bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2023–02–05
sixty-six papers selected by
Viktor Korolchuk, Newcastle University
  1. Autophagy disruption reduces mTORC1 activation leading to retinal ganglion cell neurodegeneration associated with glaucoma.
  2. Deciphering functional roles and interplay between Beclin1 and Beclin2 in autophagosome formation and mitophagy.
  3. Farnesoid X Receptor (FXR) Regulates mTORC1 Signaling and Autophagy by Inhibiting SESN2 Expression.
  4. Rapamycin and Alzheimer disease: a hypothesis for the effective use of rapamycin for treatment of neurodegenerative disease.
  5. AMPK-dependent phosphorylation of the GATOR2 component WDR24 suppresses glucose-mediated mTORC1 activation.
  6. The participation of non-canonical autophagic proteins in the autophagy process and their potential as therapeutic targets.
  7. Mechanisms Controlling Selective Elimination of Damaged Lysosomes.
  8. Arf5 mediated regulation of mTORC1 at the plasma membrane.
  9. Autophagy-dependent ferroptosis in cancer.
  10. Autophagic structures revealed by cryo-electron tomography: New clues about autophagosome biogenesis.
  11. Reduced hepatocyte mitophagy is an early feature of NAFLD pathogenesis and hastens the onset of steatosis, inflammation and fibrosis.
  12. mTOR signaling inhibition decreases lysosome migration and impairs the success of Trypanosoma cruzi infection and replication in cardiomyocytes.
  13. Regulation of mTOR by phosphatidic acid.
  14. CCPG1 recognizes ER luminal proteins for selective ER-phagy.
  15. LINC01278 Induces Autophagy to Inhibit Tumour Progression by Suppressing the mTOR Signalling Pathway.
  16. Brain-protective mechanisms of autophagy associated circRNAs: Kick starting self-cleaning mode in brain cells via circRNAs as a potential therapeutic approach for neurodegenerative diseases.
  17. Metabolic function of autophagy is essential for cell survival.
  18. Autophagy collaborates with apoptosis pathways to control myelination specificity and function.
  19. Beyond housekeeping: autophagy regulates PKA signaling at synapses.
  20. Transcription factor EB regulates phosphatidylinositol-3-phosphate levels that control lysosome positioning in the bladder cancer model.
  21. Frontotemporal Dementia Patient Neurons With Progranulin Deficiency Display Protein Dyshomeostasis.
  22. Dock7 regulates AKT and mTOR/S6K activity required for the transformed phenotypes and survival of cancer cells.
  23. Lysosomal quality control: molecular mechanisms and therapeutic implications.
  24. Phosphorylation of EIF2S1 (eukaryotic translation initiation factor 2 subunit alpha) is indispensable for nuclear translocation of TFEB and TFE3 during ER stress.
  25. A distinct linker mediating ER-autophagosome membrane contact site (EACS) in plants.
  26. Application of Novel Degraders Employing Autophagy for Expediting Medicinal Research.
  27. Modeling Huntington disease through microRNA-mediated neural reprogramming identifies age-associated autophagy dysfunction driving the onset of neurodegeneration.
  28. Autophagy regulates inflammation in intracerebral hemorrhage: Enemy or friend?
  29. Quantitative assessment of mitophagy in irradiated cancer cells.
  30. BORC complex specific components and Kinesin-1 mediate autophagy evasion by the autophagy-resistant Mycobacterium tuberculosis Beijing strain.
  31. A genome-wide CRISPR functional survey of the human phagocytosis molecular machinery.
  32. A single dose of exercise stimulates skeletal muscle mitochondrial plasticity in myotonic dystrophy type 1.
  33. Recent advances of tanshinone in regulating autophagy for medicinal research.
  34. PI5P4Kα supports prostate cancer metabolism and exposes a survival vulnerability during androgen receptor inhibition.
  35. Claspin is Required for Growth Recovery from Serum Starvation through Regulating the PI3K-PDK1-mTOR Pathway in Mammalian Cells.
  36. Dysregulation of endoplasmic reticulum stress response in skin wounds in a streptozotocin-induced diabetes mouse model.
  37. Effect of ATG12-ATG5-ATG16L1 autophagy E3-like complex on the ability of LC3/GABARAP proteins to induce vesicle tethering and fusion.
  38. ANP promotes HTR-8/SVneo cell invasion by upregulating protein kinase N 3 via autophagy inhibition.
  39. Pharmacological inhibition of lysosomal two-pore channel 2 (TPC2) confers neuroprotection in stroke via autophagy regulation.
  40. Oleoylethanolamide facilitates PPARa and TFEB signaling and attenuates Ab pathology in a mouse model of Alzheimer's disease.
  41. MANF stimulates autophagy and restores mitochondrial homeostasis to treat toxic proteinopathy.
  42. TPPU inhibits inflammation-induced excessive autophagy to restore the osteogenic differentiation potential of stem cells and improves alveolar ridge preservation.
  43. Identification of autophagy-associated genes and prognostic implications in adults with acute myeloid leukemia by integrated bioinformatics analysis.
  44. Genome-wide screens identify SEL1L as an intracellular rheostat controlling collagen turnover.
  45. Mesopore-encaged active MnOx in nano-silica selectively suppresses lung cancer cells by inducing autophagy.
  46. Antiretroviral treatment reveals a novel role for lysosomes in oligodendrocyte maturation.
  47. The many hats of transmembrane emp24 domain protein TMED9 in secretory pathway homeostasis.
  48. Lipophagy: Molecular Mechanisms and Implications in Hepatic Lipid Metabolism.
  49. Chlamydia psittaci inclusion membrane protein CPSIT_0842 induces macrophage apoptosis through MAPK/ERK-mediated autophagy.
  50. Targeting VPS41 induces methuosis and inhibits autophagy in cancer cells.
  51. TRPV1 regulates ApoE4-disrupted intracellular lipid homeostasis and decreases synaptic phagocytosis by microglia.
  52. Chemical mimetics of the N-degron pathway alleviate systemic inflammation by activating mitophagy and immunometabolic remodeling.
  53. An explanation of how mutant and wild-type mitochondria might stably co-exist in inherited mitochondrial diseases.
  54. mTORC1 syndrome (TorS): unified paradigm for diabetes/metabolic syndrome.
  55. TNEA therapy promotes the autophagic degradation of NLRP3 inflammasome in a transgenic mouse model of Alzheimer's disease via TFEB/TFE3 activation.
  56. TSC2 regulates tumor susceptibility to TRAIL-mediated T-cell killing by orchestrating mTOR signaling.
  57. Post-fast refeeding enhances intestinal stem cell-mediated regeneration and tumourigenesis through mTORC1-dependent polyamine synthesis.
  58. Skeletal diseases caused by mutations in PTH1R show aberrant differentiation of skeletal progenitors due to dysregulation of DEPTOR.
  59. Molecular Engineering of pH-Responsive NIR Oxazine Assemblies for Evoking Tumor Ferroptosis via Triggering Lysosomal Dysfunction.
  60. Tracking endoplasmic reticulum viscosity during ferroptosis and autophagy using a molecular rotor probe.
  61. NFATc2-dependent Epigenetic Downregulation of the TSC2/Beclin-1 Pathway is Involved in Neuropathic Pain Induced by Oxaliplatin.
  62. Age-dependent nuclear lipid droplet deposition is a cellular hallmark of aging in Caenorhabditis elegans.
  63. Autophagy in the pathogenesis and therapeutic potential of post-traumatic osteoarthritis.
  64. Dysregulation of the mTOR pathway by mechlorethamine.
  65. Mitochondrial protein import machinery conveys stress signals to the cytosol and beyond.
  66. Editorial: mTOR pathway malfunctions in neurodevelopmental disorders.
  1. bioRxiv. 2023 Jan 04. pii: 2023.01.04.522687. [Epub ahead of print]
    Autophagy disruption reduces mTORC1 activation leading to retinal ganglion cell neurodegeneration associated with glaucoma.
    Kang-Chieh Huang, Cátia Gomes, Yukihiro Shiga, Nicolas Belforte, Kirstin B VanderWall, Sailee S Lavekar, Clarisse M Fligor, Jade Harkin, Adriana Di Polo, Jason S Meyer.
      Autophagy dysfunction has been associated with several neurodegenerative diseases including glaucoma, characterized by the degeneration of retinal ganglion cells (RGCs). However, the mechanisms by which autophagy dysfunction promotes RGC damage remain unclear. Here, we hypothesized that perturbation of the autophagy pathway results in increased autophagic demand, thereby downregulating signaling through mammalian target of rapamycin complex 1 (mTORC1), a negative regulator of autophagy, contributing to the degeneration of RGCs. We identified an impairment of autophagic-lysosomal degradation and decreased mTORC1 signaling via activation of the stress sensor adenosine monophosphate-activated protein kinase (AMPK), along with subsequent neurodegeneration in RGCs differentiated from human pluripotent stem cells (hPSCs) with a glaucoma-associated variant of Optineurin (OPTN-E50K). Similarly, the microbead occlusion model of glaucoma resulting in ocular hypertension also exhibited autophagy disruption and mTORC1 downregulation. Pharmacological inhibition of mTORC1 in hPSC-derived RGCs recapitulated disease-related neurodegenerative phenotypes in otherwise healthy RGCs, while the mTOR-independent induction of autophagy reduced protein accumulation and restored neurite outgrowth in diseased OPTN-E50K RGCs. Taken together, these results highlight an important balance between autophagy and mTORC1 signaling essential for RGC homeostasis, while disruption to these pathways contributes to neurodegenerative features in glaucoma, providing a potential therapeutic target to prevent neurodegeneration.
    DOI:  https://doi.org/10.1101/2023.01.04.522687
  2. Sci Signal. 2023 Jan 31. 16(770): eabo4457
    Deciphering functional roles and interplay between Beclin1 and Beclin2 in autophagosome formation and mitophagy.
    Justin M Quiles, Rita H Najor, Eileen Gonzalez, Monica Jeung, Wenjing Liang, Sarah M Burbach, Erika A Zumaya, Rachel Y Diao, Mark A Lampert, Åsa B Gustafsson.
      The degradation of macromolecules and organelles by the process of autophagy is critical for cellular homeostasis and is often compromised during aging and disease. Beclin1 and Beclin2 are implicated in autophagy induction, and these homologs share a high degree of amino acid sequence similarity but have divergent N-terminal regions. Here, we investigated the functions of the Beclin homologs in regulating autophagy and mitophagy, a specialized form of autophagy that targets mitochondria. Both Beclin homologs contributed to autophagosome formation, but a mechanism of autophagosome formation independent of either Beclin homolog occurred in response to starvation or mitochondrial damage. Mitophagy was compromised only in Beclin1-deficient HeLa cells and mouse embryonic fibroblasts because of defective autophagosomal engulfment of mitochondria, and the function of Beclin1 in mitophagy required the phosphorylation of the conserved Ser15 residue by the kinase Ulk1. Mitochondria-ER-associated membranes (MAMs) are important sites of autophagosome formation during mitophagy, and Beclin1, but not Beclin2 or a Beclin1 mutant that could not be phosphorylated at Ser15, localized to MAMs during mitophagy. Our findings establish a regulatory role for Beclin1 in selective mitophagy by initiating autophagosome formation adjacent to mitochondria, a function facilitated by Ulk1-mediated phosphorylation of Ser15 in its distinct N-terminal region.
