bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2023–11–26
58 papers selected by
Viktor Korolchuk, Newcastle University
  1. Using Drosophila melanogaster to Dissect the Roles of the mTOR Signaling Pathway in Cell Growth.
  2. Lysosomes as coordinators of cellular catabolism, metabolic signalling and organ physiology.
  3. A Surge of Cytosolic Calcium Dysregulates Lysosomal Function and Impairs Autophagy Flux during Cupric Chloride-Induced Neuronal Death.
  4. An atypical GABARAP binding module drives the pro-autophagic potential of the AML-associated NPM1c variant.
  5. Unraveling the Janus-Faced Role of Autophagy in Hepatocellular Carcinoma: Implications for Therapeutic Interventions.
  6. Autophagy Modulation and Its Implications on Glioblastoma Treatment.
  7. The tRNA-GCN2-FBXO22-axis-mediated mTOR ubiquitination senses amino acid insufficiency.
  8. Docosahexaenoic Acid-Acylated Astaxanthin Monoester Ameliorates Amyloid-β Pathology and Neuronal Damage by Restoring Autophagy in Alzheimer's Disease Models.
  9. The ribosome-associated chaperone Zuo1 controls translation upon TORC1 inhibition.
  10. Molecular Mechanism of Autophagy, Cytoplasmic Zoning by Lipid Membranes.
  11. Autophagy drives the conversion of developmental neural stem cells to the adult quiescent state.
  12. Microautophagy regulated by STK38 and GABARAPs is essential to repair lysosomes and prevent aging.
  13. Deacetylation of ATG7 drives the induction of macroautophagy and LC3-associated microautophagy.
  14. Epigenetic modification and exosome effects on autophagy in osteoarthritis.
  15. The PB1 and the ZZ domain of the autophagy receptor p62/SQSTM1 regulate the interaction of p62/SQSTM1 with the autophagosome protein LC3B.
  16. Targeting protein methylation in pancreatic cancer cells results in KRAS signaling imbalance and inhibition of autophagy.
  17. TFEB-vacuolar ATPase signaling regulates lysosomal function and microglial activation in tauopathy.
  18. Hypoxia stabilizes the H2 O2 -producing oxidase Nox4 in cardiomyocytes via suppressing autophagy-related lysosomal degradation.
  19. Coiled-coil-mediated dimerization of Atg16 is required for binding to the PROPPIN Atg21.
  20. ULK1 seen at the single-molecule level during autophagy initiation.
  21. Examining the Role of a Functional Deficiency of Iron in Lysosomal Storage Disorders with Translational Relevance to Alzheimer's Disease.
  22. Pathology of hereditary renal cell carcinoma syndromes: Tuberous sclerosis complex (TSC).
  23. A conserved nutrient responsive axis mediates autophagic degradation of miRNA-mRNA hybrids in blood cell progenitors.
  24. Drp1 regulated PINK1-dependent mitophagy protected duck follicular granulosa cells from acute heat stress injury.
  25. OPTN gene therapy increases autophagy and protects mitochondria in SOD1-G93A-expressing transgenic mice and cells.
  26. Induction of Autophagy and Its Role in Peripheral Nerve Regeneration after Peripheral Nerve Injury.
  27. The Important Role of Protein Kinases in the p53 Sestrin Signaling Pathway.
  28. Clostridioides difficile PCR ribotypes 001 and 084 can trigger autophagy process in human intestinal Caco-2 cells.
  29. Antidepressants as Autophagy Modulators for Cancer Therapy.
  30. Correction of symptoms of Huntington disease by genistein through FOXO3-mediated autophagy stimulation.
  31. SMYD3 Modulates AMPK-mTOR Signaling Balance in Cancer Cell Response to DNA Damage.
  32. The Natural Alkaloid Palmatine Selectively Induces Mitophagy and Restores Mitochondrial Function in an Alzheimer's Disease Mouse Model.
  33. Lysosome regulation of microglia in Alzheimer's disease via TFEB-vacuolar ATPase.
  34. Sphingolipid-Based Synergistic Interactions to Enhance Chemosensitivity in Lung Cancer Cells.
  35. Age-related macular degeneration and neurodegenerative disorders: Shared pathways in complex interactions.
  36. Modulation of hepatic transcription factor EB activity during cold exposure uncovers direct regulation of bis(monoacylglycero)phosphate lipids by Pla2g15.
  37. Effects of Everolimus in Modulating the Host Immune Responses against Mycobacterium tuberculosis Infection.
  38. 3,4-dimethoxychalcone induces autophagy and reduces neointimal hyperplasia and aortic lesions in mouse models of atherosclerosis.
  39. Amino Acid-Starved Cancer Cells Utilize Macropinocytosis and Ubiquitin-Proteasome System for Nutrient Acquisition.
  40. Identification of mitophagy-associated proteins profile as potential plasma biomarkers of idiopathic Parkinson's disease.
  41. Improvement Effect of Mitotherapy on the Cognitive Ability of Alzheimer's Disease through NAD+/SIRT1-Mediated Autophagy.
  42. Mitochondrial nucleoid condensates drive peripheral fission through high membrane curvature.
  43. Carbon black nanoparticles and cadmium co-exposure aggravates bronchial epithelial cells inflammation via autophagy-lysosome pathway.
  44. Iron derived from NCOA4-mediated ferritinophagy causes cellular senescence via the cGAS-STING pathway.
  45. Kynurenine attenuates mitochondrial depolarization and neuronal cell death induced by rotenone exposure independently of AhR-mediated parkin induction in SH-SY5Y differentiated cells.
  46. PTK2B promotes TBK1 and STING oligomerization and enhances the STING-TBK1 signaling.
  47. Seneca Valley Virus Degrades STING via PERK and ATF6-Mediated Reticulophagy.
  48. Acne Transcriptomics: Fundamentals of Acne Pathogenesis and Isotretinoin Treatment.
  49. Amelioration of Tau and ApoE4-linked glial lipid accumulation and neurodegeneration with an LXR agonist.
  50. Multiomics of GCN4-Dependent Replicative Lifespan Extension Models Reveals Gcn4 as a Regulator of Protein Turnover in Yeast.
  51. Autophagy indicators in oral squamous cell carcinoma.
  52. Ovatodiolide induces autophagy-mediated cell death through the p62-Keap1-Nrf2 signaling pathway in chronic myeloid leukemia cells.
  53. Mitochondrial GpC and CpG DNA Hypermethylation Cause Metabolic Stress-Induced Mitophagy and Cholestophagy.
  54. ATG9A regulates the dissociation of recycling endosomes from microtubules to form liquid influenza A virus inclusions.
  55. β-hydroxybutyrate administered at reperfusion reduces infarct size and preserves cardiac function by improving mitochondrial function through autophagy in male mice.
  56. Structure of the DDB1-AMBRA1 E3 ligase receptor complex linked to cell cycle regulation.
  57. C. elegans hedgehog/patched-like morphogen-receptor pair GRD-1/PTR-11 modulates developmental rate.
  58. DLG1 promotes the antiviral innate immune response by inhibiting p62-mediated autophagic degradation of IKKε.
  1. Cells. 2023 Nov 14. pii: 2622. [Epub ahead of print]12(22):
    Using Drosophila melanogaster to Dissect the Roles of the mTOR Signaling Pathway in Cell Growth.
    Anna Frappaolo, Maria Grazia Giansanti.
      The evolutionarily conserved target of rapamycin (TOR) serine/threonine kinase controls eukaryotic cell growth, metabolism and survival by integrating signals from the nutritional status and growth factors. TOR is the catalytic subunit of two distinct functional multiprotein complexes termed mTORC1 (mechanistic target of rapamycin complex 1) and mTORC2, which phosphorylate a different set of substrates and display different physiological functions. Dysregulation of TOR signaling has been involved in the development and progression of several disease states including cancer and diabetes. Here, we highlight how genetic and biochemical studies in the model system Drosophila melanogaster have been crucial to identify the mTORC1 and mTORC2 signaling components and to dissect their function in cellular growth, in strict coordination with insulin signaling. In addition, we review new findings that involve Drosophila Golgi phosphoprotein 3 in regulating organ growth via Rheb-mediated activation of mTORC1 in line with an emerging role for the Golgi as a major hub for mTORC1 signaling.
    Keywords:  Drosophila; GOLPH3; Golgi; mTOR signaling
    DOI:  https://doi.org/10.3390/cells12222622
  2. Nat Rev Mol Cell Biol. 2023 Nov 24.
    Lysosomes as coordinators of cellular catabolism, metabolic signalling and organ physiology.
    Carmine Settembre, Rushika M Perera.
      Every cell must satisfy basic requirements for nutrient sensing, utilization and recycling through macromolecular breakdown to coordinate programmes for growth, repair and stress adaptation. The lysosome orchestrates these key functions through the synchronised interplay between hydrolytic enzymes, nutrient transporters and signalling factors, which together enable metabolic coordination with other organelles and regulation of specific gene expression programmes. In this Review, we discuss recent findings on lysosome-dependent signalling pathways, focusing on how the lysosome senses nutrient availability through its physical and functional association with mechanistic target of rapamycin complex 1 (mTORC1) and how, in response, the microphthalmia/transcription factor E (MiT/TFE) transcription factors exert feedback regulation on lysosome biogenesis. We also highlight the emerging interactions of lysosomes with other organelles, which contribute to cellular homeostasis. Lastly, we discuss how lysosome dysfunction contributes to diverse disease pathologies and how inherited mutations that compromise lysosomal hydrolysis, transport or signalling components lead to multi-organ disorders with severe metabolic and neurological impact. A deeper comprehension of lysosomal composition and function, at both the cellular and organismal level, may uncover fundamental insights into human physiology and disease.
    DOI:  https://doi.org/10.1038/s41580-023-00676-x
  3. J Biol Chem. 2023 Nov 17. pii: S0021-9258(23)02507-3. [Epub ahead of print] 105479
    A Surge of Cytosolic Calcium Dysregulates Lysosomal Function and Impairs Autophagy Flux during Cupric Chloride-Induced Neuronal Death.
    Yoonkyung Kim, Yangsin Lee, Minjung Choo, Nuri Yun, Jin Won Cho, Young J Oh.
      Autophagy is a degradative pathway that plays an important role in maintaining cellular homeostasis. Dysfunction of autophagy is associated with the progression of neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Although one of the typical features of brain aging is an accumulation of redox-active metals that eventually lead to neurodegeneration, a plausible link between trace metal-induced neurodegeneration and dysregulated autophagy has not been clearly determined. Here, we used a cupric chloride-induced neurodegeneration model in MN9D dopaminergic neuronal cells along with ultrastructural and biochemical analyses to demonstrate impaired autophagic flux with accompanying lysosomal dysfunction. We found that a surge of cytosolic calcium was involved in cupric chloride-induced dysregulated autophagy. Consequently, buffering of cytosolic calcium by calbindin-D28K overexpression or co-treatment with the calcium chelator BAPTA attenuated the cupric chloride-induced impairment in autophagic flux by ameliorating dysregulation of lysosomal function. Thus, these events allowed the rescue of cells from cupric chloride-induced neuronal death. These phenomena were largely confirmed in cupric chloride-treated primary cultures of cortical neurons. Taken together, these results suggest that abnormal accumulation of trace metal elements and a resultant surge of cytosolic calcium leads to neuronal death by impairing autophagic flux at the lysosomal level.
    Keywords:  autophagy; copper; cytosolic calcium; lysosome; neurodegeneration
    DOI:  https://doi.org/10.1016/j.jbc.2023.105479
  4. Cell Rep. 2023 Nov 22. pii: S2211-1247(23)01496-1. [Epub ahead of print]42(12): 113484
    An atypical GABARAP binding module drives the pro-autophagic potential of the AML-associated NPM1c variant.
    Hannah Mende, Anshu Khatri, Carolin Lange, Sergio Alejandro Poveda-Cuevas, Georg Tascher, Adriana Covarrubias-Pinto, Frank Löhr, Sebastian E Koschade, Ivan Dikic, Christian Münch, Anja Bremm, Lorenzo Brunetti, Christian H Brandts, Hannah Uckelmann, Volker Dötsch, Vladimir V Rogov, Ramachandra M Bhaskara, Stefan Müller.
      The nucleolar scaffold protein NPM1 is a multifunctional regulator of cellular homeostasis, genome integrity, and stress response. NPM1 mutations, known as NPM1c variants promoting its aberrant cytoplasmic localization, are the most frequent genetic alterations in acute myeloid leukemia (AML). A hallmark of AML cells is their dependency on elevated autophagic flux. Here, we show that NPM1 and NPM1c induce the autophagy-lysosome pathway by activating the master transcription factor TFEB, thereby coordinating the expression of lysosomal proteins and autophagy regulators. Importantly, both NPM1 and NPM1c bind to autophagy modifiers of the GABARAP subfamily through an atypical binding module preserved within its N terminus. The propensity of NPM1c to induce autophagy depends on this module, likely indicating that NPM1c exerts its pro-autophagic activity by direct engagement with GABARAPL1. Our data report a non-canonical binding mode of GABARAP family members that drives the pro-autophagic potential of NPM1c, potentially enabling therapeutic options.
    Keywords:  AML; ATG8; Autophagy; CP: Cancer; CP: Molecular biology; GABARAP; LC3; NPM1; NPM1c; TFEB; atypical LIR; lysosome
    DOI:  https://doi.org/10.1016/j.celrep.2023.113484
  5. Int J Mol Sci. 2023 Nov 13. pii: 16255. [Epub ahead of print]24(22):
    Unraveling the Janus-Faced Role of Autophagy in Hepatocellular Carcinoma: Implications for Therapeutic Interventions.
