaperone BiP/GRP78 retrotranslocated from the endoplasmic reticulum (ER). R-BiP, the Nt-arginylated species of BiP, is associated with cytosolic mtDNA to accelerate its targeting to autophagic membranes for lysosomal degradation. Thus, cytosolic mtDNA activates the N-degron pathway to facilitate its own degradation and form a negative feedback loop, by which the cell can turn off sterile immune responses at the right time.
    Keywords:  ATE1; CP: Immunology; DNA-PK; KU70; R-BiP; autophagy; mitochondrial DNA; proteasomal dysfunction; sterile immune response; the N-degron pathway; type I interferon
    DOI:  https://doi.org/10.1016/j.celrep.2024.115094
  26. Autophagy Rep. 2024 ;pii: 2285214. [Epub ahead of print]3(1):
    Autophagy deficiency protects against ocular hypertension and glaucoma.
    Angela Dixon, Myoung Sup Shim, April Nettesheim, Aislyn Coyne, Chien-Chia Su, Haiyan Gong, Paloma B Liton.
      Glaucoma encompasses a spectrum of disorders characterized by the chronic degeneration of retinal ganglion cell (RGC) axons and the progressive loss of RGCs, resulting in visual impairment. In this study, we investigated the effect of autophagy deficiency on two glaucoma hypertensive models, the DBA/2J spontaneous glaucoma model, and the TGFβ2 (transforming growth factor β2) chronic ocular hypertensive model. For this, we used the Atg4b -/- and DBA/2J-Atg4b -/- mice, this latter generated in our laboratory via CRISPR/Cas9 technology, which display impaired autophagy. In contrast to littermate WT controls, mice deficient in Atg4B, did not develop glaucomatous elevation of intraocular pressure (IOP). Moreover, autophagy deficiency protected against RGC death and optic nerve atrophy. Collectively, our data supports a pathogenic role of autophagy in the context of ocular hypertension and glaucoma.
    Keywords:  Autophagy; DBA/2J; RGC; glaucoma; ocular hypertension; optic nerve
    DOI:  https://doi.org/10.1080/27694127.2023.2285214
  27. Chembiochem. 2024 Dec 23. e202400887
    NOVEL APPROACHES IN TARGETING MEMBRANE AND SECRETED PROTEINS FOR LYSOSOMAL DEGRADATION.
    Mohamed Eldeeb, Grace Hohman, Michael Shahid.
      Protein degradation is pivotal for all biochemical aspects of cellular function. In mammalian cells, protein degradation is mediated mainly by the ubiquitin proteasome system (UPS) and the autophagic-lysosomal system (ALS). Over the last two decades, different types of targeted protein degradation approaches have been developed including proteolysis targeting chimeras (PROTACs) and lysosome targeting chimeras (LYTACs), which employ the UPS to degrade intracellular proteins and the ALS to degrade extracellular and membrane proteins respectively. Nevertheless, current targeted membrane protein degradation approaches face some inherent challenges including limited target protein degradation efficacy and cell type specific applicability. Herein, we highlight a recent development of novel targeted membrane protein degradation modalities that exhibit wide-applicability and high protein degradation efficiency. These novel membrane protein degraders hold tremendous promise as new pharmacological and biochemical tools in targeting membrane and secretory proteins for lysosomal degradation.
    Keywords:  Lysosome; Protein degradation; Proteolysis; autophagy; membrane proteins
    DOI:  https://doi.org/10.1002/cbic.202400887
  28. J Biol Chem. 2024 Dec 18. pii: S0021-9258(24)02595-X. [Epub ahead of print] 108093
    The steroid hormone 20-hydroxyecdysone inhibits RAPTOR expression by repressing Hox gene transcription to induce autophagy.
    Tianwen Liu, Can Tian, Yanxue Li, Jinxing Wang, Xiaofan Zhao.
      Regulatory-associated protein of TOR (RAPTOR) is a key component of TOR complex 1 (TORC1), which determines the lysosomal location and substrate recruitment of TORC1 to promote cell growth and prevent autophagy. Many studies in recent decades have focused on the posttranslational modification of RAPTOR; however, little is known about the transcriptional regulatory mechanism of Raptor. Using the lepidopteran insect cotton bollworm (Helicoverpa armigera) as model, we reveal the transcriptional regulatory mechanism of Raptor. RAPTOR has different expression profiles in tissues during development from larva to late pupa, with high expression levels at larval feeding stages but low expression levels during metamorphic stages in the epidermis, midgut and fat body. RAPTOR is localized in the larval midgut at the feeding stage but is localized in the imaginal midgut at metamorphic stages. The knockdown of Raptor at the feeding stage results in the production of small pupae, early autophagy of the midgut and fat body, and decreased cell proliferation. However, Raptor knockdown at metamorphic stage represses the development of the epidermis, adult fat body and brain. 20-Hydroxecdysone (20E) represses Raptor transcription. Homeobox (HOX) proteins promote Raptor transcription by binding to its promoter. Overexpression of HOX proteins represses ATG expression and autophagy but increases cell proliferation. 20E represses Hox genes transcription via its nuclear receptor EcR binding to its promoters. Together, these findings suggest that HOX proteins are positive regulators that upregulate Raptor transcription. 20E represses Hox gene transcription, thus repressing Raptor expression, resulting in autophagy and repressing cell proliferation during metamorphosis.
    Keywords:  20-hydroxyecdysone; RAPTOR; autophagy; cell proliferation; homeobox
    DOI:  https://doi.org/10.1016/j.jbc.2024.108093
  29. Neuro Oncol. 2024 Dec 28. pii: noae280. [Epub ahead of print]
    Autophagy Modulates Glioblastoma Cell Sensitivity to Selinexor-mediated XPO1 inhibition.
    Yongjian Tang, Lisa Sprinzen, Yukinori Terada, Karrie M Kiang, Chuntao Li, Yu Zeng, Fangkun Liu, Hongshu Zhou, Xisong Liang, Jianzhong Zhang, Russell O Pieper, Bo Chen, Liyang Zhang.
       BACKGROUND: Selinexor is a selective inhibitor of exportin-1 (XPO1), a key mediator of the nucleocytoplasmic transport for molecules critical to tumor cell survival. Selinexor's lethality is generally associated with the induction of apoptosis, and in some cases, with autophagy-induced apoptosis. We performed this study to determine Selinexor's action in glioblastoma (GBM) cells, which are notoriously resistant to apoptosis.
    METHODS: Patient-derived GBM cells were treated with Selinexor, and drug response and autophagy levels were monitored. Homozygous C528S XPO1 mutant GBM43 cells were generated by CRISPR/Cas9 editing. Single Selinexor or combination treatment with autophagy inhibitors was evaluated. In addition, bulk-tissue, single-cell, and spatial transcriptome were analyzed, and molecular docking was performed.
    RESULTS: Although all cell lines exhibited a dose- and time-dependent reduction of cell viability, the most profound molecular response to Selinexor was induction of autophagy instead of apoptosis. Selinexor-induced autophagy was an on-target consequence of XPO1 inhibition, and could be mitigated by expression of a mutant, Selinexor-resistant form of XPO1, and Selinexor-induced autophagy was related at least in part to nuclear trapping of the transcription factor TFEB. Furthermore, genetic or pharmacologic suppression of autophagy sensitized the cells to Selinexor-induced toxicity in association with the induction of apoptosis. Finally, in intracranial PDX studies, the combination of Selinexor with the autophagy inhibitor chloroquine significantly impeded tumor growth and extended mouse survival relative to single-agent treatment.
    CONCLUSION: These results suggest that activation of autophagy confers a protective mechanism against Selinexor in GBM cells, and that the combination of Selinexor with autophagy inhibitors may serve as a viable means to enhance Selinexor-induced cell death.
    Keywords:  Selinexor; XPO1; autophagy; glioma; nuclear export
    DOI:  https://doi.org/10.1093/neuonc/noae280
  30. Front Cell Dev Biol. 2024 ;12 1499457
    The pro-fibrotic role of autophagy in renal intrinsic cells: mechanisms and therapeutic potential in chronic kidney disease.
    Ying-Ying Zhang, Xiao-Tao Zhou, Geng-Zhen Huang, Wen-Jun Liao, Xian Chen, Yue-Rong Ma.
      Chronic kidney disease (CKD) represents a significant global public health burden, affecting over 10% of the world's population. Its high morbidity, multifactorial complications, and substantial mortality impose significant burdens on healthcare systems and patients, necessitating considerable investment in healthcare resources. Renal fibrosis (RF) is a key pathological feature and driver of CKD progression. Extensive research indicates that autophagy participates in the complete pathogenesis of RF. Under physiological conditions, autophagy is essential for maintaining renal cellular homeostasis. However, under pathological conditions, perhaps aberrant and sustained activation of autophagy contributes to oxidative stress, apoptosis, inflammation, etc. Ultimately, they accelerate the development of RF. The role of autophagy in RF is currently controversial. This review investigates the molecular mechanisms by which intrinsic renal cell autophagy contributes to RF across diverse disease models, suggesting that autophagy and its associated regulatory pathways represent potential diagnostic and therapeutic targets for CKD.
    Keywords:  autophagy; chronic kidney disease; mechanism; renal fibrosis; therapeutic targets
    DOI:  https://doi.org/10.3389/fcell.2024.1499457
  31. iScience. 2024 Dec 20. 27(12): 111447
    Hyperaminoacidemia from interrupted glucagon signaling increases pancreatic acinar cell proliferation and size via mTORC1 and YAP pathways.