    DOI:  https://doi.org/10.1126/scisignal.abo4457
  3. Mol Nutr Food Res. 2023 Jan 30. e2200517
    Farnesoid X Receptor (FXR) Regulates mTORC1 Signaling and Autophagy by Inhibiting SESN2 Expression.
    GuoYan Wang, Lei Chen, SenLin Qin, HuiJun Geng, Chao Xia, YiNing Zheng, XinJian Lei, Jun Zhang, ShengRu Wu, JunHu Yao, Lu Deng.
       SCOPE: The mechanistic target of rapamycin complex 1 (mTORC1), as a link between nutrients and autophagy, senses many nutrients in the microenvironment. A growing body of recent literature describes the function of bile acids (BAs) as versatile signaling molecules, while it remains largely unclear whether mTORC1 can sense BAs and the mechanism has not been studied.
    METHODS AND RESULTS: After treating LO2 cells with indicated concentration of chenodeoxycholic acid (CDCA) and farnesoid X receptor (FXR) inhibitor/activator for 6 h, it finds that CDCA and FXR significantly accelerate mTORC1 activation. The results of immunofluorescence indicate that CDCA and FXR inhibit cellular autophagy through activating mTORC1 pathway. In particular, these findings show that CDCA and FXR promote the lysosomal translocation and activation of mTORC1 in an amino acid-sensitive manner. Mechanistically, the transcriptomics data indicate that SESN2 is a checkpoint for mTORC1 lysosome translocation and activation induced by FXR, and knockdown SESN2 with siRNA suppresses the regulation of FXR on autophagy.
    CONCLUSION: These results indicate that FXR-induced decrease in SESN2 expression and activation of the mTORC1 pathway can control autophagy and be explored as potential therapeutic targets for enterohepatic and metabolic disorders.
    Keywords:  SESN2; autophagy; farnesoid X receptor (FXR); lysosomal translocation; mTORC1
    DOI:  https://doi.org/10.1002/mnfr.202200517
  4. Autophagy. 2023 Feb 02.
    Rapamycin and Alzheimer disease: a hypothesis for the effective use of rapamycin for treatment of neurodegenerative disease.
    Julian M Carosi, Timothy J Sargeant.
      In 2019 we summarized work relating to the potential use of rapamycin for treating Alzheimer disease (AD). We considered the commentary necessary because use of rapamycin in people with AD is a very real prospect and we wanted to present a balanced view of the likely consequences of MTOR (mechanistic target of rapamycin kinase) inhibition in the AD brain. We concluded that use of rapamycin, an MTOR inhibitor that increases macroautophagy/autophagy, could hold promise for prevention of AD if used early enough. However, MTOR inhibition appeared ineffectual in resolving existing amyloid pathology in AD mouse models. In this View article, we update these observations with new studies that have used rapamycin in AD models and provide evidence both for and against its use in AD. We also discuss rapamycin in the light of new research that describes rapamycin-induced autophagic stress in the ageing brain and autophagic stress as the origin of the amyloid plaque itself. We conclude that rapamycin will have complex effects on the brain in AD. Further, we hypothesize that lysosomal degradative capacity in the brain will likely determine how effective or detrimental rapamycin will be as a treatment of AD.
    Keywords:  Alzheimer disease; autophagy; dementia; lysosome; rapamycin
    DOI:  https://doi.org/10.1080/15548627.2023.2175569
  5. Nat Metab. 2023 Feb 02.
    AMPK-dependent phosphorylation of the GATOR2 component WDR24 suppresses glucose-mediated mTORC1 activation.
    Xiaoming Dai, Cong Jiang, Qiwei Jiang, Lan Fang, Haihong Yu, Jinhe Guo, Peiqiang Yan, Fangtao Chi, Tao Zhang, Hiroyuki Inuzuka, John M Asara, Ping Wang, Jianping Guo, Wenyi Wei.
      The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth in response to amino acid and glucose levels. However, how mTORC1 senses glucose availability to regulate various downstream signalling pathways remains largely elusive. Here we report that AMP-activated protein kinase (AMPK)-mediated phosphorylation of WDR24, a core component of the GATOR2 complex, has a role in the glucose-sensing capability of mTORC1. Mechanistically, glucose deprivation activates AMPK, which directly phosphorylates WDR24 on S155, subsequently disrupting the integrity of the GATOR2 complex to suppress mTORC1 activation. Phosphomimetic Wdr24S155D knock-in mice exhibit early embryonic lethality and reduced mTORC1 activity. On the other hand, compared to wild-type littermates, phospho-deficient Wdr24S155A knock-in mice are more resistant to fasting and display elevated mTORC1 activity. Our findings reveal that AMPK-mediated phosphorylation of WDR24 modulates glucose-induced mTORC1 activation, thereby providing a rationale for targeting AMPK-WDR24 signalling to fine-tune mTORC1 activation as a potential therapeutic means to combat human diseases with aberrant activation of mTORC1 signalling including cancer.
    DOI:  https://doi.org/10.1038/s42255-022-00732-4
  6. Expert Opin Ther Targets. 2023 Feb 03.
    The participation of non-canonical autophagic proteins in the autophagy process and their potential as therapeutic targets.
    Yiming Yin, Yourong Zhou, Xiaochun Yang, Zhifei Xu, Bo Yang, Peihua Luo, Hao Yan, Qiaojun He.
       INTRODUCTION: : Autophagy is a conserved catabolic process that help recycles intracellular component to maintain homeostasis. The completion of autophagy requires the synergistic effect of multiple canonical autophagic proteins. Defects in autophagy machinery have been reported to promote diseases, rendering autophagy a bone fide health-modifying agent. However, the clinical implication of canonical pan-autophagic activators or inhibitors has often led to undesirable side effects, making it urgent to find a safer autophagy-related therapeutic target. The discovery of the non-canonical autophagic proteins has been found to specifically affect the development of diseases without causing a universal impact on autophagy and has shed light on finding a safer way to utilize autophagy in the therapeutic context.
    AREAS COVERED: This review summarizes recently discovered non-canonical autophagic proteins, how these proteins influence autophagy, and their potential therapeutic role in the disease due to their interaction with autophagy.
    EXPERT OPINION: Several therapies have been studied thus far, and continued research is needed to identify the potential that non-canonical autophagic proteins have for treating certain diseases. In the meantime, continue to uncover new non-canonical autophagic proteins and examine which are likely to have therapeutic implications.
    Keywords:  Autophagy; Diseases; Non-canonical autophagic proteins; Therapeutic targets
    DOI:  https://doi.org/10.1080/14728222.2023.2177151
  7. Curr Opin Physiol. 2022 Oct;pii: 100590. [Epub ahead of print]29
    Mechanisms Controlling Selective Elimination of Damaged Lysosomes.
    Melissa J Hoyer, Sharan Swarup, J Wade Harper.
      Lysosomes are subjected to physiological and patho-physiological insults over the course of their life cycle and are accordingly repaired or recycled. Lysophagy, the selective degradation of lysosomes via autophagy, occurs upon unrepairable lysosomal membrane rupture; galectins bind to glycosylated macromolecules in the lysosome lumen, orchestrating a series of cellular responses to promote autophagic recycling of damaged lysosomes and transcriptional upregulation of lysosomal genes. Damaged lysosomes are ubiquitylated, resulting in the recruitment of ubiquitin-binding autophagy receptors, which promote assembly of an autophagosome around damaged lysosomes for delivery to healthy lysosomes for degradation. Here, we review the current state of our understanding of mechanisms used to mark and eliminate damaged lysosomes, and discuss the complexities of galectin function and ubiquitin-chain linkage types. Finally, we discuss the limitations of available data and challenges with the goal of understanding the mechanistic basis of key steps in lysophagic flux.
    DOI:  https://doi.org/10.1016/j.cophys.2022.100590
  8. Mol Biol Cell. 2023 Feb 03. mbcE22070302
    Arf5 mediated regulation of mTORC1 at the plasma membrane.
    Christian Makhoul, Fiona J Houghton, Elizabeth Hinde, Paul A Gleeson.
      The mechanistic target of rapamycin (mTOR) kinase regulates a major signalling pathway in eukaryotic cells. In addition to regulation of mTORC1 at lysosomes, mTORC1 is also localised at other locations. However, little is known about the recruitment and activation of mTORC1 at non-lysosomal sites. To identify regulators of mTORC1 recruitment to non-lysosomal compartments, novel interacting partners with the mTORC1 subunit, Raptor, were identified using immunoprecipitation and mass spectrometry. We show that one of the interacting partners, Arf5, is a novel regulator of mTORC1 signalling at plasma membrane ruffles. Arf5-GFP localizes with endogenous mTOR at PI3,4P2 enriched membrane ruffles together the GTPase required for mTORC1 activation, Rheb. Knockdown of Arf5 reduced the recruitment of mTOR to membrane ruffles. The activation of mTORC1 at membrane ruffles was directly demonstrated using a plasma membrane-targeted mTORC1 biosensor and Arf5 shown to enhance the phosphorylation of the mTORC1 biosensor substrate. In addition, endogenous Arf5 was shown to be required for rapid activation of mTORC1-mediated S6 phosphorylation following nutrient starvation and re-feeding. Our findings reveal a novel Arf5-dependent pathway for recruitment and activation of mTORC1 at plasma membrane ruffles, a process relevant for spatial and temporal regulation of mTORC1 by receptor and nutrient stimuli.
    DOI:  https://doi.org/10.1091/mbc.E22-07-0302
  9. Antioxid Redox Signal. 2023 Feb 03.
    Autophagy-dependent ferroptosis in cancer.
    Fangquan Chen, Xiutao Cai, Rui Kang, Jiao Liu, Doalin Tang.
       SIGNIFICANCE: Autophagy is a self-degrading process that determines cell fate in response to various environmental stresses. In contrast to autophagy-mediated cell survival, the signals, mechanisms, and effects of autophagy-dependent cell death remain obscure. The discovery of autophagy-dependent ferroptosis provides a paradigm for understanding the relationship between aberrant degradation pathways and excessive lipid peroxidation in driving regulated cell death.