    Thi Ha Nguyen, Tuan Minh Nguyen, Dinh Thi Minh Ngoc, Taesik You, Mi Kyung Park, Chang Hoon Lee.
      This review aims to provide a comprehensive understanding of the molecular mechanisms underlying autophagy and mitophagy in hepatocellular carcinoma (HCC). Autophagy is an essential cellular process in maintaining cell homeostasis. Still, its dysregulation is associated with the development of liver diseases, including HCC, which is one of leading causes of cancer-related death worldwide. We focus on elucidating the dual role of autophagy in HCC, both in tumor initiation and progression, and highlighting the complex nature involved in the disease. In addition, we present a detailed analysis of a small subset of autophagy- and mitophagy-related molecules, revealing their specific functions during tumorigenesis and the progression of HCC cells. By understanding these mechanisms, we aim to provide valuable insights into potential therapeutic strategies to manipulate autophagy effectively. The goal is to improve the therapeutic response of liver cancer cells and overcome drug resistance, providing new avenues for improved treatment options for HCC patients. Overall, this review serves as a valuable resource for researchers and clinicians interested in the complex role of autophagy in HCC and its potential as a target for innovative therapies aimed to combat this devastating disease.
    Keywords:  autophagy; autophagy inducer; autophagy inhibitors; hepatocellular carcinoma; mitophagy
    DOI:  https://doi.org/10.3390/ijms242216255
  6. Curr Issues Mol Biol. 2023 Oct 29. 45(11): 8687-8703
    Autophagy Modulation and Its Implications on Glioblastoma Treatment.
    Johnny Chen, Andrea Salinas Rodriguez, Maximiliano Arath Morales, Xiaoqian Fang.
      Autophagy is a vital cellular process that functions to degrade and recycle damaged organelles into basic metabolites. This allows a cell to adapt to a diverse range of challenging conditions. Autophagy assists in maintaining homeostasis, and it is tightly regulated by the cell. The disruption of autophagy has been associated with many diseases, such as neurodegenerative disorders and cancer. This review will center its discussion on providing an in-depth analysis of the current molecular understanding of autophagy and its relevance to brain tumors. We will delve into the current literature regarding the role of autophagy in glioma pathogenesis by exploring the major pathways of JAK2/STAT3 and PI3K/AKT/mTOR and summarizing the current therapeutic interventions and strategies for glioma treatment. These treatments will be evaluated on their potential for autophagy induction and the challenges associated with their utilization. By understanding the mechanism of autophagy, clinical applications for future therapeutics in treating gliomas can be better targeted.
    Keywords:  JAK2/STAT3 signaling pathway; PI3K/AKT/mTOR signaling pathway; autophagy; glioblastoma; treatment
    DOI:  https://doi.org/10.3390/cimb45110546
  7. Cell Metab. 2023 Nov 11. pii: S1550-4131(23)00385-6. [Epub ahead of print]
    The tRNA-GCN2-FBXO22-axis-mediated mTOR ubiquitination senses amino acid insufficiency.
    Meng-Kai Ge, Cheng Zhang, Na Zhang, Ping He, Hai-Yan Cai, Song Li, Shuai Wu, Xi-Li Chu, Yu-Xue Zhang, Hong-Ming Ma, Li Xia, Shuo Yang, Jian-Xiu Yu, Shi-Ying Yao, Xiao-Long Zhou, Bing Su, Guo-Qiang Chen, Shao-Ming Shen.
      Mammalian target of rapamycin complex 1 (mTORC1) monitors cellular amino acid changes for function, but the molecular mediators of this process remain to be fully defined. Here, we report that depletion of cellular amino acids, either alone or in combination, leads to the ubiquitination of mTOR, which inhibits mTORC1 kinase activity by preventing substrate recruitment. Mechanistically, amino acid depletion causes accumulation of uncharged tRNAs, thereby stimulating GCN2 to phosphorylate FBXO22, which in turn accrues in the cytoplasm and ubiquitinates mTOR at Lys2066 in a K27-linked manner. Accordingly, mutation of mTOR Lys2066 abolished mTOR ubiquitination in response to amino acid depletion, rendering mTOR insensitive to amino acid starvation both in vitro and in vivo. Collectively, these data reveal a novel mechanism of amino acid sensing by mTORC1 via a previously unknown GCN2-FBXO22-mTOR pathway that is uniquely controlled by uncharged tRNAs.
    Keywords:  FBXO22; GCN2; amino acids; mTOR; mTORC1; ubiquitination; uncharged tRNA
    DOI:  https://doi.org/10.1016/j.cmet.2023.10.016
  8. Mol Nutr Food Res. 2023 Nov 22. e2300414
    Docosahexaenoic Acid-Acylated Astaxanthin Monoester Ameliorates Amyloid-β Pathology and Neuronal Damage by Restoring Autophagy in Alzheimer's Disease Models.
    Xiaoxu Wang, Yu Song, Peixu Cong, Zhigao Wang, Yanjun Liu, Jie Xu, Changhu Xue.
       SCOPE: Astaxanthin (AST) is ubiquitous in aquatic foods and microorganisms. The study previously finds that docosahexaenoic acid-acylated AST monoester (AST-DHA) improves cognitive function in Alzheimer's disease (AD), although the underlying mechanism remains unclear. Moreover, autophagy is reportedly involved in amyloid-β (Aβ) clearance and AD pathogenesis. Therefore, this study aims to evaluate the preventive effect of AST-DHA and elucidates the mechanism of autophagy modulation in Aβ pathology.
    METHODS AND RESULTS: In the cellular AD model, AST-DHA significantly reduces toxic Aβ1-42 levels and alleviated the accumulation of autophagic markers (LC3II/I and p62) in Aβ25-35 -induced SH-SY5Y cells. Notably, AST-DHA restores the autophagic flux in SH-SY5YmRFP-GFP-LC3 cells. In APP/PS1 mice, a 3-month dietary supplementation of AST-DHA exceeded free-astaxanthin (F-AST) capacity to increase hippocampal and cortical autophagy. Mechanistically, AST-DHA restores autophagy by activating the ULK1 signaling pathway and restoring autophagy-lysosome fusion. Moreover, AST-DHA relieves ROS production and mitochondrial stress affecting autophagy in AD. As a favorable outcome of restored autophagy, AST-DHA mitigates cerebral Aβ and p-Tau deposition, ultimately improving neuronal function.
    CONCLUSION: The findings demonstrate that AST-DHA can rectify autophagic impairment in AD, and confer neuroprotection in Aβ-related pathology, which supports the future application of AST as an autophagic inducer for maintaining brain health.
    Keywords:  astaxanthin; autophagosome-lysosome fusion; autophagy; mitochondria; neuronal function
    DOI:  https://doi.org/10.1002/mnfr.202300414
  9. EMBO J. 2023 Nov 20. e113240
    The ribosome-associated chaperone Zuo1 controls translation upon TORC1 inhibition.
    Ailsa Black, Thomas D Williams, Flavie Soubigou, Ifeoluwapo M Joshua, Houjiang Zhou, Frederic Lamoliatte, Adrien Rousseau.
      Protein requirements of eukaryotic cells are ensured by proteostasis, which is mediated by tight control of TORC1 activity. Upon TORC1 inhibition, protein degradation is increased and protein synthesis is reduced through inhibition of translation initiation to maintain cell viability. Here, we show that the ribosome-associated complex (RAC)/Ssb chaperone system, composed of the HSP70 chaperone Ssb and its HSP40 co-chaperone Zuo1, is required to maintain proteostasis and cell viability under TORC1 inhibition in Saccharomyces cerevisiae. In the absence of Zuo1, translation does not decrease in response to the loss of TORC1 activity. A functional interaction between Zuo1 and Ssb is required for proper translational control and proteostasis maintenance upon TORC1 inhibition. Furthermore, we have shown that the rapid degradation of eIF4G following TORC1 inhibition is mediated by autophagy and is prevented in zuo1Δ cells, contributing to decreased survival in these conditions. We found that autophagy is defective in zuo1Δ cells, which impedes eIF4G degradation upon TORC1 inhibition. Our findings identify an essential role for RAC/Ssb in regulating translation in response to changes in TORC1 signalling.
    Keywords:  TORC1; proteostasis; ribosome-associated chaperones; stress; translation
    DOI:  https://doi.org/10.15252/embj.2022113240
  10. J Biochem. 2023 Nov 20. pii: mvad099. [Epub ahead of print]
    Molecular Mechanism of Autophagy, Cytoplasmic Zoning by Lipid Membranes.
    Tetsuya Kotani, Yuri Yasuda, Hitoshi Nakatogawa.
      Autophagy is a highly conserved intracellular degradation mechanism. The most distinctive feature of autophagy is the formation of double-membrane structures called autophagosomes, which compartmentalize portions of the cytoplasm. The outer membrane of the autophagosome fuses with the vacuolar/lysosomal membrane, leading to the degradation of the contents of the autophagosome. Approximately 30 years have passed since the identification of autophagy-related (ATG) genes and Atg proteins essential for autophagosome formation, and the primary functions of these Atg proteins have been elucidated. These achievements have significantly advanced our understanding of the mechanism of autophagosome formation. This article summarizes our current knowledge on how the autophagosome precursor is generated, and how the membrane expands and seals to complete the autophagosome.
    Keywords:  autophagosome; autophagy; intracellular degradation; membrane dynamics; vacuole/lysosome
    DOI:  https://doi.org/10.1093/jb/mvad099
  11. Nat Commun. 2023 Nov 24. 14(1): 7541
    Autophagy drives the conversion of developmental neural stem cells to the adult quiescent state.
    Isabel Calatayud-Baselga, Lucía Casares-Crespo, Carmina Franch-Ibáñez, José Guijarro-Nuez, Pascual Sanz, Helena Mira.
      Neurogenesis in the adult mammalian brain relies on the lifelong persistence of quiescent neural stem cell (NSC) reservoirs. Little is known about the mechanisms that lead to the initial establishment of quiescence, the main hallmark of adult stem cells, during development. Here we show that protein aggregates and autophagy machinery components accumulate in developmental radial glia-like NSCs as they enter quiescence and that pharmacological or genetic blockade of autophagy disrupts quiescence acquisition and maintenance. Conversely, increasing autophagy through AMPK/ULK1 activation instructs the acquisition of the quiescent state without affecting BMP signaling, a gatekeeper of NSC quiescence during adulthood. Selective ablation of Atg7, a critical gene for autophagosome formation, in radial glia-like NSCs at early and late postnatal stages compromises the initial acquisition and maintenance of quiescence during the formation of the hippocampal dentate gyrus NSC niche. Therefore, we demonstrate that autophagy is cell-intrinsically required to establish NSC quiescence during hippocampal development. Our results uncover an important role of autophagy in the transition of developmental NSCs into their dormant adult form, paving the way for studies directed at further understanding the mechanisms of stem cell niche formation and maintenance in the mammalian brain.
    DOI:  https://doi.org/10.1038/s41467-023-43222-1
  12. EMBO Rep. 2023 Nov 21. e57300
    Microautophagy regulated by STK38 and GABARAPs is essential to repair lysosomes and prevent aging.
    Monami Ogura, Tatsuya Kaminishi, Takayuki Shima, Miku Torigata, Nao Bekku, Keisuke Tabata, Satoshi Minami, Kohei Nishino, Akiko Nezu, Maho Hamasaki, Hidetaka Kosako, Tamotsu Yoshimori, Shuhei Nakamura.
      Lysosomes are degradative organelles and signaling hubs that maintain cell and tissue homeostasis, and lysosomal dysfunction is implicated in aging and reduced longevity. Lysosomes are frequently damaged, but their repair mechanisms remain unclear. Here, we demonstrate that damaged lysosomal membranes are repaired by microautophagy (a process termed "microlysophagy") and identify key regulators of the first and last steps. We reveal the AGC kinase STK38 as a novel microlysophagy regulator. Through phosphorylation of the scaffold protein DOK1, STK38 is specifically required for the lysosomal recruitment of the AAA+ ATPase VPS4, which terminates microlysophagy by promoting the disassembly of ESCRT components. By contrast, microlysophagy initiation involves non-canonical lipidation of ATG8s, especially the GABARAP subfamily, which is required for ESCRT assembly through interaction with ALIX. Depletion of STK38 and GABARAPs accelerates DNA damage-induced cellular senescence in human cells and curtails lifespan in C. elegans, respectively. Thus, microlysophagy is regulated by STK38 and GABARAPs and could be essential for maintaining lysosomal integrity and preventing aging.
    Keywords:  ESCRT; lysosome; microautophagy; non-canonical ATG8 lipidation
    DOI:  https://doi.org/10.15252/embr.202357300
  13. Autophagy. 2023 Nov 24.
    Deacetylation of ATG7 drives the induction of macroautophagy and LC3-associated microautophagy.
    Yinfeng Xu, Chuying Qian, Qian Wang, Lijiang Song, Zhengfu He, Wei Liu, Wei Wan.
      LC3 lipidation plays an important role in the regulation of macroautophagy and LC3-associated microautophagy. The E1-like enzyme ATG7 is one of the core components that are directly involved in LC3 lipidation reaction. Here, we provide evidence showing that acetylation of ATG7 tightly controls its enzyme activity to regulate the induction of macroautophagy and LC3-associated microautophagy. Mechanistically, acetylation of ATG7 disrupts its interaction with the E2-like enzyme ATG3, leading to an inhibition of LC3 lipidation in vitro and in vivo. Functionally, in response to various different stimuli, cellular ATG7 undergoes deacetylation to induce macroautophagy and LC3-associated microautophagy, which are necessary for cells to eliminate cytoplasmic DNA and degrade lysosome membrane proteins, respectively. Taken together, these findings reveal that ATG7 acetylation acts as a critical rheostat in controlling LC3 lipidation and related cellular processes.