    Chunhua Dai, Yue Zhang, Yulong Gong, Amber Bradley, Zihan Tang, Katelyn Sellick, Shristi Shrestha, Erick Spears, Brittney A Covington, Jade Stanley, Regina Jenkins, Tiffany M Richardson, Rebekah A Brantley, Katie Coate, Diane C Saunders, Jordan J Wright, Marcela Brissova, E Danielle Dean, Alvin C Powers, Wenbiao Chen.
      Increased blood amino acid levels (hyperaminoacidemia) stimulate pancreas expansion by unclear mechanisms. Here, by genetic and pharmacological disruption of glucagon receptor (GCGR) in mice and zebrafish, we found that the ensuing hyperaminoacidemia promotes pancreatic acinar cell proliferation and cell hypertrophy, which can be mitigated by a low protein diet in mice. In addition to mammalian target of rapamycin complex 1 (mTORC1) signaling, acinar cell proliferation required slc38a5, the most highly expressed amino acid transporter gene in both species. Transcriptomics data revealed the activation signature of yes-associated protein (YAP) in acinar cells of mice with hyperaminoacidemia, consistent with the observed increase in YAP-expressing acinar cells. Yap1 activation also occurred in acinar cells in gcgr-/- zebrafish, which was reversed by rapamycin. Knocking down yap1 in gcgr-/- zebrafish decreased mTORC1 activity and acinar cell proliferation and hypertrophy. Thus, the study discovered a previously unrecognized role of the YAP/Taz pathway in hyperaminoacidemia-induced acinar cell hypertrophy and hyperplasia.
    Keywords:  Biomolecules; Cell biology; Model organism; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2024.111447
  32. J Biomed Sci. 2024 Dec 23. 31(1): 105
    Regulating the regulators: long non-coding RNAs as autophagic controllers in chronic disease management.
    Aviral Kumar, Kenneth Chun-Hong Yap, Bandari BharathwajChetty, Juncheng Lyu, Mangala Hegde, Mohamed Abbas, Mohammed S Alqahtani, Soham Khadlikar, Ali Zarrabi, Arezoo Khosravi, Alan Prem Kumar, Ajaikumar B Kunnumakkara.
      The increasing prevalence of chronic diseases and their associated morbidities demands a deeper understanding of underlying mechanism and causative factors, with the hope of developing novel therapeutic strategies. Autophagy, a conserved biological process, involves the degradation of damaged organelles or protein aggregates to maintain cellular homeostasis. Disruption of this crucial process leads to increased genomic instability, accumulation of reactive oxygen species (ROS), decreased mitochondrial functions, and suppression of ubiquitination, leading to overall decline in quality of intracellular components. Such deregulation has been implicated in a wide range of pathological conditions such as cancer, cardiovascular, inflammatory, and neurological disorders. This review explores the role of long non-coding RNAs (lncRNAs) as modulators of transcriptional and post-transcriptional gene expression, regulating diverse physiological process like proliferation, development, immunity, and metabolism. Moreover, lncRNAs are known to sequester autophagy related microRNAs by functioning as competing endogenous RNAs (ceRNAs), thereby regulating this vital process. In the present review, we delineate the multitiered regulation of lncRNAs in the autophagic dysfunction of various pathological diseases. Moreover, by highlighting recent findings on the modulation of lncRNAs in different stages of autophagy, and the emerging clinical landscape that recognizes lncRNAs in disease diagnosis and therapy, this review highlights the potential of lncRNAs as biomarkers and therapeutic targets in clinical settings of different stages of autophagic process by regulating ATG and its target genes. This focus on lncRNAs could lead to breakthroughs in personalized medicine, offering new avenues for diagnosis and treatment of complex diseases.
    Keywords:  Autophagy; Chronic diseases; Clinical management; Long non-coding RNAs; MicroRNAs
    DOI:  https://doi.org/10.1186/s12929-024-01092-9
  33. Int J Biol Macromol. 2024 Dec 20. pii: S0141-8130(24)09868-4. [Epub ahead of print] 139057
    Regulation of autophagy and cellular signaling through non-histone protein methylation.
    Yongfen Bao, Yaoyao Ma, Wentao Huang, Yujie Bai, Siying Gao, Luyao Xiu, Yuyang Xie, Xinrong Wan, Shigang Shan, Chao Chen, Lihua Qu.
      Autophagy is a highly conserved catabolic pathway that is precisely regulated and plays a significant role in maintaining cellular metabolic balance and intracellular homeostasis. Abnormal autophagy is directly linked to the development of various diseases, particularly immune disorders, neurodegenerative conditions, and tumors. The precise regulation of proteins is crucial for proper cellular function, and post-translational modifications (PTMs) are key epigenetic mechanisms in the regulation of numerous biological processes. Multiple proteins undergo PTMs that influence autophagy regulation. Methylation modifications on non-histone lysine and arginine residues have been identified as common PTMs critical to various life processes. This paper focused on the regulatory effects of non-histone methylation modifications on autophagy, summarizing related research on signaling pathways involved in autophagy-related non-histone methylation, and discussing current challenges and clinical significance. Our review concludes that non-histone methylation plays a pivotal role in the regulation of autophagy and its associated signaling pathways. Targeting non-histone methylation offers a promising strategy for therapeutic interventions in diseases related to autophagy dysfunction, such as cancer and neurodegenerative disorders. These findings provide a theoretical basis for the development of non-histone-methylation-targeted drugs for clinical use.
    Keywords:  Arginine methylation; Autophagy; Lysine methylation; Non-histone; Post-translational modification; Signaling pathway
    DOI:  https://doi.org/10.1016/j.ijbiomac.2024.139057
  34. J Basic Microbiol. 2024 Dec 25. e2400603
    Autophagy Activated by Atg1 Interacts With Atg9 Promotes Biofilm Formation and Resistance of Candida albicans.
    Yun Huang, Shenjun Yu, Siqi Liu, Xiao Zhao, Xueyi Chen, Xin Wei.
      Autophagy regulates the development of Candida albicans (C. albicans) biofilms and their sensitivity to antifungals. Atg1, a serine/threonine protein kinase, recruits autophagy-related proteins for autophagosome formation. Atg9, the only transmembrane protein, is phosphorylated by Atg1 during autophagy. The specific roles of Atg1 and Atg9 in biofilm formation and resistance of C. albicans remain unclear. The study used RT-qPCR and Western blotting to assess the correlation between Atg1, Atg9 and biofilm formation, XTT reduction assays to evaluate biofilm formation and antifungal resistance, commercial kits to detect reactive oxygen species (ROS), mitochondrial membrane potential (MMP), and autophagy activity, transmission electron microscopy (TEM) to study the morphological changes, protein-protein interaction (PPI) analysis to analyze the interaction between Atg1 and Atg9. Results demonstrated that Atg1 and Atg9 were highly expressed in biofilms than planktonic cells. Biofilm formation, antifungal resistance, MMP and autophagy activity decreased and ROS increased in atg1Δ/Δ and atg9Δ/Δ. TORC1 inhibition with rapamycin rescued the reduced biofilm formation of atg1Δ/Δ and increased antifungal resistance of atg1Δ/Δ and atg9Δ/Δ. PPI analysis and TEM observation indicated that Atg1 interacted with Atg9, which was certified by RT-qPCR and Western blotting. This study suggested that Atg1 interacts with Atg9, activates the autophagy regulating the formation and sensitivity of C. albicans biofilms.
    Keywords:  Atg1; Atg9; Candida albicans; antifungal resistance; biofilm formation
    DOI:  https://doi.org/10.1002/jobm.202400603
  35. J Biol Chem. 2024 Dec 24. pii: S0021-9258(24)02628-0. [Epub ahead of print] 108126
    HSP90 stabilizes visual cycle retinol dehydrogenase 5 in the endoplasmic reticulum by inhibiting its degradation during autophagy.
    Xiaolin Jia, Yuxuan Wang, Mingjun Jiang, Dan-Dan Chen, Guohui Shang, Baixue Liu, Mengjiao Xue, Youfei Lang, Guiling Zhou, Yichen Dong, Fengyan Zhang, Xuyan Peng, Yanzhong Hu.
      Genetic mutations in retinol dehydrogenase 5 (RDH5), a rate-limiting enzyme of the visual cycle, is associated with nyctalopia, AMD and stationary congenital fundus albipunctatus (FA). A majority of these mutations impair RDH5 protein expression and intracellular localization. However, the regulatory mechanisms underlying RDH5 metabolism remain unclear. Here, we find that RDH5 undergoes degradation via the autophagy-lysosomal pathway, and its stability is regulated by interacting with HSP90. Deletion of HSP90α or HSP90β by CRISPR-Cas9 or inhibition of HSP90 activity by IPI-504 down-regulates RDH5 protein level, but not its mRNA expression, and this downregulation is restored by autophagic inhibitors (3-MA, CQ and Baf-A1) and siRNA of ATG5 or ATG7, but not by the proteasome inhibitor MG132. RDH5 can physically interact with SQSTM1/P62, and this interaction is enhanced in HSP90-deficient cells as well as in CQ-treated cells. Knocking down SQSTM1/P62 by siRNA induces RDH5 protein accumulation. Moreover, HSP90, RDH5 and Calnexin form a complex through intermolecular interactions. Deficiency of HSP90α or HSP90β dissociates RDH5 from Calnexin, and increases RDH5 translocation from the endoplasmic reticulum (ER) to the cytosol. Taken together, we propose that dysfunction of HSP90 leads to RDH5 release from Calnexin in the ER into the cytosol, where it binds to the adaptor SQSTM1/P62 for degradation in the autolysosome. RDH5 is a novel client candidate of HSP90. The downregulation of RDH5 may be responsible for the nyctalopia side effect noted in cancer patients receiving HSP90 inhibitor treatment currently in the clinical trial.
