bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2024–02–04
71 papers selected by
Viktor Korolchuk, Newcastle University
  1. Mitophagy in plants: Emerging regulators of mitochondrial targeting for selective autophagy.
  2. Arginyltransferase 1 modulates p62-driven autophagy via mTORC1/AMPk signaling.
  3. The role of autophagy in insulin resistance and glucolipid metabolism and potential use of autophagy modulating natural products in the treatment of type 2 diabetes mellitus.
  4. mTORC1 controls murine postprandial hepatic glycogen synthesis via Ppp1r3b.
  5. Regulation of autophagy by perilysosomal calcium: a new player in β-cell lipotoxicity.
  6. Optineurin provides a mitophagy contact site for TBK1 activation.
  7. Translocator protein (TSPO) ligands attenuate mitophagy deficits in the SH-SY5Y cellular model of Alzheimer's disease via the autophagy adaptor P62.
  8. A novel therapeutic target for kidney diseases: Lessons learned from starvation response.
  9. DENND6A links Arl8b to a Rab34/RILP/dynein complex, regulating lysosomal positioning and autophagy.
  10. Mitophagy Activation by Rapamycin Enhances Mitochondrial Function and Cognition in 5×FAD Mice.
  11. The Contributions of the Endolysosomal Compartment and Autophagy to APOEɛ4 Allele-Mediated Increase in Alzheimer's Disease Risk.
  12. ANXA2 (annexin A2) is crucial to ATG7-mediated autophagy, leading to tumor aggressiveness in triple-negative breast cancer cells.
  13. Deregulated mitochondrial quality control, the heel of Achilles in elucidating the role of autophagy in SARM1-mediated axon degeneration.
  14. Leukemia and mitophagy: a novel perspective for understanding oncogenesis and resistance.
  15. The role of autophagy in prostate cancer and prostatic diseases: a new therapeutic strategy.
  16. Targeting the mammalian target of rapamycin pathway in neurological manifestations of Covid-19.
  17. Axonal distribution of mitochondria maintains neuronal autophagy during aging via eIF2β.
  18. Folate depletion induces erythroid differentiation through perturbation of de novo purine synthesis.
  19. Rab11 regulates autophagy at dendritic spines in an mTOR- and NMDA-dependent manner.
  20. Development and characterization of phospho-ubiquitin antibodies to monitor PINK1-PRKN signaling in cells and tissue.
  21. Selective disruption of mTORC1 and mTORC2 in VTA astrocytes induces depression and anxiety-like behaviors in mice.
  22. FREE1 regulates phagophore closure in plants.
  23. Glp-1 Mimetics and Autophagy in Diabetic Milieu: State-of-the-Art.
  24. Autophagy prevents graft failure during murine Graft versus Host Disease.
  25. Exploring the ATG9A interactome uncovers interaction with VPS13A.
  26. Identifying Autophagy-Associated Proteins and Chemicals with a Random Walk-Based Method within Heterogeneous Interaction Network.
  27. 5-ALA localises to the autophagy compartment and increases its fluorescence upon autophagy enhancement through caloric restriction and spermidine treatment in human glioblastoma.
  28. Degradative autophagy regulates the homeostasis of miRnas to control cancer development.
  29. Mechanistic exploration of autophagy and aging by RNA interference.
  30. OTUD3 suppresses the mTORC1 signaling by deubiquitinating KPTN.
  31. Complex Topology of Ubiquitin Chains Mediates Lysosomal Degradation of MrgC Proteins.
  32. The C9orf72-SMCR8 complex suppresses primary ciliogenesis as a RAB8A GAP.
  33. The N-terminal region of the ATG8 autophagy protein LC3C is essential for its membrane fusion properties.
  34. G-quadruplexes in MTOR and induction of autophagy.
  35. Mitochondrial damage and impaired mitophagy contribute to disease progression in SCA6.
  36. FGF21-mediated autophagy: Remodeling the homeostasis in response to stress in liver diseases.
  37. Mitophagy curtails cytosolic mtDNA-dependent activation of cGAS/STING inflammation during aging.
  38. The p24-family and COPII subunit SEC24C facilitate the clearance of alpha1-antitrypsin Z from the endoplasmic reticulum to lysosomes.
  39. The dual role of autophagy in HPV-positive head and neck squamous cell carcinoma: a systematic review.
  40. Restoration of autophagy activity by dipsacoside B alleviates exhaustive exercise-induced kidney injury via the AMPK/mTOR pathway.
  41. Natural products targeting macroautophagy signaling in hepatocellular carcinoma therapy: Recent evidence and perspectives.
  42. Novel exosomal circEGFR facilitates triple negative breast cancer autophagy via promoting TFEB nuclear trafficking and modulating miR-224-5p/ATG13/ULK1 feedback loop.
  43. GPI-anchored Gas1 protein regulates cytosolic proteostasis in budding yeast.
  44. Sirtuin3 promotes the degradation of hepatic Z alpha-1 antitrypsin through lipophagy.
  45. Regulation of ULK1 by WTAP/IGF2BP3 axis enhances mitophagy and progression in epithelial ovarian cancer.
  46. Molecular mechanisms underlying the BIRC6-mediated regulation of apoptosis and autophagy.
  47. Lipid droplets and fatty acid-induced lipotoxicity: in a nutshell.
  48. HIF-1 contributes to autophagy activation via BNIP3 to facilitate renal fibrosis in hypoxia in vitro and UUO in vivo.
  49. Mitochondrial protein C15ORF48 is a stress-independent inducer of autophagy that regulates oxidative stress and autoimmunity.
  50. Role of autophagy and mitophagy of group 2 innate lymphoid cells in allergic and local allergic rhinitis.
  51. Edwardsiella piscicida causes iron storage disorders by an autophagy pathway in fish monocytes/macrophages.
  52. Silver nanoparticles induce endothelial cytotoxicity through ROS-mediated mitochondria-lysosome damage and autophagy perturbation: The protective role of N-acetylcysteine.
  53. Loss of interleukin 1 signaling causes impairment of microglia- mediated synapse elimination and autistic-like behaviour in mice.
  54. miRNA family miR-29 inhibits PINK1-PRKN dependent mitophagy via ATG9A.
  55. OPA1 mutation affects autophagy and triggers senescence in autosomal dominant optic atrophy plus fibroblasts.
  56. Lucanthone, a Potential PPT1 inhibitor, Perturbs Stemness, Reduces Tumor Microtube Formation and Slows the Growth of Temozolomide-Resistant Gliomas in Vivo.
  57. The cocoon into a butterfly: why the HVA22 family proteins turned out to be the reticulophagy receptors in plants？.
  58. Mitochondrial dysfunction in NPC1-deficiency is not rescued by drugs targeting the glucosylceramidase GBA2 and the cholesterol-binding proteins TSPO and StARD1.
  59. Loss of mitogen-activated protein kinase phosphate-5 aggravates islet dysfunction in mice with type 1 and type 2 diabetes.
  60. Migrasomal autophagosomes relieve endoplasmic reticulum stress in glioblastoma cells.
  61. DUSP4 maintains the survival and LSD1 protein stability in esophageal squamous cell carcinoma cells by inhibiting JNK signaling-dependent autophagy.
  62. Unveiling the Intricacies of Autophagy in Asthma: Unraveling Novel Therapeutic Avenues.
  63. NUPR1 contributes to activate TFE3-dependent autophagy leading to cervical cancer proliferation.
  64. Meeting summary of The NYO3 5th NO-Age/AD meeting and the 1st Norway-UK joint meeting on ageing and dementia: recent progress on the mechanisms and interventional strategies.
  65. Cell biology of Parkinson's disease: Mechanisms of synaptic, lysosomal, and mitochondrial dysfunction.
  66. Lentiviral gene therapy with IGF2-tagged GAA normalizes the skeletal muscle proteome in murine Pompe disease.
  67. Comparative analysis of primate and pig cells reveals primate-specific PINK1 expression and phosphorylation.
  68. Autophagy-dependent alternative splicing of ribosomal protein S24 produces a more stable isoform that aids in hypoxic cell survival.
  69. Multiple mechanisms activate GCN2 eIF2 kinase in response to diverse stress conditions.
  70. Q-switched 1064 nm Nd: YAG laser restores skin photoageing by activating autophagy by TGFβ1 and ITGB1.
  71. The Parkinson's Disease related mutant VPS35 (D620N) amplifies the LRRK2 response to endolysosomal stress.
  1. J Microsc. 2024 Jan 31.
    Mitophagy in plants: Emerging regulators of mitochondrial targeting for selective autophagy.
    Patrick J Duckney, Pengwei Wang, Patrick J Hussey.
      The degradation and turnover of mitochondria is fundamental to Eukaryotes and is a key homeostatic mechanism for maintaining functional mitochondrial populations. Autophagy is an important pathway by which mitochondria are degraded, involving their sequestration into membrane-bound autophagosomes and targeting to lytic endosomal compartments (the lysosome in animals, the vacuole in plants and yeast). Selective targeting of mitochondria for autophagy, also known as mitophagy, distinguishes mitochondria from other cell components for degradation and is necessary for the regulation of mitochondria-specific cell processes. In mammals and yeast, mitophagy has been well characterised and is regulated by numerous pathways with diverse and important functions in the regulation of cell homeostasis, metabolism and responses to specific stresses. In contrast, we are only just beginning to understand the importance and functions of mitophagy in plants, chiefly as the proteins that target mitochondria for autophagy in plants are only recently emerging. Here, we discuss the current progress of our understanding of mitophagy in plants, the importance of mitophagy for plant life and the regulatory autophagy proteins involved in mitochondrial degradation. In particular, we will discuss the recent emergence of mitophagy receptor proteins that selectively target mitochondria for autophagy, and discuss the missing links in our knowledge of mitophagy-regulatory proteins in plants compared to animals and yeast.
    Keywords:  Arabidopsis; TRB1; TraB; autophagy; contact site; homeostasis; mitochondria; mitophagy; plant; stress
    DOI:  https://doi.org/10.1111/jmi.13267
  2. Cell Commun Signal. 2024 Jan 31. 22(1): 87
    Arginyltransferase 1 modulates p62-driven autophagy via mTORC1/AMPk signaling.
    Laura V Bonnet, Anabela Palandri, Jesica B Flores-Martin, Marta E Hallak.
       BACKGROUND: Arginyltransferase (Ate1) orchestrates posttranslational protein arginylation, a pivotal regulator of cellular proteolytic processes. In eukaryotic cells, two interconnected systems-the ubiquitin proteasome system (UPS) and macroautophagy-mediate proteolysis and cooperate to maintain quality protein control and cellular homeostasis. Previous studies have shown that N-terminal arginylation facilitates protein degradation through the UPS. Dysregulation of this machinery triggers p62-mediated autophagy to ensure proper substrate processing. Nevertheless, how Ate1 operates through this intricate mechanism remains elusive.
    METHODS: We investigated Ate1 subcellular distribution through confocal microscopy and biochemical assays using cells transiently or stably expressing either endogenous Ate1 or a GFP-tagged Ate1 isoform transfected in CHO-K1 or MEFs, respectively. To assess Ate1 and p62-cargo clustering, we analyzed their colocalization and multimerization status by immunofluorescence and nonreducing immunoblotting, respectively. Additionally, we employed Ate1 KO cells to examine the role of Ate1 in autophagy. Ate1 KO MEFs cells stably expressing GFP-tagged Ate1-1 isoform were used as a model for phenotype rescue. Autophagy dynamics were evaluated by analyzing LC3B turnover and p62/SQSTM1 levels under both steady-state and serum-starvation conditions, through immunoblotting and immunofluorescence. We determined mTORC1/AMPk activation by assessing mTOR and AMPk phosphorylation through immunoblotting, while mTORC1 lysosomal localization was monitored by confocal microscopy.
    RESULTS: Here, we report a multifaceted role for Ate1 in the autophagic process, wherein it clusters with p62, facilitates autophagic clearance, and modulates its signaling. Mechanistically, we found that cell-specific inactivation of Ate1 elicits overactivation of the mTORC1/AMPk signaling hub that underlies a failure in autophagic flux and subsequent substrate accumulation, which is partially rescued by ectopic expression of Ate1. Statistical significance was assessed using a two-sided unpaired t test with a significance threshold set at P<0.05.
    CONCLUSIONS: Our findings uncover a critical housekeeping role of Ate1 in mTORC1/AMPk-regulated autophagy, as a potential therapeutic target related to this pathway, that is dysregulated in many neurodegenerative and cancer diseases.
    Keywords:  Arginylation; Arginyltransferase 1; Autophagy; Posttranslational modification; mTORC1; p62/SQSTM1
    DOI:  https://doi.org/10.1186/s12964-024-01499-9
  3. Diabetes Metab Res Rev. 2024 Jan;40(1): e3762
    The role of autophagy in insulin resistance and glucolipid metabolism and potential use of autophagy modulating natural products in the treatment of type 2 diabetes mellitus.
    Xiaoxue Yang, Wenwen Ding, Ziyi Chen, Kaiyi Lai, Ying Liu.
      Type 2 diabetes mellitus (T2DM) is a severe, long-term condition characterised by disruptions in glucolipid and energy metabolism. Autophagy, a fundamental cellular process, serves as a guardian of cellular health by recycling and renewing cellular components. To gain a comprehensive understanding of the vital role that autophagy plays in T2DM, we conducted an extensive search for high-quality publications across databases such as Web of Science, PubMed, Google Scholar, and SciFinder and used keywords like 'autophagy', 'insulin resistance', and 'type 2 diabetes mellitus', both individually and in combinations. A large body of evidence underscores the significance of activating autophagy in alleviating T2DM symptoms. An enhanced autophagic activity, either by activating the adenosine monophosphate-activated protein kinase and sirtuin-1 signalling pathways or inhibiting the mechanistic target of rapamycin complex 1 signalling pathway, can effectively improve insulin resistance and balance glucolipid metabolism in key tissues like the hypothalamus, skeletal muscle, liver, and adipose tissue. Furthermore, autophagy can increase β-cell mass and functionality in the pancreas. This review provides a narrative summary of autophagy regulation with an emphasis on the intricate connection between autophagy and T2DM symptoms. It also discusses the therapeutic potentials of natural products with autophagy activation properties for the treatment of T2DM conditions. Our findings suggest that autophagy activation represents an innovative approach of treating T2DM.
    Keywords:  autophagy; cell metabolism; insulin resistance; natural products; type 2 diabetes mellitus
    DOI:  https://doi.org/10.1002/dmrr.3762
  4. J Clin Invest. 2024 Jan 30. pii: e173782. [Epub ahead of print]
    mTORC1 controls murine postprandial hepatic glycogen synthesis via Ppp1r3b.
    Kahealani Uehara, Won Dong Lee, Megan Stefkovich, Dipsikha Biswas, Dominic Santoleri, Anna E Garcia Whitlock, William J Quinn Iii, Talia N Coopersmith, Kate Townsend Creasy, Daniel J Rader, Kei Sakamoto, Joshua D Rabinowitz, Paul M Titchenell.
      In response to a meal, insulin drives hepatic glycogen synthesis to help regulate systemic glucose homeostasis. The mechanistic target of rapamycin complex 1 (mTORC1) is a well-established insulin target and contributes to the postprandial control of liver lipid metabolism, autophagy, and protein synthesis. However, its role in hepatic glucose metabolism is less understood. Here, we used metabolomics, isotope tracing, and mouse genetics to define a role for liver mTORC1 signaling in the control of postprandial glycolytic intermediates and glycogen deposition. We show that mTORC1 is required for glycogen synthase activity and glycogenesis. Mechanistically, hepatic mTORC1 activity promotes the feeding-dependent induction of Ppp1r3b, a gene encoding a phosphatase important for glycogen synthase activity whose polymorphisms are linked to human diabetes. Re-expression of Ppp1r3b in livers lacking mTORC1 signaling enhances glycogen synthase activity and restores postprandial glycogen content. mTORC1-dependent transcriptional control of Ppp1r3b is facilitated by FOXO1, a well characterized transcriptional regulator involved in the hepatic response to nutrient intake. Collectively, we identify a role for mTORC1 signaling in the transcriptional regulation of Ppp1r3b and the subsequent induction of postprandial hepatic glycogen synthesis.
    Keywords:  Endocrinology; Glucose metabolism; Insulin signaling; Metabolism
    DOI:  https://doi.org/10.1172/JCI173782
  5. Exp Mol Med. 2024 Feb 01.
    Regulation of autophagy by perilysosomal calcium: a new player in β-cell lipotoxicity.