    Keywords:  ATG7; Acetylation; LC3 lipidation; macroautophagy; microautophagy
    DOI:  https://doi.org/10.1080/15548627.2023.2287932
  14. Biochem Pharmacol. 2023 Nov 17. pii: S0006-2952(23)00523-3. [Epub ahead of print]218 115930
    Epigenetic modification and exosome effects on autophagy in osteoarthritis.
    Chenglong Cheng, Yajie Wu, Yurong Huang, Qiuyun Xue, Yuting Wang, Faxue Liao, Xiaomei Wang, Chenggui Miao.
      Osteoarthritis (OA) is a degenerative disease that leads to joint pain and stiffness and is one of the leading causes of disability and pain worldwide. Autophagy is a highly conserved self-degradation process, and its abnormal function is closely related to human diseases, including OA. Abnormal autophagy regulates cell aging, matrix metalloproteinase metabolism, and reactive oxygen metabolism, which are key in the occurrence and development of OA. There is evidence that drugs directly or indirectly targeting autophagy significantly hinder the progress of OA. In addition, the occurrence and development of autophagy in OA are regulated by many factors, including epigenetic modification, exosomes, crucial autophagy molecules, and signaling pathway regulation. Autophagy, as a new therapeutic target for OA, has widely influenced the pathological mechanism of OA. However, determining how autophagy affects OA pathology and its use in the treatment and diagnosis of targets still need further research.
    Keywords:  Autophagy; Epigenetic inheritance; Exosome; Osteoarthritis; Therapeutic drug
    DOI:  https://doi.org/10.1016/j.bcp.2023.115930
  15. Protein Sci. 2023 Nov 20. e4840
    The PB1 and the ZZ domain of the autophagy receptor p62/SQSTM1 regulate the interaction of p62/SQSTM1 with the autophagosome protein LC3B.
    Lucia Alcober-Boquet, Tabea Zang, Larissa Pietsch, Evelyn Suess, Markus Hartmann, Ewgenij Proschak, Lissy Z F Gross, Mariana Sacerdoti, Stefan Zeuzem, Vladimir V Rogov, Alejandro E Leroux, Albrecht Piiper, Ricardo M Biondi.
      Autophagy is a highly conserved cellular process that allows degradation of large macromolecules. p62/SQSTM1 is a key adaptor protein that interacts both with material to be degraded and with LC3 at the autophagosome, enabling degradation of cargos such as protein aggregates, lipid droplets and damaged organelles by selective autophagy. Dysregulation of autophagy contributes to the pathogenesis of many diseases. In this study we investigated if the interaction of p62/SQSTM1 with LC3B could be regulated. We purified full-length p62/SQSTM1 and established an in vitro assay that measures the interaction with LC3B. We used the assay to determine the role of the different domains of p62/SQSTM1 in the interaction with LC3B. We identified a mechanism of regulation of p62/SQSTM1 where the ZZ and the PB1 domains regulate the exposure of the LIR-sequence to enable or inhibit the interaction with LC3B. A mutation to mimic the phosphorylation of a site on the ZZ domain leads to increased interaction with LC3B. Also, a small compound that binds to the ZZ domain enhances interaction with LC3B. Dysregulation of these mechanisms in p62/SQSTM1 could have implications for diseases where autophagy is affected. In conclusion, our study highlights the regulated nature of p62/SQSTM1 and its ability to modulate the interaction with LC3B through a LIR-sequence Accessibility Mechanism (LAM). Furthermore, our findings suggest the potential for pharmacological modulation of the exposure of LIR, paving the way for future therapeutic strategies. This article is protected by copyright. All rights reserved.
    Keywords:  LC3 and GABARAP proteins; LIR; XRK3F2; chemical biology; molecular mechanism; p62/SQSTM1
    DOI:  https://doi.org/10.1002/pro.4840
  16. Cell Death Dis. 2023 Nov 23. 14(11): 761
    Targeting protein methylation in pancreatic cancer cells results in KRAS signaling imbalance and inhibition of autophagy.
    María F Montenegro, Román Martí-Díaz, Ana Navarro, Jorge Tolivia, Luis Sánchez-Del-Campo, Juan Cabezas-Herrera, José Neptuno Rodríguez-López.
      Pancreatic cancer cells with mutant KRAS require strong basal autophagy for viability and growth. Here, we observed that some processes that allow the maintenance of basal autophagy in pancreatic cancer cells are controlled by protein methylation. Thus, by maintaining the methylation status of proteins such as PP2A and MRAS, these cells can sustain their autophagic activity. Protein methylation disruption by a hypomethylating treatment (HMT), which depletes cellular S-adenosylmethionine levels while inducing S-adenosylhomocysteine accumulation, resulted in autophagy inhibition and endoplasmic reticulum stress-induced apoptosis in pancreatic cancer cells. We observed that by reducing the membrane localization of MRAS, hypomethylation conditions produced an imbalance in KRAS signaling, resulting in the partial inactivation of ERK and hyperactivation of the PI3K/AKT-mTORC1 pathway. Interestingly, HMT impeded CRAF activation by disrupting the ternary SHOC2 complex (SHOC2/MRAS/PP1), which functions as a CRAF-S259 holophosphatase. The demethylation events that resulted in PP2A inactivation also favored autophagy inhibition by preventing ULK1 activation while restoring the cytoplasmic retention of the MiT/TFE transcription factors. Since autophagy provides pancreatic cancer cells with metabolic plasticity to cope with various metabolic stress conditions, while at the same time promoting their pathogenesis and resistance to KRAS pathway inhibitors, this hypomethylating treatment could represent a therapeutic opportunity for pancreatic adenocarcinomas.
    DOI:  https://doi.org/10.1038/s41419-023-06288-9
  17. Nat Neurosci. 2023 Nov 20.
    TFEB-vacuolar ATPase signaling regulates lysosomal function and microglial activation in tauopathy.
    Baiping Wang, Heidi Martini-Stoica, Chuangye Qi, Tzu-Chiao Lu, Shuo Wang, Wen Xiong, Yanyan Qi, Yin Xu, Marco Sardiello, Hongjie Li, Hui Zheng.
      Transcription factor EB (TFEB) mediates gene expression through binding to the coordinated lysosome expression and regulation (CLEAR) sequence. TFEB targets include subunits of the vacuolar ATPase (v-ATPase), which are essential for lysosome acidification. Single-nucleus RNA sequencing of wild-type and PS19 (Tau) transgenic mice expressing the P301S mutant tau identified three unique microglia subclusters in Tau mice that were associated with heightened lysosome and immune pathway genes. To explore the lysosome-immune relationship, we specifically disrupted the TFEB-v-ATPase signaling by creating a knock-in mouse line in which the CLEAR sequence of one of the v-ATPase subunits, Atp6v1h, was mutated. CLEAR mutant exhibited a muted response to TFEB, resulting in impaired lysosomal acidification and activity. Crossing the CLEAR mutant with Tau mice led to higher tau pathology but diminished microglia response. These microglia were enriched in a subcluster low in mTOR and HIF-1 pathways and were locked in a homeostatic state. Our studies demonstrate a physiological function of TFEB-v-ATPase signaling in maintaining lysosomal homeostasis and a critical role of the lysosome in mounting a microglia and immune response in tauopathy and Alzheimer's disease.
    DOI:  https://doi.org/10.1038/s41593-023-01494-2
  18. Genes Cells. 2023 Nov 20.
    Hypoxia stabilizes the H2 O2 -producing oxidase Nox4 in cardiomyocytes via suppressing autophagy-related lysosomal degradation.
    Shogo Matsunaga, Akira Kohda, Sachiko Kamakura, Junya Hayase, Kei Miyano, Akira Shiose, Hideki Sumimoto.
      The hydrogen peroxide (H2 O2 )-producing NADPH oxidase Nox4, forming a heterodimer with p22phox , is expressed in a variety of cells including those in the heart to mediate adaptive responses to cellular stresses such as hypoxia. Since Nox4 is constitutively active, H2 O2 production is controlled by its protein abundance. Hypoxia-induced Nox4 expression is observed in various types of cells and generally thought to be regulated at the transcriptional level. Here we show that hypoxia upregulates the Nox4 protein level and Nox4-catalyzed H2 O2 production without increasing the Nox4 mRNA in rat H9c2 cardiomyocytes. In these cells, the Nox4 protein is stabilized under hypoxic conditions in a manner dependent on the presence of p22phox . Cell treatment with the proteasome inhibitor MG132 results in a marked decrease of the Nox4 protein under both normoxic and hypoxic conditions, indicating that the proteasome pathway does not play a major role in Nox4 degradation. The decrease is partially restored by the autophagy inhibitor 3-methyladenine. Furthermore, the Nox4 protein level is upregulated by the lysosome inhibitors bafilomycin A1 and chloroquine. Thus, in cardiomyocytes, Nox4 appears to be degraded via an autophagy-related pathway, and its suppression by hypoxia likely stabilizes Nox4, leading to upregulation of Nox4-catalyzed H2 O2 production.
    Keywords:  Nox4; autophagy; cardiomyocytes; hypoxia; lysosome; p22phox
    DOI:  https://doi.org/10.1111/gtc.13085
  19. Open Biol. 2023 Nov;13(11): 230192
    Coiled-coil-mediated dimerization of Atg16 is required for binding to the PROPPIN Atg21.
    Miranda Bueno-Arribas, Celia Cruz-Cuevas, María-Angeles Navas, Ricardo Escalante, Olivier Vincent.
      PROPPINs/WIPIs are β-propeller proteins that bind phosphoinositides and contribute to the recruitment of protein complexes involved in membrane remodelling processes such as autophagosome formation and endosomal trafficking. Yeast Atg21 and mammalian WIPI2 interact with Atg16/ATG16L1 to mediate recruitment of the lipidation machinery to the autophagosomal membrane. Here, we used the reverse double two-hybrid method (RD2H) to identify residues in Atg21 and Atg16 critical for protein-protein binding. Although our results are generally consistent with the crystal structure of the Atg21-Atg16 complex reported previously, they also reveal that dimerization of the Atg16 coiled-coil domain is required for Atg21 binding. Furthermore, most of the residues identified in Atg21 are conserved in WIPI2 and we showed that these residues also mediate ATG16L1 binding. Strikingly, these residues occupy the same position in the β-propeller structure as residues in PROPPINs/WIPIs Hsv2 and WIPI4 that mediate Atg2/ATG2A binding, supporting the idea that these proteins use different amino acids at the same position to interact with different autophagic proteins. Finally, our findings demonstrate the effectiveness of the RD2H system to identify critical residues for protein-protein interactions and the utility of this method to generate combinatory mutants with a complete loss of binding capacity.
    Keywords:  ATG16; ATG21; WIPI; autophagy; proppin; reverse two-hybrid
    DOI:  https://doi.org/10.1098/rsob.230192
  20. Autophagy. 2023 Nov 22.
    ULK1 seen at the single-molecule level during autophagy initiation.
    Chiranjib Banerjee, Elias M Puchner, Do-Hyung Kim.
      Macroautophagy/autophagy research often involves overexpressing proteins to investigate their localization, function and activity. However, this approach can disturb the inherent balance of cellular components, potentially affecting the integrity of the autophagy process. With the advent of genome-editing techniques like CRISPR-Cas9, it is now possible to tag endogenous proteins with fluorescent markers, enabling the study of their behaviors under more physiologically relevant conditions. Nevertheless, conventional microscopy methods have limitations in characterizing the behaviors of proteins expressed at endogenous levels. This challenge can be overcome by single-molecule localization microscopy (SMLM) methods, which provide single-molecule sensitivity and super-resolution imaging capabilities. In our recent study, we used SMLM in combination with genome editing to explore the behavior of endogenous ULK1 during autophagy initiation, yielding unprecedented insights into the autophagy initiation process.
    Keywords:  Genome editing; PALM; SMLM; ULK1; single molecule
    DOI:  https://doi.org/10.1080/15548627.2023.2286078
  21. Cells. 2023 Nov 16. pii: 2641. [Epub ahead of print]12(22):
    Examining the Role of a Functional Deficiency of Iron in Lysosomal Storage Disorders with Translational Relevance to Alzheimer's Disease.
    Steven M LeVine.
      The recently presented Azalea Hypothesis for Alzheimer's disease asserts that iron becomes sequestered, leading to a functional iron deficiency that contributes to neurodegeneration. Iron sequestration can occur by iron being bound to protein aggregates, such as amyloid β and tau, iron-rich structures not undergoing recycling (e.g., due to disrupted ferritinophagy and impaired mitophagy), and diminished delivery of iron from the lysosome to the cytosol. Reduced iron availability for biochemical reactions causes cells to respond to acquire additional iron, resulting in an elevation in the total iron level within affected brain regions. As the amount of unavailable iron increases, the level of available iron decreases until eventually it is unable to meet cellular demands, which leads to a functional iron deficiency. Normally, the lysosome plays an integral role in cellular iron homeostasis by facilitating both the delivery of iron to the cytosol (e.g., after endocytosis of the iron-transferrin-transferrin receptor complex) and the cellular recycling of iron. During a lysosomal storage disorder, an enzyme deficiency causes undigested substrates to accumulate, causing a sequelae of pathogenic events that may include cellular iron dyshomeostasis. Thus, a functional deficiency of iron may be a pathogenic mechanism occurring within several lysosomal storage diseases and Alzheimer's disease.