    RECENT ADVANCES: Ferroptosis was originally described as an autophagy-independent and iron-mediated non-apoptotic cell death. Current studies reveal that the level of intracellular autophagy is positively correlated with ferroptosis sensitivity. Selective autophagic degradation of proteins (e.g., ferritin, SLC40A1, ARNTL, GPX4, and CDH2) or organelles (e.g., lipid droplets or mitochondria) promotes ferroptosis by inducing iron overload and/or lipid peroxidation. Several upstream autophagosome regulators (e.g., TMEM164), downstream autophagy receptors (e.g., HPCAL1), or danger signals (e.g., DCN) are selectively required for ferroptosis-related autophagy, but not for starvation-induced autophagy. The induction of autophagy-dependent ferroptosis is an effective approach to eliminate drug-resistant cancer cells.
    CRITICAL ISSUES: How different organelles selectively activate autophagy to modulate ferroptosis sensitivity is not fully understood. Identifying direct protein effectors of ferroptotic cell death remains a challenge.
    FUTURE DIRECTIONS: Further understanding of the molecular mechanics and immune consequences of autophagy-dependent ferroptosis is critical for the development of precision antitumor therapies.
    DOI:  https://doi.org/10.1089/ars.2022.0202
  10. Autophagy. 2023 Feb 01.
    Autophagic structures revealed by cryo-electron tomography: New clues about autophagosome biogenesis.
    Hana Popelka, Daniel J Klionsky.
      Transitions from the early to late phagophore, which occur to engulf cytoplasmic material within an autophagosome for macroautophagic/autophagic degradation, involve dynamic ultrastructural changes that are not fully understood. A recent study combined cryo-electron tomography (cryo-ET) with extensive computational analysis to get a better insight into autophagosome biogenesis in situ within yeast cells. This approach disclosed new information on the shape of autophagic structures, their contacts with surrounding organelles, membrane sources, and mechanisms of transition. Together, these results provide new directions for autophagy research, and show the potential of cryo-ET in cell biology.
    Keywords:  Endoplasmic reticulum; membrane organelle; phagophore; vacuole; vesicle
    DOI:  https://doi.org/10.1080/15548627.2023.2175305
  11. Res Sq. 2023 Jan 16. pii: rs.3.rs-2469234. [Epub ahead of print]
    Reduced hepatocyte mitophagy is an early feature of NAFLD pathogenesis and hastens the onset of steatosis, inflammation and fibrosis.
    Ramya Undamatla, Olayemi G Fagunloye, Jeffrey Chen, Lia R Edmunds, Anjana Murali, Amanda Mills, Bingxian Xie, Martha M Pangburn, Ian Sipula, Gregory Gibson, Claudette St Croix, Michael J Jurczak.
      Nonalcoholic fatty liver disease (NAFLD) encompasses a spectrum of pathologies that includes steatosis, steatohepatitis (NASH) and fibrosis and is strongly associated with insulin resistance and type 2 diabetes. Changes in mitochondrial function are implicated in the pathogenesis of NAFLD, particularly in the transition from steatosis to NASH. Mitophagy is a mitochondrial quality control mechanism that allows for the selective removal of damaged mitochondria from the cell via the autophagy pathway. While past work demonstrated a negative association between liver fat content and rates of mitophagy, when changes in mitophagy occur during the pathogenesis of NAFLD and whether such changes contribute to the primary endpoints associated with the disease are currently poorly defined. We therefore undertook the studies described here to establish when alterations in mitophagy occur during the pathogenesis of NAFLD, as well as to determine the effects of genetic inhibition of mitophagy via conditional deletion of a key mitophagy regulator, PARKIN, on the development of steatosis, insulin resistance, inflammation and fibrosis. We find that loss of mitophagy occurs early in the pathogenesis of NAFLD and that loss of PARKIN hastens the onset but not severity of key NAFLD disease features. These observations suggest that loss of mitochondrial quality control in response to nutritional stress may contribute to mitochondrial dysfunction and the pathogenesis of NAFLD.
    DOI:  https://doi.org/10.21203/rs.3.rs-2469234/v1
  12. Acta Trop. 2023 Jan 26. pii: S0001-706X(23)00032-3. [Epub ahead of print]240 106845
    mTOR signaling inhibition decreases lysosome migration and impairs the success of Trypanosoma cruzi infection and replication in cardiomyocytes.
    Juliana M Alvim, Gabriela Venturini, Theo G M Oliveira, Jonathan G Seidman, Christine E Seidman, José E Krieger, Alexandre C Pereira.
      Chagas disease is caused by the parasite Trypanosoma cruzi (T. cruzi) and, among all the chronic manifestations of the disease, Chronic Chagas Cardiomyopathy (CCC) is the most severe outcome. Despite high burden and public health importance in Latin America, there is a gap in understanding the molecular mechanisms that results in CCC development. Previous studies showed that T. cruzi uses the host machinery for infection and replication, including the repurposing of the responses to intracellular infection such as mitochondrial activity, vacuolar membrane, and lysosomal activation in benefit of parasite infection and replication. One common signaling upstream to many responses to parasite infection is mTOR pathway, previous associated to several downstream cellular mechanisms including autophagy, mitophagy and lysosomal activation. Here, using human iPSC derived cardiomyocytes (hiPSCCM), we show the mTOR pathway is activated in hiPSCCM after T. cruzi infection, and the inhibition of mTOR with rapamycin reduced number of T. cruzi 48 h post infection (hpi). Rapamycin treatment also reduced lysosome migration from nuclei region to cell periphery resulting in less T. cruzi inside the parasitophorous vacuole (PV) in the first hour of infection. In addition, the number of parasites leaving the PV to the cytoplasm to replicate in later times of infection was also lower after rapamycin treatment. Altogether, our data suggest that host's mTOR activation concomitant with parasite infection modulates lysosome migration and that T. cruzi uses this mechanism to achieve infection and replication. Modulating this mechanism with rapamycin impaired the success of T. cruzi life cycle independent of mitophagy.
    Keywords:  Cardiomyocyte infection; Chagas disease; Lysosomes; Rapamycin; Trypanosoma cruzi; mTOR
    DOI:  https://doi.org/10.1016/j.actatropica.2023.106845
  13. Trends Endocrinol Metab. 2023 Jan 31. pii: S1043-2760(23)00015-2. [Epub ahead of print]
    Regulation of mTOR by phosphatidic acid.
    Maria A Frias, Ahmet Hatipoglu, David A Foster.
      mTORC1, the mammalian target of rapamycin complex 1, is a key regulator of cellular physiology. The lipid metabolite phosphatidic acid (PA) binds to and activates mTORC1 in response to nutrients and growth factors. We review structural findings and propose a model for PA activation of mTORC1. PA binds to a highly conserved sequence in the α4 helix of the FK506 binding protein 12 (FKBP12)/rapamycin-binding (FRB) domain of mTOR. It is proposed that PA binding to two adjacent positively charged amino acids breaks and shortens the C-terminal region of helix α4. This has profound consequences for both substrate binding and the catalytic activity of mTORC1.
    Keywords:  FRB; Rheb; mTOR; phosphatidic acid; phospholipase D; structure
    DOI:  https://doi.org/10.1016/j.tem.2023.01.004
  14. Mol Biol Cell. 2023 Feb 03. mbcE22090432
    CCPG1 recognizes ER luminal proteins for selective ER-phagy.
    Shunsuke Ishii, Haruka Chino, Koji L Ode, Yoshitaka Kurikawa, Hiroki R Ueda, Akira Matsuura, Noboru Mizushima, Eisuke Itakura.
      The endoplasmic reticulum (ER) is a major cell compartment where protein synthesis, folding and post-translational modifications occur with assistance from a wide variety of chaperones and enzymes. Quality control systems selectively eliminate abnormal proteins that accumulate inside the ER due to cellular stresses. ER-phagy, i.e., selective autophagy of the ER, is a mechanism that maintains or re-establishes cellular and ER-specific homeostasis through removal of abnormal proteins. However, how ER luminal proteins are recognized by the ER-phagy machinery remains unclear. Here, we applied the aggregation-prone protein, six-repeated islet amyloid polypeptide (6xIAPP), as a model ER-phagy substrate, and found that cell cycle progression 1 (CCPG1), which is an ER-phagy receptor, efficiently mediates its degradation via ER-phagy. We also identified prolyl 3-hydroxylase family member 4 (P3H4) as an endogenous cargo of CCPG1-dependent ER-phagy. The ER luminal region of CCPG1 contains several highly conserved regions that we refer to as cargo interaction regions (CIRs); these directly interact with specific luminal cargos for ER-phagy. Notably, 6xIAPP and P3H4 directly interact with different CIRs. These findings indicate that CCPG1 is a bispecific ER-phagy receptor for ER luminal proteins and the autophagosomal membrane that contributes to the efficient removal of aberrant ER-resident proteins through ER-phagy.
    DOI:  https://doi.org/10.1091/mbc.E22-09-0432
  15. Oxid Med Cell Longev. 2023 ;2023 8994901
    LINC01278 Induces Autophagy to Inhibit Tumour Progression by Suppressing the mTOR Signalling Pathway.
    Bo Liu, Xueting Yao, Chaoyang Zhang, Wenzhe Li, Yanan Wang, Qianling Liao, Ziwei Li, Qinying Huang, Yanchen Zhang, Wencan Wu.
      Uveal melanoma (UM) is an aggressive intraocular malignant tumour that is closely related to autophagic dysfunction. We aimed to identify autophagy-related long noncoding RNAs (lncRNAs) to elucidate the molecular mechanism of UM. Here, we show that LINC01278 is a new potential biomarker with clinical prognostic value in UM through bioinformatics analysis. Application of an autophagy inhibitor (3-MA) and an autophagy agonist (MG-132) indicated that LINC01278 can inhibit UM cell proliferation, migration, and invasion by inducing autophagy. A xenograft nude mouse model was used to examine the tumorigenesis of UM cells in vivo. Mechanistically, LINC01278 can inhibit the mTOR signalling pathway to activate autophagy, as shown by experiments with an mTOR agonist (MHY1485) and mTOR inhibitor (rapamycin) treatment. Our findings indicate that LINC01278 functions as a tumour suppressor by inhibiting the mTOR signalling pathway to induce autophagy. Targeting the LINC01278-mTOR axis might be a novel and promising therapeutic approach for UM.
    DOI:  https://doi.org/10.1155/2023/8994901
  16. Front Mol Neurosci. 2022 ;15 1078441
    Brain-protective mechanisms of autophagy associated circRNAs: Kick starting self-cleaning mode in brain cells via circRNAs as a potential therapeutic approach for neurodegenerative diseases.
    Rabea Basri, Faryal Mehwish Awan, Burton B Yang, Usman Ayub Awan, Ayesha Obaid, Anam Naz, Aqsa Ikram, Suliman Khan, Ijaz Ul Haq, Sadiq Noor Khan, Muslim Bin Aqeel.