    Ha Thu Nguyen, Andreas Wiederkehr, Claes B Wollheim, Kyu-Sang Park.
      Autophagy is an essential quality control mechanism for maintaining organellar functions in eukaryotic cells. Defective autophagy in pancreatic beta cells has been shown to be involved in the progression of diabetes through impaired insulin secretion under glucolipotoxic stress. The underlying mechanism reveals the pathologic role of the hyperactivation of mechanistic target of rapamycin (mTOR), which inhibits lysosomal biogenesis and autophagic processes. Moreover, accumulating evidence suggests that oxidative stress induces Ca2+ depletion in the endoplasmic reticulum (ER) and cytosolic Ca2+ overload, which may contribute to mTOR activation in perilysosomal microdomains, leading to autophagic defects and β-cell failure due to lipotoxicity. This review delineates the antagonistic regulation of autophagic flux by mTOR and AMP-dependent protein kinase (AMPK) at the lysosomal membrane, and both of these molecules could be activated by perilysosomal calcium signaling. However, aberrant and persistent Ca2+ elevation upon lipotoxic stress increases mTOR activity and suppresses autophagy. Therefore, normalization of autophagy is an attractive therapeutic strategy for patients with β-cell failure and diabetes.
    DOI:  https://doi.org/10.1038/s12276-024-01161-x
  6. EMBO J. 2024 Jan 29.
    Optineurin provides a mitophagy contact site for TBK1 activation.
    Koji Yamano, Momoha Sawada, Reika Kikuchi, Kafu Nagataki, Waka Kojima, Ryu Endo, Hiroki Kinefuchi, Atsushi Sugihara, Tomoshige Fujino, Aiko Watanabe, Keiji Tanaka, Gosuke Hayashi, Hiroshi Murakami, Noriyuki Matsuda.
      Tank-binding kinase 1 (TBK1) is a Ser/Thr kinase that is involved in many intracellular processes, such as innate immunity, cell cycle, and apoptosis. TBK1 is also important for phosphorylating the autophagy adaptors that mediate the selective autophagic removal of damaged mitochondria. However, the mechanism by which PINK1-Parkin-mediated mitophagy activates TBK1 remains largely unknown. Here, we show that the autophagy adaptor optineurin (OPTN) provides a unique platform for TBK1 activation. Both the OPTN-ubiquitin and the OPTN-pre-autophagosomal structure (PAS) interaction axes facilitate assembly of the OPTN-TBK1 complex at a contact sites between damaged mitochondria and the autophagosome formation sites. At this assembly point, a positive feedback loop for TBK1 activation is initiated that accelerates hetero-autophosphorylation of the protein. Expression of monobodies engineered here to bind OPTN impaired OPTN accumulation at contact sites, as well as the subsequent activation of TBK1, thereby inhibiting mitochondrial degradation. Taken together, these data show that a positive and reciprocal relationship between OPTN and TBK1 initiates autophagosome biogenesis on damaged mitochondria.
    Keywords:  Autophagy; Mitochondria; PINK1; Parkin; Ubiquitin
    DOI:  https://doi.org/10.1038/s44318-024-00036-1
  7. Biochimie. 2024 Jan 25. pii: S0300-9084(24)00030-0. [Epub ahead of print]
    Translocator protein (TSPO) ligands attenuate mitophagy deficits in the SH-SY5Y cellular model of Alzheimer's disease via the autophagy adaptor P62.
    Lauren H Fairley, Amandine Grimm, Steffen A Herff, Anne Eckert.
      Mitochondrial dysfunction has been widely implicated in the pathogenesis of Alzheimer's disease (AD), with accumulation of damaged and dysfunctional mitochondria occurring early in the disease. Mitophagy, which governs mitochondrial turnover and quality control, is impaired in the AD brain, and strategies aimed at enhancing mitophagy have been identified as promising therapeutic targets. The translocator protein (TSPO) is an outer mitochondrial membrane protein that is upregulated in AD, and ligands targeting TSPO have been shown to exert neuroprotective effects in mouse models of AD. However, whether TSPO ligands modulate mitophagy in AD has not been explored. Here, we provide evidence that the TSPO-specific ligands Ro5-4864 and XBD173 attenuate mitophagy deficits and mitochondrial fragmentation in a cellular model of AD overexpressing the human amyloid precursor protein (APP). Ro5-4864 and XBD173 appear to enhance mitophagy via modulation of the autophagic cargo receptor P62/SQSTM1, in the absence of an effect on PARK2, PINK1, or LC3 level. Taken together, these findings indicate that TSPO ligands may be promising therapeutic agents for ameliorating mitophagy deficits in AD.
    Keywords:  Alzheimer's disease; Amyloid; Autophagy; Mitochondria; Mitophagy; TSPO; Translocator protein
    DOI:  https://doi.org/10.1016/j.biochi.2024.01.012
  8. Pharmacol Ther. 2024 Jan 28. pii: S0163-7258(24)00010-X. [Epub ahead of print]254 108590
    A novel therapeutic target for kidney diseases: Lessons learned from starvation response.
    Kosuke Yamahara, Mako Yasuda-Yamahara, Shinji Kume.
      The prevalence of chronic kidney disease (CKD) is increasing worldwide, making the disease an urgent clinical challenge. Caloric restriction has various anti-aging and organ-protective effects, and unraveling its molecular mechanisms may provide insight into the pathophysiology of CKD. In response to changes in nutritional status, intracellular nutrient signaling pathways show adaptive changes. When nutrients are abundant, signals such as mechanistic target of rapamycin complex 1 (mTORC1) are activated, driving cell proliferation and other processes. Conversely, others, such as sirtuins and AMP-activated protein kinase, are activated during energy scarcity, in an attempt to compensate. Autophagy, a cellular self-maintenance mechanism that is regulated by such signals, has also been reported to contribute to the progression of various kidney diseases. Furthermore, in recent years, ketone bodies, which have long been considered to be detrimental, have been reported to play a role as starvation signals, and thereby to have renoprotective effects, via the inhibition of mTORC1. Therefore, in this review, we discuss the role of mTORC1, which is one of the most extensively studied nutrient-related signals associated with kidney diseases, autophagy, and ketone body metabolism; and kidney energy metabolism as a novel therapeutic target for CKD.
    Keywords:  Autophagy; CKD; Ketone body; Starvation response; mTORC1
    DOI:  https://doi.org/10.1016/j.pharmthera.2024.108590
  9. Nat Commun. 2024 Jan 31. 15(1): 919
    DENND6A links Arl8b to a Rab34/RILP/dynein complex, regulating lysosomal positioning and autophagy.
    Rahul Kumar, Maleeha Khan, Vincent Francis, Adriana Aguila, Gopinath Kulasekaran, Emily Banks, Peter S McPherson.
      Lysosomes help maintain cellular proteostasis, and defects in lysosomal positioning and function can cause disease, including neurodegenerative disorders. The spatiotemporal distribution of lysosomes is regulated by small GTPases including Rabs, which are activated by guanine nucleotide exchange factors (GEFs). DENN domain proteins are the largest family of Rab GEFs. Using a cell-based assay, we screened DENND6A, a member of the DENN domain protein family against all known Rabs and identified it as a potential GEF for 20 Rabs, including Rab34. Here, we demonstrate that DENND6A activates Rab34, which recruits a RILP/dynein complex to lysosomes, promoting lysosome retrograde transport. Further, we identify DENND6A as an effector of Arl8b, a major regulatory GTPase on lysosomes. We demonstrate that Arl8b recruits DENND6A to peripheral lysosomes to activate Rab34 and initiate retrograde transport, regulating nutrient-dependent lysosomal juxtanuclear repositioning. Loss of DENND6A impairs autophagic flux. Our findings support a model whereby Arl8b/DENND6A/Rab34-dependent lysosomal retrograde trafficking controls autophagy.
    DOI:  https://doi.org/10.1038/s41467-024-44957-1
  10. Behav Brain Res. 2024 Jan 30. pii: S0166-4328(24)00045-7. [Epub ahead of print] 114889
    Mitophagy Activation by Rapamycin Enhances Mitochondrial Function and Cognition in 5×FAD Mice.
    Wenrong Zheng, Kualiang Li, Meihua Zhong, Kejun Wu, Lele Zhou, Jie Huang, Libin Liu, Zhou Chen.
      Alzheimer's disease (AD) is the most prevalent form of dementia, characterized by severe mitochondrial dysfunction, which is an intracellular process that is significantly compromised in the early stages of AD. Mitophagy, the selective removal of damaged mitochondria, is a potential therapeutic strategy for AD. Rapamycin, a mammalian target of rapamycin (mTOR) inhibitor, augmented autophagy and mitigated cognitive impairment. Our study revealed that rapamycin enhances cognitive function by activating mitophagy, alleviating neuronal loss, and improving mitochondrial dysfunction in 5×FAD mice. Interestingly, the neuroprotective effect of rapamycin in AD were negated by treatment with 3-MA, a mitophagy inhibitor. Overall, our findings suggest that rapamycin ameliorates cognitive impairment in 5×FAD mice via mitophagy activation and its downstream PINK1-Parkin pathway, which aids in the clearance of amyloid-β (Aβ) and damaged mitochondria. This study reveals a novel mechanism involving mitophagy regulation underlying the therapeutic effect of rapamycin in AD. This study provides new insights and therapeutic targets for rapamycin in the treatment of AD. However, there are still some shortcomings in this topic; if we can further knock out the PINK1/Parkin gene in animals or use siRNA technology, we can further confirm the experimental results.
    Keywords:  5×FAD mice; Cognitive impairment; Mitochondrial dysfunction; Mitophagy; Rapamycin
    DOI:  https://doi.org/10.1016/j.bbr.2024.114889
  11. J Alzheimers Dis. 2024 ;97(3): 1007-1031
    The Contributions of the Endolysosomal Compartment and Autophagy to APOEɛ4 Allele-Mediated Increase in Alzheimer's Disease Risk.
    Ernest Amponsah Asiamah, Baofeng Feng, Ruiyun Guo, Xu Yaxing, Xiaofeng Du, Xin Liu, Jinyu Zhang, Huixian Cui, Jun Ma.
      Apolipoprotein E4 (APOE4), although yet-to-be fully understood, increases the risk and lowers the age of onset of Alzheimer's disease (AD), which is the major cause of dementia among elderly individuals. The endosome-lysosome and autophagy pathways, which are necessary for homeostasis in both neurons and glia, are dysregulated even in early AD. Nonetheless, the contributory roles of these pathways to developing AD-related pathologies in APOE4 individuals and models are unclear. Therefore, this review summarizes the dysregulations in the endosome-lysosome and autophagy pathways in APOE4 individuals and non-human models, and how these anomalies contribute to developing AD-relevant pathologies. The available literature suggests that APOE4 causes endosomal enlargement, increases endosomal acidification, impairs endosomal recycling, and downregulates exosome production. APOE4 impairs autophagy initiation and inhibits basal autophagy and autophagy flux. APOE4 promotes lysosome formation and trafficking and causes ApoE to accumulate in lysosomes. APOE4-mediated changes in the endosome, autophagosome and lysosome could promote AD-related features including Aβ accumulation, tau hyperphosphorylation, glial dysfunction, lipid dyshomeostasis, and synaptic defects. ApoE4 protein could mediate APOE4-mediated endosome-lysosome-autophagy changes. ApoE4 impairs vesicle recycling and endosome trafficking, impairs the synthesis of autophagy genes, resists being dissociated from its receptors and degradation, and forms a stable folding intermediate that could disrupt lysosome structure. Drugs such as molecular correctors that target ApoE4 molecular structure and enhance autophagy may ameliorate the endosome-lysosome-autophagy-mediated increase in AD risk in APOE4 individuals.
    Keywords:  Alzheimer’s disease; Apolipoprotein E; endosomes; lysosomes
    DOI:  https://doi.org/10.3233/JAD-230658
  12. Autophagy. 2024 Jan 30. 1-16
    ANXA2 (annexin A2) is crucial to ATG7-mediated autophagy, leading to tumor aggressiveness in triple-negative breast cancer cells.
    Minsoo Koh, Hyesol Lim, Hao Jin, Minjoo Kim, Yeji Hong, Young Keun Hwang, Yunjung Woo, Eun-Sook Kim, Sun Young Kim, Kyung Mee Kim, Hyun Kyung Lim, Joohee Jung, Sujin Kang, Boyoun Park, Han-Byoel Lee, Wonshik Han, Myung-Shik Lee, Aree Moon.
      Triple-negative breast cancer (TNBC) is associated with a poor prognosis and metastatic growth. TNBC cells frequently undergo macroautophagy/autophagy, contributing to tumor progression and chemotherapeutic resistance. ANXA2 (annexin A2), a potential therapeutic target for TNBC, has been reported to stimulate autophagy. In this study, we investigated the role of ANXA2 in autophagic processes in TNBC cells. TNBC patients exhibited high levels of ANXA2, which correlated with poor outcomes. ANXA2 increased LC3B-II levels following bafilomycin A1 treatment and enhanced autophagic flux in TNBC cells. Notably, ANXA2 upregulated the phosphorylation of HSF1 (heat shock transcription factor 1), resulting in the transcriptional activation of ATG7 (autophagy related 7). The mechanistic target of rapamycin kinase complex 2 (MTORC2) played an important role in ANXA2-mediated ATG7 transcription by HSF1. MTORC2 did not affect the mRNA level of ANXA2, but it was involved in the protein stability of ANXA2. HSPA (heat shock protein family A (Hsp70)) was a potential interacting protein with ANXA2, which may protect ANXA2 from lysosomal proteolysis. ANXA2 knockdown significantly increased sensitivity to doxorubicin, the first-line chemotherapeutic regimen for TNBC treatment, suggesting that the inhibition of autophagy by ANXA2 knockdown may overcome doxorubicin resistance. In a TNBC xenograft mouse model, we demonstrated that ANXA2 knockdown combined with doxorubicin administration significantly inhibited tumor growth compared to doxorubicin treatment alone, offering a promising avenue to enhance the effectiveness of chemotherapy. In summary, our study elucidated the molecular mechanism by which ANXA2 modulates autophagy, suggesting a potential therapeutic approach for TNBC treatment.Abbreviation: ATG: autophagy related; ChIP: chromatin-immunoprecipitation; HBSS: Hanks' balanced salt solution; HSF1: heat shock transcription factor 1; MTOR: mechanistic target of rapamycin kinase; TNBC: triple-negative breast cancer; TFEB: transcription factor EB; TFE3: transcription factor binding to IGHM enhancer 3.
    Keywords:  ATG7; Annexin A2; HSF1; MTOR; autophagy; triple-negative breast cancer
    DOI:  https://doi.org/10.1080/15548627.2024.2305063
  13. J Neurosci Res. 2024 Jan;102(1): e25292
    Deregulated mitochondrial quality control, the heel of Achilles in elucidating the role of autophagy in SARM1-mediated axon degeneration.
    Shuai Wang, Yifan Zhang, Mingxue Song, Xiulan Zhao, Fuyong Song.
      Autophagic dysfunction in neurodegenerative diseases is being extensively studied, yet the exact mechanism of macroautophagy/autophagy in axon degeneration is still elusive. A recent study by Kim et al. links autophagic stress to the sterile α and toll/interleukin 1 receptor motif containing protein 1 (SARM1)-dependent core axonal degeneration program, providing a new insight into the role of autophagy in axon degeneration. In the classical Wallerian axon degeneration model of axotomy, disruption of axonal transport destroys the coordinated activity of pro-survival and pro-degenerative factors in the axoplasm and activates the NADase activity of SARM1, thus triggering the axonal self-destruction program. However, the mechanism for SARM1 activation in the chronic neurodegenerative disorders is more complex. Mitochondrial defects and oxidative stress contribute to the activation of SARM1, while mitophagy can inhibit mitochondrial dysfunction and promote the clearance of SARM1 on mitochondria, thus protecting against neuronal degeneration. Therefore, in-depth elucidation of the underlying mechanisms of mitophagy during axonal degeneration can help develop promising strategies for the prevention and treatment of various neurodegenerative disorders.
    Keywords:  SARM1; autophagy; axon degeneration; mitochondrial dysfunction; mitophagy
    DOI:  https://doi.org/10.1002/jnr.25292
  14. Ann Hematol. 2024 Jan 29.
    Leukemia and mitophagy: a novel perspective for understanding oncogenesis and resistance.
    Yueyao Liu, Zhigui Ma.