    Keywords:  Alzheimer’s disease; Gaucher’s disease; Krabbe’s disease; Niemann–Pick type C disease; iron; lysosome; mucolipidosis type IV; neuronal ceroid lipofuscinosis
    DOI:  https://doi.org/10.3390/cells12222641
  22. Semin Diagn Pathol. 2023 Sep 20. pii: S0740-2570(23)00093-X. [Epub ahead of print]
    Pathology of hereditary renal cell carcinoma syndromes: Tuberous sclerosis complex (TSC).
    Miranda E Machacek, Chin-Lee Wu, Kristine M Cornejo.
      Tuberous sclerosis complex (TSC) is an autosomal dominant genetic disease characterized by hamartomatous tumors involving multiple organs such as the brain, skin, heart, lung and kidney. TSC is caused by inactivating mutations in TSC1/TSC2, which encodes hamartin and tuberin, respectively, and forms a complex that regulates mechanistic target of rapamycin complex 1 (mTORC1), resulting in cell overgrowth and oncogenesis. Since a leading cause of morbidity and mortality in TSC relates to chronic kidney disease and the ability to preserve renal function, this review describes the important pathologic findings in TSC-associated renal neoplasms and their correlating sporadic counterparts. The most common renal tumor in TSC patients are AMLs, followed by a heterogeneous spectrum of renal epithelial tumors, which may provide clues to establishing a diagnosis of TSC.
    Keywords:  Eosinophilic solid and cystic RCC (ESC-RCC); Eosinophilic vacuolated tumor (EVT); Low-grade oncocytic tumor (LOT); RCC with leiomyomatous stroma (RCC-LMS); Renal cell carcinoma (RCC); Tuberous sclerosis complex (TSC)
    DOI:  https://doi.org/10.1053/j.semdp.2023.09.001
  23. Nucleic Acids Res. 2023 Nov 22. pii: gkad1047. [Epub ahead of print]
    A conserved nutrient responsive axis mediates autophagic degradation of miRNA-mRNA hybrids in blood cell progenitors.
    Sushmit Ghosh, Sreemoyee Chakraborti, Devki Devi, Rajesh Sahu, Sudip Mandal, Lolitika Mandal.
      In animals, microRNAs are amongst the primary non-coding RNAs involved in regulating the gene expression of a cell. Most mRNAs in a cell are targeted by one or many miRNAs. Although several mechanisms can be attributed to the degradation of miRNA and mRNA within a cell, but the involvement of autophagy in the clearance of miRNA and its target mRNA is not known. We discover a leucine-responsive axis in blood cell progenitors that can mediate an autophagy-directed degradation of miRNA-bound mRNA in Drosophila melanogaster and Homo sapiens. This previously unknown miRNA clearance axis is activated upon amino acid deprivation that can traffic miRNA-mRNA-loaded Argonaute for autophagic degradation in a p62-dependent manner. Thus, our research not only reports a novel axis that can address the turnover of a catalytically active miRISC but also elucidates a slicer-independent mechanism through which autophagy can selectively initiate the clearance of target mRNA.
    DOI:  https://doi.org/10.1093/nar/gkad1047
  24. Poult Sci. 2023 Oct 28. pii: S0032-5791(23)00766-6. [Epub ahead of print]103(1): 103247
    Drp1 regulated PINK1-dependent mitophagy protected duck follicular granulosa cells from acute heat stress injury.
    Chen Yang, Pei Luo, You-Tian Yang, Xin-Liang Fu, Bing-Xin Li, Xu Shen, Dan-Ning Xu, Yun-Mao Huang, Yun-Bo Tian, Wen-Jun Liu.
      The mitochondrial quality control system is crucial in maintaining cellular homeostasis during environmental stress. Granulosa cells are the main cells secreting steroid hormones, and mitochondria are the key organelles for steroid hormone synthesis. The impact of the mitochondrial quality control system on granulosa cells' steroid hormone synthesis and survival under heat stress is still unclear. Here, we showed that acute heat stress induces mitochondrial damage and significantly increases the number of mitophagy-like vesicles in the cytoplasm of duck ovary granulosa cells at the ultra-structural level. Meanwhile, we also found heat stress significantly increased mitochondrial fission and mitophagy-related protein expression levels both in vivo and in vitro. Furthermore, by confocal fluorescence analysis, we discovered that LC3 was distributed spot-like manner near the nucleus in the heat treatment group, and the LC3 spots and lysosomes were colocalized with Mito-Tracker in the heat treatment group. We further detected the mitophagy-related protein in the cytoplasm and mitochondria, respectively. Results showed that the PINK1 protein was significantly increased both in cytoplasm and mitochondria, while the LC3-Ⅱ/LC3-Ⅰ ratio increase only occurred in mitochondrial. In addition, the autophagy protein induced by acute heat treatment was effectively inhibited by the mitophagy inhibitor CysA. Finally, we demonstrated that the alteration of cellular mitophagy by siRNA interference with Drp1 and PINK1 inhibited the steroid synthesis of granulosa cells and increased cell apoptosis. Study provides strong evidence that the Drp1 regulated PINK1-dependent mitophagy pathway protects follicular granulosa cells from acute heat stress-induced injury.
    Keywords:  Drp1; PINK1; granulosa cells; heat stress; mitophagy
    DOI:  https://doi.org/10.1016/j.psj.2023.103247
  25. FEBS J. 2023 Nov 20.
    OPTN gene therapy increases autophagy and protects mitochondria in SOD1-G93A-expressing transgenic mice and cells.
    Di Wen, Yingxiao Ji, Yuanyuan Li, Weisong Duan, Yanyan Wang, Zhongyao Li, Meichun Tao, Yakun Liu.
      Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by progressive motor neuron (MN) death. Mutation of the superoxide dismutase 1 (SOD1) gene, which results in abnormal protein aggregation, is one of the causes of familial ALS. Autophagic dysfunction occurs in SOD1-G93A mutant mice as the disease progresses, but the aetiology of this disease is still unclear. Optineurin (OPTN) is an adaptor that is involved in autophagy and participates in aggrephagy and mitophagy. Previous studies have established that OPTN mutations contribute to diseases such as glaucoma and ALS. However, the function of OPTN in autophagy and mitophagy has not been intensively investigated in models of ALS. In this study, we assessed the beneficial effect of OPTN on autophagy and mitochondrial function by intrathecally injecting adeno-associated virus 9 (AAV9)-OPTN into SOD1-G93A transgenic mice, and by administering lentivirus (LV)-OPTN to cells expressing the SOD1-G93A mutant protein. The expression of voltage dependent anion channel 1 (VDAC1) was increased and autophagy was elevated after OPTN gene therapy, as shown by a lower level of p62 and a higher level of microtubule-associated protein 1A/1B-light chain 3 (LC3)-II. Moreover, using electron microscopy, we observed a hyperpolarized mitochondrial transmembrane potential and reversal of mitochondrial morphological abnormalities. Furthermore, the protein level of TANK-binding kinase 1 (TBK1) was increased, suggesting that mitophagy was increased. Our findings from both animal and cell line studies strongly suggest that OPTN gene therapy is a powerful strategy to increase autophagy and protect mitochondria to prevent the progression of ALS, and could be effective in the treatment of ALS.
    Keywords:  MMP; OPTN; SOD1-G93A transgenic mice; amyotrophic lateral sclerosis; autophagy pathway
    DOI:  https://doi.org/10.1111/febs.17009
  26. Int J Mol Sci. 2023 Nov 11. pii: 16219. [Epub ahead of print]24(22):
    Induction of Autophagy and Its Role in Peripheral Nerve Regeneration after Peripheral Nerve Injury.
    Dong Keon Yon, Yong Jun Kim, Dong Choon Park, Su Young Jung, Sung Soo Kim, Joon Hyung Yeo, Jeongmin Lee, Jae Min Lee, Seung Geun Yeo.
      No matter what treatment is used after nerve transection, a complete cure is impossible, so basic and clinical research is underway to find a cure. As part of this research, autophagy is being investigated for its role in nerve regeneration. Here, we review the existing literature regarding the involvement and significance of autophagy in peripheral nerve injury and regeneration. A comprehensive literature review was conducted to assess the induction and role of autophagy in peripheral nerve injury and subsequent regeneration. Studies were included if they were prospective or retrospective investigations of autophagy and facial or peripheral nerves. Articles not mentioning autophagy or the facial or peripheral nerves, review articles, off-topic articles, and those not written in English were excluded. A total of 14 peripheral nerve studies that met these criteria, including 11 involving sciatic nerves, 2 involving facial nerves, and 1 involving the inferior alveolar nerve, were included in this review. Studies conducted on rats and mice have demonstrated activation of autophagy and expression of related factors in peripheral nerves with or without stimulation of autophagy-inducing factors such as rapamycin, curcumin, three-dimensional melatonin nerve scaffolds, CXCL12, resveratrol, nerve growth factor, lentinan, adipose-derived stem cells and melatonin, basic fibroblast growth factor, and epothilone B. Among the most studied of these factors in relation to degeneration and regeneration of facial and sciatic nerves are LC3II/I, PI3K, mTOR, Beclin-1, ATG3, ATG5, ATG7, ATG9, and ATG12. This analysis indicates that autophagy is involved in the process of nerve regeneration following facial and sciatic nerve damage. Inadequate autophagy induction or failure of autophagy responses can result in regeneration issues after peripheral nerve damage. Animal studies suggest that autophagy plays an important role in peripheral nerve degeneration and regeneration.
    Keywords:  autophagy; degeneration; facial nerve; regeneration
    DOI:  https://doi.org/10.3390/ijms242216219
  27. Cancers (Basel). 2023 Nov 13. pii: 5390. [Epub ahead of print]15(22):
    The Important Role of Protein Kinases in the p53 Sestrin Signaling Pathway.
    Karsten Gülow, Deniz Tümen, Claudia Kunst.
      p53, a crucial tumor suppressor and transcription factor, plays a central role in the maintenance of genomic stability and the orchestration of cellular responses such as apoptosis, cell cycle arrest, and DNA repair in the face of various stresses. Sestrins, a group of evolutionarily conserved proteins, serve as pivotal mediators connecting p53 to kinase-regulated anti-stress responses, with Sestrin 2 being the most extensively studied member of this protein family. These responses involve the downregulation of cell proliferation, adaptation to shifts in nutrient availability, enhancement of antioxidant defenses, promotion of autophagy/mitophagy, and the clearing of misfolded proteins. Inhibition of the mTORC1 complex by Sestrins reduces cellular proliferation, while Sestrin-dependent activation of AMP-activated kinase (AMPK) and mTORC2 supports metabolic adaptation. Furthermore, Sestrin-induced AMPK and Unc-51-like protein kinase 1 (ULK1) activation regulates autophagy/mitophagy, facilitating the removal of damaged organelles. Moreover, AMPK and ULK1 are involved in adaptation to changing metabolic conditions. ULK1 stabilizes nuclear factor erythroid 2-related factor 2 (Nrf2), thereby activating antioxidative defenses. An understanding of the intricate network involving p53, Sestrins, and kinases holds significant potential for targeted therapeutic interventions, particularly in pathologies like cancer, where the regulatory pathways governed by p53 are often disrupted.
    Keywords:  Sestrins; autophagy; mTORC; mitophagy; nuclear factor erythroid 2-related factor 2 (Nrf2); p53; stress response
    DOI:  https://doi.org/10.3390/cancers15225390
  28. Microb Pathog. 2023 Nov 16. pii: S0882-4010(23)00483-7. [Epub ahead of print]185 106450
    Clostridioides difficile PCR ribotypes 001 and 084 can trigger autophagy process in human intestinal Caco-2 cells.
    Masoumeh Azimirad, Maryam Noori, Sahar Amirkamali, Gelareh Nasiri, Hamid Asadzadeh Aghdaei, Abbas Yadegar, Daniel J Klionsky, Mohammad Reza Zali.
      Autophagy is a homeostatic process that can promote cell survival or death. However, the exact role of autophagy in Clostridioides difficile infection (CDI) is still not precisely elucidated. Here, we investigate the role of distinct C. difficile ribotypes (RTs) in autophagy induction using Caco-2 cells. The expression analysis of autophagy-associated genes and related miRNAs were examined following treatment of Caco-2 cells with C. difficile after 4 and 8 h using RT-qPCR. Toxin production was assessed using enzyme-linked immunosorbent assay (ELISA). Immunofluorescence analysis was performed to detect MAP1LC3B/LC3B, followed by an autophagic flux analysis. C. difficile significantly reduced the viability of Caco-2 cells in comparison with untreated cells. Elevated levels of LC3-II and SQSTM1/p62 by C. difficile RT001 and RT084 in the presence of E64d/leupeptin confirmed the induction of autophagy activity. Similarly, the immunofluorescence analysis demonstrated that C. difficile RT001 and RT084 significantly increased the amount of LC3-positive structures in Caco-2 cells. The induction of autophagy was further demonstrated by increased levels of LC3B, ULK1, ATG12, PIK3C3/VPS34, BECN1 (beclin 1), ATG5, and ATG16L1 transcripts and reduced levels of AKT and MTOR gene expression. The expression levels of MIR21 and MIR30B, microRNAs that suppress autophagy, were differentially affected by C. difficile. In conclusion, the present work revealed that C. difficile bacteria can induce autophagy through both toxin-dependent and -independent mechanisms. Also, our results suggest the potential role of other C. difficile virulence factors in autophagy modulation using intestinal cells in vitro.