      Altered autophagy is a hallmark of neurodegeneration but how autophagy is regulated in the brain and dysfunctional autophagy leads to neuronal death has remained cryptic. Being a key cellular waste-recycling and housekeeping system, autophagy is implicated in a range of brain disorders and altering autophagy flux could be an effective therapeutic strategy and has the potential for clinical applications down the road. Tight regulation of proteins and organelles in order to meet the needs of complex neuronal physiology suggests that there is distinct regulatory pattern of neuronal autophagy as compared to non-neuronal cells and nervous system might have its own separate regulator of autophagy. Evidence has shown that circRNAs participates in the biological processes of autophagosome assembly. The regulatory networks between circRNAs, autophagy, and neurodegeneration remains unknown and warrants further investigation. Understanding the interplay between autophagy, circRNAs and neurodegeneration requires a knowledge of the multiple steps and regulatory interactions involved in the autophagy pathway which might provide a valuable resource for the diagnosis and therapy of neurodegenerative diseases. In this review, we aimed to summarize the latest studies on the role of brain-protective mechanisms of autophagy associated circRNAs in neurodegenerative diseases (including Alzheimer's disease, Parkinson's disease, Huntington's disease, Spinal Muscular Atrophy, Amyotrophic Lateral Sclerosis, and Friedreich's ataxia) and how this knowledge can be leveraged for the development of novel therapeutics against them. Autophagy stimulation might be potential one-size-fits-all therapy for neurodegenerative disease as per considerable body of evidence, therefore future research on brain-protective mechanisms of autophagy associated circRNAs will illuminate an important feature of nervous system biology and will open the door to new approaches for treating neurodegenerative diseases.
    Keywords:  autophagy; circRNAs; nervous system; neurodegeneration; therapeutics
    DOI:  https://doi.org/10.3389/fnmol.2022.1078441
  17. Autophagy. 2023 Feb 01. 1-3
    Metabolic function of autophagy is essential for cell survival.
    Lucia Sedlackova, Tetsushi Kataura, Sovan Sarkar, Viktor I Korolchuk.
      Age-related human pathologies present with a multitude of molecular and metabolic phenotypes, which individually or synergistically contribute to tissue degeneration. However, current lack of understanding of the interdependence of these molecular pathologies limits the potential range of existing therapeutic intervention strategies. In our study, we set out to understand the chain of molecular events, which underlie the loss of cellular viability in macroautophagy/autophagy deficiency associated with aging and age-related disease. We discover a novel axis linking autophagy, a cellular waste disposal pathway, and a metabolite, nicotinamide adenine dinucleotide (NAD). The axis connects multiple organelles, molecules and stress response pathways mediating cellular demise when autophagy becomes dysfunctional. By elucidating the steps on the path from efficient mitochondrial recycling to NAD maintenance and ultimately cell viability, we highlight targets potentially receptive to therapeutic interventions in a range of genetic and age-related diseases associated with autophagy dysfunction.Abbreviations: IMM: inner mitochondrial membrane; NAD: nicotinamide dinucleotide; OXPHOS: oxidative phosphorylation; PARP: poly(ADP-ribose) polymerase; ROS: reactive oxygen species.
    Keywords:  Aging; DNA damage; NAD; PARP; ROS; autophagy; mitochondria; mitophagy; sirtuins
    DOI:  https://doi.org/10.1080/15548627.2023.2165753
  18. bioRxiv. 2023 Jan 02. pii: 2022.12.31.522394. [Epub ahead of print]
    Autophagy collaborates with apoptosis pathways to control myelination specificity and function.
    Tingxin Zhang, Han-Gyu Bae, Aksheev Bhambri, Yihe Zhang, Daniela Barbosa, Jumin Xue, Sabeen Wazir, Sara B Mulinyawe, Jun Hee Kim, Lu O Sun.
      Oligodendrocytes are the sole myelin producing cells in the central nervous system. Oligodendrocyte numbers are tightly controlled across diverse brain regions to match local axon type and number, but the underlying mechanisms and functional significance remain unclear. Here, we show that autophagy, an evolutionarily conserved cellular process that promotes cell survival under canonical settings, elicits premyelinating oligodendrocyte apoptosis during development and regulates critical aspects of nerve pulse propagation. Autophagy flux is increased in premyelinating oligodendrocytes, and its genetic blockage causes ectopic oligodendrocyte survival throughout the entire brain. Autophagy acts in the TFEB-Bax/Bak pathway and elevates PUMA mRNA levels to trigger premyelinating oligodendrocyte apoptosis cell-autonomously. Autophagy continuously functions in the myelinating oligodendrocytes to limit myelin sheath numbers and fine-tune nerve pulse propagation. Our results provide in vivo evidence showing that autophagy promotes apoptosis in mammalian cells under physiological conditions and reveal key intrinsic mechanisms governing oligodendrocyte number.
    HIGHLIGHTS: Autophagy flux increases in the premyelinating and myelinating oligodendrocytesAutophagy promotes premyelinating oligodendrocyte (pre-OL) apoptosis to control myelination location and timing Autophagy acts in the TFEB-PUMA-Bax/Bak pathway and elevates PUMA mRNA levels to determine pre-OL fate Autophagy continuously functions in the myelinating oligodendrocytes to limit myelin sheath thickness and finetune nerve pulse propagation.
    DOI:  https://doi.org/10.1101/2022.12.31.522394
  19. Trends Neurosci. 2023 Jan 28. pii: S0166-2236(23)00016-4. [Epub ahead of print]
    Beyond housekeeping: autophagy regulates PKA signaling at synapses.
    Maeve Louise Coughlan, Sandra Maday.
      Autophagy modulates synaptic function and plasticity, but the molecular basis for this process is largely unknown. A recent tour de force study by Overhoff and colleagues identifies a novel role for autophagy in regulating PKA signaling at synapses to modulate the organization of the postsynaptic proteome and neuronal excitability.
    Keywords:  AMPAR; ATG5; PKA; proteome; synaptic plasticity; synaptic transmission
    DOI:  https://doi.org/10.1016/j.tins.2023.01.002
  20. Commun Biol. 2023 Jan 28. 6(1): 114
    Transcription factor EB regulates phosphatidylinositol-3-phosphate levels that control lysosome positioning in the bladder cancer model.
    Pallavi Mathur, Camilla De Barros Santos, Hugo Lachuer, Julie Patat, Bruno Latgé, François Radvanyi, Bruno Goud, Kristine Schauer.
      Lysosomes orchestrate degradation and recycling of exogenous and endogenous material thus controlling cellular homeostasis. Little is known how this organelle changes during cancer. Here we investigate the intracellular landscape of lysosomes in a cellular model of bladder cancer. Employing standardized cell culture on micropatterns we identify a phenotype of peripheral lysosome positioning prevailing in bladder cancer cell lines but not normal urothelium. We show that lysosome positioning is controlled by phosphatidylinositol-3-phosphate (PtdIns3P) levels on endomembranes which recruit FYVE-domain containing proteins for lysosomal dispersion. We identify transcription factor EB (TFEB) as an upstream regulator of PtdIns3P production by VPS34 that is activated in aggressive bladder cancer cells with peripheral lysosomes. This conceptually clarifies the dual role of TFEB as regulator of endosomal maturation and autophagy, two distinct processes controlled by PtdIns3P. Altogether, our findings uncover peripheral lysosome positioning, resulting from PtdIns3P production downstream of TFEB activation, as a potential biomarker for bladder cancer.
    DOI:  https://doi.org/10.1038/s42003-023-04501-1
  21. bioRxiv. 2023 Jan 20. pii: 2023.01.18.524611. [Epub ahead of print]
    Frontotemporal Dementia Patient Neurons With Progranulin Deficiency Display Protein Dyshomeostasis.
    Lisa Elia, Bianca Herting, Amela Alijagic, Christina Buselli, Leela Wong, Grace Morrison, Miguel A Prado, Joao A Paulo, Steven P Gygi, Daniel Finley, Steven Finkbeiner.
      Haploinsufficiency of progranulin (PGRN) causes frontotemporal dementia (FTD), a devastating neurodegenerative disease with no effective treatment. PGRN is required for efficient proteostasis, as loss of neuronal PGRN results in dysfunctional lysosomes and impaired clearance and cytoplasmic aggregation of TDP-43, a protein involved in neurodegeneration in FTD. These and other events lead to neurodegeneration and neuroinflammation. However, the detailed mechanisms leading to protein dyshomeostasis in PGRN-deficient cells remain unclear. We report here the development of human cell models of FTD with PGRN-deficiency to explore the molecular mechanisms underlying proteostasis breakdown and TDP-43 aggregation in FTD. Neurons differentiated from FTD patient induced pluripotent stem cells (iPSCs) have reduced PGRN levels, and the neurons recapitulate key disease features, including impaired lysosomal function, defective TDP-43 turnover and accumulation, neurodegeneration, and death. Proteomic analysis revealed altered levels of proteins linked to the autophagy-lysosome pathway (ALP) and the ubiquitin-proteasome system (UPS) in FTD patient neurons, providing new mechanistic insights into the link between PGRN-deficiency and disease pathobiology.
    DOI:  https://doi.org/10.1101/2023.01.18.524611
  22. bioRxiv. 2023 Jan 03. pii: 2023.01.03.522657. [Epub ahead of print]
    Dock7 regulates AKT and mTOR/S6K activity required for the transformed phenotypes and survival of cancer cells.
    Oriana Y Teran, Matthew R Zanotelli, Miao-Chong Joy Lin, Richard A Cerione, Kristin F Wilson.
      Cancer cells, both within a developing tumor and during metastatic spread, encounter many stresses that require adaptive mechanisms to survive and maintain malignant progression. Here we describe a signaling complex involving the small GTPase Cdc42 and Dock7, a Cdc42/Rac GEF and unique Cdc42-effector, that has a previously unappreciated role in regulating AKT, mTOR, and other mTOR signaling and regulatory partners including the TSC1/TCS2 complex and S6K during serum starvation. Dock7 is highly expressed in triple-negative breast cancers and is essential for the malignant properties in nutrient-deprived growth conditions of several cancer cell lines. We find that Dock7 interacts with phosphorylated AKT to maintain a low, but critical activation of a rapamycin-sensitive and Raptor-independent mTORC1-like activity required for survival during nutrient stress. Following the knock-out of Dock7 from cancer cells, interactions between AKT and the phosphatase PHLPP increased while phosphorylation of AKT at Ser473 decreased, suggesting Dock7 protects AKT from dephosphorylation. The DHR1 domain of Dock7, previously of unknown function, is responsible for maintaining AKT Ser473 phosphorylation during serum starvation through an interaction requiring its C2-like motif. Together, these findings indicate that Dock7 protects and maintains the phosphorylation of AKT to sustain a tonic mTOR/S6K activity in cancer cells necessary for their resistance to anoikis and to prevent them from undergoing apoptosis during stressful conditions.