      Mitophagy, the selective autophagic process that specifically degrades mitochondria, serves as a vital regulatory mechanism for eliminating damaged mitochondria and maintaining cellular balance. Emerging research underscores the central role of mitophagy in the initiation, advancement, and treatment of cancer. Mitophagy is widely acknowledged to govern mitochondrial homeostasis in hematopoietic stem cells (HSCs), influencing their metabolic dynamics. In this article, we integrate recent data to elucidate the regulatory mechanisms governing mitophagy and its intricate significance in the context of leukemia. An in-depth molecular elucidation of the processes governing mitophagy may serve as a basis for the development of pioneering approaches in targeted therapeutic interventions.
    Keywords:  Autophagy; HSCs; Leukemia; Mitophagy; Resistance; Therapy
    DOI:  https://doi.org/10.1007/s00277-024-05635-w
  15. Prostate Cancer Prostatic Dis. 2024 Jan 31.
    The role of autophagy in prostate cancer and prostatic diseases: a new therapeutic strategy.
    Guilherme Lemos, Cícera Madri Alves de Souza Fernandes, Fábio Henrique Silva, Fabiano Beraldi Calmasini.
       BACKGROUND: Autophagy is a well-conserved catabolic process that plays a key role in cell homeostasis. In the prostate, defective autophagy has been implicated in the genesis and progression of several pathological conditions.
    AIM: The present review explored the autophagy pathway in prostate-related dysfunctions, focusing on prostate cancer (PCa), benign prostatic hyperplasia (BPH) and prostatitis.
    RESULTS: Impaired autophagy activity has been shown in animal models of BPH and prostatitis. Moreover, autophagy activation by specific and non-specific drugs improved both conditions in pre-clinical studies. Conversely, the efficacy of autophagy inducers in PCa remains controversial, depending on intrinsic PCa characteristics and stage of progression. Intriguingly, autophagy inhibitors have shown beneficial effects in PCa suppression or even to overcome chemotherapy resistance. However, there are still open questions regarding the upstream mechanisms by which autophagy is deregulated in the prostate and the exact role of autophagy in PCa. The lack of specificity and increased toxicity associated with the currently autophagy inhibitors limits its use clinically, reflecting in reduced number of clinical data.
    CONCLUSION: New therapeutic strategies to treat prostatic diseases involving new autophagy modulators, combination therapy and new drug formulations should be explored. Understanding the autophagy signaling in each prostatic disease is crucial to determine the best pharmacological approach.
    DOI:  https://doi.org/10.1038/s41391-024-00793-4
  16. Rev Med Virol. 2024 Jan;34(1): e2503
    Targeting the mammalian target of rapamycin pathway in neurological manifestations of Covid-19.
    Han Wang, Li Cheng, Lanlan Yu, Zhigang Guo.
      The diverse and severe nature of neurological manifestations associated with coronavirus disease 2019 (Covid-19) has garnered increasing attention. Exploring the potential to decrease neurological complications in Covid-19 patients involves targeting the mammalian target of rapamycin (mTOR) pathway as a therapeutic strategy. The mTOR pathway, widely recognised for its central role in essential cellular processes like synthesising proteins, facilitating autophagy, and modulating immune responses, has implications in various neurological disorders. Drawing parallels between these disorders and the observed neurological complications in Covid-19, we present a comprehensive review on the current understanding of mTOR signalling in the context of severe acute respiratory syndrome coronavirus 2 infection and neuroinflammation.
    Keywords:  Covid-19; mTOR pathway; neurological manifestations; therapeutic targeting
    DOI:  https://doi.org/10.1002/rmv.2503
  17. bioRxiv. 2024 Jan 20. pii: 2024.01.20.576435. [Epub ahead of print]
    Axonal distribution of mitochondria maintains neuronal autophagy during aging via eIF2β.
    Kanako Shinno, Yuri Miura, Koichi M Iijima, Emiko Suzuki, Kanae Ando.
      Neuronal aging and neurodegenerative diseases are accompanied by proteostasis collapse, while cellular factors that trigger it are not identified. Impaired mitochondrial transport in the axon is another feature of aging and neurodegenerative diseases. Using Drosophila , we found that genetic depletion of axonal mitochondria causes dysregulation of translation and protein degradation. Axons with mitochondrial depletion showed abnormal protein accumulation, and autophagic defects. Lowering neuronal ATP levels by blocking glycolysis did not reduce autophagy, suggesting that autophagic defects are associated with mitochondrial distribution. We found eIF2β was upregulated by depletion of axonal mitochondria via proteome analysis. Phosphorylation of eIF2α, another subunit of eIF2, was lowered, and global translation was suppressed. Neuronal overexpression of eIF2β phenocopied the autophagic defects and neuronal dysfunctions, and lowering eIF2β expression rescued those perturbations caused by depletion of axonal mitochondria. These results indicate the mitochondria-eIF2β axis maintains proteostasis in the axon, of which disruption may underly the onset and progression of age-related neurodegenerative diseases.
    Highlights: Loss of axonal mitochondria impairs autophagy and accumulates proteins in the axonLoss of axonal mitochondria upregulates eIF2β and downregulates p-eIF2αNeuronal upregulation of eIF2β induces autophagic defects and locomotor dysfunctionLowering eIF2β rescues autophagic defects caused by loss of axonal mitochondria.
    DOI:  https://doi.org/10.1101/2024.01.20.576435
  18. Sci Adv. 2024 Feb 02. 10(5): eadj9479
    Folate depletion induces erythroid differentiation through perturbation of de novo purine synthesis.
    Adam G Maynard, Nancy K Pohl, Annabel P Mueller, Boryana Petrova, Alan Y L Wong, Peng Wang, Andrew J Culhane, Jeannette R Brook, Leah M Hirsch, Ngoc Hoang, Orville Kirkland, Tatum Braun, Sarah Ducamp, Mark D Fleming, Hojun Li, Naama Kanarek.
      Folate, an essential vitamin, is a one-carbon acceptor and donor in key metabolic reactions. Erythroid cells harbor a unique sensitivity to folate deprivation, as revealed by the primary pathological manifestation of nutritional folate deprivation: megaloblastic anemia. To study this metabolic sensitivity, we applied mild folate depletion to human and mouse erythroid cell lines and primary murine erythroid progenitors. We show that folate depletion induces early blockade of purine synthesis and accumulation of the purine synthesis intermediate and signaling molecule, 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR), followed by enhanced heme metabolism, hemoglobin synthesis, and erythroid differentiation. This is phenocopied by inhibition of folate metabolism using the inhibitor SHIN1, and by AICAR supplementation. Mechanistically, the metabolically driven differentiation is independent of mechanistic target of rapamycin complex 1 (mTORC1) and adenosine 5'-monophosphate-activated protein kinase (AMPK) and is instead mediated by protein kinase C. Our findings suggest that folate deprivation-induced premature differentiation of erythroid progenitor cells is a molecular etiology to folate deficiency-induced anemia.
    DOI:  https://doi.org/10.1126/sciadv.adj9479
  19. Mol Biol Cell. 2024 Jan 31. mbcE23020060
    Rab11 regulates autophagy at dendritic spines in an mTOR- and NMDA-dependent manner.
    Aleksandra Janusz-Kaminska, Agnieszka Brzozowska, Aleksandra Tempes, Malgorzata Urbanska, Magdalena Blazejczyk, Jacek Miłek, Bozena Kuzniewska, Juan Zeng, Jan Wesławski, Katarzyna Kisielewska, Gary J Bassell, Jacek Jaworski.
      Synaptic plasticity is a process that shapes neuronal connections during neurodevelopment and learning and memory. Autophagy is a mechanism that allows the cell to degrade its unnecessary or dysfunctional components. Autophagosomes appear at dendritic spines in response to plasticity-inducing stimuli. Autophagy defects contribute to altered dendritic spine development, autistic-like behavior in mice, and neurological disease. While several studies have explored the involvement of autophagy in synaptic plasticity, the initial steps of the emergence of autophagosomes at the postsynapse remain unknown. Here we demonstrate a postsynaptic association of autophagy-related protein 9A (Atg9A), known to be involved in the early stages of autophagosome formation, with Rab11, a small GTPase that regulates endosomal trafficking. Rab11 activity was necessary to maintain Atg9A-positive structures at dendritic spines. Inhibition of mTOR increased Rab11 and Atg9A interaction and increased the emergence of LC3 positive vesicles, an autophagosome membrane-associated protein marker, in dendritic spines when coupled to NMDA receptor stimulation. Dendritic spines with newly formed LC3+ vesicles were more resistant to NMDA-induced morphologic change. Rab11 DN overexpression suppressed appearance of LC3+ vesicles. Collectively, these results suggest that initiation of autophagy in dendritic spines depends on neuronal activity and Rab11a-dependent Atg9A interaction that is regulated by mTOR activity. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E23-02-0060
  20. bioRxiv. 2024 Jan 16. pii: 2024.01.15.575715. [Epub ahead of print]
    Development and characterization of phospho-ubiquitin antibodies to monitor PINK1-PRKN signaling in cells and tissue.
    Jens O Watzlawik, Xu Hou, Tyrique Richardson, Szymon L Lewicki, Joanna Siuda, Zbigniew K Wszolek, Casey N Cook, Leonard Petrucelli, Michael DeTure, Dennis W Dickson, Odetta Antico, Miratul M K Muqit, Jordan B Fishman, Karima Pirani, Ravindran Kumaran, Nicole K Polinski, Fabienne C Fiesel, Wolfdieter Springer.
      The selective removal of dysfunctional mitochondria, a process termed mitophagy, is critical for cellular health and impairments have been linked to aging, Parkinson disease, and other neurodegenerative conditions. A central mitophagy pathway is orchestrated by the ubiquitin (Ub) kinase PINK1 together with the E3 Ub ligase PRKN/Parkin. The decoration of damaged mitochondrial domains with phosphorylated Ub (p-S65-Ub) mediates their elimination though the autophagy system. As such p-S65-Ub has emerged as a highly specific and quantitative marker of mitochondrial damage with significant disease relevance. Existing p-S65-Ub antibodies have been successfully employed as research tools in a range of applications including western blot, immunocytochemistry, immunohistochemistry, and ELISA. However, physiological levels of p-S65-Ub in the absence of exogenous stress are very low, therefore difficult to detect and require reliable and ultrasensitive methods. Here we generated and characterized a collection of novel recombinant, rabbit monoclonal p-S65-Ub antibodies with high specificity and affinity in certain applications that allow the field to better understand the molecular mechanisms and disease relevance of PINK1-PRKN signaling. These antibodies may also serve as novel diagnostic or prognostic tools to monitor mitochondrial damage in various clinical and pathological specimens.
    DOI:  https://doi.org/10.1101/2024.01.15.575715
  21. Behav Brain Res. 2024 Jan 31. pii: S0166-4328(24)00044-5. [Epub ahead of print] 114888
    Selective disruption of mTORC1 and mTORC2 in VTA astrocytes induces depression and anxiety-like behaviors in mice.
    Ziteng Zheng, Han Zhou, Lu Yang, Lanlan Zhang, Ming Guo.
      Dysfunction of the mechanistic target of rapamycin (mTOR) signaling pathway is implicated in neuropsychiatric disorders including depression and anxiety. Most studies have been focusing on neurons, and the function of mTOR signaling pathway in astrocytes is less investigated. mTOR forms two distinct complexes, mTORC1 and mTORC2, with key scaffolding protein Raptor and Rictor, respectively. The ventral tegmental area (VTA), a vital component of the brain reward system, is enrolled in regulating both depression and anxiety. In the present study, we aimed to examine the regulation effect of VTA astrocytic mTOR signaling pathway on depression and anxiety. We specifically deleted Raptor or Rictor in VTA astrocytes in mice and performed a series of behavioral tests for depression and anxiety. Deletion of Raptor and Rictor both decreased the immobility time in the tail suspension test and the latency to eat in the novelty suppressed feeding test, and increased the horizontal activity and the movement time in locomotor activity. Deletion of Rictor decreased the number of total arm entries in the elevated plus-maze test and the vertical activity in locomotor activity. These data suggest that VTA astrocytic mTORC1 plays a role in regulating depression-related behaviors and mTORC2 is involved in both depression and anxiety-related behaviors. Our results indicate that VTA astrocytic mTOR signaling pathway might be new targets for the treatment of psychiatric disorders.
    Keywords:  anxiety; astrocyte; depression; mTORC1; mTORC2; ventral tegmental area
    DOI:  https://doi.org/10.1016/j.bbr.2024.114888
  22. Autophagy. 2024 Feb 02.
    FREE1 regulates phagophore closure in plants.
    Ying Zhu, Yonglun Zeng, Liwen Jiang.
      Adenosine monophosphate-activated protein kinase (AMPK), the central energy sensor in more complex eukaryotes, can activate macroautophagy/autophagy upon cellular energy deficiency. However, the regulatory role of nutrient sensing in mediating phagophore closure to generate an autophagosome remains unknown. The evolutionarily conserved endosomal sorting complexes required for transport (ESCRT) machinery has been postulated to regulate phagophore sealing, yet the signaling pathway modulating the ESCRT complex relocation from multivesicular body (MVB) to phagophore for closure remains unknown. We recently identified a plant unique pleiotropic protein FREE1 (FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1), which is phosphorylated by the plant energy sensor SnRK1 (SNF1-related kinase 1) and bridges the ATG conjugation system and ESCRT machinery to regulate phagophore sealing upon nutrient starvation. This study elucidated the bona fide roles and underlying mechanism of cellular energy-sensing pathways in regulating compartment sealing.
    Keywords:  Arabidopsis; ESCRT; autophagosome closure; autophagy
    DOI:  https://doi.org/10.1080/15548627.2024.2312793
  23. Curr Diabetes Rev. 2024 Jan 25.
    Glp-1 Mimetics and Autophagy in Diabetic Milieu: State-of-the-Art.
    Habib Yaribeygi, Mina Maleki, Raul D Santos, Tannaz Jamialahmadi, Amirhossein Sahebkar.
      The diabetic milieu is associated with cascades of pathophysiological pathways that culminate in diabetic complications and tissue injuries. Autophagy is an essential process mandatory for cell survival and tissue homeostasis by degrading damaged organelles and removing injured cells. However, it may turn into a pathological process in an aberrant mode in the diabetic and/or malignant milieu. Moreover, autophagy could serve as a promising therapeutic target for many complications related to tissue injury. Glp-1 mimetics are a class of newer antidiabetic agents that reduce blood glucose through several pathways. However, some evidence suggests that they can provide extra glycemic benefits by modulating autophagy, although there is no complete understanding of this mechanism and its underlying molecular pathways. Hence, in the current review, we aimed to provide new insights on the possible impact of Glp-1 mimetics on autophagy and consequent benefits as well as mediating pathways.
    Keywords:  Diabetes mellitus; Glp-1 mimetic; Glucagon-like peptide-1; autophagy; molecular pathways; sitagliptin
    DOI:  https://doi.org/10.2174/0115733998276570231222105959
  24. Blood Adv. 2024 Jan 31. pii: bloodadvances.2023010972. [Epub ahead of print]
    Autophagy prevents graft failure during murine Graft versus Host Disease.
    Katie E Lineburg, Lucie Leveque-El Mouttie, Christopher R Hunter, Laeitia Le Texier, Crystal McGirr, Bianca Teal, Bruce R Blazar, Steven W Lane, Geoffrey R Hill, Jean-Pierre Levesque, Kelli P A MacDonald.
      Autophagy is an intracellular survival process that has established roles in the long-term survival and function of hematopoietic stem cells (HSC). We investigated the contribution of autophagy to HSC fitness during allogeneic transplantation and GVHD. We demonstrate in vitro that both TNF and IL-1β, major components of GVHD cytokine storm, synergistically promote autophagy in both HSC and their more mature hematopoietic progenitor cells (HPC). In vivo we demonstrate that autophagy is increased in donor HSC and HPC during GVHD. Competitive transplant experiments demonstrated that autophagy deficient cells display reduced capacity to reconstitute the hematopoietic system compared to wild-type counterparts. In an MHC mismatched model of GVHD and associated cytokine dysregulation, we demonstrate that autophagy-deficient HSC and progenitors fail to establish durable hematopoiesis, leading to primary graft failure and universal transplant related mortality. Using several different models, we confirm that autophagy activity is increased in early progenitor and HSC populations in the presence of T cell-derived inflammatory cytokines and that these HSC populations require autophagy to survive. Thus autophagy serves as a key survival mechanism in HSC and progenitor populations after allogeneic SCT and may represent a therapeutic target to prevent graft failure during GVHD.