    Keywords:  Autophagy; Caco-2 cells; Clostridioides difficile; LC3B; MIR21; MIR30B; RT001; RT084
    DOI:  https://doi.org/10.1016/j.micpath.2023.106450
  29. Molecules. 2023 Nov 14. pii: 7594. [Epub ahead of print]28(22):
    Antidepressants as Autophagy Modulators for Cancer Therapy.
    Leping He, Yuanfeng Fu, Yuxi Tian, Xiaofeng Wang, Xuejun Zhou, Ren-Bo Ding, Xingzhu Qi, Jiaolin Bao.
      Cancer is a major global public health problem with high morbidity. Depression is known to be a high-frequency complication of cancer diseases that decreases patients' life quality and increases the mortality rate. Therefore, antidepressants are often used as a complementary treatment during cancer therapy. During recent decades, various studies have shown that the combination of antidepressants and anticancer drugs increases treatment efficiency. In recent years, further emerging evidence has suggested that the modulation of autophagy serves as one of the primary anticancer mechanisms for antidepressants to suppress tumor growth. In this review, we introduce the anticancer potential of antidepressants, including tricyclic antidepressants (TCAs), tetracyclic antidepressants (TeCAs), selective serotonin reuptake inhibitors (SSRIs), and serotonin-norepinephrine reuptake inhibitors (SNRIs). In particular, we focus on their autophagy-modulating mechanisms for regulating autophagosome formation and lysosomal degradation. We also discuss the prospect of repurposing antidepressants as anticancer agents. It is promising to repurpose antidepressants for cancer therapy in the future.
    Keywords:  antidepressants; autophagy; cancer therapy; drug repurposing; molecular mechanism
    DOI:  https://doi.org/10.3390/molecules28227594
  30. Autophagy. 2023 Nov 22.
    Correction of symptoms of Huntington disease by genistein through FOXO3-mediated autophagy stimulation.
    Karolina Pierzynowska, Magdalena Podlacha, Lidia Gaffke, Estera Rintz, Karolina Wiśniewska, Zuzanna Cyske, Grzegorz Węgrzyn.
      Huntington disease (HD) is a neurodegenerative disorder caused by a mutation in the HTT gene. The expansion of CAG triplets leads to the appearance of misfolded HTT (huntingtin) forming aggregates and leading to impairment of neuronal functions. Here we demonstrate that stimulation of macroautophagy/autophagy by genistein (4',5,7-trihydroxyisoflavone or 5,7-dihydroxy-3-(4-hydroxyphenyl)-4 H-1-benzopyran-4-one) caused a reduction of levels of mutated HTT in brains of HD mice and correction of their behavior as assessed in a battery of cognitive, anxiety and motor tests, even if the compound was administered after symptoms had developed in the animals. Biochemical and immunological parameters were also improved in HD mice. Studies on molecular mechanisms of genistein-mediated stimulation of autophagy in HD cells indicated the involvement of the FOXO3-related pathway. In conclusion, treatment with genistein stimulates the autophagy process in the brains of HD mice, leading to correction of symptoms of HD, suggesting that it might be considered as a potential drug for this disease. Combined with a very recently published report indicating that impaired autophagy may be a major cause of neurodegenerative changes, these results may indicate the way to the development of effective therapeutic approaches for different neurodegenerative diseases by testing compounds (or possibly combinations of compounds) capable of stimulating autophagy and/or unblocking this process.
    Keywords:  Autophagy activation; FOXO3; Huntington disease mouse model; correction of neurodegenerative disease symptoms; genistein (4′,5,7-trihydroxyisoflavone)
    DOI:  https://doi.org/10.1080/15548627.2023.2286116
  31. Cells. 2023 Nov 17. pii: 2644. [Epub ahead of print]12(22):
    SMYD3 Modulates AMPK-mTOR Signaling Balance in Cancer Cell Response to DNA Damage.
    Martina Lepore Signorile, Paola Sanese, Elisabetta Di Nicola, Candida Fasano, Giovanna Forte, Katia De Marco, Vittoria Disciglio, Marialaura Latrofa, Antonino Pantaleo, Greta Varchi, Alberto Del Rio, Valentina Grossi, Cristiano Simone.
      Cells respond to DNA damage by activating a complex array of signaling networks, which include the AMPK and mTOR pathways. After DNA double-strand breakage, ATM, a core component of the DNA repair system, activates the AMPK-TSC2 pathway, leading to the inhibition of the mTOR cascade. Recently, we showed that both AMPK and mTOR interact with SMYD3, a methyltransferase involved in DNA damage response. In this study, through extensive molecular characterization of gastrointestinal and breast cancer cells, we found that SMYD3 is part of a multiprotein complex that is involved in DNA damage response and also comprises AMPK and mTOR. In particular, upon exposure to the double-strand break-inducing agent neocarzinostatin, SMYD3 pharmacological inhibition suppressed AMPK cascade activation and thereby promoted the mTOR pathway, which reveals the central role played by SMYD3 in the modulation of AMPK-mTOR signaling balance during cancer cell response to DNA double-strand breaks. Moreover, we found that SMYD3 can methylate AMPK at the evolutionarily conserved residues Lys411 and Lys424. Overall, our data revealed that SMYD3 can act as a bridge between the AMPK and mTOR pathways upon neocarzinostatin-induced DNA damage in gastrointestinal and breast cancer cells.
    Keywords:  AMPK; DNA damage; SMYD3; breast cancer; gastrointestinal cancer; mTOR
    DOI:  https://doi.org/10.3390/cells12222644
  32. Int J Mol Sci. 2023 Nov 20. pii: 16542. [Epub ahead of print]24(22):
    The Natural Alkaloid Palmatine Selectively Induces Mitophagy and Restores Mitochondrial Function in an Alzheimer's Disease Mouse Model.
    Da-Ye Lee, Kang-Min Lee, Jee-Hyun Um, Young-Yeon Kim, Dong-Hyun Kim, Jeanho Yun.
      Palmatine, a natural alkaloid found in various plants, has been reported to have diverse pharmacological and biological effects, including anti-inflammatory, antioxidant, and cardiovascular effects. However, the role of palmatine in mitophagy, a fundamental process crucial for maintaining mitochondrial function, remains elusive. In this study, we found that palmatine efficiently induces mitophagy in various human cell lines. Palmatine specifically induces mitophagy and subsequently stimulates mitochondrial biogenesis. Palmatine did not interfere with mitochondrial function, similar to CCCP, suggesting that palmatine is not toxic to mitochondria. Importantly, palmatine treatment alleviated mitochondrial dysfunction in PINK1-knockout MEFs. Moreover, the administration of palmatine resulted in significant improvements in cognitive function and restored mitochondrial function in an Alzheimer's disease mouse model. This study identifies palmatine as a novel inducer of selective mitophagy. Our results suggest that palmatine-mediated mitophagy induction could be a potential strategy for Alzheimer's disease treatment and that natural alkaloids are potential sources of mitophagy inducers.
    Keywords:  Alzheimer’s disease; mitochondrial dysfunction; mitophagy; palmatine
    DOI:  https://doi.org/10.3390/ijms242216542
  33. Nat Neurosci. 2023 Nov 24.
    Lysosome regulation of microglia in Alzheimer's disease via TFEB-vacuolar ATPase.
      
    DOI:  https://doi.org/10.1038/s41593-023-01495-1
  34. Cells. 2023 Nov 08. pii: 2588. [Epub ahead of print]12(22):
    Sphingolipid-Based Synergistic Interactions to Enhance Chemosensitivity in Lung Cancer Cells.
    Susana Mesén-Porras, Andrea Rojas-Céspedes, José Arturo Molina-Mora, José Vega-Baudrit, Francisco Siles, Steve Quiros, Rodrigo Mora-Rodríguez.
      Tumor heterogeneity leads to drug resistance in cancer treatment with the crucial role of sphingolipids in cell fate and stress signaling. We analyzed sphingolipid metabolism and autophagic flux to study chemotherapeutic interactions on the A549 lung cancer model. Loaded cells with fluorescent sphingomyelin analog (BODIPY) and mCherry-EGFP-LC3B were used to track autophagic flux and assess cytotoxicity when cells are exposed to chemotherapy (epirubicin, cisplatin, and paclitaxel) together with sphingolipid pathway inhibitors and autophagy modulators. Our cell model approach employed fluorescent sphingolipid biosensors and a Gaussian Mixture Model of cell heterogeneity profiles to map the influence of chemotherapy on the sphingolipid pathway and infer potential synergistic interactions. Results showed significant synergy, especially when combining epirubicin with autophagy inducers (rapamycin and Torin), reducing cell viability. Cisplatin also synergized with a ceramidase inhibitor. However, paclitaxel often led to antagonistic effects. Our mapping model suggests that combining chemotherapies with autophagy inducers increases vesicle formation, possibly linked to ceramide accumulation, triggering cell death. However, the in silico model proposed ceramide accumulation in autophagosomes, and kinetic analysis provided evidence of sphingolipid colocalization in autophagosomes. Further research is needed to identify specific sphingolipids accumulating in autophagosomes. These findings offer insights into potential strategies for overcoming chemotherapy resistance by targeting the sphingolipid pathway.
    Keywords:  BODIPY; autophagy; cancer; sphingolipids pathway; synergisms
    DOI:  https://doi.org/10.3390/cells12222588
  35. Surv Ophthalmol. 2023 Nov 22. pii: S0039-6257(23)00162-5. [Epub ahead of print]
    Age-related macular degeneration and neurodegenerative disorders: Shared pathways in complex interactions.
    Sayena Jabbehdari, Anthony C Oganov, Fateme Rezagholi, Soheil Mohammadi, Hamid Harandi, Ghasem Yazdanpanah, J Fernando Arevalo.
      Age-related macular degeneration (AMD) is a leading cause of irreversible blindness in the elderly, and neurodegenerative disorders such as Alzheimer' disease and Parkinson disease are debilitating conditions that affect millions worldwide. Despite the different clinical manifestations of these diseases, growing evidence suggests that they share common pathways in their pathogenesis including inflammation, oxidative stress, and impaired autophagy. In this review, we explore the complex interactions between AMD and neurodegenerative disorders, focusing on their shared mechanisms and potential therapeutic targets. We also discuss the current opportunities and challenges for developing effective treatments that can target these pathways to prevent or slow down disease progression in AMD. Some of the promising strategies that we explore include modulating the immune response, reducing oxidative stress, enhancing autophagy and lysosomal function, and targeting specific protein aggregates or pathways. Ultimately, a better understanding of the shared pathways between AMD and neurodegenerative disorders may pave the way for novel and more efficacious treatments.
    Keywords:  Alzheimer's disease; Parkinson's disease; Retina; age related macular degeneration
    DOI:  https://doi.org/10.1016/j.survophthal.2023.11.003
  36. bioRxiv. 2023 Nov 10. pii: 2023.11.03.565498. [Epub ahead of print]
    Modulation of hepatic transcription factor EB activity during cold exposure uncovers direct regulation of bis(monoacylglycero)phosphate lipids by Pla2g15.
    Raghav Jain, Gisela Geoghegan, Jessica Davidson, Daniel J Nesbitt, Akira Abe, Xiaojuan Chao, Isabella James, Amy Cavanagh, Sylwia Michorowska, Rakesh Verma, Kathryn Scheuler, Vania Hinkovska-Galcheva, Evgenia Shishkova, Wen-Xing Ding, Joshua J Coon, James A Shayman, Judith A Simcox.
      Cold exposure is an environmental stress that elicits a rapid metabolic shift in endotherms and is required for survival. The liver provides metabolic flexibility through its ability to rewire lipid metabolism to respond to an increased demand in energy for thermogenesis. We leveraged cold exposure to identify novel lipids contributing to energy homeostasis and found that lysosomal bis(monoacylglycero)phosphate (BMP) lipids were significantly increased in the liver during acute cold exposure. BMP lipid changes occurred independently of lysosomal abundance but were dependent on the lysosomal transcriptional regulator transcription factor EB (TFEB). Knockdown of TFEB in hepatocytes decreased BMP lipid levels. Through molecular biology and biochemical assays, we found that TFEB regulates lipid catabolism during cold exposure and that TFEB knockdown mice were cold intolerant. To identify how TFEB regulates BMP lipid levels, we used a combinatorial approach to identify TFEB target Pla2g15 , a lysosomal phospholipase, as capable of degrading BMP lipids in in vitro liposome assays. Knockdown of Pla2g15 in hepatocytes led to a decrease in BMP lipid species. Together, our studies uncover a required role of TFEB in mediating lipid liver remodeling during cold exposure and identified Pla2g15 as an enzyme that regulates BMP lipid catabolism.
    DOI:  https://doi.org/10.1101/2023.11.03.565498
  37. Cells. 2023 Nov 18. pii: 2653. [Epub ahead of print]12(22):
    Effects of Everolimus in Modulating the Host Immune Responses against Mycobacterium tuberculosis Infection.
    Anmol Raien, Sofia Davis, Michelle Zhang, David Zitser, Michelle Lin, Graysen Pitcher, Krishna Bhalodia, Selvakumar Subbian, Vishwanath Venketaraman.
      The phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin (P13K/AKT/mTOR) pathway plays a key role in tuberculosis (TB) pathogenesis and infection. While the activity levels of this pathway during active infection are still debated, manipulating this pathway shows potential benefit for host-directed therapies. Some studies indicate that pathway inhibitors may have potential for TB treatment through upregulation of autophagy, while other studies do not encourage the use of these inhibitors due to possible host tissue destruction by Mycobacterium tuberculosis (M. tb) and increased infection risk. Investigating further clinical trials and their use of pathway inhibitors is necessary in order to ascertain their potential for TB treatment. This paper is particularly focused on the drug everolimus, an mTOR inhibitor. One of the first clinical trials sponsored by the Aurum Institute showed potential benefit in using everolimus as an adjunctive therapy for tuberculosis. Infection with tuberculosis is associated with a metabolic shift from oxidative phosphorylation towards glycolysis. The everolimus arm in the clinical trial showed further reduction than the control for both maximal and peak glycolytic activity. Compared with control, those receiving everolimus demonstrated increased lung function through forced expiratory volume in 1 s (FEV1) measurements, suggesting that everolimus may mitigate inflammation contributing to lung damage.