    DOI:  https://doi.org/10.1101/2023.01.03.522657
  23. Trends Cell Biol. 2023 Jan 28. pii: S0962-8924(23)00004-1. [Epub ahead of print]
    Lysosomal quality control: molecular mechanisms and therapeutic implications.
    Haoxiang Yang, Jay Xiaojun Tan.
      Lysosomes are essential catabolic organelles with an acidic lumen and dozens of hydrolytic enzymes. The detrimental consequences of lysosomal leakage have been well known since lysosomes were discovered during the 1950s. However, detailed knowledge of lysosomal quality control mechanisms has only emerged relatively recently. It is now clear that lysosomal leakage triggers multiple lysosomal quality control pathways that replace, remove, or directly repair damaged lysosomes. Here, we review how lysosomal damage is sensed and resolved in mammalian cells, with a focus on the molecular mechanisms underlying different lysosomal quality control pathways. We also discuss the clinical implications and therapeutic potential of these pathways.
    Keywords:  ESCRT; PITT; TFEB/TFE3; lysophagy; lysosomal biogenesis; lysosomal repair
    DOI:  https://doi.org/10.1016/j.tcb.2023.01.001
  24. Autophagy. 2023 Jan 31.
    Phosphorylation of EIF2S1 (eukaryotic translation initiation factor 2 subunit alpha) is indispensable for nuclear translocation of TFEB and TFE3 during ER stress.
    Thao Thi Dang, Mi-Jeong Kim, Yoon Young Lee, Hien Thi Le, Kook Hwan Kim, Somi Nam, Seung Hwa Hyun, Hong Lim Kim, Su Wol Chung, Hun Taeg Chung, Eek-Hoon Jho, Hiderou Yoshida, Kyoungmi Kim, Chan Young Park, Myung-Shik Lee, Sung Hoon Back.
      There are diverse links between macroautophagy/autophagy pathways and unfolded protein response (UPR) pathways under endoplasmic reticulum (ER) stress conditions to restore ER homeostasis. Phosphorylation of EIF2S1/eIF2α is an important mechanism that can regulate all three UPR pathways through transcriptional and translational reprogramming to maintain cellular homeostasis and overcome cellular stresses. In this study, to investigate the roles of EIF2S1 phosphorylation in regulation of autophagy during ER stress, we used EIF2S1 phosphorylation-deficient (A/A) cells in which residue 51 was mutated from serine to alanine. A/A cells exhibited defects in several steps of autophagic processes (such as autophagosome and autolysosome formation) that are regulated by the transcriptional activities of the autophagy master transcription factors TFEB and TFE3 under ER stress conditions. EIF2S1 phosphorylation was required for nuclear translocation of TFEB and TFE3 during ER stress. In addition, EIF2AK3/PERK, PPP3/calcineurin-mediated dephosphorylation of TFEB and TFE3, and YWHA/14-3-3 dissociation were required for their nuclear translocation, but were insufficient to induce their nuclear retention during ER stress. Overexpression of the activated ATF6/ATF6α form, XBP1s, and ATF4 differentially rescued defects of TFEB and TFE3 nuclear translocation in A/A cells during ER stress. Consequently, overexpression of the activated ATF6 or TFEB form more efficiently rescued autophagic defects, although XBP1s and ATF4 also displayed an ability to restore autophagy in A/A cells during ER stress. Our results suggest that EIF2S1 phosphorylation is important for autophagy and UPR pathways, to restore ER homeostasis and reveal how EIF2S1 phosphorylation connects UPR pathways to autophagy.
    Keywords:  ATF6; EIF2S1 phosphorylation; ER stress; TFEB; autophagy; nuclear translocation; phosphorylation TFE3; transcription factor E3; transcription factor EB
    DOI:  https://doi.org/10.1080/15548627.2023.2173900
  25. Autophagy. 2023 Feb 02.
    A distinct linker mediating ER-autophagosome membrane contact site (EACS) in plants.
    Hao Ye, Jiayang Gao, Liwen Jiang.
      Endoplasmic reticulum (ER) membrane contacts play a central role in regulating autophagosome formation in yeast and mammals. However, a direct functional linkage between the ER and autophagosomes in plants remains elusive. We have recently identified and characterized a plant-unique protein complex consisting of AT4G22540/OSBP2A/ORP2A (oxysterol binding protein-related protein 2A), the ER resident protein AT3G60600/VAP27-1 (vesicle-associated protein 27-1) and AT2G45170/ATG8e (autophagy related 8e) that mediate the ER-autophagosome membrane contact site (EACS) in the model plant Arabidopsis thaliana. Knockdown (KD) of ORP2A affects autophagosome formation and seedling development, whereas ORP2A KD root cells show accumulation of the macroautophagic/autophagic core machinery and PtdIns3P in enlarged ER membranes under autophagy conditions. This study reveals the molecular architecture and functions of a distinct plant EACS in regulating autophagosome formation via lipid redistribution.
    Keywords:  Arabidopsis; ORP; PtdIns3P; autophagosome; membrane contact site
    DOI:  https://doi.org/10.1080/15548627.2023.2176028
  26. J Med Chem. 2023 Jan 30.
    Application of Novel Degraders Employing Autophagy for Expediting Medicinal Research.
    Xiang Li, Qian Liu, Xin Xie, Cheng Peng, Qiwen Pang, Bo Liu, Bo Han.
      Targeted protein degradation (TPD) technology is based on a unique pharmacological mechanism that has profoundly revolutionized medicinal research by overcoming limitations associated with traditional small-molecule drugs. Autophagy, a mechanism for intracellular waste disposal and recovery, is an important biological process in medicinal research. Recently, studies have demonstrated that several emerging autophagic degraders can treat human diseases. Herein we summarize the progress in medicinal research on autophagic degraders, including autophagosome-tethering compounds (ATTEC), autophagy-targeting chimeras (AUTAC), and AUTOphagy-TArgeting chimeras (AUTOTAC), for treating human diseases. These autophagic degraders exhibit excellent potential for treating neurodegenerative diseases. Our research on autophagic degraders provides a new avenue for medicinal research on TPD via autophagy.
    DOI:  https://doi.org/10.1021/acs.jmedchem.2c01712
  27. Autophagy. 2023 Feb 02.
    Modeling Huntington disease through microRNA-mediated neural reprogramming identifies age-associated autophagy dysfunction driving the onset of neurodegeneration.
    Young Mi Oh, Seong Won Lee, Andrew S Yoo.
      Huntington disease (HD) is an inherited neurodegenerative disease with adult-onset clinical symptoms. However, the mechanism by which aging triggers the onset of neurodegeneration in HD patients remains unclear. Modeling the age-dependent progression of HD with striatal medium spiny neurons (MSNs) generated by direct reprogramming of fibroblasts from HD patients at different disease stages identifies age-dependent decline in critical cellular functions such as autophagy/macroautophagy and onset of neurodegeneration. Mechanistically, MSNs derived from symptomatic HD patients (HD-MSNs) are characterized by increased chromatin accessibility proximal to the MIR29B-3p host gene and its upregulation compared to MSNs from younger pre-symptomatic patients. MIR29B-3p in turn targets and represses STAT3 (signal transducer and activator of transcription 3) that controls the biogenesis of autophagosomes, leading to HD-MSN degeneration. Our recent study demonstrates age-associated microRNA (miRNA) and autophagy dysregulation linked to MSN degeneration, and potential approaches for protecting MSNs by enhancing autophagy in HD.
    Keywords:  Huntington disease; aging; autophagy/macroautophagy; microRNA-mediated neuronal reprogramming; neurodegeneration
    DOI:  https://doi.org/10.1080/15548627.2023.2175572
  28. Front Cell Neurosci. 2022 ;16 1036313
    Autophagy regulates inflammation in intracerebral hemorrhage: Enemy or friend?
    Kaijing Fu, Weilin Xu, Cameron Lenahan, Yong Mo, Jing Wen, Teng Deng, Qianrong Huang, Fangzhou Guo, Ligen Mo, Jun Yan.
      Intracerebral hemorrhage (ICH) is the second-largest stroke subtype and has a high mortality and disability rate. Secondary brain injury (SBI) is delayed after ICH. The main contributors to SBI are inflammation, oxidative stress, and excitotoxicity. Harmful substances from blood and hemolysis, such as hemoglobin, thrombin, and iron, induce SBI. When cells suffer stress, a critical protective mechanism called "autophagy" help to maintain the homeostasis of damaged cells, remove harmful substances or damaged organelles, and recycle them. Autophagy plays a critical role in the pathology of ICH, and its function remains controversial. Several lines of evidence demonstrate a pro-survival role for autophagy in ICH by facilitating the removal of damaged proteins and organelles. However, many studies have found that heme and iron can aggravate SBI by enhancing autophagy. Autophagy and inflammation are essential culprits in the progression of brain injury. It is a fascinating hypothesis that autophagy regulates inflammation in ICH-induced SBI. Autophagy could degrade and clear pro-IL-1β and apoptosis-associated speck-like protein containing a CARD (ASC) to antagonize NLRP3-mediated inflammation. In addition, mitophagy can remove endogenous activators of inflammasomes, such as reactive oxygen species (ROS), inflammatory components, and cytokines, in damaged mitochondria. However, many studies support the idea that autophagy activates microglia and aggravates microglial inflammation via the toll-like receptor 4 (TLR4) pathway. In addition, autophagy can promote ICH-induced SBI through inflammasome-dependent NLRP6-mediated inflammation. Moreover, some resident cells in the brain are involved in autophagy in regulating inflammation after ICH. Some compounds or therapeutic targets that regulate inflammation by autophagy may represent promising candidates for the treatment of ICH-induced SBI. In conclusion, the mutual regulation of autophagy and inflammation in ICH is worth exploring. The control of inflammation by autophagy will hopefully prove to be an essential treatment target for ICH.
    Keywords:  NLRP3 inflammasome; autophagy; intracerebral hemorrhage; microglia; mitophagy; neuroinflammatory; secondary brain injury
    DOI:  https://doi.org/10.3389/fncel.2022.1036313
  29. Methods Cell Biol. 2023 ;pii: S0091-679X(22)00143-1. [Epub ahead of print]174 93-111
    Quantitative assessment of mitophagy in irradiated cancer cells.
    Emma Guilbaud, Sheila Spada, Norma Bloy, Claudia Galassi, Ai Sato, Carlos Jiménez-Cortegana, Artur Aretz, Aitziber Buqué, Takahiro Yamazaki, Sandra Demaria, Lorenzo Galluzzi.