    DOI:  https://doi.org/10.1182/bloodadvances.2023010972
  25. J Cell Sci. 2024 Jan 31. pii: jcs.261081. [Epub ahead of print]
    Exploring the ATG9A interactome uncovers interaction with VPS13A.
    Alexander R van Vliet, Harold B J Jefferies, Peter A Faull, Jessica Chadwick, Fairouz Ibrahim, Mark J Skehel, Sharon A Tooze.
      ATG9A, the only transmembrane protein of the core autophagy pathway, cycles between the Golgi, endosomes and a vesicular compartment. ATG9A was recently shown to act as a lipid scramblase and this function is thought to require its interaction with another core autophagy protein ATG2A, which acts as a lipid transfer protein. Together ATG9A and ATG2A are proposed to function to expand the growing autophagosome. However, ATG9A is implicated in other pathways including membrane repair and lipid droplet homeostasis. To elucidate other ATG9A interactors within the autophagy pathway, or interactors beyond autophagy we performed an interactome analysis through mass spectrometry. This analysis revealed a host of proteins involved in lipid synthesis and trafficking, including ACSL3 and VPS13A and C. Furthermore, we show that ATG9A directly interacts with VPS13A and forms a complex distinct from the ATG9A:ATG2A complex.
    Keywords:  ATG9A interactome; Autophagy; VPS13; Lipid Trafficking; Mass Spectrometry
    DOI:  https://doi.org/10.1242/jcs.261081
  26. Front Biosci (Landmark Ed). 2024 Jan 17. 29(1): 21
    Identifying Autophagy-Associated Proteins and Chemicals with a Random Walk-Based Method within Heterogeneous Interaction Network.
    FeiMing Huang, Wei Guo, Lei Chen, KaiYan Feng, Tao Huang, Yu-Dong Cai.
       BACKGROUND: Autophagy is instrumental in various health conditions, including cancer, aging, and infections. Therefore, examining proteins and compounds associated with autophagy is paramount to understanding cellular biology and the origins of diseases, paving the way for potential therapeutic and disease prediction strategies. However, the complexity of autophagy, its intersection with other cellular pathways, and the challenges in monitoring autophagic activity make the experimental identification of these elements arduous.
    METHODS: In this study, autophagy-related proteins and chemicals were catalogued on the basis of Human Autophagy-dedicated Database. These entities were mapped to their respective PubChem identifications (IDs) for chemicals and Ensembl IDs for proteins, yielding 563 chemicals and 779 proteins. A network comprising protein-protein, protein-chemical, and chemical-chemical interactions was probed employing the Random-Walk-with-Restart algorithm using the aforementioned proteins and chemicals as seed nodes to unearth additional autophagy-associated proteins and chemicals. Screening tests were performed to exclude proteins and chemicals with minimal autophagy associations.
    RESULTS: A total of 88 inferred proteins and 50 inferred chemicals of high autophagy relevance were identified. Certain entities, such as the chemical prostaglandin E2 (PGE2), which is recognized for modulating cell death-induced inflammatory responses during pathogen invasion, and the protein G Protein Subunit Alpha I1 (GNAI1), implicated in ether lipid metabolism influencing a range of cellular processes including autophagy, were associated with autophagy.
    CONCLUSIONS: The discovery of novel autophagy-associated proteins and chemicals is of vital importance because it enhances the understanding of autophagy, provides potential therapeutic targets, and fosters the development of innovative therapeutic strategies and interventions.
    Keywords:  autophagy; chemical; network; protein; random walk with restart
    DOI:  https://doi.org/10.31083/j.fbl2901021
  27. Biochem Biophys Rep. 2024 Mar;37 101642
    5-ALA localises to the autophagy compartment and increases its fluorescence upon autophagy enhancement through caloric restriction and spermidine treatment in human glioblastoma.
    Kim Fredericks, Jurgen Kriel, Lize Engelbrecht, Petra Andreea Mercea, Georg Widhalm, Brad Harrington, Ian Vlok, Ben Loos.
      Glioblastoma Multiforme (GBM) is the most invasive and prevalent Central Nervous System (CNS) malignancy. It is characterised by diffuse infiltrative growth and metabolic dysregulation that impairs the extent of surgical resection (EoR), contributing to its poor prognosis. 5-Aminolevulinic acid (5-ALA) fluorescence-guided surgical resection (FGR) takes advantage of the preferential generation of 5-ALA-derived fluorescence signal in glioma cells, thereby improving visualisation and enhancing the EoR. However, despite 5-ALA FGR is a widely used technique in the surgical management of malignant gliomas, the infiltrative tumour margins usually show only vague or no visible fluorescence and thus a significant amount of residual tumour tissue may hence remain in the resection cavity, subsequently driving tumour recurrence. To investigate the molecular mechanisms that govern the preferential accumulation of 5-ALA in glioma cells, we investigated the precise subcellular localisation of 5-ALA signal using Correlative Light and Electron Microscopy (CLEM) and colocalisation analyses in U118MG glioma cells. Our results revealed strong 5-ALA signal localisation in the autophagy compartment - specifically autolysosomes and lysosomes. Flow cytometry was employed to investigate whether autophagy enhancement through spermidine treatment (SPD) or nutrient deprivation/caloric restriction (CR) would enhance 5-ALA fluorescence signal generation. Indeed, SPD, CR and a combination of SPD/CR treatment significantly increased 5-ALA signal intensity, with a most robust increase in signal intensity observed in the combination treatment of SPD/CR. When using 3-D glioma spheroids to assess the effect of 5-ALA on cellular ultrastructure, we demonstrate that 5-ALA exposure leads to cytoplasmic disruption, vacuolarisation and large-scale mitophagy induction. These findings not only suggest a critical role for the autophagy compartment in 5-ALA engagement and signal generation but also point towards a novel and practically feasible approach to enhance 5-ALA fluorescence signal intensity. The findings may highlight that indeed autophagy control may serve as a promising avenue to promote an improved resection and GBM prognosis.
    Keywords:  5-Aminolevulinic acid fluorescence; Autolysosomes; Autophagic activity; Autophagosomes; Autophagy; Glioblastoma; Lysosomes
    DOI:  https://doi.org/10.1016/j.bbrep.2024.101642
  28. Autophagy. 2024 Jan 31.
    Degradative autophagy regulates the homeostasis of miRnas to control cancer development.
    Shan-Ying Wu, Chien-An Chu, Sheng-Hui Lan, Hsiao-Sheng Liu.
      Macroautophagy/autophagy acts as an anti-tumor mechanism in early cancer stages but promotes growth in established tumors. Similarly, miRNAs function as tumor suppressors or oncogenes, depending on their target genes. This reciprocal relationship between autophagy and miRNAs is a well-studied area, primarily focused on how miRNAs regulate autophagy-related genes. Our research provides innovative insights into how autophagy selectively controls miRNAs. For instance, MIR224 is preferentially degraded within autophagosomes, leading to the upregulation of SMAD4 and suppressing hepatocellular carcinoma (HCC) tumorigenesis. Conversely, autophagy positively regulates MIR449A by degrading EP300/p300 to activate FOXO1 and facilitate MIR449A transcription in colorectal cancer (CRC). In conclusion, our findings reveal the role of autophagy in maintaining the cellular balance of two miRNAs to mitigate tumorigenic stresses and highlight that autophagy-regulated miRNA profiles may serve as diagnostic and therapeutic markers for cancer development.
    Keywords:  Cancer; MIR224; MIR449A; macroautophagy
    DOI:  https://doi.org/10.1080/15548627.2024.2312035
  29. Methods Cell Biol. 2024 ;pii: S0091-679X(23)00065-1. [Epub ahead of print]181 213-226
    Mechanistic exploration of autophagy and aging by RNA interference.
    Hui Pan, Oliver Kepp, Guido Kroemer.
      Cellular senescence is a cellular process with organismal impact that is mechanistically counterbalanced to a certain extent by frequent episodes of autophagy. Here we describe a detailed, automation-compatible method for the use of RNA-interference (RNAi; also called post-transcriptional gene silencing (PTGS))-mediated silencing of autophagy related protein-coding gene expression. RNAi is a conserved biological response to double-stranded RNA that mediates resistance to endogenous parasites and exogenous pathogenic nucleic acids. RNAi mediated by short interfering RNA (siRNA) is widely used for gene function analysis. The accurate use of RNAi for the inference of gene function necessitates that both specificity and efficacy of the siRNA-mediated knockdown are monitored. In this manuscript, we exemplify these crucial steps employing siRNAs targeting the autophagy and lysosomal biogenesis associated transcription factor TFE3 and validate their specificity on protein and mRNA level.
    Keywords:  Aging; Autophagy; Cancer; Screening
    DOI:  https://doi.org/10.1016/bs.mcb.2023.03.003
  30. Front Pharmacol. 2023 ;14 1337732
    OTUD3 suppresses the mTORC1 signaling by deubiquitinating KPTN.
    Jiatao Li, Dan Yang, Yan Lin, Wei Xu, Shi-Min Zhao, Chenji Wang.
      Background: Ubiquitination and deubiquitination modifications play pivotal roles in eukaryotic life processes, regulating protein dynamics via the ubiquitin-proteasome pathway. Dysregulation can impact disease development, including cancer and neurodegenerative disorders. Increasing evidence highlights their role in tumorigenesis, modulating key proteins. OTUD3, a deubiquitinase, stabilizes PTEN, suppressing tumor growth by inhibiting PI3K-AKT signaling. Yet, further OTUD3 substrates remain underexplored. Methods: We employed the In vivo ubiquitination assay to investigate the ubiquitination role of OTUD3 on KPTN within the cellular context. Additionally, CRISPR/Cas9 editing and Immunofluorescence were utilized to study the impact of OTUD3 on the mTOR signaling pathway in cells. Furthermore, Cell proliferation assay and NMR were employed to explore the effects of OTUD3 on cellular growth and proliferation. Results: OTUD3 serves as a deubiquitinase for KPTN. OTUD3 interacts with KPTN, facilitated by the OTU domain within OTUD3. Further investigations confirmed KPTN's ubiquitination modification, primarily at lysine residue 49. Ubiquitination experiments demonstrated OTUD3's ability to mediate KPTN's deubiquitination without affecting its protein levels. This suggests KPTN's ubiquitination is a function-regulated, non-degradable modification. Under various amino acid starvation or stimulation conditions, overexpressing OTUD3 reduces mTORC1 signaling activation, while knocking out OTUD3 further enhances it. Notably, OTUD3's regulation of mTORC1 signaling relies on its deubiquitinase activity, and this effect is observed even in PTEN KO cells, confirming its independence from PTEN, a reported substrate. OTUD3 also promotes GATOR1's lysosomal localization, a process requiring KPTN's involvement. Ultimately, OTUD3 affects cellular metabolic pool products by downregulating the mTORC1 pathway, significantly inhibiting tumor cell growth and proliferation. Discussion: Our experiments shed light on an alternative perspective regarding the intrinsic functions of OTUD3 in inhibiting tumor development. We propose a novel mechanism involving KPTN-mediated regulation of the mTORC1 signaling pathway, offering fresh insights into the occurrence and progression of tumor diseases driven by related genes. This may inspire new approaches for drug screening and cancer treatment, potentially guiding future therapies for relevant tumors.
    Keywords:  KICSTOR; KPTN; OTU domain-containing protein 3; deubiquitination; mTORC1
    DOI:  https://doi.org/10.3389/fphar.2023.1337732
  31. Cell Biochem Biophys. 2024 Jan 30.
    Complex Topology of Ubiquitin Chains Mediates Lysosomal Degradation of MrgC Proteins.
    Jiacheng Yu, Dan Li, Mingming Xie, Jun Xie, Zhen Wang, Xiaoping Gu, Zhengliang Ma, Yu'e Sun.
       BACKGROUND: Activation of Mas-related G protein-coupled receptor C (MrgC) receptors relieves pain, but also leads to ubiquitination of MrgC receptors. Ubiquitination mediates MrgC receptor endocytosis and degradation. However, MrgC degradation pathways and ubiquitin-linked chain types are not known.
    METHODS: N2a cells were treated with cycloheximide (CHX, protein synthesis inhibitor), Mg132 (proteasome inhibitor), 3-Methyladenine (3MA, autophagy lysosome inhibitor) and Chloroquine (CQ, autophagy lysosome inhibitor) to observe the half-life and degradation pathway of MrgC. The location of internalized MrgC receptors and lysosomes (Lyso-Tracker) was observed by immunofluorescence staining. N2a cells were transfected with Myc-MrgC and a series of HA-tagged ubiquitin mutants to study the ubiquitin-linked chain type of MrgC.
    RESULTS: The amount of MrgC protein decreased with time after CHX treatment of N2a cells. Autophagy lysosome inhibitors can inhibit the degradation of MrgC. The amount of MrgC protein decreased with time after CHX treatment of N2a cells. 3-MA and CQ inhibited the degradation of MrgC protein, whereas Mg-132 did not inhibit it. Partially internalized MrgC receptors were co-labeled with lysosomes. MrgC proteins have multiple topologies of ubiquitin-modified chains.
    CONCLUSION: As a member of the G protein-coupled receptor family, MrgC receptors can be degraded over time. The complex topology of the ubiquitin-linked chain mediates the lysosomal degradation of MrgC proteins.
    Keywords:  Degradation; MrgC; Ubiquitin; Ubiquitin chain
    DOI:  https://doi.org/10.1007/s12013-023-01204-6
  32. Autophagy. 2024 Jan 31.
    The C9orf72-SMCR8 complex suppresses primary ciliogenesis as a RAB8A GAP.
    Dan Tang, Hui Bao, Shiqian Qi.
      Approximately half of the familial cases of amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD) are attributed to the abnormal GGGGCC repeat expansion within the first intron of C9orf72, potentializing C9orf72 and its product as the most promising target for ALS therapeutics. Nevertheless, the biological function of C9orf72 remains unclear. Previously, we reported that C9orf72 and its binding partner, SMCR8, form a GTPase-activating protein (GAP) complex, which is proposed to regulate membrane trafficking and autophagy. Hereby, we found that the C9orf72-SMCR8 complex negatively regulates primary ciliogenesis and hedgehog (HH) signaling. Furthermore, the biochemical analysis and cell biology experiments identified C9orf72 as the RAB8A binding subunit and SMCR8 as the GAP subunit within the complex. Further, we discussed the relationship among the C9orf72-SMCR8 complex, primary ciliogenesis, and autophagy.
    Keywords:  ALS; FTD; GAP; HH signaling; RAB; SHH; primary cilia
    DOI:  https://doi.org/10.1080/15548627.2024.2311541
  33. Int J Biol Macromol. 2024 Jan 30. pii: S0141-8130(24)00638-X. [Epub ahead of print] 129835
    The N-terminal region of the ATG8 autophagy protein LC3C is essential for its membrane fusion properties.
    Uxue Ballesteros, Marina N Iriondo, Yaiza R Varela, Félix M Goñi, Alicia Alonso, L Ruth Montes, Asier Etxaniz.
      Autophagy is a catabolic process in which a double-membrane organelle, the autophagosome (AP), engulfs cellular components that will be degraded in the lysosomes. ATG8 protein family members participate at various stages of AP formation. The present study compares the capacity to induce lipid-vesicle tethering and fusion of two ATG8 family members, LC3B and LC3C, with model membranes. LC3B is the most thoroughly studied ATG8 protein. It is generally considered as an autophagosomal marker and a canonical representative of the LC3 subfamily. LC3C is less studied, but recent data have reported its implication in various processes, crucial to cellular homeostasis. The results in this paper show that LC3C induces higher levels of tethering and of intervesicular lipid mixing than LC3B. As the N-terminus of LC3C is different from that of the other family members, various mutants of the N-terminal region of both LC3B and LC3C were designed, and their activities compared. It was concluded that the N-terminal region of LC3C was responsible for the enhanced vesicle tethering, membrane perturbation and vesicle-vesicle fusion activities of LC3C as compared to LC3B. The results suggest a specialized function of LC3C in the AP expansion process.
    Keywords:  ATG8; Autophagy; LC3C; Membrane fusion
    DOI:  https://doi.org/10.1016/j.ijbiomac.2024.129835
  34. Sci Rep. 2024 01 30. 14(1): 2525
    G-quadruplexes in MTOR and induction of autophagy.
    Piyali Majumder, Chinmayee Shukla, Arjun Arya, Shubham Sharma, Bhaskar Datta.