    Keywords:  autophagy and endoplasmic reticulum; calnexin; heat shock protein 90; retinol dehydrogenase 5; visual cycle
    DOI:  https://doi.org/10.1016/j.jbc.2024.108126
  36. Phytomedicine. 2024 Dec 18. pii: S0944-7113(24)00992-9. [Epub ahead of print]136 156337
    Sanguinarine suppresses oral squamous cell carcinoma progression by targeting the PKM2/TFEB aix to inhibit autophagic flux.
    Yong-Chun Peng, Zhi-Jing He, Lun-Cai Yin, Hui-Feng Pi, Yi Jiang, Ke-Yan Li, Li Tian, Jia Xie, Jian-Bo Zhang, Chen-Yao Li, Guan-Ying Feng, Kai Wang, Ding-Zhou Zhou, Xiao-Wei Xie, Zhi-Yuan Zhang, Teng-Fei Fan.
       BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the most common malignancies. However, there is no effective treatment for OSCC.
    PURPOSE: This study aimed to identify a natural compound with significant efficacy against OSCC and elucidate its primary mechanism of action.
    METHODS: An FDA-approved drug library and an MCE autophagy-related molecular compound library were screened through high-throughput screening to identify an effective natural compound against OSCC. The IC50 value of sanguinarine (Sang) in OSCC cells was determined using a CCK8 assay. Immunoblotting and immunofluorescence staining were used to assess the effect of Sang on autophagic flux in OSCC cells. Changes in the acidic lysosomal environment were evaluated using RFP-GFP-LC3B and LysoSensor Green DND-189. Furthermore, limited proteolysis-coupled mass spectrometry (LiP-MS) and virtual screening techniques were utilized to identify direct binding targets of Sang, which were subsequently validated by surface plasmon resonance (SPR) and microscale thermophoresis (MST). Molecular docking combined with molecular dynamics analysis identified the binding site between the target protein and Sang. In vitro and in vivo investigations with mutant plasmids confirmed this finding.
    RESULTS: Screening led to the identification of the naturally occurring autophagy modulator Sang as a potent inhibitor of OSCC progression. Moreover, Sang impaired lysosomal function through reducing lysosomal-associated membrane proteins, inhibiting lysosomal proteolysis, and altering the lysosomal pH. These effects contributed to defects in autophagic clearance and subsequently suppressed OSCC progression. Notably, Sang bound the phenylalanine 26 (F26) residue in pyruvate kinase M2 (PKM2) and inhibited PKM2 enzymatic activity, subsequently suppressing transcription factor EB (TFEB) expression to inhibit lysosomal function and blocking autophagic flux in OSCC cells.
    CONCLUSION: Our results demonstrate for the first time that Sang can suppress the PKM2/TFEB axis, and influence lysosomal function, thereby blocking autophagy and inhibiting the progression of OSCC, making it a promising therapeutic option for the treatment of OSCC.
    Keywords:  Autophagy; Oral squamous cell carcinoma (OSCC); Sanguinarine (Sang); Transcription factor EB (TFEB); pyruvate kinase M2 (PKM2)
    DOI:  https://doi.org/10.1016/j.phymed.2024.156337
  37. Autophagy. 2024 Dec 26.
    Regulation of N-Degron Recognin-Mediated Autophagy by the sars-cov-2 plpro ubiquitin deconjugase.
    Carlos Ayala Torres, Jiangnan Liu, Nico P Dantuma, Maria G Masucci.
      Viral proteases play critical roles in the host cell and immune remodeling that allows virus production. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) papain-like protease (PLpro) encoded in the large nonstructural protein 3 (Nsp3) also possesses isopeptidase activity with specificity for ubiquitin and ISG15 conjugates. Here, we interrogated the cellular interactome of the SARS-CoV-2 PLpro catalytic domain to gain insight into the putative substrates and cellular functions affected by the viral deubiquitinase. PLpro was detected in protein complexes that control multiple ubiquitin and ubiquitin-like (UbL) regulated signaling and effector pathways. By restricting the analysis to cytosolic and membrane-associated ubiquitin ligases, we found that PLpro interacts with N-recognin ubiquitin ligases and preferentially rescues type I N-degron substrates from proteasomal degradation. PLpro stabilized N-degron carrying HSPA5/BiP/GRP78, which is arginylated in the cytosol upon release from the endoplasmic reticulum (ER) upon ER stress and enhanced the Arg-HSPA5-driven oligomerization of the N-recognin SQSTM1/p62 that serves as a platform for phagophore assembly. However, while in addition to Arg-HSPA5 and SQSTM1/p62, ATG9A, WIPI2, and BECN1/Beclin 1 were detected in PLpro immunoprecipitates, other components of the autophagosome biogenesis machinery, such as the ATG12-ATG5-ATG16L1 complex and MAP1LC3/LC3 were absent, which correlated with proteolytic inactivation of ULK1, impaired production of lipidated LC3-II, and inhibition of reticulophagy. The findings highlight a novel mechanism by which, through the reprogramming of autophagy, the PLpro deubiquitinase may contribute to the remodeling of intracellular membranes in coronavirus-infected cells.
    Keywords:  HSPA5/BiP/GRP78; N-degron; Plpro; SARS-CoV-2; SQSTM1/p62; reticulophagy
    DOI:  https://doi.org/10.1080/15548627.2024.2442849
  38. iScience. 2024 Dec 20. 27(12): 111406
    Spns1-dependent endocardial lysosomal function drives valve morphogenesis through Notch1-signaling.
    Myra N Chávez, Prateek Arora, Marco Meer, Ines J Marques, Alexander Ernst, Rodrigo A Morales Castro, Nadia Mercader.
      Autophagy-lysosomal degradation is a conserved homeostatic process considered to be crucial for cardiac morphogenesis. However, both its cell specificity and functional role during heart development remain unclear. Here, we introduced zebrafish models to visualize autophagic vesicles in vivo and track their temporal and cellular localization in the larval heart. We observed a significant accumulation of autolysosomal and lysosomal vesicles in the atrioventricular and bulboventricular regions and their respective valves. We addressed the role of lysosomal degradation based on the Spinster homolog 1 (spns1) mutant (not really started, nrs). n rs larvae displayed morphological and functional cardiac defects, including abnormal endocardial organization, impaired valve formation and retrograde blood flow. Single-nuclear transcriptome analyses revealed endocardial-specific differences in lysosome-related genes and alterations of notch1-signalling. Endocardial-specific overexpression of spns1 and notch1 rescued features of valve formation and function. Altogether, our results reveal a cell-autonomous role of lysosomal processing during cardiac valve formation affecting notch1-signalling.
    Keywords:  Cell biology; Developmental biology; Model organism; Molecular biology; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2024.111406
  39. Transl Neurodegener. 2024 Dec 24. 13(1): 66
    Endosomal traffic disorders: a driving force behind neurodegenerative diseases.
    Jianru Dong, Weiwei Tong, Mingyan Liu, Mengyu Liu, Jinyue Liu, Xin Jin, Ju Chen, Huachao Jia, Menglin Gao, Minjie Wei, Ying Duan, Xin Zhong.
      Endosomes are crucial sites for intracellular material sorting and transportation. Endosomal transport is a critical process involved in the selective uptake, processing, and intracellular transport of substances. The equilibrium between endocytosis and circulation mediated by the endosome-centered transport pathway plays a significant role in cell homeostasis, signal transduction, and immune response. In recent years, there have been hints linking endosomal transport abnormalities to neurodegenerative diseases, including Alzheimer's disease. Nonetheless, the related mechanisms remain unclear. Here, we provide an overview of endosomal-centered transport pathways and highlight potential physiological processes regulated by these pathways, with a particular focus on the correlation of endosomal trafficking disorders with common pathological features of neurodegenerative diseases. Additionally, we summarize potential therapeutic agents targeting endosomal trafficking for the treatment of neurodegenerative diseases.
    Keywords:  Autophagy; DNA and RNA defects; Dysfunctional synapses and neural network; Endosomal traffic disorders; Glycolipid metabolism; Immunity; Neurodegenerative disease; Neuroinflammation; Pathological protein aggregation; Therapeutic drugs
    DOI:  https://doi.org/10.1186/s40035-024-00460-7
  40. Autophagy Rep. 2024 Dec 31. pii: 27694127.2024.2306766. [Epub ahead of print]3(1):
    TANGO2-related rhabdomyolysis symptoms are associated with abnormal autophagy functioning.
    Hortense de Calbiac, Sebastian Montealegre, Marjolène Straube, Solène Renault, Hugo Debruge, Loïc Chentout, Sorana Ciura, Apolline Imbard, Edouard Le Guillou, Anca Marian, Nicolas Goudin, Laure Caccavelli, Sylvie Fabrega, Arnaud Hubas, Peter van Endert, Nicolas Dupont, Julien Diana, Edor Kabashi, Pascale de Lonlay.