    Keywords:  Mycobacterium tuberculosis; autophagy; everolimus; host-directed therapy; mTOR
    DOI:  https://doi.org/10.3390/cells12222653
  38. Cell Death Dis. 2023 Nov 22. 14(11): 758
    3,4-dimethoxychalcone induces autophagy and reduces neointimal hyperplasia and aortic lesions in mouse models of atherosclerosis.
    Giulia Cerrato, Carlota Alvarez-Lucena, Allan Sauvat, Yanhua Hu, Sabrina Forveille, Guo Chen, Sylvère Durand, Fanny Aprahamian, Marion Leduc, Omar Motiño, Lisardo Boscá, Qingbo Xu, Oliver Kepp, Guido Kroemer.
      Autophagy inducers can prevent cardiovascular aging and age-associated diseases including atherosclerosis. Therefore, we hypothesized that autophagy-inducing compounds that act on atherosclerosis-relevant cells might have a protective role in the development of atherosclerosis. Here we identified 3,4-dimethoxychalcone (3,4-DC) as an inducer of autophagy in several cell lines from endothelial, myocardial and myeloid/macrophagic origin, as demonstrated by the aggregation of the autophagosome marker GFP-LC3 in the cytoplasm of cells, as well as the downregulation of its nuclear pool indicative of autophagic flux. In this respect, 3,4-DC showed a broader autophagy-inducing activity than another chalcone (4,4- dimethoxychalcone), spermidine and triethylene tetramine. Thus, we characterized the potential antiatherogenic activity of 3,4-DC in two different mouse models, namely, (i) neointima formation with smooth muscle expansion of vein segments grafted to the carotid artery and (ii) genetically predisposed ApoE-/- mice fed an atherogenic diet. In the vein graft model, local application of 3,4-DC was able to maintain the lumen of vessels and to reduce neointima lesions. In the diet-induced model, intraperitoneal injections of 3,4-DC significantly reduced the number of atherosclerotic lesions in the aorta. In conclusion, 3,4-DC stands out as an autophagy inducer with potent antiatherogenic activity.
    DOI:  https://doi.org/10.1038/s41419-023-06305-x
  39. Adv Sci (Weinh). 2023 Nov 20. e2304791
    Amino Acid-Starved Cancer Cells Utilize Macropinocytosis and Ubiquitin-Proteasome System for Nutrient Acquisition.
    Tianyi Wang, Yaming Zhang, Yuwei Liu, Yi Huang, Weiping Wang.
      To grow in nutrient-deprived tumor microenvironment, cancer cells often internalize and degrade extracellular proteins to refuel intracellular amino acids. However, the nutrient acquisition routes reported by previous studies are mainly restricted in autophagy-lysosomal pathway. It remains largely unknown if other protein degradation systems also contribute to the utilization of extracellular nutrients. Herein, it is demonstrated that under amino acid starvation, extracellular protein internalization through macropinocytosis and protein degradation through ubiquitin-proteasome system are activated as a nutrient supply route, sensitizing cancer cells to proteasome inhibition. By inhibiting both macropinocytosis and ubiquitin-proteasome system, an innovative approach to intensify amino acid starvation for cancer therapy is presented. To maximize therapeutic efficacy and minimize systemic side effects, a pH-responsive polymersome nanocarrier is developed to deliver therapeutic agents specifically to tumor tissues. This nanoparticle system provides an approach to exacerbate amino acid starvation for cancer therapy, which represents a promising strategy for cancer treatment.
    Keywords:  amino acid starvation; cancer starvation therapy; macropinocytosis; pH-responsive polymersomes; ubiquitin-proteasome system
    DOI:  https://doi.org/10.1002/advs.202304791
  40. CNS Neurosci Ther. 2023 Nov 21.
    Identification of mitophagy-associated proteins profile as potential plasma biomarkers of idiopathic Parkinson's disease.
    Shuangjie Qian, Haijun He, Xi Xiong, Ruixue Ai, Wenwen Wang, Huimin Zhu, Qianqian Ye, Shuoting Zhou, Hilde Nilsen, Chenglong Xie.
       BACKGROUND: Despite extensive work to identify diagnostic plasma markers for Parkinson's disease (PD), there are still no accepted and validated surrogate biomarkers. Mitophagy-associated proteins (MAPs), including PTEN-induced putative kinase 1 (PINK1), Parkin, phosphoglycerate mutase 5 (PGAM5), BCL2 interacting protein 3 (BNIP3), and phosphorylated-TBK1 (p-TBK1), are, to our best knowledge, not well studied as a panel of biomarkers of neurodegeneration in PD.
    METHODS: The study population comprised 116 age-matched controls (HC), 179 PD patients, alongside and 90 PD syndromes (PDs) divided between two cohorts: (i) the modeling cohort (cohort 1), including 150 PD, 97 HC, and 80 PDs; and (ii) the validated cohort (cohort 2), including 29 PD, 19 HC, and 10 PDs.
    RESULTS: MAPs are elevated in the plasma of PD patients. PINK1, Parkin, and PGAM5 displayed the top three measurable increase trends in amplitude compared to BNIP3 and p-TBK1. Moreover, the area under the curve (AUC) values of PINK1, PGAM5, and Parkin were ranked the top three MAP candidates in diagnosis accuracy for PD from HC, but the MAPs make it hard to differentiate PD from PDs. In addition, there are higher plasma PINK1-Parkin levels and prominent diagnostic accuracy in A-synuclein (+) subjects than in A-synuclein (-) subjects.
    CONCLUSIONS: These results uncover that plasma MAPs (PINK1, Parkin, and PGAM5) may be potentially useful diagnostic biomarkers for PD diagnosis. Studies on larger cohorts would be required to test whether elevated plasma MAP levels are related to PD risk or prognosis.
    Keywords:  MAPs; Parkinson's disease; biomarkers; diagnosis; mitophagy-associated proteins
    DOI:  https://doi.org/10.1111/cns.14532
  41. Antioxidants (Basel). 2023 Nov 16. pii: 2006. [Epub ahead of print]12(11):
    Improvement Effect of Mitotherapy on the Cognitive Ability of Alzheimer's Disease through NAD+/SIRT1-Mediated Autophagy.
    Xiaoxi Yang, Peiyu Zhou, Zizhen Zhao, Jingli Li, Zhigang Fan, Xiaorong Li, Zhihong Cui, Ailing Fu.
      To date, Alzheimer's disease (AD) has grown to be a predominant health challenge that disturbs the elderly population. Studies have shown that mitochondrial dysfunction is one of the most significant features of AD. Transplantation therapy of healthy mitochondria (mitotherapy), as a novel therapeutic strategy to restore mitochondrial function, is proposed to treat the mitochondria-associated disease. Also, the molecular mechanism of mitotherapy remains unclear. Here, we applied the mitotherapy in AD model mice induced by amyloid-β (Aβ) plaque deposition and suggested that autophagy would be an important mechanism of the mitotherapy. After the healthy mitochondria entered the defective neuronal cells damaged by the misfolded Aβ protein, autophagy was activated through the NAD+-dependent deacetylase sirtuin 1 (SIRT1) signal. The damaged mitochondria and Aβ protein were eliminated by autophagy, which could also decrease the content of radical oxygen species (ROS). Moreover, the levels of brain-derived neurotrophic factor (BDNF) and extracellular-regulated protein kinases (ERK) phosphorylation increased after mitotherapy, which would be beneficial to repair neuronal function. As a result, the cognitive ability of AD animals was ameliorated in a water maze test after the healthy mitochondria were administrated to the mice. The study indicated that mitotherapy would be an effective approach to AD treatment through the mechanism of autophagy activation.
    Keywords:  AD; NAD+/SIRT1; autophagy; mitotherapy
    DOI:  https://doi.org/10.3390/antiox12112006
  42. Cell Rep. 2023 Nov 23. pii: S2211-1247(23)01484-5. [Epub ahead of print]42(12): 113472
    Mitochondrial nucleoid condensates drive peripheral fission through high membrane curvature.
    Qixin Chen, Liu-Yi Liu, Zhiqi Tian, Zhou Fang, Kang-Nan Wang, Xintian Shao, Chengying Zhang, Weiwei Zou, Fiona Rowan, Kangqiang Qiu, Baohua Ji, Jun-Lin Guan, Dechang Li, Zong-Wan Mao, Jiajie Diao.
      Mitochondria are dynamic organelles that undergo fusion and fission events, in which the mitochondrial membrane and DNA (mtDNA) play critical roles. The spatiotemporal organization of mtDNA reflects and impacts mitochondrial dynamics. Herein, to study the detailed dynamics of mitochondrial membrane and mtDNA, we rationally develop a dual-color fluorescent probe, mtGLP, that could be used for simultaneously monitoring mitochondrial membrane and mtDNA dynamics via separate color outputs. By combining mtGLP with structured illumination microscopy to monitor mitochondrial dynamics, we discover the formation of nucleoid condensates in damaged mitochondria. We further reveal that nucleoid condensates promoted the peripheral fission of damaged mitochondria via asymmetric segregation. Through simulations, we find that the peripheral fission events occurred when the nucleoid condensates interacted with the highly curved membrane regions at the two ends of the mitochondria. Overall, we show that mitochondrial nucleoid condensates utilize peripheral fission to maintain mitochondrial homeostasis.
    Keywords:  CP: Cell biology; chemical biology
    DOI:  https://doi.org/10.1016/j.celrep.2023.113472
  43. Environ Res. 2023 Nov 22. pii: S0013-9351(23)02537-9. [Epub ahead of print] 117733
    Carbon black nanoparticles and cadmium co-exposure aggravates bronchial epithelial cells inflammation via autophagy-lysosome pathway.
    Liting Zheng, Rulin Mao, Xiaohong Liang, Yangyang Jia, Zehao Chen, Shuwei Yao, Yiguo Jiang, Yueting Shao.
      Carbon black nanoparticles (CBNPs) and cadmium (Cd) are major components of various air pollutants and cigarette smoke. Autophagy and inflammation both play critical roles in understanding the toxicity of particles and their components, as well as maintaining body homeostasis. However, the effects and mechanisms of CBNPs and Cd (CBNPs-Cd) co-exposure on the human respiratory system remain unclear. In this study, a CBNPs-Cd exposure model was constructed to explore the respiratory toxicity and combined mechanism of these chemicals on the autophagy-lysosome pathway in the context of respiratory inflammation. Co-exposure of CBNPs and Cd significantly increased the number of autophagosomes and lysosomes in human bronchial epithelial cells (16HBE) and mouse lung tissues compared to the control group, as well as the groups exposed to CBNPs and Cd alone. Autophagic markers, LC3II and P62 proteins, were up-regulated in 16HBE cells and mouse lung tissues after CBNPs-Cd co-exposure. However, treatment with Cq inhibitor (an indicator of lysosomal acid environment) resulted in a substantial decreased co-localization fluorescence of LC3 and lysosomes in the CBNPs-Cd combination group compared with the CBNPs-Cd single and control groups. No difference in LAMP1 protein expression was observed among the exposed groups. Adding 3 MA alleviated inflammatory responses, while applying the Baf-A1 inhibitor aggravated inflammation both in vitro and in vivo following CBNPs-Cd co-exposure. Factorial analysis showed no interaction between CBNPs and Cd in their effects on 16HBE cells. We demonstrated that co-exposure to CBNPs-Cd increases the synthesis of autophagosomes and regulates the acidic environment of lysosomes, thereby inhibiting autophagy-lysosome fusion and enhancing the inflammatory response in both 16HBE cells and mouse lung. These findings provide evidence for a comprehensive understanding of the interaction between CBNPs and Cd in mixed pollutants, as well as for the prevention and control of occupational exposure to these two chemicals.
    Keywords:  Autophagy; Cadmium; Carbon black nanoparticles; Inflammation; Lysosome
    DOI:  https://doi.org/10.1016/j.envres.2023.117733
  44. Cell Death Discov. 2023 Nov 18. 9(1): 419
    Iron derived from NCOA4-mediated ferritinophagy causes cellular senescence via the cGAS-STING pathway.
    Hong-Ying Li, Ting-Ting Wei, Miao Zhuang, Cheng-Ye Tan, Tian-Hua Xie, Jiping Cai, Yong Yao, Lingpeng Zhu.
      Cellular senescence is a hallmark of aging and has been linked to age-related diseases. Age-related macular degeneration (AMD), the most common aging-related retinal disease, is prospectively associated with retinal pigment epithelial (RPE) senescence. However, the mechanism of RPE cell senescence remains unknown. In this study, tert-butyl hydroperoxide (TBH)-induced ARPE-19 cells and D-galactose-treated C57 mice were used to examine the cause of elevated iron in RPE cell senescence. Ferric ammonium citrate (FAC)-treated ARPE-19 cells and C57 mice were used to elucidated the mechanism of iron overload-induced RPE cell senescence. Molecular biology techniques for the assessment of iron metabolism, cellular senescence, autophagy, and mitochondrial function in vivo and in vitro. We found that iron level was increased during the senescence process. Ferritin, a major iron storage protein, is negatively correlated with intracellular iron levels and cell senescence. NCOA4, a cargo receptor for ferritinophagy, mediates degradation of ferritin and contributes to iron accumulation. Besides, we found that iron overload leads to mitochondrial dysfunction. As a result, mitochondrial DNA (mtDNA) is released from damaged mitochondria to cytoplasm. Cytoplasm mtDNA activates the cGAS-STING pathway and promotes inflammatory senescence-associated secretory phenotype (SASP) and cell senescence. Meanwhile, iron chelator Deferoxamine (DFO) significantly rescues RPE senescence and retinopathy induced by FAC or D-gal in mice. Taken together, these findings imply that iron derived from NCOA4-mediated ferritinophagy causes cellular senescence via the cGAS-STING pathway. Inhibiting iron accumulation may represent a promising therapeutic approach for age-related diseases such as AMD.