      G-quadruplex (G4) structures have emerged as singular therapeutic targets for cancer and neurodegeneration. Autophagy, a crucial homeostatic mechanism of the cell, is often dysregulated in neurodegenerative diseases and cancers. We used QGRS mapper to identify 470 G4 sequences in MTOR, a key negative regulator of autophagy. We sought to identify a functional context by leveraging the effect of G4-targeting ligands on MTOR G4 sequences. The effect of Bis-4,3, a G4 selective dimeric carbocyanine dye, was compared with the known G4-stabilizing activity of the porphyrin, TMPyP4 in HeLa and SHSY-5Y cells. Our results show that treatment with G4-selective ligands downregulates MTOR RNA and mTOR protein expression levels. This is the first report describing G4 motifs in MTOR. This study indicates a possible role of G4 stabilizing ligands in induction of autophagy by downregulation of mTOR levels, albeit not precluding MTOR independent pathways.
    DOI:  https://doi.org/10.1038/s41598-024-52561-y
  35. Acta Neuropathol. 2024 Jan 29. 147(1): 26
    Mitochondrial damage and impaired mitophagy contribute to disease progression in SCA6.
    Tsz Chui Sophia Leung, Eviatar Fields, Namrata Rana, Ru Yi Louisa Shen, Alexandra E Bernstein, Anna A Cook, Daniel E Phillips, Alanna J Watt.
      Spinocerebellar ataxia type 6 (SCA6) is a neurodegenerative disease that manifests in midlife and progressively worsens with age. SCA6 is rare, and many patients are not diagnosed until long after disease onset. Whether disease-causing cellular alterations differ at different disease stages is currently unknown, but it is important to answer this question in order to identify appropriate therapeutic targets across disease duration. We used transcriptomics to identify changes in gene expression at disease onset in a well-established mouse model of SCA6 that recapitulates key disease features. We observed both up- and down-regulated genes with the major down-regulated gene ontology terms suggesting mitochondrial dysfunction. We explored mitochondrial function and structure and observed that changes in mitochondrial structure preceded changes in function, and that mitochondrial function was not significantly altered at disease onset but was impaired later during disease progression. We also detected elevated oxidative stress in cells at the same disease stage. In addition, we observed impairment in mitophagy that exacerbates mitochondrial dysfunction at late disease stages. In post-mortem SCA6 patient cerebellar tissue, we observed metabolic changes that are consistent with mitochondrial impairments, supporting our results from animal models being translatable to human disease. Our study reveals that mitochondrial dysfunction and impaired mitochondrial degradation likely contribute to disease progression in SCA6 and suggests that these could be promising targets for therapeutic interventions in particular for patients diagnosed after disease onset.
    Keywords:  Ataxia; Disease progression; Metabolomics; Mitochondria; Purkinje cell; Transcriptome
    DOI:  https://doi.org/10.1007/s00401-023-02680-z
  36. Genes Dis. 2024 May;11(3): 101027
    FGF21-mediated autophagy: Remodeling the homeostasis in response to stress in liver diseases.
    Wei Shen, Modan Yang, Hao Chen, Chiyu He, Huigang Li, Xinyu Yang, Jianyong Zhuo, Zuyuan Lin, Zhihang Hu, Di Lu, Xiao Xu.
      Liver diseases are worldwide problems closely associated with various stresses, such as endoplasmic reticulum stress. The exact interplay between stress and liver diseases remains unclear. Autophagy plays an essential role in maintaining homeostasis, and recent studies indicate tight crosstalk between stress and autophagy in liver diseases. Once the balance between damage and autophagy is broken, autophagy can no longer resist injury or maintain homeostasis. In recent years, FGF21 (fibroblast growth factor 21)-induced autophagy has attracted much attention. FGF21 is regarded as a stress hormone and can be up-regulated by an abundance of signaling pathways in response to stress. Also, increased FGF21 activates autophagy by a complicated signaling network in which mTOR plays a pivotal role. This review summarizes the mechanism of FGF21-mediated autophagy and its derived application in the defense of stress in liver diseases and offers a glimpse into its promising prospect in future clinical practice.
    Keywords:  Autophagy; Fibroblast growth factor 21; Liver diseases; Stress
    DOI:  https://doi.org/10.1016/j.gendis.2023.05.019
  37. Nat Commun. 2024 Jan 27. 15(1): 830
    Mitophagy curtails cytosolic mtDNA-dependent activation of cGAS/STING inflammation during aging.
    Juan Ignacio Jiménez-Loygorri, Beatriz Villarejo-Zori, Álvaro Viedma-Poyatos, Juan Zapata-Muñoz, Rocío Benítez-Fernández, María Dolores Frutos-Lisón, Francisco A Tomás-Barberán, Juan Carlos Espín, Estela Area-Gómez, Aurora Gomez-Duran, Patricia Boya.
      Macroautophagy decreases with age, and this change is considered a hallmark of the aging process. It remains unknown whether mitophagy, the essential selective autophagic degradation of mitochondria, also decreases with age. In our analysis of mitophagy in multiple organs in the mito-QC reporter mouse, mitophagy is either increased or unchanged in old versus young mice. Transcriptomic analysis shows marked upregulation of the type I interferon response in the retina of old mice, which correlates with increased levels of cytosolic mtDNA and activation of the cGAS/STING pathway. Crucially, these same alterations are replicated in primary human fibroblasts from elderly donors. In old mice, pharmacological induction of mitophagy with urolithin A attenuates cGAS/STING activation and ameliorates deterioration of neurological function. These findings point to mitophagy induction as a strategy to decrease age-associated inflammation and increase healthspan.
    DOI:  https://doi.org/10.1038/s41467-024-45044-1
  38. Mol Biol Cell. 2024 Jan 31. mbcE23060257
    The p24-family and COPII subunit SEC24C facilitate the clearance of alpha1-antitrypsin Z from the endoplasmic reticulum to lysosomes.
    Benjamin S Roberts, Debashree Mitra, Sudhanshu Abishek, Richa Beher, Prasanna Satpute-Krishnan.
      A subpopulation of the alpha-1-antitrypsin misfolding Z mutant (ATZ) is cleared from the endoplasmic reticulum (ER) via an ER-to-lysosome-associated degradation (ERLAD) pathway. Here, we report that the COPII subunit SEC24C and the p24-family of proteins facilitate the clearance of ATZ via ERLAD. In addition to the previously reported ERLAD components calnexin and FAM134B, we discovered that ATZ co-immunoprecipitates with the p24-family members TMP21 and TMED9. This contrasts with wild type alpha1-antitrypsin, which did not co-immunoprecipitate with FAM134B, calnexin or the p24-family members. Live-cell imaging revealed that ATZ and the p24-family members traffic together from the ER to lysosomes. Using chemical inhibitors to block ER exit or autophagy, we demonstrated that p24-family members and ATZ co-accumulate at SEC24C marked ER-exit sites or in ER-derived compartments, respectively. Furthermore, depletion of SEC24C, TMP21 or TMED9 inhibited lysosomal trafficking of ATZ and resulted in the increase of intracellular ATZ levels. Conversely, overexpression of these p24-family members resulted in the reduction of ATZ levels. Intriguingly, the p24-family members co-immunoprecipitate with ATZ, FAM134B and SEC24C. Thus, we propose a model in which the p24-family functions in an adaptor complex linking SEC24C with the ERLAD machinery for the clearance of ATZ. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E23-06-0257
  39. J Cancer Res Clin Oncol. 2024 Jan 31. 150(2): 56
    The dual role of autophagy in HPV-positive head and neck squamous cell carcinoma: a systematic review.
    Sam Augustine Kandathil, Arian Akhondi, Lorenz Kadletz-Wanke, Gregor Heiduschka, Nikolai Engedal, Faris F Brkic.
       PURPOSE: Human papilloma virus (HPV)-positive head and neck squamous cell carcinoma (HNSCC) displays distinct epidemiological, clinical, and molecular characteristics compared to the negative counterpart. Alterations in autophagy play an important role in cancer, and emerging evidence indicates an interplay of autophagy in HNSCC carcinogenesis and tumor promotion. However, the influence of HPV infection on autophagy in HNSCC has received less attention and has not been previously reviewed. Therefore, we here aimed to systematically review the role of autophagy explicitly in HPV+ HNSCC.
    METHODS: Studies accessible in PubMed, Embase, Scopus, and Web of Science investigating HNSCC, highlighting the molecular biological differences between HPV- and HPV+ HNSCC and its influences on autophagy in HNSCC were analyzed according to the PRISMA statement. A total of 10 articles were identified, included, and summarized.
    RESULTS: The HPV16 E7 oncoprotein was reported to be involved in the degradation of AMBRA1 and STING, and to enhance chemotherapy-induced cell death via lethal mitophagy in HNSCC cells. Autophagy-associated gene signatures correlated with HPV-subtype and overall survival. Additionally, immunohistochemical (IHC) analyses indicate that high LC3B expression correlates with poor overall survival in oropharyngeal HNSCC patients.
    CONCLUSION: HPV may dampen general bulk autophagic flux via degradation of AMBRA1 but may promote selective autophagic degradation of STING and mitochondria. Interpretations of correlations between autophagy-associated gene expressions or IHC analyses of autophagy-related (ATG) proteins in paraffin embedded tissue with clinicopathological features without biological validation need to be taken with caution.
    Keywords:  ATG; Autophagy; HNSCC; HPV; Radiosensitivity; Survival
    DOI:  https://doi.org/10.1007/s00432-023-05514-3
  40. Nat Prod Res. 2024 Jan 31. 1-7
    Restoration of autophagy activity by dipsacoside B alleviates exhaustive exercise-induced kidney injury via the AMPK/mTOR pathway.
    Zhenyu Li, Zhuang Tian.
      Exhaustive exercise (EE) induces kidney injury, but its concrete mechanism has not been fully elucidated. Hepatoprotective effects of dipsacoside B (DB) have been found previously, involving in autophagy induction. However, whether DB exerts renal protective effect and its potential mechanism are still unknown. The present study aimed to investigate the benefit of DB in EE-induced kidney injury and decipher its underlying mechanism. Here, we found that DB ameliorated EE-induced renal dysfunction and renal histopathological injury in rats. DB possessed anti-inflammatory, anti-oxidative, and anti-apoptotic functions in kidneys of exercise-induced exhausted rats. Besides, DB improved autophagy function in kidneys of EE rats. Mechanically, activation of the adenylate-activating protein kinase (AMPK)/mammalian target of rapamycin (mTOR) pathway was implicated in the kidney injury-relieving effects and autophagy restoration induced by DB. Collectively, these findings provide reference for the clinical application of DB in preventing and managing EE-induced kidney injury.
    Keywords:  AMPK/mTOR signalling; Exhaustive exercise; autophagy; dipsacoside B; kidney injury
    DOI:  https://doi.org/10.1080/14786419.2024.2308002
  41. Phytother Res. 2024 Feb 01.
    Natural products targeting macroautophagy signaling in hepatocellular carcinoma therapy: Recent evidence and perspectives.
    Yuan Chen, Xiyue Tan, Wenwen Zhang, Yubing Li, Xinyu Deng, Jinhao Zeng, Lihua Huang, Xiao Ma.
      Hepatocellular carcinoma (HCC), presently the second leading cause of global cancer-related mortality, continues to pose significant challenges in the realm of medical oncology, impacting both clinical drug selection and mechanistic research. Recent investigations have unveiled autophagy-related signaling as a promising avenue for HCC treatment. A growing body of research has highlighted the pivotal role of autophagy-modulating natural products in inhibiting HCC progression. In this context, we provide a concise overview of the fundamental autophagy mechanism and delineate the involvement of autophagic signaling pathways in HCC development. Additionally, we review pertinent studies demonstrating how natural products regulate autophagy to mitigate HCC. Our findings indicate that natural products exhibit cytotoxic effects through the induction of excessive autophagy, simultaneously impeding HCC cell proliferation by autophagy inhibition, thereby depriving HCC cells of essential energy. These effects have been associated with various signaling pathways, including PI3K/AKT, MAPK, AMPK, Wnt/β-catenin, Beclin-1, and ferroautophagy. These results underscore the considerable therapeutic potential of natural products in HCC treatment. However, it is important to note that the present study did not establish definitive thresholds for autophagy induction or inhibition by natural products. Further research in this domain is imperative to gain comprehensive insights into the dual role of autophagy, equipping us with a better understanding of this double-edged sword in HCC management.
    Keywords:  autophagy-related genes; liver cancer; mTOR signaling pathway; macroautophagy; natural compounds; phosphorylation
    DOI:  https://doi.org/10.1002/ptr.8103
  42. Oncogene. 2024 Jan 27.
    Novel exosomal circEGFR facilitates triple negative breast cancer autophagy via promoting TFEB nuclear trafficking and modulating miR-224-5p/ATG13/ULK1 feedback loop.
    Huachen Song, Zitong Zhao, Liying Ma, Weihong Zhao, Yi Hu, Yongmei Song.
      Triple-negative breast cancer (TNBC) cells are in a more hypoxic and starved state than non-TNBC cells, which makes TNBC cells always maintain high autophagy levels. Emerging evidence has demonstrated that circular RNAs (circRNAs) are involved in the progress of tumorigenesis. However, the regulation and functions of autophagy-induced circRNAs in TNBC remain unclear. In our study, autophagy-responsive circRNA candidates in TNBC cells under amino acid starved were identified by RNA sequencing. The results showed that circEGFR expression was significantly upregulated in autophagic cells. Knockdown of circEGFR inhibited autophagy in TNBC cells, and circEGFR derived from exosomes induced autophagy in recipient cells in the tumor microenvironment. In vitro and in vivo functional assays identified circEGFR as an oncogenic circRNA in TNBC. Clinically, circEGFR was significantly upregulated in TNBC and was positively associated with lymph node metastasis. CircEGFR in plasma-derived exosomes was upregulated in breast cancer patients compared with healthy people. Mechanistically, circEGFR facilitated the translocation of Annexin A2 (ANXA2) toward the plasma membrane in TNBC cells, which led to the release of Transcription Factor EB (a transcription factor of autophagy-related proteins, TFEB) from ANXA2-TFEB complex, causing nuclear translocation of TFEB, thereby promoting autophagy in TNBC cells. Meanwhile, circEGFR acted as ceRNA by directly binding to miR-224-5p and inhibited the expression of miR-224-5p, which weakened the suppressive role of miR-224-5p/ATG13/ULK1 axis on autophagy. Overall, our study demonstrates the key role of circEGFR in autophagy, malignant progression, and metastasis of TNBC. These indicate circEGFR is a potential diagnosis biomarker and therapeutic target for TNBC.
    DOI:  https://doi.org/10.1038/s41388-024-02950-4
  43. G3 (Bethesda). 2024 Jan 30. pii: jkad263. [Epub ahead of print]
    GPI-anchored Gas1 protein regulates cytosolic proteostasis in budding yeast.
    Yuhao Wang, Linhao Ruan, Rong Li.
      The decline in protein homeostasis (proteostasis) is a hallmark of cellular aging and aging-related diseases. Maintaining a balanced proteostasis requires a complex network of molecular machineries that govern protein synthesis, folding, localization, and degradation. Under proteotoxic stress, misfolded proteins that accumulate in cytosol can be imported into mitochondria for degradation through the "mitochondrial as guardian in cytosol" (MAGIC) pathway. Here, we report an unexpected role of Gas1, a cell wall-bound glycosylphosphatidylinositol (GPI)-anchored β-1,3-glucanosyltransferase in the budding yeast, in differentially regulating MAGIC and ubiquitin-proteasome system (UPS). Deletion of GAS1 inhibits MAGIC but elevates protein ubiquitination and UPS-mediated protein degradation. Interestingly, we found that the Gas1 protein exhibits mitochondrial localization attributed to its C-terminal GPI anchor signal. But this mitochondria-associated GPI anchor signal is not required for mitochondrial import and degradation of misfolded proteins through MAGIC. By contrast, catalytic inactivation of Gas1 via the gas1-E161Q mutation inhibits MAGIC but not its mitochondrial localization. These data suggest that the glucanosyltransferase activity of Gas1 is important for regulating cytosolic proteostasis.
    Keywords:  GPI; Gas1; MAGIC; budding yeast; mitochondria; proteostasis
    DOI:  https://doi.org/10.1093/g3journal/jkad263
  44. Hepatol Commun. 2024 Feb 01. pii: e0370. [Epub ahead of print]8(2):
    Sirtuin3 promotes the degradation of hepatic Z alpha-1 antitrypsin through lipophagy.