      Patients with pathogenic variants in the TANGO2 gene suffer from severe and recurrent rhabdomyolysis episodes precipitated by fasting. Autophagy functioning was analyzed in vitro, in primary skeletal myoblasts from TANGO2 patients, in basal and fasting conditions, and TANGO2 mutations were associated with reduced LC3-II levels upon starvation. In zebrafish larvae, tango2 inhibition induced locomotor defects which were exacerbated by exposure to atorvastatin, a compound known to cause rhabdomyolysis. Importantly, rhabdomyolysis features of tango2 knockdown were associated with autophagy and mitophagy defects in zebrafish. Calpeptin treatment was sufficient to rescue the locomotor properties thanks to its beneficial effect on autophagy functioning in zebrafish and to improve LC3-II levels in starved primary muscle cells of TANGO2 patients. Overall, we demonstrated that TANGO2 plays an important role in autophagy thus giving rise to new therapeutic perspectives in the prevention of RM life-threatening episodes.
    Keywords:  Autophagy; TANGO2; calpeptin; myoblasts; rhabdomyolysis; zebrafish
    DOI:  https://doi.org/10.1080/27694127.2024.2306766
  41. Cell Death Differ. 2024 Dec 23.
    Temporal dissection of the roles of Atg4 and ESCRT in autophagosome formation in yeast.
    Hui Li, Jing-Zhen Song, Cheng-Wen He, Meng-Xi Xie, Zheng-Tan Zhang, You Zhou, Xin-Jing Li, Li Cui, Jing Zhu, Qingqiu Gong, Zhiping Xie.
      Autophagosomes are formed by the enlargement and sealing of phagophores. This is accompanied by the recruitment and release of autophagy-related (Atg) proteins that function therein. Presently, the relationship among factors that act after the initial emergence of the phagophore is unclear. The endosomal sorting complexes required for transport (ESCRT) machinery and Atg4 are known to function in phagophore sealing and Atg8 release, respectively. Here we show that biochemically, both Atg4 and ESCRT promoted phagophore sealing. Intriguingly, Atg4-mediated release of Atg8 from the phagophore promoted phagophore sealing even in the absence of ESCRT. This sealing activity could be reconstituted in vitro using cell lysate and purified Atg4. To elucidate the temporal relationship between Atg4 and ESCRT, we charted a timeline of the autophagosome formation cycle based on the trafficking of Atg proteins and mapped the actions of Atg4 and ESCRT to specific stages. The temporal impact of Atg4-mediated release of Atg8 from phagophore was mapped to the stage after the assembly of phagophore assembly site (PAS) scaffold and phosphatidylinositol-3-kinase (PtdIns-3-K) complex; its retardation only extended the duration of Atg8 release stage, leading to delayed phagophore sealing and accumulation of multiple phagophores. The impacts of ESCRT were mapped to two stages. In addition to promoting phagophore sealing, it also dictates whether PtdIns-3-K recruitment can occur by controlling Atg9 trafficking, thereby determining the incidence of autophagosome formation. Accordingly, ESCRT deficiency led to a combination of reduced autophagosome frequency and extended autophagosome formation duration, manifesting as reduced autophagic flux but normal apparent Atg8 puncta number. Our study thus identifies Atg4-mediated Atg8 shedding as a novel membrane scission mechanism and reveals a new early-stage role for ESCRT in autophagy.
    DOI:  https://doi.org/10.1038/s41418-024-01438-8
  42. Elife. 2024 Dec 23. pii: RP86194. [Epub ahead of print]12
    Impairment of lipid homeostasis causes lysosomal accumulation of endogenous protein aggregates through ESCRT disruption.
    John Yong, Jacqueline E Villalta, Ngoc Vu, Matthew A Kukurugya, Niclas Olsson, Magdalena Preciado López, Julia R Lazzari-Dean, Kayley Hake, Fiona E McAllister, Bryson D Bennett, Calvin H Jan.
      Protein aggregation increases during aging and is a pathological hallmark of many age-related diseases. Protein homeostasis (proteostasis) depends on a core network of factors directly influencing protein production, folding, trafficking, and degradation. Cellular proteostasis also depends on the overall composition of the proteome and numerous environmental variables. Modulating this cellular proteostasis state can influence the stability of multiple endogenous proteins, yet the factors contributing to this state remain incompletely characterized. Here, we performed genome-wide CRISPRi screens to elucidate the modulators of proteostasis state in mammalian cells, using a fluorescent dye to monitor endogenous protein aggregation. These screens identified known components of the proteostasis network and uncovered a novel link between protein and lipid homeostasis. Increasing lipid uptake and/or disrupting lipid metabolism promotes the accumulation of sphingomyelins and cholesterol esters and drives the formation of detergent-insoluble protein aggregates at the lysosome. Proteome profiling of lysosomes revealed ESCRT accumulation, suggesting disruption of ESCRT disassembly, lysosomal membrane repair, and microautophagy. Lipid dysregulation leads to lysosomal membrane permeabilization but does not otherwise impact fundamental aspects of lysosomal and proteasomal functions. Together, these results demonstrate that lipid dysregulation disrupts ESCRT function and impairs proteostasis.
    Keywords:  CRISPR; ESCRT; aggregation; cell biology; human; lipid dysregulation; lysosome; proteostasis
    DOI:  https://doi.org/10.7554/eLife.86194
  43. bioRxiv. 2024 Dec 14. pii: 2024.12.13.628212. [Epub ahead of print]
    Leucine Aminopeptidase LyLAP enables lysosomal degradation of membrane proteins.
    Aakriti Jain, Isaac Heremans, Gilles Rademaker, Tyler C Detomasi, Grace A Hernandez, Justin Zhang, Suprit Gupta, Teresa von Linde, Mike Lange, Martina Spacci, Peter Rohweder, Dashiell Anderson, Y Rose Citron, James A Olzmann, David W Dawson, Charles S Craik, Guido Bommer, Rushika M Perera, Roberto Zoncu.
      Proteolysis of hydrophobic helices is required for complete breakdown of every transmembrane protein trafficked to the lysosome and sustains high rates of endocytosis. However, the lysosomal mechanisms for degrading hydrophobic domains remain unknown. Combining lysosomal proteomics with functional genomic data mining, we identify Lysosomal Leucine Aminopeptidase (LyLAP; formerly Phospholipase B Domain-Containing 1) as the hydrolase most tightly associated with elevated endocytic activity. Untargeted metabolomics and biochemical reconstitution demonstrate that LyLAP is not a phospholipase, but a processive monoaminopeptidase with strong preference for N-terminal leucine - an activity necessary and sufficient for breakdown of hydrophobic transmembrane domains. LyLAP is upregulated in pancreatic ductal adenocarcinoma (PDA), which relies on macropinocytosis for nutrient uptake, and its ablation led to buildup of undigested hydrophobic peptides, which compromised lysosomal membrane integrity and inhibited PDA cell growth. Thus, LyLAP enables lysosomal degradation of membrane proteins, and may represent a vulnerability in highly endocytic cancer cells.
    One sentence summary: LyLAP degrades transmembrane proteins to sustain high endocytosis and lysosomal membrane stability in pancreatic cancer.
    DOI:  https://doi.org/10.1101/2024.12.13.628212
  44. Int J Biol Macromol. 2024 Dec 22. pii: S0141-8130(24)09888-X. [Epub ahead of print] 139077
    The effect of molecular chaperone mediated autophagy on ApoE expression in retinal pigment epithelial cells: Molecular structure and protein action mechanism.
    Yifan Zhong, Yun Zhou, Zuoqian Jing, Xianjie Liu, Kaibo Yang, Guijie Ren, Haijie Chen, Siyu Jiang, Xue Shen, Xinying Du, Hongzhe Liu, Yunping Pan, Xiaoli Ma.
      Chaperone mediated autophagy (CMA) represents a specialized mechanism of lysosomal protein breakdown, playing a crucial role as a metabolic pathway that helps to regulate and sustain cellular and systemic physiological equilibrium. Within the CMA process, proteins that contain sequences similar to KFERQ are specifically identified by the heat shock cognate protein 70. These proteins are then chaperoned to the lysosomes for subsequent degradation, a process facilitated by the lysosome associated membrane protein 2A. This particular research employed bioinformatics techniques to systematically screen for potential substrates of CMA. ApoE has a KFERQ like motif, which may be a substrate for CMA. Under conditions of starvation, hypoxia, H2O2, PA, and NaIO3, the expression of the rate limiting factor LAMP2A in CMA and ApoE increased significantly (P < 0.05). Under conditions of NaIO3, the expression of CMA related gene mRNA increased significantly (P < 0.05). When we use lysosomal blocker CQ to inhibit CMA activity, the expression level of ApoE in retinal pigment epithelial cells increased, and the difference was statistically significant (P < 0.05). When we inhibit CMA, the accumulation of ApoE in retinal pigment epithelial cells increases and cell viability decreases. When we activate CMA, the accumulation of ApoE decreases and cell viability increases. In retinal pigment epithelial cells, the drusen associated protein ApoE can be degraded through the CMA pathway.
    Keywords:  Age related macular degeneration; ApoE; LAMP2A; Molecular chaperone autophagy
    DOI:  https://doi.org/10.1016/j.ijbiomac.2024.139077
  45. PNAS Nexus. 2025 Jan;4(1): pgae556
    Antibody-mediated clearance of an ER-resident aggregate that causes glaucoma.