      Mitophagy is a finely regulated mechanism through which eukaryotic cells selectively dispose of supernumerary, permeabilized or otherwise damaged mitochondria through lysosomal degradation. Dysfunctional mitochondria are prone to release potentially cytotoxic factors including reactive oxygen species (ROS) and caspase activators, such as cytochrome c, somatic (CYCS). Thus, proficient mitophagic responses mediate prominent cytoprotective functions. Moreover, the rapid degradation of permeabilized mitochondria limits the release of mitochondrial components that may drive inflammatory reactions, such as mitochondrial DNA (mtDNA) and transcription factor A, mitochondrial (TFAM), implying that mitophagy also mediates potent anti-inflammatory effects. Here, we detail a simple, flow cytometry-assisted protocol for the specific measurement of mitophagic responses as driven by radiation therapy (RT) in mouse hormone receptor (HR)+ mammary carcinoma TS/A cells. With some variations, this method - which relies on the mitochondria-restricted expression of a fluorescent reporter that is sensitive to pH and hence changes excitation wavelength within lysosomes (mt-mKeima) - can be adapted to a variety of human and mouse cancer cell lines and/or straightforwardly implemented on fluorescence microscopy platforms.
    Keywords:  Antimycin; Autophagy; CGAS/STING1; NLRP3 inflammasome; Oligomycin; PRKN; SARRP
    DOI:  https://doi.org/10.1016/bs.mcb.2022.09.002
  30. Sci Rep. 2023 Jan 30. 13(1): 1663
    BORC complex specific components and Kinesin-1 mediate autophagy evasion by the autophagy-resistant Mycobacterium tuberculosis Beijing strain.
    Janpen Tunganuntarat, Phongthon Kanjanasirirat, Tanawadee Khumpanied, Salisa Benjaskulluecha, Benjawan Wongprom, Tanapat Palaga, Tegar Adriansyah Putra Siregar, Suparerk Borwornpinyo, Angkana Chaiprasert, Prasit Palittapongarnpim, Marisa Ponpuak.
      Autophagy induction by starvation has been shown to enhance lysosomal delivery to mycobacterial phagosomes, resulting in the restriction of the Mycobacterium tuberculosis reference strain H37Rv. In contrast to H37Rv, our previous study showed that strains belonging to the notorious M. tuberculosis Beijing genotype could evade autophagic elimination. Our recent RNA-Seq analysis also discovered that the autophagy-resistant M. tuberculosis Beijing strain (BJN) evaded autophagic control by upregulating the expression of Kxd1, a BORC complex component, and Plekhm2, both of which function in lysosome positioning towards the cell periphery in host macrophages, thereby suppressing enhanced lysosomal delivery to its phagosome and sparing the BJN from elimination as a result. In this work, we further characterised the other specific components of the BORC complex, BORC5-8, and Kinesin proteins in autophagy resistance by the BJN. Depletion of BORCS5-8 and Kinesin-1, but not Kinesin-3, reverted autophagy avoidance by the BJN, resulting in increased lysosomal delivery to the BJN phagosomes. In addition, the augmented lysosome relocation towards the perinuclear region could now be observed in the BJN-infected host cells depleted in BORCS5-8 and Kinesin-1 expressions. Taken together, the data uncovered new roles for BORCS5-8 and Kinesin-1 in autophagy evasion by the BJN.
    DOI:  https://doi.org/10.1038/s41598-023-28983-5
  31. Life Sci Alliance. 2023 Apr;pii: e202201715. [Epub ahead of print]6(4):
    A genome-wide CRISPR functional survey of the human phagocytosis molecular machinery.
    Patrick Essletzbichler, Vitaly Sedlyarov, Fabian Frommelt, Didier Soulat, Leonhard X Heinz, Adrijana Stefanovic, Benedikt Neumayer, Giulio Superti-Furga.
      Phagocytosis, the process by which cells engulf large particles, plays a vital role in driving tissue clearance and host defense. Its dysregulation is connected to autoimmunity, toxic accumulation of proteins, and increased risks for infections. Despite its importance, we lack full understanding of all molecular components involved in the process. To create a functional map in human cells, we performed a genome-wide CRISPRko FACS screen that identified 716 genes. Mapping those hits to a comprehensive protein-protein interaction network annotated for functional cellular processes allowed retrieval of protein complexes identified multiple times and detection of missing phagocytosis regulators. In addition to known components, such as the Arp2/3 complex, the vacuolar-ATPase-Rag machinery, and the Wave-2 complex, we identified and validated new phagocytosis-relevant functions, including the oligosaccharyltransferase complex (MAGT1/SLC58A1, DDOST, STT3B, and RPN2) and the hypusine pathway (eIF5A, DHPS, and DOHH). Overall, our phagocytosis network comprises elements of cargo uptake, shuffling, and biotransformation through the cell, providing a resource for the identification of potential novel drivers for diseases of the endo-lysosomal system. Our approach of integrating protein-protein interaction offers a broadly applicable way to functionally interpret genome-wide screens.
    DOI:  https://doi.org/10.26508/lsa.202201715
  32. Acta Physiol (Oxf). 2023 Feb 01. e13943
    A single dose of exercise stimulates skeletal muscle mitochondrial plasticity in myotonic dystrophy type 1.
    Andrew I Mikhail, Alexander Manta, Sean Y Ng, Aislin K Osborne, Stephanie R Mattina, Mark R Mackie, Vladimir Ljubicic.
       AIM: Myotonic dystrophy type 1 (DM1) is the second most common muscular dystrophy after Duchenne and is the most prevalent muscular dystrophy in adults. DM1 patients that participate in aerobic exercise training experience several physiological benefits concomitant with improved muscle mitochondrial function without alterations in typical DM1-specific disease mechanisms, which suggests that correcting organelle health is key to ameliorate the DM1 pathology. However, our understanding of the molecular mechanisms of mitochondrial turnover and dynamics in DM1 skeletal muscle is lacking.
    METHODS: Skeletal muscle tissue were sampled from healthy and DM1 mice under sedentary conditions and at several recovery time-points following an exhaustive treadmill run.
    RESULTS: We demonstrate that DM1 patients exhibit an imbalance in the transcriptional apparatus for mitochondrial turnover and dynamics in skeletal muscle. Additionally, DM1 mice displayed elevated expression of autophagy and mitophagy regulators. A single dose of exercise successfully enhanced canonical exercise molecular pathways and skeletal muscle mitochondrial biogenesis despite failing to alter the cellular pathology in DM1 mice. However, treadmill running stimulated coordinated organelle fusion and fission signaling, as well as improved alternative splicing of Optic atrophy 1. Exercise also evoked autophagy and mitophagy pathways in DM1 skeletal muscle resulting in the normalized expression of autophagy- and lysosome-related machinery responsible for the clearance of dysfunctional organelles.
    CONCLUSION: Collectively, our data indicate that mitochondrial dynamics and turnover processes in DM1 skeletal muscle are initiated with a single dose of exercise, which may underlie the adaptive benefits previously documented in DM1 mice and patients.
    Keywords:  AMP-activated protein kinase; autophagy; biogenesis; dynamics; mitophagy
    DOI:  https://doi.org/10.1111/apha.13943
  33. Front Pharmacol. 2022 ;13 1059360
    Recent advances of tanshinone in regulating autophagy for medicinal research.
    Sha Wu, Kui Zhao, Jie Wang, Nannan Liu, Kaidi Nie, Luming Qi, Lina Xia.
      Initially described as an ancient and highly conserved catabolic biofunction, autophagy plays a significant role in disease pathogenesis and progression. As the bioactive ingredient of Salvia miltiorrhiza, tanshinone has recently shown profound effects in alleviating and treating various diseases by regulating autophagy. However, compared to the remarkable achievements in the known pharmacological effects of this traditional Chinese medicine, there is a lack of a concise and comprehensive review deciphering the mechanism by which tanshinone regulates autophagy for medicinal research. In this context, we concisely review the advances of tanshinone in regulating autophagy for medicinal research, including human cancer, the nervous system, and cardiovascular diseases. The pharmacological effects of tanshinone targeting autophagy involve the regulation of autophagy-related proteins, such as Beclin-1, LC3-II, P62, ULK1, Bax, ATG3, ATG5, ATG7, ATG9, and ATG12; the regulation of the PI3K/Akt/mTOR, MEK/ERK/mTOR, Beclin-1-related, and AMPK-related signaling pathways; the accumulation of reactive oxygen species (ROS); and the activation of AMPK. Notably, we found that tanshinone played a dual role in human cancers in an autophagic manner, which may provide a new avenue for potential clinical application. In brief, these findings on autophagic tanshinone and its derivatives provide a new clue for expediting medicinal research related to tanshinone compounds and autophagy.
    Keywords:  Salvia miltiorrhiza; autophagy; human cancers; medicinal research; tanshinone; traditional Chinese medicine
    DOI:  https://doi.org/10.3389/fphar.2022.1059360
  34. Sci Adv. 2023 Feb 03. 9(5): eade8641
    PI5P4Kα supports prostate cancer metabolism and exposes a survival vulnerability during androgen receptor inhibition.
    Joanna Triscott, Matthias Reist, Lukas Küng, Francielle C Moselle, Marika Lehner, John Gallon, Archna Ravi, Gurpreet K Arora, Simone de Brot, Mark Lundquist, Hector Gallart-Ayala, Julijana Ivanisevic, Salvatore Piscuoglio, Lewis C Cantley, Brooke M Emerling, Mark A Rubin.
      Phosphatidylinositol (PI)regulating enzymes are frequently altered in cancer and have become a focus for drug development. Here, we explore the phosphatidylinositol-5-phosphate 4-kinases (PI5P4K), a family of lipid kinases that regulate pools of intracellular PI, and demonstrate that the PI5P4Kα isoform influences androgen receptor (AR) signaling, which supports prostate cancer (PCa) cell survival. The regulation of PI becomes increasingly important in the setting of metabolic stress adaptation of PCa during androgen deprivation (AD), as we show that AD influences PI abundance and enhances intracellular pools of PI-4,5-P2. We suggest that this PI5P4Kα-AR relationship is mitigated through mTORC1 dysregulation and show that PI5P4Kα colocalizes to the lysosome, the intracellular site of mTORC1 complex activation. Notably, this relationship becomes prominent in mouse prostate tissue following surgical castration. Finally, multiple PCa cell models demonstrate marked survival vulnerability following stable PI5P4Kα inhibition. These results nominate PI5P4Kα as a target to disrupt PCa metabolic adaptation to castrate resistance.
    DOI:  https://doi.org/10.1126/sciadv.ade8641
  35. Mol Cell Biol. 2023 Jan;43(1): 1-21
    Claspin is Required for Growth Recovery from Serum Starvation through Regulating the PI3K-PDK1-mTOR Pathway in Mammalian Cells.
    Chi-Chun Yang, Hisao Masai.