    Brittney Poole, Regina Oshins, Zhiguang Huo, Alek Aranyos, Jesse West, Sergio Duarte, Virginia C Clark, Thiago Beduschi, Ali Zarrinpar, Mark Brantly, Nazli Khodayari.
       BACKGROUND: Alpha-1 antitrypsin deficiency (AATD) is a genetic disease caused by misfolding and accumulation of mutant alpha-1 antitrypsin (ZAAT) in the endoplasmic reticulum of hepatocytes. Hepatic ZAAT aggregates acquire a toxic gain-of-function that impacts the endoplasmic reticulum which is theorized to cause liver disease in individuals with AATD who present asymptomatic until late-stage cirrhosis. Currently, there is no treatment for AATD-mediated liver disease except liver transplantation. In our study of mitochondrial RNA, we identified that Sirtuin3 (SIRT3) plays a role in the hepatic phenotype of AATD.
    METHODS: Utilizing RNA and protein analysis in an in vitro AATD model, we investigated the role of SIRT3 in the pathophysiology of AATD-mediated liver disease while also characterizing our novel, transgenic AATD mouse model.
    RESULTS: We show lower expression of SIRT3 in ZAAT-expressing hepatocytes. In contrast, the overexpression of SIRT3 increases hepatic ZAAT degradation. ZAAT degradation mediated by SIRT3 appeared independent of proteasomal degradation and regular autophagy pathways. We observed that ZAAT-expressing hepatocytes have aberrant accumulation of lipid droplets, with ZAAT polymers localizing on the lipid droplet surface in a direct interaction with Perilipin2, which coats intracellular lipid droplets. SIRT3 overexpression also induced the degradation of lipid droplets in ZAAT-expressing hepatocytes. We observed that SIRT3 overexpression induces lipophagy by enhancing the interaction of Perilipin2 with HSC70. ZAAT polymers then degrade as a consequence of the mobilization of lipids through this process.
    CONCLUSIONS: In this context, SIRT3 activation may eliminate the hepatic toxic gain-of-function associated with the polymerization of ZAAT, providing a rationale for a potential novel therapeutic approach to the treatment of AATD-mediated liver disease.
    DOI:  https://doi.org/10.1097/HC9.0000000000000370
  45. Cell Death Dis. 2024 Jan 29. 15(1): 97
    Regulation of ULK1 by WTAP/IGF2BP3 axis enhances mitophagy and progression in epithelial ovarian cancer.
    Jiao Wang, Fei Zheng, Dandan Wang, Qing Yang.
      There is a pressing need for innovative therapeutic strategies for patients with epithelial ovarian cancer (EOC). Previous studies have shown that UNC-51-like kinase 1 (ULK1), a serine/threonine kinase, is crucial in regulating cellular autophagy and mitophagy across various tumor types. However, the clinical implications, biological functions, and potential mechanisms of ULK1 in EOC remain poorly understood. This study demonstrates that ULK1 expression is upregulated in EOC tissue samples and EOC cell lines, with increased ULK1 expression correlating with poor prognosis. Functionally, overexpressed ULK1 enhances the proliferation and migration abilities of EOC cells both in vitro and in vivo. Mechanistically, ULK1 was identified as an m6A target of WTAP. WTAP-mediated m6A modification of ULK1 enhanced its mRNA stability in an IGF2BP3-dependent manner, leading to elevated ULK1 expression and enhanced mitophagy in EOC. In summary, our research reveals that the WTAP/IGF2BP3-ULK1 axis significantly influences protective mitophagy in EOC, contributing to its progression. Therefore, the regulatory mechanisms and biological function of ULK1 identify it as a potential molecular target for therapeutic intervention in EOC.
    DOI:  https://doi.org/10.1038/s41419-024-06477-0
  46. Nat Commun. 2024 Jan 30. 15(1): 891
    Molecular mechanisms underlying the BIRC6-mediated regulation of apoptosis and autophagy.
    Shuo-Shuo Liu, Tian-Xia Jiang, Fan Bu, Ji-Lan Zhao, Guang-Fei Wang, Guo-Heng Yang, Jie-Yan Kong, Yun-Fan Qie, Pei Wen, Li-Bin Fan, Ning-Ning Li, Ning Gao, Xiao-Bo Qiu.
      Procaspase 9 is the initiator caspase for apoptosis, but how its levels and activities are maintained remains unclear. The gigantic Inhibitor-of-Apoptosis Protein BIRC6/BRUCE/Apollon inhibits both apoptosis and autophagy by promoting ubiquitylation of proapoptotic factors and the key autophagic protein LC3, respectively. Here we show that BIRC6 forms an anti-parallel U-shaped dimer with multiple previously unannotated domains, including a ubiquitin-like domain, and the proapoptotic factor Smac/DIABLO binds BIRC6 in the central cavity. Notably, Smac outcompetes the effector caspase 3 and the pro-apoptotic protease HtrA2, but not procaspase 9, for binding BIRC6 in cells. BIRC6 also binds LC3 through its LC3-interacting region, probably following dimer disruption of this BIRC6 region. Mutation at LC3 ubiquitylation site promotes autophagy and autophagic degradation of BIRC6. Moreover, induction of autophagy promotes autophagic degradation of BIRC6 and caspase 9, but not of other effector caspases. These results are important to understand how the balance between apoptosis and autophagy is regulated under pathophysiological conditions.
    DOI:  https://doi.org/10.1038/s41467-024-45222-1
  47. FEBS Lett. 2024 Jan 28.
    Lipid droplets and fatty acid-induced lipotoxicity: in a nutshell.
    Eseiwi Obaseki, Daniel Adebayo, Sumit Bandyopadhyay, Hanaa Hariri.
      Lipid droplets (LDs) are fat storage organelles that are conserved from bacteria to humans. LDs are broken down to supply cells with fatty acids (FAs) that can be used as an energy source or membrane synthesis. An overload of FAs disrupts cellular functions and causes lipotoxicity. Thus, by acting as hubs for storing excess fat, LDs prevent lipotoxicity and preserve cellular homeostasis. LD synthesis and turnover have to be precisely regulated to maintain a balanced lipid distribution and allow for cellular adaptation during stress. Here, we discuss how prolonged exposure to excess lipids affects cellular functions, and the roles of LDs in buffering cellular stress focusing on lipotoxicity.
    Keywords:  autophagy; fatty acid; lipid droplet; lipolysis; lipophagy; lipotoxicity
    DOI:  https://doi.org/10.1002/1873-3468.14808
  48. Am J Physiol Cell Physiol. 2024 Jan 29.
    HIF-1 contributes to autophagy activation via BNIP3 to facilitate renal fibrosis in hypoxia in vitro and UUO in vivo.
    Jing Liu, Man J Livingston, Guie Dong, Qingqing Wei, Ming Zhang, Shuqin Mei, Jiefu Zhu, Chun Zhang, Zheng Dong.
      The molecular basis of renal interstitial fibrosis, a major pathological feature of progressive kidney diseases, remains poorly understood. Autophagy has been implicated in renal fibrosis, but whether it promotes or inhibits fibrosis remains controversial. Moreover, it is unclear how autophagy is activated and sustained in renal fibrosis. The present study was designed to address these questions using the in vivo mouse model of unilateral ureteral obstruction model and the in vitro model of hypoxia in renal tubular cells. Both models showed the activation of hypoxia-inducible factors-1 (HIF-1) and autophagy along with fibrotic changes. Inhibition of autophagy with chloroquine reduced renal fibrosis in unilateral ureteral obstruction model, while chloroquine and autophagy-related gene 7 knockdown decreased fibrotic changes in cultured BUMPT renal proximal tubular cells, supporting a pro-fibrotic role of autophagy. Notably, pharmacological and genetic inhibition of HIF-1 led to the suppression of autophagy and renal fibrosis in these models. Mechanistically, knockdown of BCL2 and adenovirus E1B 19-kDa-interacting protein 3(BNIP3), a down-stream target gene of HIF-1, decreased autophagy and fibrotic changes during hypoxia in BUMPT cells. Together, these results suggest that HIF-1 may activate autophagy via BNIP3 in renal tubular cells to facilitate the development of renal interstitial fibrosis.
    Keywords:  BNIP3; autophagy; hypoxia-inducible factor-1; renal fibrosis
    DOI:  https://doi.org/10.1152/ajpcell.00458.2023
  49. Nat Commun. 2024 Feb 01. 15(1): 953
    Mitochondrial protein C15ORF48 is a stress-independent inducer of autophagy that regulates oxidative stress and autoimmunity.
    Yuki Takakura, Moeka Machida, Natsumi Terada, Yuka Katsumi, Seika Kawamura, Kenta Horie, Maki Miyauchi, Tatsuya Ishikawa, Nobuko Akiyama, Takao Seki, Takahisa Miyao, Mio Hayama, Rin Endo, Hiroto Ishii, Yuya Maruyama, Naho Hagiwara, Tetsuya J Kobayashi, Naoto Yamaguchi, Hiroyuki Takano, Taishin Akiyama, Noritaka Yamaguchi.
      Autophagy is primarily activated by cellular stress, such as starvation or mitochondrial damage. However, stress-independent autophagy is activated by unclear mechanisms in several cell types, such as thymic epithelial cells (TECs). Here we report that the mitochondrial protein, C15ORF48, is a critical inducer of stress-independent autophagy. Mechanistically, C15ORF48 reduces the mitochondrial membrane potential and lowers intracellular ATP levels, thereby activating AMP-activated protein kinase and its downstream Unc-51-like kinase 1. Interestingly, C15ORF48-dependent induction of autophagy upregulates intracellular glutathione levels, promoting cell survival by reducing oxidative stress. Mice deficient in C15orf48 show a reduction in stress-independent autophagy in TECs, but not in typical starvation-induced autophagy in skeletal muscles. Moreover, C15orf48-/- mice develop autoimmunity, which is consistent with the fact that the stress-independent autophagy in TECs is crucial for the thymic self-tolerance. These results suggest that C15ORF48 induces stress-independent autophagy, thereby regulating oxidative stress and self-tolerance.
    DOI:  https://doi.org/10.1038/s41467-024-45206-1
  50. World Allergy Organ J. 2024 Feb;17(2): 100852
    Role of autophagy and mitophagy of group 2 innate lymphoid cells in allergic and local allergic rhinitis.
    Chen Wang, Jin-Jing Zhuo, Wen-Qian Li, Min-Li Zhou, Ke-Jia Cheng.
       Background: Roles of ILC2s in allergic rhinitis (AR) and local allergic rhinitis (LAR) are unclear. In this study, we are determined to find the levels of autophagy and mitophagy of ILC2s in allergic nasal inflammation.
    Methods: ELISA was used to detect type 2 inflammatory cytokines. Hematoxylin and eosin (H&E) staining were used to compare the eosinophil (EOS) infiltration of nasal tissue specimens. Flow cytometry was used to detect the levels of ILC2s and Th2 cells. Immunohistochemistry (IHC) and Western blot (WB) were used to detect the levels of Beclin1, LC3, p62, PINK1, Parkin, FUNDC1, and BNIP3 in nasal mucosa. The levels of autophagy related proteins and mitophagy related proteins of the ILC2s were detected by WB. The number of autophagosomes of ILC2s was observed by transmission electron microscopy. The co-localization levels of GFP-LC3 and Mito tracker in ILC2s were observed by confocal microscopy using immunofluorescence.
    Results: We found that the level of type 2 inflammation in AR and LAR mice was significantly increased. The levels of autophagy and mitophagy of AR and LAR mice in nasal mucosa and ILC2s were both increased.
    Conclusions: ILC2s may be associated with the occurrence and development of nasal allergic inflammation. The abnormal increase of autophagy and mitophagy levels in the nose may be associated with the incidence of AR and LAR. Abnormal autophagy and mitophagy levels of ILC2s cells may be one of the causes of allergic nasal inflammation.
    Keywords:  Allergic rhinitis; Autophagy; Local allergic rhinitis; Mitophagy; Type 2 inflammation
    DOI:  https://doi.org/10.1016/j.waojou.2023.100852
  51. Fish Shellfish Immunol. 2024 Jan 30. pii: S1050-4648(24)00061-5. [Epub ahead of print]146 109417
    Edwardsiella piscicida causes iron storage disorders by an autophagy pathway in fish monocytes/macrophages.
    Jingqi Ren, Xiaoyu Ma, Hengyi Hu, Dan Wang, Hao Sun, Jiaxi Liu, Xinyan Wang, Hong Zhou.
      Edwardsiella piscicida (E. piscicida) is a gram-negative pathogen that survives in intracellular environment. Currently, the interplay between E. piscicida and host cells has not been completely explored. In this study, we found that E. piscicida disturbed iron homeostasis in grass carp monocytes/macrophages to maintain its own growth. Further investigation revealed the bacteria induced an increase of intracellular iron, which was subjected to the degradation of ferritin. Moreover, the autophagy inhibitor impeded the degradation of ferritin and increase of intracellular iron in E. piscicida-infected monocytes/macrophages, implying possible involvement of autophagy response in the process of E. piscicida-broken iron homeostasis. Along this line, confocal microscopy observed that E. piscicida elicited the colocalization of ferritin with LC3-positive autophagosome in the monocytes/macrophages, indicating that E. piscicida mediated the degradation of ferritin possibly through the autophagic pathway. These results deepened our understanding of the interaction between E. piscicida and fish cells, hinting that the disruption of iron homeostasis was an important factor for pathogenicity of E. piscicida. They also indicated that autophagy was a possible mechanism governing intracellular iron metabolism in response to E. piscicida infection and might offer a new avenue for anti-E. piscicida strategies in the future.
    Keywords:  Autophagy; Edwardsiella piscicida; Ferritin; Grass carp; Iron homeostasis
    DOI:  https://doi.org/10.1016/j.fsi.2024.109417
  52. Toxicology. 2024 Jan 28. pii: S0300-483X(24)00015-5. [Epub ahead of print] 153734
    Silver nanoparticles induce endothelial cytotoxicity through ROS-mediated mitochondria-lysosome damage and autophagy perturbation: The protective role of N-acetylcysteine.
    Jing He, Yunyun Ma, Xudong Niu, Jiansheng Pei, Ru Yan, Fangjing Xu, Jing Ma, Xiaojuan Ma, Shaobin Jia, Wanrui Ma.
      Silver nanoparticles (AgNPs) are used increasingly often in the biomedical field, but their potential deleterious effects on the cardiovascular system remain to be elucidated. The primary aim of this study was to evaluate the toxic effects, and the underlying mechanisms of these effects, of AgNPs on human umbilical vein endothelial cells (HUVECs), as well as the protective role of N-acetylcysteine (NAC) against cytotoxicity induced by AgNPs. In this study, we found that exposure to AgNPs affects the morphology and function of endothelial cells which manifests as decreased cell proliferation, migration, and angiogenesis ability. Mechanistically, AgNPs can induce excessive cellular production of reactive oxygen species (ROS), leading to damage to cellular sub-organs such as mitochondria and lysosomes. More importantly, our data suggest that AgNPs causes autophagy defect, inhibits mitophagy, and finally activates the mitochondria-mediated apoptosis signaling pathway and evokes cell death. Interestingly, treatment with ROS scavenger-NAC can effectively suppress AgNP-induced endothelial damage.Our results indicate that ROS-mediated mitochondria-lysosome injury and autophagy dysfunction are potential factors of endothelial toxicity induced by AgNPs. This study may provide new evidence for the cardiovascular toxicity of AgNPs and serve as a reference for the safe use of nanoparticles(NPs) in the future.
    Keywords:  Apoptosis; Autophagy; N-acetylcysteine; ROS; Silver nanoparticles
    DOI:  https://doi.org/10.1016/j.tox.2024.153734
  53. Brain Behav Immun. 2024 Jan 31. pii: S0889-1591(24)00233-2. [Epub ahead of print]
    Loss of interleukin 1 signaling causes impairment of microglia- mediated synapse elimination and autistic-like behaviour in mice.
    Antonella Borreca, Cristina Mantovani, Genni Desiato, Irene Corradini, Fabia Filipello, Chiara Elia, Francesca D'Autilia, Giulia Santamaria, Cecilia Garlanda, Raffaella Morini, Davide Pozzi, Michela Matteoli.