    Minh Thu Ma, Ahlam N Qerqez, Kamisha R Hill, Laura R Azouz, Hannah A Youngblood, Shannon E Hill, Yemo Ku, Donna M Peters, Jennifer A Maynard, Raquel L Lieberman.
      Recombinant antibodies are a promising class of therapeutics to treat protein misfolding associated with neurodegenerative diseases, and several antibodies that inhibit aggregation are approved or in clinical trials to treat Alzheimer's disease. Here, we developed antibodies targeting the aggregation-prone β-propeller olfactomedin (OLF) domain of myocilin, variants of which comprise the strongest genetic link to glaucoma and cause early onset vision loss for several million individuals worldwide. Mutant myocilin aggregates intracellularly in the endoplasmic reticulum (ER). Subsequent ER stress causes cytotoxicity that hastens dysregulation of intraocular pressure, the primary risk factor for most forms of glaucoma. Our antibody discovery campaign yielded two recombinant antibodies: anti-OLF1 recognizes a linear epitope, while anti-OLF2 is selective for natively folded OLF and inhibits aggregation in vitro. By binding OLF, these antibodies engage autophagy/lysosomal degradation to promote degradation of two pathogenic mutant myocilins. This work demonstrates the potential for therapeutic antibodies to disrupt ER-localized protein aggregates by altering the fate of folding intermediates. This approach could be translated as a precision medicine to treat myocilin-associated glaucoma with in situ antibody expression. More generally, the study supports the approach of enhancing lysosomal degradation to treat proteostasis decline in glaucoma and other diseases.
    Keywords:  autophagy; molecular recognition; myocilin; protein misfolding; proteostasis
    DOI:  https://doi.org/10.1093/pnasnexus/pgae556
  46. Inflammation. 2024 Dec 27.
    TFEB Phase Separation Mediates the Amelioration Effect of Intermittent Fasting on Inflammatory Colitis.
    Xiujuan Zhao, Minghui Xia, Zhengxin Peng, Qiuyang Du, Yang Liu, Yu Xia, Panjing Lv, Xiao Zhang, Shijie Yuan, Xiaorong Xie, Jing Wang, Shuguo Sun, Xiang-Ping Yang, Ran He.
      Intermittent fasting (IF) has been shown to ameliorate inflammation including DSS-induced colitis. It is well known that autophagy can limit inflammation and TFEB is a master transcriptional factor that regulates the processes of autophagy. However, whether TFEB is involved in the regulation of IF-mediated amelioration of inflammation and its mechanism remained unclear. In this study, we found that IF ameliorated DSS-induced colitis and induced TFEB. Nutrition deprivation induced TFEB puncta formation, which processes the characteristics of liquid-liquid phase separation (LLPS) showed by fluorescence recovery after photobleaching (FRAP) assay and 1,6-hexanediol treatment. We found the 24-33 amino acids of Coiled-Coil (CC) domain located in N terminus is essential for TFEB phase separation. Deletion of 24-33 amino acids within the CC domain inhibited TFEB-mediated target gene expression. In addition, we found transcription co-activators, EP300 and MED1, co-localized with TFEB condensate to formed a transcriptional hub that promotes the efficient expression of target genes. More importantly, TFEB inhibitor with ability to suppress TFEB puncta formation abolished the IF-mediated amelioration of DSS colitis. Together, these findings revealed a critical role of TFEB phase separation in the regulation of its transcriptional activity and anti-inflammatory functions induced by IF.
    Keywords:  Autophagy; Colitis; Phase separation; Transcription factor EB; Transcriptional activity
    DOI:  https://doi.org/10.1007/s10753-024-02202-3
  47. Acta Neuropathol Commun. 2024 Dec 21. 12(1): 199
    CHMP2B promotes CHMP7 mediated nuclear pore complex injury in sporadic ALS.
    Olivia Keeley, Emma Mendoza, Druv Menon, Alyssa N Coyne.
      Alterations to the composition and function of neuronal nuclear pore complexes (NPCs) have been documented in multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis (ALS). Moreover, recent work has suggested that injury to the NPC can at least in part contribute to TDP-43 loss of function and mislocalization, a pathological hallmark of ALS and related neurodegenerative diseases. Collectively, these studies highlight a role for disruptions in NPC homeostasis and surveillance as a significant pathophysiologic event in neurodegeneration. The ESCRT-III nuclear surveillance pathway plays a critical role in the surveillance and maintenance of NPCs and the surrounding nuclear environment. Importantly, pathologic alterations to this pathway and its protein constituents have been implicated in neurodegenerative diseases such as ALS. However, the mechanism by which this pathway contributes to disease associated alterations in the NPC remains unknown. Here we use an induced pluripotent stem cell (iPSC) derived neuron (iPSN) model of sALS to demonstrate that CHMP7/ESCRT-III nuclear maintenance/surveillance is overactivated in sALS neurons. This overactivation is dependent upon the ESCRT-III protein CHMP2B and sustained CHMP2B dependent "activation" is sufficient to contribute to pathologic CHMP7 nuclear accumulation and POM121 reduction. Importantly, partial knockdown of CHMP2B was sufficient to alleviate NPC injury and downstream TDP-43 dysfunction in sALS neurons thereby highlighting CHMP2B as a potential therapeutic target in disease.
    DOI:  https://doi.org/10.1186/s40478-024-01916-7
  48. Cell Biol Int. 2024 Dec 20.
    Calcium level and autophagy defect in GNE mutants of rare neuromuscular disorder.
    Shweta Sharma, Fluencephila Mashangva, Jyoti Oswalia, Shagun Singh, Rohan Alag, Ranjana Arya.
      Rare genetic disorders are low in prevalence and hence there is little or no attention paid to them in the mainstream medical industry. One of the ultra-rare neuromuscular disorders, GNE myopathy is caused due to biallelic mutations in the bifunctional enzyme, GNE (UDP N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase). It catalyses the rate-limiting step in sialic acid biosynthesis. There are no effective treatments for GNE myopathy as the pathomechanism is poorly understood. Pathologically, the disease is characterized by the formation of rimmed vacuoles that contain aggregates of β-amyloid, tau, presenilin etc proteins in muscle biopsy samples. Accumulation of aggregated proteins in the cells may occur due to the failure of the regulated autophagy phenomenon. In the present study, we aim to understand the effect of GNE mutations on autophagy. The cytosolic calcium levels in GNE mutant cells were found to be altered in a GNE mutation-specific manner. The chaperone levels, such as HSP70 and PDI, as well as autophagic markers (LC3II/I ratios) were altered in the GNE mutant cells. Treatment with BAPTA-AM, calcium chelator, significantly restored cytosolic calcium levels in some GNE mutant cells as well as autophagic marker levels and autophagic punctae formation. The effect on the calcium signalling cascade involving CaMKKβ/AMPK/mTOR was studied in the GNE mutant cells. Our study provides insights into the role of calcium in autophagic vacuole formation in the cells with GNE mutations that will have significance towards understanding the pathomechanism of GNE Myopathy and drug target identification for the rare disease.
    Keywords:  GNE Myopathy; autophagy; calcium homeostasis; rare genetic disease
    DOI:  https://doi.org/10.1002/cbin.12268
  49. Genes Dis. 2025 Mar;12(2): 101260
    mTOR pathway: A key player in diabetic nephropathy progression and therapeutic targets.
    Jingxuan Shi, Xinze Liu, Yuanyuan Jiao, Jingwei Tian, Jiaqi An, Guming Zou, Li Zhuo.
      Diabetic nephropathy is a prevalent complication of diabetes and stands as the primary contributor to end-stage renal disease. The global prevalence of diabetic nephropathy is on the rise, however, due to its intricate pathogenesis, there is currently an absence of efficacious treatments to enhance renal prognosis in affected patients. The mammalian target of rapamycin (mTOR), a serine/threonine protease, assumes a pivotal role in cellular division, survival, apoptosis delay, and angiogenesis. It is implicated in diverse signaling pathways and has been observed to partake in the progression of diabetic nephropathy by inhibiting autophagy, promoting inflammation, and increasing oxidative stress. In this academic review, we have consolidated the understanding of the pathological mechanisms associated with four distinct resident renal cell types (podocytes, glomerular mesangial cells, renal tubular epithelial cells, and glomerular endothelial cells), as well as macrophages and T lymphocytes, within a diabetic environment. Additionally, we highlight the research progress in the treatment of diabetic nephropathy with drugs and various molecules interfering with the mTOR signaling pathway, providing a theoretical reference for the treatment and prevention of diabetic nephropathy.
    Keywords:  Bibliometrics; Diabetic nephropathy; Glomerular endothelial cell; Immune cell; Mesangial cell; Podocyte; Renal tubular epithelial cell; mTOR
    DOI:  https://doi.org/10.1016/j.gendis.2024.101260
  50. Contact (Thousand Oaks). 2024 Jan-Dec;7:7 25152564241308722
    The Vacuole Lipid Droplet Contact Site vCLIP.
    Duy Trong Vien Diep, Maria Bohnert.