      Claspin plays multiple important roles in regulation of DNA replication as a mediator for the cellular response to replication stress, an integral replication fork factor that facilitates replication fork progression and a factor that promotes initiation by recruiting Cdc7 kinase. Here, we report a novel role of Claspin in growth recovery from serum starvation, which requires the activation of PI3 kinase (PI3K)-PDK1-Akt-mTOR pathways. In the absence of Claspin, cells do not proceed into S phase and eventually die partially in a ROS- and p53-dependent manner. Claspin directly interacts with PI3K and mTOR, and is required for activation of PI3K-PDK1-mTOR and for that of mTOR downstream factors, p70S6K and 4EBP1, but not for p38 MAPK cascade during the recovery from serum starvation. PDK1 physically interacts with Claspin, notably with CKBD, in a manner dependent on phosphorylation of the latter protein, and is required for interaction of mTOR with Claspin. Thus, Claspin plays a novel role as a key regulator for nutrition-induced proliferation/survival signaling by activating the mTOR pathway. The results also suggest a possibility that Claspin may serve as a common mediator that receives signals from different PI3K-related kinases and transmit them to specific downstream kinases.
    Keywords:  Claspin; PDK1; PI3 kinase; mTOR; serum stimulation
    DOI:  https://doi.org/10.1080/10985549.2022.2160598
  36. J Mol Endocrinol. 2023 Feb 01. pii: JME-22-0122. [Epub ahead of print]
    Dysregulation of endoplasmic reticulum stress response in skin wounds in a streptozotocin-induced diabetes mouse model.
    Ermelindo C Leal, Tatiana Emanuelli, Diana Santos, João Moura, Ana Catarina Rg Fonseca, Ana Burgeiro, Eugenia Carvalho.
      Dysfunction in key cellular organelles has been linked to diabetic complications. This study intended to investigate the alterations in the unfolded protein response (UPR), autophagy, and mitochondrial function, which are part of the endoplasmic reticulum (ER) stress response, in wound healing under diabetes conditions. Wound healing mouse models were used to evaluate the UPR, autophagy, mitochondrial fusion, fission, and biogenesis as well as mitophagy in the skin of control and diabetic mice at baseline and 10 days after wounding. The autophagic flux in response to high glucose conditions was also evaluated in keratinocyte and fibroblast cell cultures. Wound healing was impaired in the diabetic mouse model, and we found that the UPR and autophagy pathways were activated in skin wounds of control mice and in non-wounded skin of diabetic mice. Moreover, high glucose conditions induced autophagy in the keratinocyte and fibroblast cell cultures. However, mitophagy did not change in the skin of diabetic mice or wounded skin. In addition, mitochondrial fusion was activated in control but not in the skin diabetic wounds of diabetic mice, while mitochondrial biogenesis is downregulated in the skin of diabetic mice. In conclusion, the activation of the UPR, autophagy, and mitochondrial remodeling are crucial for a proper wound healing. These results suggest that the increase in ER stress and autophagy in the skin of diabetic mice at baseline significantly escalated to pathological levels after wounding, contributing to impaired wound healing in diabetes.
    DOI:  https://doi.org/10.1530/JME-22-0122
  37. Cell Mol Life Sci. 2023 Feb 02. 80(2): 56
    Effect of ATG12-ATG5-ATG16L1 autophagy E3-like complex on the ability of LC3/GABARAP proteins to induce vesicle tethering and fusion.
    Marina N Iriondo, Asier Etxaniz, Yaiza R Varela, Uxue Ballesteros, Melisa Lázaro, Mikel Valle, Dorotea Fracchiolla, Sascha Martens, L Ruth Montes, Félix M Goñi, Alicia Alonso.
      In macroautophagy, the autophagosome (AP) engulfs portions of cytoplasm to allow their lysosomal degradation. AP formation in humans requires the concerted action of the ATG12 and LC3/GABARAP conjugation systems. The ATG12-ATG5-ATG16L1 or E3-like complex (E3 for short) acts as a ubiquitin-like E3 enzyme, promoting LC3/GABARAP proteins anchoring to the AP membrane. Their role in the AP expansion process is still unclear, in part because there are no studies comparing six LC3/GABARAP family member roles under the same conditions, and also because the full human E3 was only recently available. In the present study, the lipidation of six members of the LC3/GABARAP family has been reconstituted in the presence and absence of E3, and the mechanisms by which E3 and LC3/GABARAP proteins participate in vesicle tethering and fusion have been investigated. In the absence of E3, GABARAP and GABARAPL1 showed the highest activities. Differences found within LC3/GABARAP proteins suggest the existence of a lipidation threshold, lower for the GABARAP subfamily, as a requisite for tethering and inter-vesicular lipid mixing. E3 increases and speeds up lipidation and LC3/GABARAP-promoted tethering. However, E3 hampers LC3/GABARAP capacity to induce inter-vesicular lipid mixing or subsequent fusion, presumably through the formation of a rigid scaffold on the vesicle surface. Our results suggest a model of AP expansion in which the growing regions would be areas where the LC3/GABARAP proteins involved should be susceptible to lipidation in the absence of E3, or else a regulatory mechanism would allow vesicle incorporation and phagophore growth when E3 is present.
    Keywords:  ATG12 UBL system; Autophagosome expansion; Autophagy conjugation systems; Human ATG8; Lipid-protein interaction; Membrane fusion
    DOI:  https://doi.org/10.1007/s00018-023-04704-z
  38. FASEB J. 2023 Mar;37(3): e22779
    ANP promotes HTR-8/SVneo cell invasion by upregulating protein kinase N 3 via autophagy inhibition.
    Nan Chu, Yao Tang, Cheng-Jie Wang, Jiang-Nan Pei, Shou-Ling Luo, Yi Yu, Zhen-Zhen Liu, Hai-Yan Liu, Xue-Min Qiu, Ling Wang, Da-Jin Li, Wei-Rong Gu.
      Preeclampsia is a gestational disease characterized by two major pathological changes-shallow trophoblast invasion and impaired spiral artery remodeling. Atrial natriuretic peptide (ANP) is a kind of peptide hormone that regulates blood pressure, while the lack of active ANP participates in preeclampsia pathogenesis. However, the underlying mechanism of how ANP modulates trophoblasts function remains unclarified. Here, we performed isobaric tags for relative and absolute quantification (iTRAQ) in ANP-treated HTR-8/SVneo cells and identified Protein Kinase 3 (PKN3) as the downstream factor of ANP, which was downregulated in preeclamptic placenta. Chromatin immunoprecipitation analysis and luciferase assays showed that NFYA was one of the transcription factors for the PKN3 promoter, which was also regulated by ANP treatment in HTR-8/SVneo cells. Transmission electron microscopy and Western Blotting in HTR-8/SVneo cells indicated that ANP inhibited autophagy via AMPK-mTORC1 signaling, while excess autophagy was observed in preeclamptic placenta. The increased expression of PKN3 and enhanced cell invasion ability in HTR-8/SVneo cells induced by ANP could be abolished by autophagy activation or transfection with PKN3 shRNA or NFYA shRNA or NPR-A shRNA via regulating the invasion-related genes and the epithelial mesenchymal transition molecules. Our results demonstrated that ANP could enhance trophoblast invasion by upregulating PKN3 via NFYA promotion through autophagy inhibition in an AMPK/mTORC1 signaling-dependent manner.
    Keywords:  atrial natriuretic peptide; autophagy; preeclampsia; protein kinase N 3; trophoblast invasion
    DOI:  https://doi.org/10.1096/fj.202200833RRR
  39. Neurobiol Dis. 2023 Jan 26. pii: S0969-9961(23)00034-7. [Epub ahead of print]178 106020
    Pharmacological inhibition of lysosomal two-pore channel 2 (TPC2) confers neuroprotection in stroke via autophagy regulation.
    Valentina Tedeschi, Antonio Vinciguerra, Maria Josè Sisalli, Giuseppe Pignataro, Agnese Secondo.
      Lysosomal function and organellar Ca2+ homeostasis become dysfunctional in Stroke causing disturbances in autophagy, the major process for the degradation of abnormal protein aggregates and dysfunctional organelles. However, the role of autophagy in Stroke is controversial since excessive or prolonged autophagy activation exacerbates ischemic brain injury. Of note, glutamate evokes NAADP-dependent Ca2+ release via lysosomal TPC2 channels thus controlling basal autophagy. Considering the massive release of excitotoxins in Stroke, autophagic flux becomes uncontrolled with abnormal formation of autophagosomes causing, in turn, disruption of excitotoxins clearance and neurodegeneration. Here, a fine regulation of autophagy via a proper pharmacological modulation of lysosomal TPC2 channel has been tested in preclinical Stroke models. Primary cortical neurons were subjected to oxygen and glucose deprivation+reoxygenation to reproduce in vitro brain ischemia. Focal brain ischemia was induced in rats by transient middle cerebral artery occlusion (tMCAO). Under these conditions, TPC2 protein expression as well as autophagy and endoplasmic reticulum (ER) stress markers were studied by Western blotting, while TPC2 localization and activity were measured by immunocytochemistry and single-cell video-imaging, respectively. TPC2 protein expression and immunosignal were highly modulated in primary cortical neurons exposed to extreme hypoxic conditions causing dysfunction in organellar Ca2+ homeostasis, ER stress and autophagy-induced cell death. TPC2 knocking down and pharmacological inhibition by Ned-19 during hypoxia induced neuroprotection. The effect of Ned-19 was reversed by the permeable form of TPC2 endogenous agonist, NAADP-AM. Of note, Ned-19 prevented ER stress, as measured by GRP78 (78 kDa glucose-regulated protein) protein reduction and caspase 9 downregulation. In this way Ned-19 restored organellar Ca2+ level. Interestingly, Ned-19 reduced the infarct volume and neurological deficits in rats subjected to tMCAO and prevented hypoxia-induced cell death by blocking autophagic flux. Collectively, the pharmacological inhibition of TPC2 lysosomal channel by Ned-19 protects from focal ischemia by hampering a hyperfunctional autophagy.
    Keywords:  Autophagy; ER stress; Focal ischemia; Hypoxia; Lysosomal function; TPC2
    DOI:  https://doi.org/10.1016/j.nbd.2023.106020
  40. Res Sq. 2023 Jan 20. pii: rs.3.rs-2484513. [Epub ahead of print]
    Oleoylethanolamide facilitates PPARa and TFEB signaling and attenuates Ab pathology in a mouse model of Alzheimer's disease.
    Michele Comerota, Manasee Gedam, Wen Xiong, Feng Jin, Lisheng Deng, Meng Wang, Jin Wang, Hui Zheng.