      In the last year, the hypothesis that elevated levels of proinflammatory cytokines contribute to the pathogenesis of neurodevelopmental diseases has gained popularity. IL-1 is one of the main cytokines found to be elevated in ASD Autism spectrum disorder, a complex neurodevelopmental condition characterized by defects in social communication and cognitive impairments. In this study, we demonstrate that mice lacking IL-1 signaling display autistic-like defects associated with an excessive number of synapses. We also show that microglia lacking IL-1 signaling at early neurodevelopmental stages are unable to properly perform the process of synapse engulfment and display excessive activation of mammalian target of rapamycin (mTOR) signaling. Notably, even the acute inhibition of IL-1R1 by IL-1Ra is sufficient to enhance mTOR signaling and reduce synaptosome phagocytosis in WT microglia. Finally, we demonstrate that rapamycin treatment rescues the defects in IL-1R deficient mice. These data unveil an exclusive role of microglial IL-1 in synapse refinement via mTOR signaling and indicate a novel mechanism possibly involved in neurodevelopmental disorders associated with defects in the IL-1 pathway.
    Keywords:  Autism spectrum disorder (ASD); IL-1 signaling; IL-1Ra (Interleukin-1 receptor antagonist); Microglia; Neurodevelopmental disorders; Proinflammatory cytokines; Rapamycin treatment; Synapse engulfment; Synaptic density; mTOR signaling
    DOI:  https://doi.org/10.1016/j.bbi.2024.01.221
  54. bioRxiv. 2024 Jan 19. pii: 2024.01.17.576122. [Epub ahead of print]
    miRNA family miR-29 inhibits PINK1-PRKN dependent mitophagy via ATG9A.
    Briana N Markham, Chloe Ramnarine, Songeun Kim, William E Grever, Alexandra I Soto-Beasley, Michael Heckman, Yingxue Ren, Andrew C Osborne, Aditya V Bhagwate, Yuanhang Liu, Chen Wang, Jungsu Kim, Zbigniew K Wszolek, Owen A Ross, Wolfdieter Springer, Fabienne C Fiesel.
      Loss-of-function mutations in the genes encoding PINK1 and PRKN result in early-onset Parkinson disease (EOPD). Together the encoded enzymes direct a neuroprotective pathway that ensures the elimination of damaged mitochondria via autophagy. We performed a genome-wide high content imaging miRNA screen for inhibitors of the PINK1-PRKN pathway and identified all three members of the miRNA family 29 (miR-29). Using RNAseq we identified target genes and found that siRNA against ATG9A phenocopied the effects of miR-29 and inhibited the initiation of PINK1-PRKN mitophagy. Furthermore, we discovered two rare, potentially deleterious, missense variants (p.R631W and p.S828L) in our EOPD cohort and tested them experimentally in cells. While expression of wild-type ATG9A was able to rescue the effects of miR-29a, the EOPD-associated variants behaved like loss-of-function mutations. Together, our study validates miR-29 and its target gene ATG9A as novel regulators of mitophagy initiation. It further serves as proof-of-concept of finding novel, potentially disease-causing EOPD-linked variants specifically in mitophagy regulating genes. The nomination of genetic variants and biological pathways is important for the stratification and treatment of patients that suffer from devastating diseases, such as EOPD.
    DOI:  https://doi.org/10.1101/2024.01.17.576122
  55. Hum Mol Genet. 2024 Jan 27. pii: ddae008. [Epub ahead of print]
    OPA1 mutation affects autophagy and triggers senescence in autosomal dominant optic atrophy plus fibroblasts.
    Paola Zanfardino, Alessandro Amati, Stefano Doccini, Sharon N Cox, Apollonia Tullo, Giovanna Longo, Annamaria D'Erchia, Ernesto Picardi, Claudia Nesti, Filippo M Santorelli, Vittoria Petruzzella.
      In several cases of mitochondrial diseases, the underlying genetic and bioenergetic causes of reduced oxidative phosphorylation (OxPhos) in mitochondrial dysfunction are well understood. However, there is still limited knowledge about the specific cellular outcomes and factors involved for each gene and mutation, which contributes to the lack of effective treatments for these disorders. This study focused on fibroblasts from a patient with Autosomal Dominant Optic Atrophy (ADOA) plus syndrome harboring a mutation in the Optic Atrophy 1 (OPA1) gene. By combining functional and transcriptomic approaches, we investigated the mitochondrial function and identified cellular phenotypes associated with the disease. Our findings revealed that fibroblasts with the OPA1 mutation exhibited a disrupted mitochondrial network and function, leading to altered mitochondrial dynamics and reduced autophagic response. Additionally, we observed a premature senescence phenotype in these cells, suggesting a previously unexplored role of the OPA1 gene in inducing senescence in ADOA plus patients. This study provides novel insights into the mechanisms underlying mitochondrial dysfunction in ADOA plus and highlights the potential importance of senescence in disease progression.
    Keywords:  ADOA plus; Autophagy; OPA1; mitochondria; mitophagy; senescence
    DOI:  https://doi.org/10.1093/hmg/ddae008
  56. J Pharmacol Exp Ther. 2024 Jan 31. pii: JPET-AR-2023-002021. [Epub ahead of print]
    Lucanthone, a Potential PPT1 inhibitor, Perturbs Stemness, Reduces Tumor Microtube Formation and Slows the Growth of Temozolomide-Resistant Gliomas in Vivo.
    Daniel P Radin, Sophie Shifman, Ian R Outhwaite, Aryan Sharma, Robert Bases, Markus A Seeliger, Stella E Tsirka.
      Glioblastoma (GBM) is the most frequently diagnosed primary CNS tumor in adults. Despite the standard of care therapy which includes surgical resection, temozolomide chemotherapy, radiation and the newly added tumor treating fields, median survival remains only ~20 months. Unfortunately, GBM has a ~100% recurrence rate, but after recurrence there are no FDA-approved therapies to limit tumor growth and enhance patient survival, as these tumors are resistant to TMZ. Recently, our laboratory reported that lucanthone slows GBM by inhibiting autophagic flux through lysosome targeting and decreases the number of Olig2+ glioma stem-like cells (GSC) in vitro and in vivo. We now additionally report that lucanthone efficiently abates stemness in patient-derived GSC and reduces tumor microtube formation in GSC, an emerging hallmark of treatment resistance in GBM. In glioma tumors derived from cells with acquired resistance to TMZ, lucanthone retains the ability to perturb tumor growth, inhibits autophagy by targeting lysosomes and reduces Olig2 positivity. We also find that lucanthone may act as an inhibitor of protein palmitoyl thioesterase 1 (PPT1). Our results suggest that lucanthone may function as a potential treatment option for GBM tumors that are not amenable to TMZ treatment. Significance Statement We report that the anti-schistosome agent lucanthone impedes tumor growth in a preclinical model of temozolomide-resistant glioblastoma, and reduces the numbers of stem-like glioma cells. It acts as an autophagy inhibitor and its mechanism of action may be via inhibition of palmitoyl protein thioesterase 1. As there are no defined therapies approved for recurrent, TMZ-resistant tumor, lucanthone could emerge as a treatment for glioblastoma tumors that may not be amenable to TMZ both in the newly diagnosed and recurrent settings.
    Keywords:  Autophagy; cancer stem cells; glioblastoma cells
    DOI:  https://doi.org/10.1124/jpet.123.002021
  57. Autophagy. 2024 Jan 31.
    The cocoon into a butterfly: why the HVA22 family proteins turned out to be the reticulophagy receptors in plants？.
    Ning Xu, Yingbo Liang, Jun Liu.
      Selective degradation of the endoplasmic reticulum (ER) by macroautophagy/autophagy (reticulophagy) is essential for maintaining ER morphology and homeostasis under environmental stresses. Several reticulophagy receptors have been identified in mammals and yeast, but their counterparts in plants have not been extensively explored yet. Recently, we demonstrated that the HVA22-family protein OsHLP1 is a reticulophagy receptor in rice plants, and its orthologs function similarly in Arabidopsis plants. In this punctum, we discuss why the HVA22 family proteins are the reticulophagy receptors in plants and how reticulophagy is highly associated with plant immune response.
    Keywords:  Defense; ER-phagy receptor; HAV22; OsHLP1; endoplasmic-reticulum; rice plants
    DOI:  https://doi.org/10.1080/15548627.2024.2311542
  58. FEBS Lett. 2024 Feb 01.
    Mitochondrial dysfunction in NPC1-deficiency is not rescued by drugs targeting the glucosylceramidase GBA2 and the cholesterol-binding proteins TSPO and StARD1.
    Simon Wheeler, Meenakshi Bhardwaj, Victor Kenyon, Maria J Ferraz, Johannes M F G Aerts, Dan J Sillence.
      Niemann-Pick type C disease (NPCD) is a rare neurodegenerative disorder most commonly caused by mutations in the lysosomal protein Niemann-Pick C1 (NPC1), which is implicated in cholesterol export. Mitochondrial insufficiency forms a significant feature of the pathology of this disease, yet studies attempting to address this are rare. The working hypothesis is that mitochondria become overloaded with cholesterol which renders them dysfunctional. We examined two potential protein targets-translocator protein (TSPO) and steroidogenic acute regulatory protein D1 (StARD1)-which are implicated in cholesterol transport to mitochondria, in addition to glucocerbrosidase 2 (GBA2), the target of miglustat, which is currently the only approved treatment for NPCD. However, inhibiting these proteins did not correct the mitochondrial defect in NPC1-deficient cells.
    Keywords:  GBA2; NPC1; Niemann-Pick C; StARD1; TSPO; mitochondria
    DOI:  https://doi.org/10.1002/1873-3468.14802
  59. FASEB J. 2024 Feb 15. 38(3): e23437
    Loss of mitogen-activated protein kinase phosphate-5 aggravates islet dysfunction in mice with type 1 and type 2 diabetes.
    Tongjian Zhao, Yafei Tian, Jianan Zhao, Dandan Sun, Yongjun Ma, Wei Wang, Weiqun Yan, Ping Jiao, Jie Ma.
      Impaired functionality and loss of islet β-cells are the primary abnormalities underlying the pathogenesis of both type 1 and 2 diabetes (T1DM and T2DM). However, specific therapeutic and preventive mechanisms underlying these conditions remain unclear. Mitogen-activated protein kinase phosphatase-5 (MKP-5) has been implicated in carcinogenesis, lipid metabolism regulation, and immune cell activation. In a previous study, we demonstrated the involvement of exogenous MKP-5 in the regulation of obesity-induced T2DM. However, the role of endogenous MKP-5 in the T1DM and T2DM processes is unclear. Thus, mice with MKP-5 knockout (KO) were generated and used to establish mouse models of both T1DM and T2DM. Our results showed that MKP-5 KO exacerbated diabetes-related symptoms in mice with both T1DM and T2DM. Given that most phenotypic studies on islet dysfunction have focused on mice with T2DM rather than T1DM, we specifically aimed to investigate the role of endoplasmic reticulum stress (ERS) and autophagy in T2DM KO islets. To accomplish this, we performed RNA sequence analysis to gain comprehensive insight into the molecular mechanisms associated with ERS and autophagy in T2DM KO islets. The results showed that the islets from mice with MKP-5 KO triggered 5' adenosine monophosphate-activated protein kinase (AMPK)-mediated autophagy inhibition and glucose-regulated protein 78 (GRP-78)-dominated ERS. Hence, we concluded that the autophagy impairment, resulting in islet dysfunction in mice with MKP-5 KO, is mediated through GRP-78 involvement. These findings provide valuable insights into the molecular pathogenesis of diabetes and highlight the significant role of MKP-5. Moreover, this knowledge holds promise for novel therapeutic strategies targeting MKP-5 for diabetes management.
    Keywords:  AMPK; GRP-78; MKP-5; diabetes mellitus; islet dysfunction; sequence analysis
    DOI:  https://doi.org/10.1096/fj.202301479R
  60. BMC Biol. 2024 Jan 30. 22(1): 23
    Migrasomal autophagosomes relieve endoplasmic reticulum stress in glioblastoma cells.
    Seon Yong Lee, Sang-Hun Choi, Yoonji Kim, Hee-Sung Ahn, Young-Gyu Ko, Kyunggon Kim, Sung Wook Chi, Hyunggee Kim.
       BACKGROUND: Glioblastoma (GBM) is more difficult to treat than other intractable adult tumors. The main reason that GBM is so difficult to treat is that it is highly infiltrative. Migrasomes are newly discovered membrane structures observed in migrating cells. Thus, they can be generated from GBM cells that have the ability to migrate along the brain parenchyma. However, the function of migrasomes has not yet been elucidated in GBM cells.
    RESULTS: Here, we describe the composition and function of migrasomes generated along with GBM cell migration. Proteomic analysis revealed that LC3B-positive autophagosomes were abundant in the migrasomes of GBM cells. An increased number of migrasomes was observed following treatment with chloroquine (CQ) or inhibition of the expression of STX17 and SNAP29, which are involved in autophagosome/lysosome fusion. Furthermore, depletion of ITGA5 or TSPAN4 did not relieve endoplasmic reticulum (ER) stress in cells, resulting in cell death.
    CONCLUSIONS: Taken together, our study suggests that increasing the number of autophagosomes, through inhibition of autophagosome/lysosome fusion, generates migrasomes that have the capacity to alleviate cellular stress.
    Keywords:  Autophagosome; Cell death; ER stress; ITGA5; Migrasome; Retraction fiber; TSPAN4
    DOI:  https://doi.org/10.1186/s12915-024-01829-w
  61. In Vitro Cell Dev Biol Anim. 2024 Jan 29.
    DUSP4 maintains the survival and LSD1 protein stability in esophageal squamous cell carcinoma cells by inhibiting JNK signaling-dependent autophagy.
    Xinxin Liu, Zhou Ye, Dingyu Rao, Qianshun Chen, Zuxiong Zhang.
      DUSP4 is a biomarker of esophageal squamous cell carcinoma (ESCC), which is responsible for the prognosis in ESCC. However, the underlying mechanism of DUSP4-regulated ESCC carcinogenesis is unknown. As a negative regulator of JNK, DUSP4 can inhibit autophagy, which contributes to tumorigenesis. This study aimed to explore the role of autophagy in DUSP4-regulated ESCC carcinogenesis. Our results showed that DUSP4 overexpression inhibited autophagy and promoted LSD1 protein expression in ESCC cells, while DUSP4 silencing showed the opposite effects. However, DUSP4 overexpression and silencing did not affect LSD1 mRNA expression. But the regulatory ability of DUSP4 overexpression on autophagy, death level, and LSD1 protein was reversed by rapamycin. In addition, DUSP4 overexpression inhibited JNK and Bcl2 phosphorylation and the dissociation of Bcl2-Beclin1 complex, while DUSP4 silencing promoted JNK and Bcl2 phosphorylation. Moreover, the regulatory ability of DUSP4 overexpression on autophagy, death, and LSD1 protein was reversed by JNK activator anisomycin. The xenograft assays also showed that DUSP4 overexpression-promoted ESCC tumor growth in vivo and LC3II and LSD1 protein expression in tumor tissues were reversed by rapamycin or anisomycin. Overall, DUSP4 inhibits Bcl2-Beclin1-autophagy signal transduction through the negative regulation of JNK, thus suppressing autophagic death and the autophagic degradation of LSD1 in ESCC, by which DUSP4 promotes ESCC carcinogenesis.
    DOI:  https://doi.org/10.1007/s11626-023-00845-4
  62. Front Biosci (Landmark Ed). 2024 Jan 18. 29(1): 22
    Unveiling the Intricacies of Autophagy in Asthma: Unraveling Novel Therapeutic Avenues.
    Junjun Peng, Na Lu, Shucheng Hua, Lei Song, Han Liu.
      Understanding the pathogenesis of different phenotypes of asthma, including glucocorticoid-dependent and glucocorticoid-resistant asthma, is crucial for the development of effective treatments. Autophagy, a fundamental cellular process involved in cell homeostasis, has been implicated in asthma, although the exact mechanisms remain unclear. Recent studies have identified autophagy activation in eosinophilic, neutrophilic, and paucigranulocytic asthma, providing novel insights into the disease. This comprehensive review examines the role of autophagy in the pathogenesis and treatment of asthma, with a focus on various cell types. The goal is to uncover potential therapeutic targets and innovative treatment modalities to improve patient outcomes in clinical settings.
    Keywords:  eosinophil; neutrophil; paucigranulocytic; phenotypes; treatment
    DOI:  https://doi.org/10.31083/j.fbl2901022
  63. Heliyon. 2024 Jan 30. 10(2): e24408
    NUPR1 contributes to activate TFE3-dependent autophagy leading to cervical cancer proliferation.
    Xiaoguang Wang, Ke Wang, Xiuli Wang.