    DOI:  https://doi.org/10.1038/s41420-023-01712-7
  45. Neurotoxicology. 2023 Nov 17. pii: S0161-813X(23)00146-8. [Epub ahead of print]99 282-291
    Kynurenine attenuates mitochondrial depolarization and neuronal cell death induced by rotenone exposure independently of AhR-mediated parkin induction in SH-SY5Y differentiated cells.
    Rosario García-Aguilar, Arturo Ortega, Esther López-Bayghen, Leticia Ramírez-Martínez, Ada Rodriguez-Campuzano, Fátima Murillo-González, Guillermo Elizondo, Libia Vega.
      Rotenone is a pesticide commonly used in agriculture that is associated with the risk of developing Parkinson's disease (PD) by inducing mitochondrial damage. As a protective cell response to different challenges, they activate mitophagy, which involves parkin activity. Parkin is an E3 ubiquitin ligase necessary in the initial steps of mitophagy, and its overexpression protects against parkinsonian effects in different models. Recent studies have reported that the aryl hydrocarbon receptor (AHR), a ligand-dependent transcription factor, induces parkin expression. Kynurenine, an endogenous AHR ligand, promotes neuroprotection in chronic neurodegenerative disorders, such as PD, although its neuroprotective mechanism needs to be fully understood. Therefore, we evaluated whether the overexpression of parkin by AHR activation with kynurenine promotes autophagy and reduces the neurotoxicity induced by rotenone in SH-SY5Y cells differentiated to dopaminergic neurons. SH-SY5Y neurons were treated with rotenone or pretreated with kynurenine or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and parkin levels, apoptosis, mitochondrial potential membrane, and autophagy were determined. The results showed that kynurenine and TCDD treatments induced parkin expression in an AHR-dependent manner. Kynurenine pretreatment inhibited rotenone-induced neuronal apoptosis in 17%, and the loss of mitochondrial membrane potential in 30% when compare to rotenone alone, together with a decrease in autophagy. By contrast, although TCDD treatment increased parkin levels, non-neuroprotective effects were observed. The kynurenine protective activity was AHR independent, suggesting that parkin induction might not be related to this effect. On the other hand, kynurenine treatment inhibited alpha amine-3-hydroxy-5-methyl-4-isoxazol propionic acid and N-methyl-D-aspartate receptors, which are well-known excitotoxicity mediators activated by rotenone exposure.
    Keywords:  Aryl hydrocarbon receptor; Autophagy; Depolarization; Kynurenine; Neuroprotection; Parkin
    DOI:  https://doi.org/10.1016/j.neuro.2023.11.007
  46. Nat Commun. 2023 Nov 21. 14(1): 7567
    PTK2B promotes TBK1 and STING oligomerization and enhances the STING-TBK1 signaling.
    Yongfang Lin, Jing Yang, Qili Yang, Sha Zeng, Jiayu Zhang, Yuanxiang Zhu, Yuxin Tong, Lin Li, Weiqi Tan, Dahua Chen, Qinmiao Sun.
      TANK-binding kinase 1 (TBK1) is a key kinase in regulating antiviral innate immune responses. While the oligomerization of TBK1 is critical for its full activation, the molecular mechanism of how TBK1 forms oligomers remains unclear. Here, we show that protein tyrosine kinase 2 beta (PTK2B) acts as a TBK1-interacting protein and regulates TBK1 oligomerization. Functional assays reveal that PTK2B depletion reduces antiviral signaling in mouse embryonic fibroblasts, macrophages and dendritic cells, and genetic experiments show that Ptk2b-deficient mice are more susceptible to viral infection than control mice. Mechanistically, we demonstrate that PTK2B directly phosphorylates residue Tyr591 of TBK1, which increases TBK1 oligomerization and activation. In addition, we find that PTK2B also interacts with the stimulator of interferon genes (STING) and can promote its oligomerization in a kinase-independent manner. Collectively, PTK2B enhances the oligomerization of TBK1 and STING via different mechanisms, subsequently regulating STING-TBK1 activation to ensure efficient antiviral innate immune responses.
    DOI:  https://doi.org/10.1038/s41467-023-43419-4
  47. Viruses. 2023 Nov 03. pii: 2209. [Epub ahead of print]15(11):
    Seneca Valley Virus Degrades STING via PERK and ATF6-Mediated Reticulophagy.
    Ling Bai, Rui Zhang, Haixue Zheng, Zhixiong Zhang, Zhidong Zhang, Yanmin Li.
      Seneca Valley Virus (SVV), a member of the Picornaviridae family, is an emerging porcine virus that can cause vesicular disease in pigs. However, the immune evasion mechanism of SVV remains unclear, as does its interaction with other pathways. STING (Stimulator of interferon genes) is typically recognized as a critical factor in innate immune responses to DNA virus infection, but its role during SVV infection remains poorly understood. In the present study, we observed that STING was degraded in SVV-infected PK-15 cells, and SVV replication in the cells was affected when STING was knockdown or overexpressed. The STING degradation observed was blocked when the SVV-induced autophagy was inhibited by using autophagy inhibitors (Chloroquine, Bafilomycin A1) or knockdown of autophagy related gene 5 (ATG5), suggesting that SVV-induced autophagy is responsible for STING degradation. Furthermore, the STING degradation was inhibited when reticulophagy regulator 1 (FAM134B), a reticulophagy related receptor, was knocked down, indicating that SVV infection induces STING degradation via reticulophagy. Further study showed that in eukaryotic translation initiation factor 2 alpha kinase 3 (PERK)/activating transcription factor 6 (ATF6) deficient cells, SVV infection failed to induce reticulophagy-medaited STING degradation, indicating that SVV infection caused STING degradation via PERK/ATF6-mediated reticulophagy. Notably, blocking reticulophagy effectively hindered SVV replication. Overall, our study suggested that SVV infection resulted in STING degradation via PERK and ATF6-mediated reticulophagy, which may be an immune escape strategy of SVV. This finding improves the understanding of the intricate interplay between viruses and their hosts and provides a novel strategy for the development of novel antiviral drugs.
    Keywords:  STING; SVV; UPR; autophagy
    DOI:  https://doi.org/10.3390/v15112209
  48. Cells. 2023 Nov 10. pii: 2600. [Epub ahead of print]12(22):
    Acne Transcriptomics: Fundamentals of Acne Pathogenesis and Isotretinoin Treatment.
    Bodo C Melnik.
      This review on acne transcriptomics allows for deeper insights into the pathogenesis of acne and isotretinoin's mode of action. Puberty-induced insulin-like growth factor 1 (IGF-1), insulin and androgen signaling activate the kinase AKT and mechanistic target of rapamycin complex 1 (mTORC1). A Western diet (hyperglycemic carbohydrates and milk/dairy products) also co-stimulates AKT/mTORC1 signaling. The AKT-mediated phosphorylation of nuclear FoxO1 and FoxO3 results in their extrusion into the cytoplasm, a critical switch which enhances the transactivation of lipogenic and proinflammatory transcription factors, including androgen receptor (AR), sterol regulatory element-binding transcription factor 1 (SREBF1), peroxisome proliferator-activated receptor γ (PPARγ) and signal transducer and activator of transcription 3 (STAT3), but reduces the FoxO1-dependent expression of GATA binding protein 6 (GATA6), the key transcription factor for infundibular keratinocyte homeostasis. The AKT-mediated phosphorylation of the p53-binding protein MDM2 promotes the degradation of p53. In contrast, isotretinoin enhances the expression of p53, FoxO1 and FoxO3 in the sebaceous glands of acne patients. The overexpression of these proapoptotic transcription factors explains isotretinoin's desirable sebum-suppressive effect via the induction of sebocyte apoptosis and the depletion of BLIMP1(+) sebocyte progenitor cells; it also explains its adverse effects, including teratogenicity (neural crest cell apoptosis), a reduced ovarian reserve (granulosa cell apoptosis), the risk of depression (the apoptosis of hypothalamic neurons), VLDL hyperlipidemia, intracranial hypertension and dry skin.
    Keywords:  FoxO1; FoxO3; acne; apoptosis; isotretinoin; mTORC1; p53; pathogenesis; therapy; transcriptomics
    DOI:  https://doi.org/10.3390/cells12222600
  49. Neuron. 2023 Nov 16. pii: S0896-6273(23)00804-8. [Epub ahead of print]
    Amelioration of Tau and ApoE4-linked glial lipid accumulation and neurodegeneration with an LXR agonist.
    Alexandra Litvinchuk, Jung H Suh, Jing L Guo, Karin Lin, Sonnet S Davis, Nga Bien-Ly, Eric Tycksen, G Travis Tabor, Javier Remolina Serrano, Melissa Manis, Xin Bao, Choonghee Lee, Megan Bosch, Enmanuel J Perez, Carla M Yuede, Anil G Cashikar, Jason D Ulrich, Gilbert Di Paolo, David M Holtzman.
      Apolipoprotein E (APOE) is a strong genetic risk factor for late-onset Alzheimer's disease (LOAD). APOE4 increases and APOE2 decreases risk relative to APOE3. In the P301S mouse model of tauopathy, ApoE4 increases tau pathology and neurodegeneration when compared with ApoE3 or the absence of ApoE. However, the role of ApoE isoforms and lipid metabolism in contributing to tau-mediated degeneration is unknown. We demonstrate that in P301S tau mice, ApoE4 strongly promotes glial lipid accumulation and perturbations in cholesterol metabolism and lysosomal function. Increasing lipid efflux in glia via an LXR agonist or Abca1 overexpression strongly attenuates tau pathology and neurodegeneration in P301S/ApoE4 mice. We also demonstrate reductions in reactive astrocytes and microglia, as well as changes in cholesterol biosynthesis and metabolism in glia of tauopathy mice in response to LXR activation. These data suggest that promoting efflux of glial lipids may serve as a therapeutic approach to ameliorate tau and ApoE4-linked neurodegeneration.
    Keywords:  Abca1; ApoE4; LXR agonist; Tau; cholesterol metabolism; lipid; microglia
    DOI:  https://doi.org/10.1016/j.neuron.2023.10.023
  50. Int J Mol Sci. 2023 Nov 10. pii: 16163. [Epub ahead of print]24(22):
    Multiomics of GCN4-Dependent Replicative Lifespan Extension Models Reveals Gcn4 as a Regulator of Protein Turnover in Yeast.
    Blaise L Mariner, Daniel P Felker, Ryla J Cantergiani, Jack Peterson, Mark A McCormick.
      We have shown that multiple tRNA synthetase inhibitors can increase lifespan in both the nematode C. elegans and the budding yeast S. cerevisiae by acting through the conserved transcription factor Gcn4 (yeast)/ATF-4 (worms). To further understand the biology downstream from this conserved transcription factor in the yeast model system, we looked at two different yeast models known to have upregulated Gcn4 and GCN4-dependent increased replicative lifespan. These two models were rpl31aΔ yeast and yeast treated with the tRNA synthetase inhibitor borrelidin. We used both proteomic and RNAseq analysis of a block experimental design that included both of these models to identify GCN4-dependent changes in these two long-lived strains of yeast. Proteomic analysis of these yeast indicate that the long-lived yeast have increased abundances of proteins involved in amino acid biosynthesis. The RNAseq of these same yeast uncovered further regulation of protein degradation, identifying the differential expression of genes associated with autophagy and the ubiquitin-proteasome system (UPS). The data presented here further underscore the important role that GCN4 plays in the maintenance of protein homeostasis, which itself is an important hallmark of aging. In particular, the changes in autophagy and UPS-related gene expression that we have observed could also have wide-ranging implications for the understanding and treatment of diseases of aging that are associated with protein aggregation.
    Keywords:  ATF-4; ATF4; Gcn4; autophagy; tRNA synthetase; ubiquitin–proteasome system
    DOI:  https://doi.org/10.3390/ijms242216163
  51. Pathology. 2023 Oct 27. pii: S0031-3025(23)00259-3. [Epub ahead of print]
    Autophagy indicators in oral squamous cell carcinoma.
    Meena Pangarkar, Uttara Wagh, Anand Pathak.
      Autophagy plays an important role in maintaining cellular homeostasis. Dysregulation of autophagy has been linked to a number of diseases, including cancer. We retrospectively evaluated immunohistochemical expression of the autophagy markers LC3B and p62 and the autophagy regulator mTOR as an indicator of autophagy in 100 surgically resected primary oral squamous cell carcinoma (OSCC) samples and sought associations with various clinicopathological factors. The expression of all three proteins was significantly higher in malignant squamous cells than in benign squamous cells in the free mucosal margin adjacent to the OSCC. Male sex, higher tumour (T) stage, node (N) stage and tumour, node, metastasis (TNM) stage were significantly associated with high marker expression; age and histological grade showed no significant association. LC3B, p62 and mTOR expression were positively correlated with one another in OSCCs, and the correlation was significant for LC3B and mTOR as well as for LC3B and p62. Disease-free survival showed an inverse correlation with high mTOR expression. Our data suggest that autophagy inhibitors and mTOR inhibitors may have a therapeutic role in the treatment of OSCCs.