      Lipid droplets frequently form contact sites with the membrane of the vacuole, the lysosome-like organelle in yeast. These vacuole lipid droplet (vCLIP) contact sites respond strongly to metabolic cues: while only a subset of lipid droplets is bound to the vacuole when nutrients are abundant, other metabolic states induce stronger contact site formation. Physical lipid droplet-vacuole binding is related to the process of lipophagy, a lipid droplet-specific form of microautophagy. The molecular basis for the formation and function of vCLIP contact sites remained enigmatic for a long time. This knowledge gap was filled when it was found that vCLIP is formed by the structurally related lipid droplet tether proteins Ldo16 and Ldo45, and the vacuolar surface protein Vac8. Ldo45 additionally recruits the phosphatidylinositol transfer protein Pdr16 to vCLIP. Here, we review the literature on the lipid droplet-vacuole contact site in light of the progress in our understanding of its molecular basis and discuss future directions for the field.
    Keywords:  LDAF1; Ldo16; Ldo45; Pdr16; Vac8; contact site; lipid droplet; lipophagy; lysosome; seipin; vCLIP; vacuole
    DOI:  https://doi.org/10.1177/25152564241308722
  51. Chem Biol Interact. 2024 Dec 24. pii: S0009-2797(24)00509-X. [Epub ahead of print] 111363
    Urolithin A attenuates Doxorubicin-induced cardiotoxicity by enhancing PINK1-regulated mitophagy via Ambra1.
    Xiaoyan Wang, Chao Ma, Keying Mi, Xinran Cao, Yinghua Tan, Haitao Yuan, Jun Ren, Xinyue Liang.
      Doxorubicin (Dox) is a widely used antineoplastics although its clinical usage is greatly limited by its cardiotoxicity. Several studies have depicted an essential role for dampened mitophagy and mitochondrial injury in Dox cardiotoxicity. However, preventative measure to alleviate Dox-evoked cardiotoxicity via targeting mitophagy and mitochondrial integrity remains elusive. Urolithin A (UA) is a newly identified mitophagy inducer with antioxidant and anti-apoptotic properties although its effect on Dox-induced cardiotoxicity is unknown. This study was designed to explore the effect of UA on Dox cardiotoxicity and mechanisms involved. Our results indicated that UA alleviated Dox-induced cardiac dysfunction exhibited by echocardiographic parameters and histological analyses, and partially relieved Dox-induced apoptosis in vitro and in vivo, and mitochondrial dysfunction including ΔΨm dissipation and ROS production in vitro. The ability of UA to facilitate restoration of mitophagy in mice and H9C2s underscored its advantageous effects, manifested as upregulation of mitophagy-related proteins, including p62, LC3, PINK1 and Parkin, as well as the co-location between LC3 and mitochondria. Incubation with 3MA nearly reversed the UA-evoked rise of mitophagy-related proteins, and inhibition of apoptosis. Given that knockdown of Ambra1 almost abolished UA-induced protective effect, the enhanced expression of Ambra1 owing to UA increased PINK1 levels by inhibiting its degradation via LONP1. Collectively, our results suggest that the cardioprotective properties of UA depend on the stimulation of PINK1-dependent mitophagy through promoting Ambra1 expression to inhibit PINK1 degradation by LONP1. This highlights UA's potential as a valuable treatment option and its importance in cardioprotective strategies against Dox-induced cardiotoxicity.
    Keywords:  Ambra1; cardiotoxicity; doxorubicin; mitophagy; urolithin A
    DOI:  https://doi.org/10.1016/j.cbi.2024.111363
  52. Brain Res. 2024 Dec 20. pii: S0006-8993(24)00671-1. [Epub ahead of print]1850 149416
    Inhibition of autophagy attenuates cognitive decline and mitochondrial dysfunction in an Alzheimer's disease mouse model with chronic cerebral hypoperfusion.
    Qin Yang, Tingting Chen, Shaofa Li, Chengmin Yang, Xingwu Zheng, Sanying Mao, Ning Liu, Shenglong Mo, Dengxing Li, Meiling Yang, Zhicheng Lu, Lina Tang, Xiaorui Huang, Xia Liu, Chongdong Jian, Yixia Yin, Jingwei Shang.
      This study aimed to investigate the impact of chronic cerebral hypoperfusion (CCH) on cognitive function, amyloid-β (Aβ) deposition, cellular autophagy, and mitochondrial dynamics in an Alzheimer's disease (AD) mouse model, and to evaluate the intervention effects of autophagy modulation on these outcomes. Utilizing the APP/PS1 mouse model combined with CCH, we assessed cognitive function, Aβ deposition, and the expression levels of relevant proteins through behavioral tests and immunohistochemical analysis. Our findings revealed pronounced cognitive deficits and increased Aβ deposition in the AD + CCH group mice, along with upregulation of mitochondrial fission proteins (Drp1, Fis1) and downregulation of mitochondrial fusion proteins (Opa1, Mfn1), indicating a shift towards mitochondrial fission and promoting cell apoptosis. Additionally, alterations were observed in the expression levels of cellular autophagy-related proteins (LC3-II, P62), which were reversed by treatment with autophagic inhibitor 3-methyladenine (3-MA). Furthermore, the expression of mitochondrial autophagy-related proteins PINK1 and Parkin was affected, with 3-MA alleviating this effect. In summary, our study elucidates the complex interplay among cognitive decline, increased Aβ deposition, and mitochondrial dysfunction in the AD + CCH model, and suggests that modulating autophagy could be a potential therapeutic strategy for treating the AD + CCH model.
    Keywords:  3-methyladenine; Alzheimer’s disease; Chronic cerebral hypoperfusion; Mitochondrial fission; Mitochondrial fusion
    DOI:  https://doi.org/10.1016/j.brainres.2024.149416
  53. Mol Neurobiol. 2024 Dec 23.
    Comparative Analysis of Human Brain RNA-seq Reveals the Combined Effects of Ferroptosis and Autophagy on Alzheimer's Disease in Multiple Brain Regions.
    Ke Ye, Xue Zhao, Lulu Liu, Fangliang Ge, Feifei Zheng, Zijie Liu, Mengjie Tian, Xinyu Han, Xu Gao, Qing Xia, Dayong Wang.
      Ferroptosis and autophagy are closely associated with Alzheimer's disease (AD). Elevated ferric ion levels can induce oxidative stress and chronic inflammatory responses, resulting in brain tissue damage and further neurological cell damage. Autophagy in Alzheimer's has a dual role. On one hand, it protects neurons by removing β-amyloid and cellular damage products caused by oxidative stress and inflammation. On the other hand, abnormal autophagy is linked to neuronal apoptosis and neurodegeneration. However, the intricate interplay between ferroptosis and autophagy in AD remains insufficiently explored. This study focuses on the roles of ferroptosis and autophagy in AD and their interconnection through bioinformatics analysis, shedding light on the disease. Ferroptosis and autophagy significantly correlate with the development and course of AD. Using PPI network analysis and unsupervised consistency clustering analysis, we uncovered a complex network of interactions between ferroptosis and autophagy during disease progression, demonstrating a significant congruence in their modification patterns. Functional analyses further demonstrated that ferroptosis and autophagy together affect the immunological status and synaptic regulation in hippocampal regions in patients with AD, which significantly impacts the start and progression of the disease.
    Keywords:  Alzheimer’s; Autophagy; Ferroptosis; Immune; Inflammation; Synapse
    DOI:  https://doi.org/10.1007/s12035-024-04642-2
  54. Cell Rep. 2024 Dec 24. pii: S2211-1247(24)01450-5. [Epub ahead of print]44(1): 115099
    The glial UDP-glycosyltransferase Ugt35b regulates longevity by maintaining lipid homeostasis in Drosophila.
    Lihong Sheng, Jianpeng Gao, Qingyuan Wei, Ye Gong, Zhi-Xiang Xu.
      Lipid droplets (LDs) are dynamic organelles essential for lipid storage and organismal survival. Studies have highlighted the importance of glial function in brain LD formation during aging; however, the genes and mechanisms involved remain elusive. Here, we found that Ugt35b, a member of the uridine diphosphate (UDP)-glycosyltransferases that catalyze the transfer of glycosyl groups to acceptors, is highly expressed in glia and crucial for Drosophila lifespan. By integrating multiomics data, we demonstrated that glial Ugt35b plays key roles in regulating glycerolipid and glycerophospholipid metabolism in the brain. Notably, we found that Ugt35b and Lsd-2 are co-expressed in glia and confirmed their protein interaction in vivo. Knockdown of Ugt35b significantly reduced LD formation by downregulating Lsd-2 expression, while overexpression of Lsd-2 partially rescued the shortened lifespan in glial Ugt35b RNAi flies. Our findings reveal the crucial role of glial Ugt35b in regulating LD formation to maintain brain lipid homeostasis and support Drosophila lifespan.
    Keywords:  CP: Metabolism; CP: Neuroscience; Drosophila; Ugt35b; glia; lifespan; lipid droplets
    DOI:  https://doi.org/10.1016/j.celrep.2024.115099
  55. Insect Mol Biol. 2024 Dec 20.
    Mechanism of starvation induced autophagy and apoptosis in the midgut of silkworm, Bombyx mori, based on calcium homeostasis.
    Jialu Cheng, Xueling Qin, Bing Han, Haoyi Gu, Hongbing Zou, Peiling Peng, Zhongxu Mao, Bing Li.