      Cervical cancer is a malignant tumor that occurs in the cervix of women and endangers their lives. In this study, we aimed to assess the roles of NUPR1 and TFE3 in cervical cancer. The Cancer Genome Atlas (TCGA) database was used to assess the correlation between NUPR1 and TFE3 expression in cervical cancer. By silencing NUPR1 and TFE3, and through 3-MA treatment, we determined whether their silencing could lead to lysosomal dysfunction, thereby inhibiting autophagy and cervical cancer cell proliferation. Their roles were further analyzed using molecular biological methods. Silencing NUPR1 and TFE3 inhibited cell proliferation and decreased the expression levels of autophagy-related genes, p62 and LC3B. By tracing lysosomes within cells, NUPR1 and TFE3 knockdown were found to induce lysosomal dysfunction, thereby inhibiting autophagy. In vivo experimental studies have shown that knockdown of NUPR1 and TFE3 can inhibit tumor growth, while reducing the ki67, p62, and LC3B expression levels and promoting apoptosis. Furthermore, the expression levels of lamp1 and lamp2, and the phosphorylation of PI3K (p-PI3K) and Akt (p-Akt) were significantly reduced after NUPR1 and TFE3 knockdown. However, treatment with 3-MA and overexpression of TFE3 could partially reverse the effect of silencing NUPR1. Overall, silencing NUPR1 reduced autophagy by inhibiting TFE3 in cervical cancer. Our results supply new evidence for the use of NUPR1 as a therapeutic target in cervical cancer.
    Keywords:  Autophagy; Cell apoptosis; PI3K/Akt signaling; Xenograft tumor
    DOI:  https://doi.org/10.1016/j.heliyon.2024.e24408
  64. J Gerontol A Biol Sci Med Sci. 2024 Jan 30. pii: glae029. [Epub ahead of print]
    Meeting summary of The NYO3 5th NO-Age/AD meeting and the 1st Norway-UK joint meeting on ageing and dementia: recent progress on the mechanisms and interventional strategies.
    He-Ling Wang, Richard Siow, Tomas Schmauck-Medina, Jianying Zhang, Per Morten Sandset, Clare Filshie, Øystein Lund, Linda Partridge, Linda Hildegard Bergersen, Lene Juel Rasmussen, Konstantinos Palikaras, Ioannis Sotiropoulos, Jon Storm-Mathisen, David C Rubinsztein, Maria Grazia Spillantini, Chris I De Zeeuw, Leiv Otto Watne, Martin Vyhnalek, Katerina Veverova, Kristina Xiao Liang, Nektarios Tavernarakis, Vilhelm A Bohr, Koutaro Yokote, Janna Saarela, Hilde Nilsen, Efstathios S Gonos, Morten Scheibye-Knudsen, Guobing Chen, Hisaya Kato, Geir Selbæk, Tormod Fladby, Per Nilsson, Anne Simonsen, Dag Aarsland, Sofie Lautrup, Ole Petter Ottersen, Lynne S Cox, Evandro F Fang.
      Unhealthy ageing poses a global challenge with profound healthcare and socioeconomic implications. Slowing down the ageing process offers a promising approach to reduce the burden of a number of age-related diseases, such as dementia, promoting healthy longevity in the old population. In response to the challenge of the ageing population and with a view to the future, Norway and the UK are fostering collaborations, supported by a "Money Follows Cooperation agreement" between the two nations. The inaugural Norway-UK joint meeting on ageing and dementia gathered leading experts on ageing and dementia from the two nations to share their latest discoveries in related fields. Since ageing is an international challenge, and to foster collaborations, we also invited leading scholars from 11 additional countries to join this event. This report provides a summary of the conference, highlighting recent progress on molecular ageing mechanisms, genetic risk factors, DNA damage and repair, mitophagy, autophagy, as well as progress on a series of clinical trials (e.g., using NAD+ precursors). The meeting facilitated dialogue among policy makers, administrative leaders, researchers, and clinical experts, aiming to promote international research collaborations and to translate findings into clinical applications and interventions to advance healthy ageing.
    Keywords:  Alzheimer’s disease; ageing; dementia; longevity; neurodegeneration
    DOI:  https://doi.org/10.1093/gerona/glae029
  65. Curr Opin Neurobiol. 2024 Feb 01. pii: S0959-4388(24)00003-5. [Epub ahead of print]85 102841
    Cell biology of Parkinson's disease: Mechanisms of synaptic, lysosomal, and mitochondrial dysfunction.
    Sarah M Brooker, Grace E Naylor, Dimitri Krainc.
      Parkinson's disease (PD) is a growing cause of disability worldwide and there is a critical need for the development of disease-modifying therapies to slow or stop disease progression. Recent advances in characterizing the genetics of PD have expanded our understanding of the cell biology of this disorder. Mitochondrial oxidative stress, defects in synaptic function, and impaired lysosomal activity have been shown to be linked in PD, resulting in a pathogenic feedback cycle involving the accumulation of toxic oxidized dopamine and alpha-synuclein. In this review, we will highlight recent data on a subset of PD-linked genes which have key roles in these pathways and the pathogenic cycle. We will furthermore discuss findings highlighting the importance of dynamic mitochondria-lysosome contact sites that mediate direct inter-organelle cross-talk in the pathogenesis of PD and related disorders.
    DOI:  https://doi.org/10.1016/j.conb.2024.102841
  66. J Proteomics. 2024 Jan 16. pii: S1874-3919(23)00226-9. [Epub ahead of print]291 105037
    Lentiviral gene therapy with IGF2-tagged GAA normalizes the skeletal muscle proteome in murine Pompe disease.
    Qiushi Liang, Eva C Vlaar, Joon M Pijnenburg, Erikjan Rijkers, Jeroen A A Demmers, Arnold G Vulto, Ans T van der Ploeg, Niek P van Til, W W M Pim Pijnappel.
      Pompe disease is a lysosomal storage disorder caused by deficiency of acid alpha-glucosidase (GAA), resulting in glycogen accumulation with profound pathology in skeletal muscle. We recently developed an optimized form of lentiviral gene therapy for Pompe disease in which a codon-optimized version of the GAA transgene (LV-GAAco) was fused to an insulin-like growth factor 2 (IGF2) peptide (LV-IGF2.GAAco), to promote cellular uptake via the cation-independent mannose-6-phosphate/IGF2 receptor. Lentiviral gene therapy with LV-IGF2.GAAco showed superior efficacy in heart, skeletal muscle, and brain of Gaa -/- mice compared to gene therapy with untagged LV-GAAco. Here, we used quantitative mass spectrometry using TMT labeling to analyze the muscle proteome and the response to gene therapy in Gaa -/- mice. We found that muscle of Gaa -/- mice displayed altered levels of proteins including those with functions in the CLEAR signaling pathway, autophagy, cytoplasmic glycogen metabolism, calcium homeostasis, redox signaling, mitochondrial function, fatty acid transport, muscle contraction, cytoskeletal organization, phagosome maturation, and inflammation. Gene therapy with LV-GAAco resulted in partial correction of the muscle proteome, while gene therapy with LV-IGF2.GAAco resulted in a near-complete restoration to wild type levels without inducing extra proteomic changes, supporting clinical development of lentiviral gene therapy for Pompe disease. SIGNIFICANCE: Lysosomal glycogen accumulation is the primary cause of Pompe disease, and leads to a cascade of pathological events in cardiac and skeletal muscle and in the central nervous system. In this study, we identified the proteomic changes that are caused by Pompe disease in skeletal muscle of a mouse model. We showed that lentiviral gene therapy with LV-IGF2.GAAco nearly completely corrects disease-associated proteomic changes. This study supports the future clinical development of lentiviral gene therapy with LV-IGF2.GAAco as a new treatment option for Pompe disease.
    Keywords:  Acid-alpha glucosidase; Glycogen storage disease type II; Lentiviral gene therapy; Lysosomal storage disease; Pompe disease; Proteome
    DOI:  https://doi.org/10.1016/j.jprot.2023.105037
  67. Zool Res. 2024 Mar 18. pii: 2095-8137(2024)02-0242-11. [Epub ahead of print]45(2): 242-252
    Comparative analysis of primate and pig cells reveals primate-specific PINK1 expression and phosphorylation.
    Xiu-Sheng Chen, Rui Han, Yan-Ting Liu, Wei Huang, Qi Wang, Xin Xiong, Ying Zhang, Jian-Guo Zhao, Shi-Hua Li, Xiao-Jiang Li, Wei-Li Yang.
      PTEN-induced putative kinase 1 (PINK1), a mitochondrial kinase that phosphorylates Parkin and other proteins, plays a crucial role in mitophagy and protection against neurodegeneration. Mutations in PINK1 and Parkin can lead to loss of function and early onset Parkinson's disease. However, there is a lack of strong in vivo evidence in rodent models to support the theory that loss of PINK1 affects mitophagy and induces neurodegeneration. Additionally, PINK1 knockout pigs ( Sus scrofa) do not appear to exhibit neurodegeneration. In our recent work involving non-human primates, we found that PINK1 is selectively expressed in primate brains, while absent in rodent brains. To extend this to other species, we used multiple antibodies to examine the expression of PINK1 in pig tissues. In contrast to tissues from cynomolgus monkeys ( Macaca fascicularis), our data did not convincingly demonstrate detectable PINK1 expression in pig tissues. Knockdown of PINK1 in cultured pig cells did not result in altered Parkin and BAD phosphorylation, as observed in cultured monkey cells. A comparison of monkey and pig striatum revealed more PINK1-phosphorylated substrates in the monkey brain. Consistently, PINK1 knockout in pigs did not lead to obvious changes in the phosphorylation of Parkin and BAD. These findings provide new evidence that PINK1 expression is specific to primates, underscoring the importance of non-human primates in investigating PINK1 function and pathology related to PINK1 deficiency.
    Keywords:  Mitochondria; Non-human primates; PINK1; Parkin; Phosphorylation; Pigs
    DOI:  https://doi.org/10.24272/j.issn.2095-8137.2023.241
  68. FEBS Lett. 2024 Jan 28.
    Autophagy-dependent alternative splicing of ribosomal protein S24 produces a more stable isoform that aids in hypoxic cell survival.
    Jenna Kerry, Erin J Specker, Morgan Mizzoni, Andrea Brumwell, Leslie Fell, Jenna Goodbrand, Michael N Rosen, James Uniacke.
      Cells remodel splicing and translation machineries to mount specialized gene expression responses to stress. Here, we show that hypoxic human cells in 2D and 3D culture models increase the relative abundance of a longer mRNA variant of ribosomal protein S24 (RPS24L) compared to a shorter mRNA variant (RPS24S) by favoring the inclusion of a 22 bp cassette exon. Mechanistically, RPS24L and RPS24S are induced and repressed, respectively, by distinct pathways in hypoxia: RPS24L is induced in an autophagy-dependent manner, while RPS24S is reduced by mTORC1 repression in a hypoxia-inducible factor-dependent manner. RPS24L produces a more stable protein isoform that aids in hypoxic cell survival and growth, which could be exploited by cancer cells in the tumor microenvironment.
    Keywords:  autophagy; hypoxia; ribosome; splicing; stress
    DOI:  https://doi.org/10.1002/1873-3468.14804
  69. Nucleic Acids Res. 2024 Jan 28. pii: gkae006. [Epub ahead of print]
    Multiple mechanisms activate GCN2 eIF2 kinase in response to diverse stress conditions.
    Jagannath Misra, Kenneth R Carlson, Dan F Spandau, Ronald C Wek.
      Diverse environmental insults induce the integrated stress response (ISR), which features eIF2 phosphorylation and translational control that serves to restore protein homeostasis. The eIF2 kinase GCN2 is a first responder in the ISR that is activated by amino acid depletion and other stresses not directly related to nutrients. Two mechanisms are suggested to trigger an ordered process of GCN2 activation during stress: GCN2 monitoring stress via accumulating uncharged tRNAs or by stalled and colliding ribosomes. Our results suggest that while ribosomal collisions are indeed essential for GCN2 activation in response to translational elongation inhibitors, conditions that trigger deacylation of tRNAs activate GCN2 via its direct association with affected tRNAs. Both mechanisms require the GCN2 regulatory domain related to histidyl tRNA synthetases. GCN2 activation by UV irradiation features lowered amino acids and increased uncharged tRNAs and UV-induced ribosome collisions are suggested to be dispensable. We conclude that there are multiple mechanisms that activate GCN2 during diverse stresses.
    DOI:  https://doi.org/10.1093/nar/gkae006
  70. Exp Dermatol. 2024 Jan;33(1): e15006
    Q-switched 1064 nm Nd: YAG laser restores skin photoageing by activating autophagy by TGFβ1 and ITGB1.
    Huiyi Xiang, Xiaorong Jia, Xiaoxia Duan, Qi Xu, Ruiqi Zhang, Yunting He, Zhi Yang.
      Excessive ultraviolet B ray (UVB) exposure to sunlight results in skin photoageing. Our previous research showed that a Q-switched 1064 nm Nd: YAG laser can alleviate skin barrier damage through miR-24-3p. However, the role of autophagy in the laser treatment of skin photoageing is still unclear. This study aims to investigate whether autophagy is involved in the mechanism of Q-switched 1064 nm Nd: YAG in the treatment of skin ageing. In vitro, primary human dermal fibroblast (HDF) cells were irradiated with different doses of UVB to establish a cell model of skin photoageing. In vivo, SKH-1 hairless mice were irradiated with UVB to establish a skin photoageing mouse model and irradiated with laser. The oxidative stress and autophagy levels were detected by western blot, immunofluorescence and flow cytometer. String was used to predict the interaction protein of TGF-β1, and CO-IP and GST-pull down were used to detect the binding relationship between TGFβ1 and ITGB1. In vitro, UVB irradiation reduced HDF cell viability, arrested cell cycle, induced cell senescence and oxidative stress compared with the control group. Laser treatment reversed cell viability, senescence and oxidative stress induced by UVB irradiation and activated autophagy. Autophagy agonists or inhibitors can enhance or attenuate the changes induced by laser treatment, respectively. In vivo, UVB irradiation caused hyperkeratosis, dermis destruction, collagen fibres reduction, increased cellular senescence and activation of oxidative stress in hairless mice. Laser treatment thinned the stratum corneum of skin tissue, increased collagen synthesis and autophagy in the dermis, and decreased the level of oxidative stress. Autophagy agonist rapamycin and autophagy inhibitor 3-methyladenine (3-MA) can enhance or attenuate the effects of laser treatment on the skin, respectively. Also, we identified a direct interaction between TGFB1 and ITGB1 and participated in laser irradiation-activated autophagy, thereby inhibiting UVB-mediated oxidative stress further reducing skin ageing. Q-switched 1064 nm Nd: YAG laser treatment inhibited UVB-induced oxidative stress and restored skin photoageing by activating autophagy, and TGFβ1 and ITGB1 directly incorporated and participated in this process.
    Keywords:  Q-switched 1064 nm Nd: YAG laser; autophagy; oxidative stress, TGF-β1; photoageing
    DOI:  https://doi.org/10.1111/exd.15006
  71. Biochem J. 2024 Feb 01. pii: BCJ20230492. [Epub ahead of print]
    The Parkinson's Disease related mutant VPS35 (D620N) amplifies the LRRK2 response to endolysosomal stress.
    Katy R McCarron, Hannah Elcocks, Heather Mortiboys, Sylvie Urbe, Michael J Clague.
      The identification of multiple genes linked to Parkinson's Disease invites the question as to how they may cooperate. We have generated isogenic cell lines that inducibly express either wild-type or a mutant form of the retromer component VPS35 (D620N), which has been linked to Parkinson's Disease. This has enabled us to test proposed effects of this mutation in a setting where the relative expression reflects the physiological occurrence. We confirm that this mutation compromises VPS35 association with the WASH complex, but find no defect in WASH recruitment to endosomes, nor in the distribution of lysosomal receptors, cation-independent mannose-6-phosphate receptor and Sortilin. We show VPS35 (D620N) enhances the activity of the Parkinson's associated kinase LRRK2 towards RAB12 under basal conditions. Furthermore, VPS35 (D620N) amplifies the LRRK2 response to endolysosomal stress resulting in enhanced phosphorylation of RABs 10 and 12. By comparing different types of endolysosomal stresses such as the ionophore nigericin and the membranolytic agent LLOMe, we are able to dissociate phospho-RAB accumulation from membrane rupture.
    Keywords:  Parkinsons disease; VPS35; endolysosome; leucine rich repeat kinase; phosphoRab
    DOI:  https://doi.org/10.1042/BCJ20230492
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