    Keywords:  LC3B; Oral squamous cell carcinoma; autophagy; mTOR; p62
    DOI:  https://doi.org/10.1016/j.pathol.2023.08.014
  52. Chem Biol Interact. 2023 Nov 22. pii: S0009-2797(23)00486-6. [Epub ahead of print] 110819
    Ovatodiolide induces autophagy-mediated cell death through the p62-Keap1-Nrf2 signaling pathway in chronic myeloid leukemia cells.
    Qingqing Xia, Jing Xie, Jianguo Zhang, Lingmin Zhang, Yingying Zhou, Bihong Zhu, Yanfang Wu, Zaixing Yang, Jie Li.
      Ovatodiolide is a macrocyclic diterpenoid compound with various biological activities that displays considerable anticancer potential in different tumor models. However, the underlying mechanism for this antineoplastic activity remains unclear. The aim of the present study was to investigate the anticancer effect and possible molecular mechanism of ovatodiolide in human chronic myeloid leukemia (CML). Ovatodiolide suppressed cell colony formation and induced apoptosis in the K562 and KU812 cells. We also observed that ovatodiolide enhanced the production of reactive oxygen species (ROS), activated Nrf2 signaling, and inhibited mTOR phosphorylation. Autophagic flux was shown to be enhanced after treatment with ovatodiolide in K562 cells. Furthermore, autophagy inhibition alleviated ovatodiolide-induced cell apoptosis, whereas autophagy promotion aggravated apoptosis in CML cells. These results demonstrated that ovatodiolide activates autophagy-mediated cell death in CML cells. Additionally, ovatodiolide transcriptionally activated the expression of p62, and the p62 levels were negatively regulated by autophagy. Moreover, p62-Keap1-Nrf2 signaling was confirmed to be involved in ovatodiolide-induced cell death. Accordingly, LC3B knockdown augmented the ovatodiolide-induced p62 expression, increased the p62-Keap1 interaction, and enhanced the translocation of Nrf2 into the nucleus. In contrast, p62 inhibition abolished the effects that were induced through ovatodiolide treatment. Nrf2 inhibition with ML385 diminished the protective effect of autophagy inhibition in CML cells. Collectively, our results indicate that ovatodiolide induces oxidative stress and provokes autophagy, which effectively decreases the expression of p62 and weakens the protective effect of Nrf2 signaling activation, thus contributing to apoptosis in CML cells.
    Keywords:  Autophagy; Autophagy-mediated cell death; Chronic myeloid leukemia; Ovatodiolide; p62-Keap1-Nrf2
    DOI:  https://doi.org/10.1016/j.cbi.2023.110819
  53. Int J Mol Sci. 2023 Nov 16. pii: 16412. [Epub ahead of print]24(22):
    Mitochondrial GpC and CpG DNA Hypermethylation Cause Metabolic Stress-Induced Mitophagy and Cholestophagy.
    Claudia Theys, Joe Ibrahim, Ligia Mateiu, Archibold Mposhi, Laura García-Pupo, Tim De Pooter, Peter De Rijk, Mojca Strazisar, İkbal Agah İnce, Iuliana Vintea, Marianne G Rots, Wim Vanden Berghe.
      Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by a constant accumulation of lipids in the liver. This hepatic lipotoxicity is associated with a dysregulation of the first step in lipid catabolism, known as beta oxidation, which occurs in the mitochondrial matrix. Eventually, this dysregulation will lead to mitochondrial dysfunction. To evaluate the possible involvement of mitochondrial DNA methylation in this lipid metabolic dysfunction, we investigated the functional metabolic effects of mitochondrial overexpression of CpG (MSssI) and GpC (MCviPI) DNA methyltransferases in relation to gene expression and (mito)epigenetic signatures. Overall, the results show that mitochondrial GpC and, to a lesser extent, CpG methylation increase bile acid metabolic gene expression, inducing the onset of cholestasis through mito-nuclear epigenetic reprogramming. Moreover, both increase the expression of metabolic nuclear receptors and thereby induce basal overactivation of mitochondrial respiration. The latter promotes mitochondrial swelling, favoring lipid accumulation and metabolic-stress-induced mitophagy and autophagy stress responses. In conclusion, both mitochondrial GpC and CpG methylation create a metabolically challenging environment that induces mitochondrial dysfunction, which may contribute to the progression of MASLD.
    Keywords:  MASLD; autophagy; bile acid metabolism; cholestasis; lipid metabolism; mitochondrial epigenetics
    DOI:  https://doi.org/10.3390/ijms242216412
  54. PLoS Biol. 2023 Nov 20. 21(11): e3002290
    ATG9A regulates the dissociation of recycling endosomes from microtubules to form liquid influenza A virus inclusions.
    Sílvia Vale-Costa, Temitope Akhigbe Etibor, Daniela Brás, Ana Laura Sousa, Mariana Ferreira, Gabriel G Martins, Victor Hugo Mello, Maria João Amorim.
      It is now established that many viruses that threaten public health establish condensates via phase transitions to complete their lifecycles, and knowledge on such processes may offer new strategies for antiviral therapy. In the case of influenza A virus (IAV), liquid condensates known as viral inclusions, concentrate the 8 distinct viral ribonucleoproteins (vRNPs) that form IAV genome and are viewed as sites dedicated to the assembly of the 8-partite genomic complex. Despite not being delimited by host membranes, IAV liquid inclusions accumulate host membranes inside as a result of vRNP binding to the recycling endocytic marker Rab11a, a driver of the biogenesis of these structures. We lack molecular understanding on how Rab11a-recycling endosomes condensate specifically near the endoplasmic reticulum (ER) exit sites upon IAV infection. We show here that liquid viral inclusions interact with the ER to fuse, divide, and slide. We uncover that, contrary to previous indications, the reported reduction in recycling endocytic activity is a regulated process rather than a competition for cellular resources involving a novel role for the host factor ATG9A. In infection, ATG9A mediates the removal of Rab11a-recycling endosomes carrying vRNPs from microtubules. We observe that the recycling endocytic usage of microtubules is rescued when ATG9A is depleted, which prevents condensation of Rab11a endosomes near the ER. The failure to produce viral inclusions accumulates vRNPs in the cytosol and reduces genome assembly and the release of infectious virions. We propose that the ER supports the dynamics of liquid IAV inclusions, with ATG9A facilitating their formation. This work advances our understanding on how epidemic and pandemic influenza genomes are formed. It also reveals the plasticity of recycling pathway endosomes to undergo condensation in response to infection, disclosing new roles for ATG9A beyond its classical involvement in autophagy.
    DOI:  https://doi.org/10.1371/journal.pbio.3002290
  55. J Mol Cell Cardiol. 2023 Nov 16. pii: S0022-2828(23)00169-4. [Epub ahead of print]186 31-44
    β-hydroxybutyrate administered at reperfusion reduces infarct size and preserves cardiac function by improving mitochondrial function through autophagy in male mice.
    Yuxin Chu, Yutao Hua, Lihao He, Jin He, Yunxi Chen, Jing Yang, Ismail Mahmoud, Fanfang Zeng, Xiaochang Zeng, Gloria A Benavides, Victor M Darley-Usmar, Martin E Young, Scott W Ballinger, Sumanth D Prabhu, Cheng Zhang, Min Xie.
      Ischemia/reperfusion (I/R) injury after revascularization contributes ∼50% of infarct size and causes heart failure, for which no established clinical treatment exists. β-hydroxybutyrate (β-OHB), which serves as both an energy source and a signaling molecule, has recently been reported to be cardioprotective when administered immediately before I/R and continuously after reperfusion. This study aims to determine whether administering β-OHB at the time of reperfusion with a single dose can alleviate I/R injury and, if so, to define the mechanisms involved. We found plasma β-OHB levels were elevated during ischemia in STEMI patients, albeit not to myocardial protection level, and decreased after revascularization. In mice, compared with normal saline, β-OHB administrated at reperfusion reduced infarct size (by 50%) and preserved cardiac function, as well as activated autophagy and preserved mtDNA levels in the border zone. Our treatment with one dose β-OHB reached a level achievable with fasting and strenuous physical activity. In neonatal rat ventricular myocytes (NRVMs) subjected to I/R, β-OHB at physiologic level reduced cell death, increased autophagy, preserved mitochondrial mass, function, and membrane potential, in addition to attenuating reactive oxygen species (ROS) levels. ATG7 knockdown/knockout abolished the protective effects of β-OHB observed both in vitro and in vivo. Mechanistically, β-OHB's cardioprotective effects were associated with inhibition of mTOR signaling. In conclusion, β-OHB, when administered at reperfusion, reduces infarct size and maintains mitochondrial homeostasis by increasing autophagic flux (potentially through mTOR inhibition). Since β-OHB has been safely tested in heart failure patients, it may be a viable therapeutic to reduce infarct size in STEMI patients.
    Keywords:  Autophagy; Ischemia-reperfusion injury; Mitochondria; β-hydroxybutyrate
    DOI:  https://doi.org/10.1016/j.yjmcc.2023.11.001
  56. Nat Commun. 2023 Nov 22. 14(1): 7631
    Structure of the DDB1-AMBRA1 E3 ligase receptor complex linked to cell cycle regulation.
    Ming Liu, Yang Wang, Fei Teng, Xinyi Mai, Xi Wang, Ming-Yuan Su, Goran Stjepanovic.
      AMBRA1 is a tumor suppressor protein that functions as a substrate receptor of the ubiquitin conjugation system with roles in autophagy and the cell cycle regulatory network. The intrinsic disorder of AMBRA1 has thus far precluded its structural determination. To solve this problem, we analyzed the dynamics of AMBRA1 using hydrogen deuterium exchange mass spectrometry (HDX-MS). The HDX results indicated that AMBRA1 is a highly flexible protein and can be stabilized upon interaction with DDB1, the adaptor of the Cullin4A/B E3 ligase. Here, we present the cryo-EM structure of AMBRA1 in complex with DDB1 at 3.08 Å resolution. The structure shows that parts of the N- and C-terminal structural regions in AMBRA1 fold together into the highly dynamic WD40 domain and reveals how DDB1 engages with AMBRA1 to create a binding scaffold for substrate recruitment. The N-terminal helix-loop-helix motif and WD40 domain of AMBRA1 associate with the double-propeller fold of DDB1. We also demonstrate that DDB1 binding-defective AMBRA1 mutants prevent ubiquitination of the substrate Cyclin D1 in vitro and increase cell cycle progression. Together, these results provide structural insights into the AMBRA1-ubiquitin ligase complex and suggest a mechanism by which AMBRA1 acts as a hub involved in various physiological processes.
    DOI:  https://doi.org/10.1038/s41467-023-43174-6
  57. Development. 2023 Nov 17. pii: dev.201974. [Epub ahead of print]
    C. elegans hedgehog/patched-like morphogen-receptor pair GRD-1/PTR-11 modulates developmental rate.
    Sinclair W Emans, Armen Yerevanian, Fasih M Ahsan, Jen Rotti, Yifei Zhou, Lucydalila Cedillo, Alexander A Soukas.
      Both Hedgehog (Hh) and target of rapamycin complex 2 (TORC2) are central, evolutionarily conserved signaling pathways that regulate development and metabolism. In C. elegans, loss of essential TORC2 component RICTOR (rict-1) causes delayed development, shortened lifespan, reduced brood, small size, and increased fat. Here we report that knockdown of Hedgehog-related morphogen grd-1 and its Patched-related receptor ptr-11 rescues delayed development in TORC2 loss of function mutants, and grd-1/ptr-11 overexpression delays wild-type development similar to TORC2 loss of function animals. These findings potentially indicate an unexpected role for grd-1/ptr-11 in slowing developmental rate downstream of a nutrient sensing pathway. Further, we implicate chronic stress transcription factor pqm-1 as a key transcriptional effector of grd-1/ptr-11 in slowing whole-organism growth. We propose that TORC2 and grd-1/ptr-11 may act linearly or converge on pqm-1 to delay organismal development.
    Keywords:  Development; Hedgehog; Metabolism; Patched; TOR complex 2 (TORC2); Target of Rapamycin (TOR)
    DOI:  https://doi.org/10.1242/dev.201974
  58. J Virol. 2023 Nov 20. e0150123
    DLG1 promotes the antiviral innate immune response by inhibiting p62-mediated autophagic degradation of IKKε.
    Huasong Chang, Hao Wu, Peili Hou, Muhammad Aizaz, Rukun Yang, Aibiao Xiang, Wenjing Qi, Hongbin He, Hongmei Wang.
       IMPORTANCE: The type-I interferon (IFN-I) signaling pathway is the first line of antiviral innate immunity. It must be precisely regulated against virus-induced damage. The tightly regulated mechanisms of action of host genes in the antiviral innate immune signaling pathway are still worth studying. Here, we report a novel role of DLG1 in positively regulating the IκB kinase epsilon (IKKε)-mediated IFN-I signaling response against negative-stranded RNA virus replication, whereas the RNA virus inhibits the expression of DLG1 for immune escape. Importantly, the E3 ligase March2 interacts with and promotes K27-linked polyubiquitination of IKKε, and p62 is a cargo receptor that recognizes ubiquitinated IKKε for eventual autophagic degradation. Together, the current findings elucidate the role of DLG1 in the antiviral IFN-I signaling pathway and viral infection repression.
    Keywords:  DLG1; IKKε; autophagy; innate immunity; interferon; ubiquitination
    DOI:  https://doi.org/10.1128/jvi.01501-23
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