      Starvation can induce autophagy and apoptosis in intestinal cells. To elucidate the underlying mechanisms, we investigated autophagy and apoptosis in the midgut of the model insect, silkworm (Bombyx mori), focusing on calcium homeostasis. The results indicated that the body weight of silkworms decreased, along with damage to the morphology of their digestive tracts and midguts after starvation treatment. Additionally, mitochondrial swelling, autophagy and apoptosis were observable. Further investigation revealed that starvation upregulated the transcription of Ca2+ release channel-associated genes (e.g., BmIP3R, BmRyR) but suppressed the expression of Ca2+ efflux genes (BmPMCA), resulting in Ca2+ overload in midgut cells and subsequent upregulation of BmCalpain transcription. In addition, starvation increased the transcription of key autophagy genes (BmATG5, BmATG7, BmATG8) and the expression of the LC3-II protein. Upon prolonged starvation, the NtATG5 protein levels increased, a process that facilitated the transition from autophagy to apoptosis. These results indicate that Ca2+ overload activates the calpain-mediated apoptosis pathway and promotes apoptosis of midgut cells. The present study reveals the significant role that Ca2+ plays in the occurrence and transformation of autophagy and apoptosis induced by starvation treatment, thus providing a new research strategy for investigating the damage caused by starvation in biological organisms.
    Keywords:  Bombyx mori; autophagy and apoptosis; calcium homeostasis; starvation treatment
    DOI:  https://doi.org/10.1111/imb.12981
  56. J Clin Invest. 2024 Dec 26. pii: e183592. [Epub ahead of print]
    Tagless LysoIP for immunoaffinity enrichment of native lysosomes from clinical samples.
    Daniel Saarela, Pawel Lis, Sara Gomes, Raja S Nirujogi, Wentao Dong, Eshaan S Rawat, Sophie Glendinning, Karolina Zeneviciute, Enrico Bagnoli, Rotimi Fasimoye, Cindy Lin, Kwamina Nyame, Fanni A Boros, Friederike Zunke, Frederic Lamoliatte, Sadik Elshani, Matthew Jaconelli, Judith Jm Jans, Margriet A Huisman, Christian Posern, Lena M Westermann, Angela Schulz, Peter M van Hasselt, Dario R Alessi, Monther Abu-Remaileh, Esther M Sammler.
      Lysosomes are implicated in a wide spectrum of human diseases including monogenic lysosomal storage disorders (LSDs), age-associated neurodegeneration and cancer. Profiling lysosomal content using tag-based lysosomal immunoprecipitation (LysoTagIP) in cell and animal models has substantially moved the field forward, but studying lysosomal dysfunction in human patients remains challenging. Here, we report the development of the 'tagless LysoIP' method, designed to enable the rapid enrichment of lysosomes, via immunoprecipitation, using the endogenous integral lysosomal membrane protein TMEM192, directly from clinical samples and human cell lines (e.g., induced pluripotent stem cell derived neurons). Isolated lysosomes were intact and suitable for subsequent multimodal omics analyses. To validate our approach, we applied the tagless LysoIP to enrich lysosomes from peripheral blood mononuclear cells derived from fresh blood of healthy donors and patients with CLN3 disease, an autosomal recessive neurodegenerative LSD. Metabolic profiling of isolated lysosomes revealed massive accumulation of glycerophosphodiesters (GPDs) in patients' lysosomes. Interestingly, a patient with a milder phenotype and genotype displayed lower accumulation of lysosomal GPDs, consistent with their potential role as disease biomarkers. Altogether, the tagless LysoIP provides a framework to study native lysosomes from patient samples, identify disease biomarkers, and discover human-relevant disease mechanisms.
    Keywords:  Cell biology; Genetic diseases; Lysosomes; Neurodegeneration; Neuroscience
    DOI:  https://doi.org/10.1172/JCI183592
  57. Biochem Biophys Res Commun. 2024 Dec 19. pii: S0006-291X(24)01755-8. [Epub ahead of print]744 151219
    Nuclear ESCRT is involved in intranuclear protein quality control by micronucleophagy.
    Most Naoshia Tasnin, Yuka Takahashi, Tsuneyuki Takuma, Takashi Ushimaru.
      Intranuclear protein quality control (PQC) is critical for protein homeostasis (or proteostasis) in non-dividing cells including brain nerve cells, but its molecular mechanism remains unresolved. In nutrient-starved conditions, elimination of nucleolar proteins is critical for cell viability in budding yeast, providing a model system to study the mechanisms involved in intranuclear PQC. The nuclear-specific endosomal sorting complex required for transport (ESCRT) CHMP7/Chm7 is linked to neurodegenerative diseases, but its known role is limited. Here, we show a novel role of nuclear ESCRT in intranuclear PQC. Chm7 and its recruiter protein Heh1 were critical for micronucleophagic degradation of nucleolar proteins and for rDNA condensation and nucleolar remodeling, which is prerequisite for proper micronucleophagic degradation of nucleolar proteins. By contrast, Chm7 was dispensable for macronucleophagy. Finally, not only authentic ESCRT but also Chm7 was crucial for the survival of quiescent cells in prolonged nutrient-starved conditions. This study uncovered that nuclear ESCRT together with authentic ESCRT orchestrate micronucleophagic degradation of nucleolar proteins, contributing to intranuclear protein homeostasis.
    Keywords:  Autophagy; Chm7; ESCRT; Nucleophagy; Protein quality control; TORC1
    DOI:  https://doi.org/10.1016/j.bbrc.2024.151219
  58. Biol Pharm Bull. 2024 ;47(12): 2143-2153
    HMGB1 Promotes Accelerated Fracture Healing in Traumatic Brain Injury through PINK1/Parkin-Mediated Mitochondrial Autophagy.
    Shiyang Chen, Aiguo Zhou, Wenlong Yan.
      We aimed to investigate the mechanism of high mobility group box 1 (HMGB1) in the accelerated fracture healing process during Traumatic brain injury (TBI). The lateral ventricles of mice in the TBI model group were injected with adenovirus-packaged short hairpin RNA (shRNA)-HMGB1 or overexpressing (ov)-HMGB1 vector. We found HMGB1 levels were higher in bone tissue at the fracture end of TBI combined with fracture model mice. Compared with the TBI combined with fracture model mice, the mice in the ov-HMGB1 group healed faster and the expression levels of mitochondrial autophagy-related proteins were higher. Compared to the ov-HMGB1 group, mice in the ov-HMGB1 + autophagy inhibitor cyclosporin A (CsA) and ov-HMGB1 + shRNA-phosphatase and tensin homolog-induced kinase 1 (PINK1) groups showed slower healing and lower expression of mitochondrial autophagy-associated proteins. The expression of osteocalcin (OCN), SOX9, and bone morphogenetic protein (BMP)-2 in bone tissue at the fracture end of the ov-HMGB1 + shRNA-PINK1 group was lower than that in the ov-HMGB1 group. The mRNA expression levels of chondrogenic differentiation markers in bone tissue at the fracture end of the ov-HMGB1 + shRNA-PINK1 group were lower than those in the ov-HMGB1 group. Fracture healing was accelerated during TBI, especially when HMGB1 was highly expressed, and HMGB1 promote accelerated fracture healing during TBI through PINK1/Parkin-mediated mitochondrial autophagy.
    Keywords:  Parkin RBR E3 ubiquitin-protein ligase pathway; high mobility group box 1 (HMGB1); mitochondrial autophagy; phosphatase and tensin homolog-induced kinase 1; traumatic brain injury combined with fracture
    DOI:  https://doi.org/10.1248/bpb.b24-00203
  59. Adv Sci (Weinh). 2024 Dec 25. e2406700
    OTUD5 Protects Dopaminergic Neurons by Promoting the Degradation of α-Synuclein in Parkinson's Disease Model.
    Xiaomeng Song, Tengfei Liu, Lu Yu, Qiuran Ji, Xin Guo, Runzhe Zong, Yiquan Li, Gan Huang, Qidi Xue, Qingyi Fu, Bingyu Liu, Yi Zheng, Lin Chen, Chengjiang Gao, Huiqing Liu.
      Defective clearance and accumulation of α-synuclein (α-Syn) is the key pathogenic factor in Parkinson's disease (PD). Recent studies emphasize the importance of E3 ligases in regulating the degradation of α-Syn. However, the molecular mechanisms by which deubiquitinases regulate α-Syn degradation are scarcely studied. In this study, it is found that the protein levels of α-Syn are negatively regulated by ovarian tumor protease deubiquitinase 5 (OTUD5) which protects dopaminergic (DA) neurons in the PD model. Mechanistically, OTUD5 promotes K63-linked polyubiquitination of α-Syn independent of its deubiquitinating enzyme activity and mediates its endolysosomal degradation by recruiting the E3 ligase neural precursor cell expressed developmentally downregulated 4 (NEDD4). Furthermore, OTUD5 conditional knockout in DA neurons results in more severe α-Syn related pathology and dyskinesia after injection of α-Syn preformed fibrils (PFF). Overall, the data unveil a novel mechanism to regulate the degradation of α-Syn and provide a new therapeutic strategy to alleviate DA neurodegeneration.
    Keywords:  deubiquitinase; endolysosomal pathway; nedd4; otud5; parkinson's disease; α‐synuclein
    DOI:  https://doi.org/10.1002/advs.202406700
  60. Cell Mol Life Sci. 2024 Dec 21. 82(1): 10
    SHIP-1 regulates the differentiation and function of Tregs via inhibiting mTORC1 activity.
    Zuochen Du, Jinzhi Wang, Qian Liu, Di Yang, Xiaoyu Sun, Lu Huang, Pei Huang, Xingye Tang, Heather Miller, Lisa Westerberg, Yoshimura Akihiko, Lu Yang, Xingrong Du, Chaohong Liu.
      Cell metabolism is crucial for orchestrating the differentiation and function of regulatory T cells (Tregs). However, the underlying mechanism that coordinates cell metabolism to regulate Treg activity is not completely understood. As a pivotal molecule in lipid metabolism, the role of SHIP-1 in Tregs remains unknown. In this study, we found SHIP-1 Treg KO mice (SHIP-1 specifically deleted in regulatory T cells) had severe autoimmunity with increased Tregs in the thymus and disrupted peripheral T cell homeostasis. Mechanistically, CD4Cre Ship-1flox/flox mice were found to have increased Treg precursors and SHIP-1 KO Tregs had reduced migration and stability, which caused decreased Tregs in the spleen. Additionally, the suppressive function of Tregs from SHIP-1 KO mice was diminished, along with their promotion of anti-tumor immunity. Interestingly, the PI3K-mTORC1, but not mTORC2, signaling axis was enhanced in SHIP-1 KO Tregs. In vivo treatment of SHIP-1 Treg KO mice with rapamycin rescued the abnormal Treg percentages and peripheral T cell homeostasis, as well as Treg suppressive function. Furthermore, the treatment of wild-type mice with SHIP-1 inhibitor enhanced anti-tumor activity. Our study highlights the SHIP-1-PI3K-mTORC1 axis that regulates Treg differentiation and function, and it is a potential target for cancer treatment.
    Keywords:  Cell metabolism; SHIP-1; Treg cells; mTOR
    DOI:  https://doi.org/10.1007/s00018-024-05470-2
  61. Trends Cancer. 2024 Dec 19. pii: S2405-8033(24)00253-X. [Epub ahead of print]
    Cancer immunotherapeutic challenges from autophagy-immune checkpoint reciprocal regulation.
    Gang Zhang, Yinfeng Chen, Xing Huang, Tingbo Liang.
      Multiple strategies have been clinically employed as combination partners to enhance the therapeutic efficacy of immune checkpoint inhibitors (ICIs). Although these combinations have demonstrated improved effectiveness in some instances, each presents its own limitations. Autophagy-targeting therapy offers several advantages when combined with ICIs, including enhanced tumor immunogenicity, reduced side effects, and broader applicability to diverse patient populations. However, emerging evidence reveals complex reciprocal regulation between autophagy and immune checkpoints which may complicate combination treatments targeting these two systems. This review focuses on the reciprocal interplay between autophagy and immune checkpoints, and provides valuable guidelines for the determination and adjustment of therapeutic regimens in the future.
    Keywords:  autophagy; cancer immunotherapy; immune checkpoint; reciprocal regulation
    DOI:  https://doi.org/10.1016/j.trecan.2024.11.001
  62. Neurosci Lett. 2024 Dec 20. pii: S0304-3940(24)00470-1. [Epub ahead of print] 138091
    Sleep deprivation activated AMPK/FOXO3a signaling mediates pineal autophagy impairment to reduce melatonin secretion in CUMS + SD rats leading to depression combined with insomnia.
    Zirong Li, Yi Shu, Qian Liu, Deguo Liu, Sheng Xie, Mingjun Wei, Lidan Lan, Xinyi Yang.
      This study established an animal model of comorbid depression and insomnia by combining chronic unpredictable mild stress (CUMS) with sleep deprivation (SD). The pathogenesis of comorbid depression and insomnia may be associated with impaired AMPK/FOXO3a signaling, which mediates autophagy inhibition, leading to decreased pineal melatonin secretion. The findings revealed that CUMS + SD rats exhibited more pronounced depression-like behaviors, sleep disorders, increased central oxidative stress, and exacerbated neuroinflammation, accompanied by reduced levels of 5-hydroxytryptophan (5-HT) and melatonin in the pineal gland. Notably, further investigations revealed that impaired mitochondrial autophagy in the pineal gland is closely linked to the significant suppression of AMPK/FOXO3a signaling. The combined intervention of venlafaxine and melatonin effectively ameliorated the impaired mitochondrial autophagy in the pineal gland of CUMS + SD rats and stimulated melatonin secretion. Consequently, the study proposes that dysfunctional mitochondrial autophagy regulated by the AMPK/FOXO3a pathway can influence melatonin secretion, thereby playing a pivotal role in the pathogenesis of depression combined with insomnia.
    Keywords:  Chronic mild unpredictable stress; Depressive insomnia comorbidity; Melatonin; Mitochondrial autophagy; Pineal gland; Sleep deprivation
    DOI:  https://doi.org/10.1016/j.neulet.2024.138091
  63. Eur J Pharmacol. 2024 Dec 18. pii: S0014-2999(24)00900-2. [Epub ahead of print]988 177210
    NRF-mediated autophagy and UPR: Exploring new avenues to overcome cancer chemo-resistance.
    Sanaz Dastghaib, Sayed Mohammad Shafiee, Fatemeh Ramezani, Niloufar Ashtari, Farhad Tabasi, Javad Saffari-Chaleshtori, Morvarid Siri, Omid Vakili, Somayeh Igder, Mozhdeh Zamani, Maryam Niknam, Mahshid Moballegh Nasery, Fariba Kokabi, Emilia Wiechec, Zohreh Mostafavi-Pour, Pooneh Mokarram, Saeid Ghavami.
      The development of chemo-resistance remains a significant hurdle in effective cancer therapy. NRF1 and NRF2, key regulators of redox homeostasis, play crucial roles in the cellular response to oxidative stress, with implications for both tumor growth and resistance to chemotherapy. This study delves into the dualistic role of NRF2, exploring its protective functions in normal cells and its paradoxical support of tumor survival and drug resistance in cancerous cells. We investigate the interplay between the PERK/NRF signaling pathway, ER stress, autophagy, and the unfolded protein response, offering a mechanistic perspective on how these processes contribute to chemoresistance. Our findings suggest that targeting NRF signaling pathways may offer new avenues for overcoming resistance to chemotherapeutic agents, highlighting the importance of a nuanced approach to redox regulation in cancer treatment. This research provides a molecular basis for the development of NRF-targeted therapies, potentially enhancing the efficacy of existing cancer treatments and offering hope for more effective management of resistant tumors.
    Keywords:  Autophagy; Drug resistance; NF-E2-related factor 2; Reactive oxygen species; Unfolded protein response
    DOI:  https://doi.org/10.1016/j.ejphar.2024.177210
  64. Free Radic Res. 2024 Dec 23. 1-32
    Exploring the Impact of Apelin and Reactive Oxygen Species on Autophagy and Cell Senescence in Pre-eclampsia.
    Xue Peng, Xi Tan, Li Dai, Wei Xia, Zhao Wu.
      This research investigates the interplay between Reactive Oxygen Species (ROS) and Apelin (APLN) in regulating autophagy, with implications for placental cell senescence and apoptosis in pre-eclampsia (PE). We manipulated APLN expression using sgRNA to study its effects on ROS levels and subsequent cellular responses. Our findings reveal that APLN overexpression elevates ROS production, accelerating cellular senescence and apoptosis. In contrast, silencing APLN enhances autophagy, thereby diminishing cellular aging and apoptosis. These outcomes were confirmed in vitro and in vivo experiments, establishing a causative relationship between ROS-mediated APLN modulation and altered placental cell dynamics in PE. The results suggest potential therapeutic targets within the ROS and APLN pathways to alleviate detrimental changes in the placenta, offering new strategies for the clinical management of PE. This study emphasizes the crucial role of autophagy in placental health and sets the stage for future investigations into therapeutic interventions for pregnancy-related complications.
    Keywords:  Apelin; Autophagy; Cellular Apoptosis; Placental Aging; Pre-eclampsia; Reactive Oxygen Species
    DOI:  https://doi.org/10.1080/10715762.2024.2446337
  65. Ann N Y Acad Sci. 2024 Dec 23.
    The role of macroautophagy in substance use disorders.
    Zhaoying Yu, Shujun Lin, Xinshuang Gong, Zhiting Zou, Xiangdong Yang, Yuer Ruan, Liyin Qian, Yu Liu, Zizhen Si.
      Macroautophagy, a universal cellular process, sends cellular material to lysosomes for breakdown and is often activated by stressors like hypoxia or drug exposure. It is vital for protein balance, neurotransmitter release, synaptic function, and neuron survival. The role of macroautophagy in substance use disorders is dual. On one hand, substances like cocaine, methamphetamine, opiates, and alcohol can activate macroautophagy pathways to degrade various neuroinflammatory factors in neuronal cells, providing a protective function. On the other hand, long-term and excessive use of addictive substances can inhibit macroautophagy pathways, obstructing the fusion of autophagosomes with lysosomes and losing the original protective function. This review first summarizes the key proteins and signaling pathways involved in macroautophagy, including mTORC1, AMPK, and endoplasmic reticulum stress, and suggests that the regulation of macroautophagy plays a central role in drug-rewarding behavior and addiction. Second, we focus on the interactions between macroautophagy and neuroinflammation induced by drugs, evaluating the potential of macroautophagy modulators as therapeutic strategies for substance use disorder (SUD), and identifying autophagy-related biomarkers that can be used for early diagnosis and monitoring of treatment response. Our review summarizes the important scientific basis involved in macroautophagy pathways for the development of new therapies for SUD.
    Keywords:  macroautophagy; neuroinflammation; neurophysiological mechanisms; neuroprotection; substance use disorder
    DOI:  https://doi.org/10.1111/nyas.15272
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