      Emerging evidence implicates impaired microglia function and dysregulation of lipid metabolism in Alzheimer's disease (AD). Oleoylethanolamide (OEA), an endogenous lipid and PPARα agonist, has been shown to promote longevity in C. elegans through regulation of lysosome-to-nucleus signaling and cellular metabolism. Using a stable OEA analog, KDS-5104, we found that OEA-PPARα signaling promotes TFEB lysosomal activity independent of mTORC1 and upregulates cell-surface receptor CD36, leading to enhanced microglial Aβ uptake and clearance. These are associated with the suppression of LPS-induced lipid droplet accumulation and inflammasome activation. Chronic treatment of the 5xFAD mice with KDS-5104 restored dysregulated profiles, reduced reactive gliosis and Aβ pathology and rescued cognitive impairments. Together, our study provides support that augmenting OEA-mediated lipid signaling may offer therapeutic benefit against aging and AD through modulating lipid metabolism and microglia phagocytosis and clearance.
    DOI:  https://doi.org/10.21203/rs.3.rs-2484513/v1
  41. bioRxiv. 2023 Jan 12. pii: 2023.01.10.523171. [Epub ahead of print]
    MANF stimulates autophagy and restores mitochondrial homeostasis to treat toxic proteinopathy.
    Yeawon Kim, Chuang Li, Chenjian Gu, Eric Tycksen, Anuradhika Puri, Terri A Pietka, Jothilingam Sivapackiam, Yili Fang, Kendrah Kidd, Sun-Ji Park, Bryce G Johnson, Stanislav Kmoch, Jeremy S Duffield, Anthony J Bleyer, Meredith E Jackrel, Fumihiko Urano, Vijay Sharma, Maria Lindahl, Ying Maggie Chen.
      Misfolded protein aggregates may cause toxic proteinopathy, including autosomal dominant tubulointerstitial kidney disease due to uromodulin mutations (ADTKD- UMOD ), one of the leading hereditary kidney diseases, and Alzheimer’s disease etc. There are no targeted therapies. ADTKD is also a genetic form of renal fibrosis and chronic kidney disease, which affects 500 million people worldwide. For the first time, in our newly generated mouse model recapitulating human ADTKD- UMOD carrying a leading UMOD deletion mutation, we show that autophagy/mitophagy and mitochondrial biogenesis are severely impaired, leading to cGAS- STING activation and tubular injury. Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a novel endoplasmic reticulum stress-regulated secreted protein. We provide the first study that inducible tubular overexpression of MANF after the onset of disease stimulates autophagy/mitophagy and clearance of the misfolded UMOD, and promotes mitochondrial biogenesis through p-AMPK enhancement, resulting in protection of kidney function. Conversely, genetic ablation of endogenous MANF upregulated in the mutant mouse and human tubular cells worsens autophagy suppression and kidney fibrosis. Together, we discover MANF as a novel biotherapeutic protein and elucidate previously unknown mechanisms of MANF in regulating organelle homeostasis to treat ADTKD, which may have broad therapeutic application to treat various proteinopathies.
    DOI:  https://doi.org/10.1101/2023.01.10.523171
  42. Sci Rep. 2023 Jan 28. 13(1): 1574
    TPPU inhibits inflammation-induced excessive autophagy to restore the osteogenic differentiation potential of stem cells and improves alveolar ridge preservation.
    Haixia Dang, Weixian Chen, Lan Chen, Xinru Huo, Fu Wang.
      Inflammation-induced autophagy is a double-edged sword. Dysfunction of autophagy impairs the differentiation capacity of mesenchymal stem cells and enhances inflammation-induced bone loss. Tooth extraction with periodontal and/or endodontic lesions exacerbates horizontal and vertical resorption of alveolar bone during the healing period. Alveolar socket preservation (ASP) procedure following tooth extraction has important clinical implications for future prosthodontic treatments. Studies have shown that epoxyeicosatrienoic acids (EETs) have significant anti-inflammatory effects and participate in autophagy. However, whether EETs can minimize alveolar bone resorption and contribute to ASP by regulating autophagy levels under inflammatory conditions remain elusive. Here, we figured out that LPS-induced inflammatory conditions increased the inflammatory cytokine and inhibited osteogenic differentiation of human dental pulp stem cells (hDPSCs), and led to excessive autophagy of hDPSCs. Moreover, we identified that increased EETs levels using TPPU, a soluble epoxide hydrolase inhibitor, reversed these negative outcomes. We further demonstrated the potential of TPPU to promote early healing of extraction sockets and ASP, and speculated that it was related to autophagy. Taken together, these results suggest that targeting inhibition of soluble epoxide hydrolase using TPPU plays a protective role in the differentiation and autophagy of mesenchymal stem cells and provides potential feasibility for applying TPPU for ASP, especially under inflammatory conditions.
    DOI:  https://doi.org/10.1038/s41598-023-28710-0
  43. Front Oncol. 2022 ;12 1074057
    Identification of autophagy-associated genes and prognostic implications in adults with acute myeloid leukemia by integrated bioinformatics analysis.
    Jing Zhang, Ying-Jun Wang, Yan-Qiu Han.
      Acute myeloid leukemia (AML) is one of the most common malignant blood neoplasma in adults. The prominent disease heterogeneity makes it challenging to foresee patient survival. Autophagy, a highly conserved degradative process, played indispensable and context-dependent roles in AML. However, it remains elusive whether autophagy-associated stratification could accurately predict prognosis of AML patients. Here, we developed a prognostic model based on autophagy-associated genes, and constructed scoring systems that help to predicte the survival of AML patients in both TCGA data and independent AML cohorts. The Nomogram model also confirmed the autophagy-associated model by showing the high concordance between observed and predicted survivals. Additionally, pathway enrichment analysis and protein-protein interaction network unveiled functional signaling pathways that were associated with autophagy. Altogether, we constructed the autophagy-associated prognostic model that might be likely to predict outcome for AML patients, providing insights into the biological risk stratification strategies and potential therapeutic targets.
    Keywords:  acute myeloid leukemia; autophagy; bioinforamtics; biomarker; prognosis
    DOI:  https://doi.org/10.3389/fonc.2022.1074057
  44. bioRxiv. 2023 Jan 14. pii: 2023.01.13.523943. [Epub ahead of print]
    Genome-wide screens identify SEL1L as an intracellular rheostat controlling collagen turnover.
    Michael J Podolsky, Benjamin Kheyfets, Afaq H Beigh, Christopher D Yang, Carlos Lizama Valenzuela, Ritwik Datta, Paul J Wolters, Michael T McManus, Ling Qi, Kamran Atabai.
      Accumulating evidence has implicated impaired extracellular matrix (ECM) clearance as a key factor in fibrotic disease. Despite decades of research elucidating the effectors of ECM clearance, relatively little is understood regarding the upstream regulation of this process. Collagen is the most abundant constituent of normal and fibrotic ECM in mammalian tissues. Its catabolism occurs through extracellular proteolysis and cell-mediated uptake of collagen fragments for intracellular degradation. Given the paucity of information regarding the regulation of this latter process, we executed unbiased genome-wide screens to understand the molecular underpinnings of cell-mediated collagen clearance. Using this approach, we discovered a previously unappreciated mechanism through which collagen biosynthesis is sensed by cells internally and directly regulates clearance of extracellular collagen. The sensing mechanism is dependent on endoplasmic reticulum-resident protein SEL1L and occurs via a noncanonical function of SEL1L. This pathway functions as a homeostatic negative feedback loop that limits collagen accumulation in tissues. In human fibrotic lung disease, the induction of this collagen clearance pathway by collagen synthesis is impaired, thereby contributing to the pathological accumulation of collagen in lung tissue. Thus cell-autonomous, rheostatic collagen clearance is a previously unidentified pathway of tissue homeostasis.
    DOI:  https://doi.org/10.1101/2023.01.13.523943
  45. Biomater Sci. 2023 Jan 30.
    Mesopore-encaged active MnOx in nano-silica selectively suppresses lung cancer cells by inducing autophagy.
    Fen Yang, Xuan Wang, Jie Sun, Sijia Tan, Shizhe Zhou, Wenlong Tu, Xuexue Dong, Qicai Xiao, Fu Yang, Liqian Gao.
      Autophagy induced by nanomaterials is one of the intracellular catabolic pathways that degrade and recycle the biomacromolecules and damaged organelles in cells and has emerged as a very promising pharmacological target critical to future drug development and anti-cancer therapy. Herein, we developed mesopore-encaged highly-dispersed active cluster-like MnOx in nanosilica entitled MnO-MS, with a size of around 130 nm. Our studies show that MnO-MS could not only obviously induce autophagy in both stable GFP-LC3 HeLa cells and GFP-LC3-mCherry HeLa cells but also could selectively inhibit lung cancer A549 cell growth at 11.19 μg mL-1 (IC50) while exhibiting little cytotoxicity in normal cells. Encouraged by these interesting results, a further mechanistic study reveals that reactive oxygen species (ROS) were excited by the active MnOx in nanosilica, leading to the disruption of mitochondrial membrane potential (MMP), enhancement of ATG5A/ATG16L/ATG4B/Beclin1, and finally, inhibition of the mTOR signaling pathways. Collectively, these findings indicate that MnO-MS-induced cell death via autophagy pathways in cancer cells. Furthermore, MnO-MS significantly inhibited tumor growth with minimal side effects in vivo, and it is envisioned that MnO-MS can be further developed as a potential autophagy inducer for the treatment of lung cancers.
    DOI:  https://doi.org/10.1039/d2bm01826h
  46. J Neurochem. 2023 Jan 31.
    Antiretroviral treatment reveals a novel role for lysosomes in oligodendrocyte maturation.
    Lindsay K Festa, Abigail E Clyde, Caela C Long, Lindsay M Roth, Judith B Grinspan, Kelly L Jordan-Sciutto.
      White matter deficits are a common neuropathologic finding in neurologic disorders, including HIV-associated neurocognitive disorders (HAND). In HAND, the persistence of white matter alterations despite suppressive antiretroviral (ARV) therapy suggests that ARVs may be directly contributing to these impairments. Here, we report that a frontline ARV, bictegravir (BIC), significantly attenuates remyelination following cuprizone-mediated demyelination, a model that recapitulates acute demyelination, but has no impact on already formed mature myelin. Mechanistic studies utilizing primary rat oligodendrocyte precursor cells (OPCs) revealed that treatment with BIC leads to significant decrease in mature oligodendrocytes accompanied by lysosomal de-acidification and impairment of lysosomal degradative capacity with no alterations in lysosomal membrane permeability or total lysosome number. Activation of the endolysosomal cation channel TRPML1 prevents both lysosomal de-acidification and impairment of oligodendrocyte differentiation by BIC. Lastly, we show that de-acidification of lysosomes by compounds that raise lysosomal pH is sufficient to prevent maturation of oligodendrocytes. Overall, this study has uncovered a critical role for lysosomal acidification in modulating oligodendrocyte function and has implications for neurologic diseases characterized by lysosomal dysfunction and white matter abnormalities.
    DOI:  https://doi.org/10.1111/jnc.15773
  47. Front Cell Dev Biol. 2022 ;10 1096899
    The many hats of transmembrane emp24 domain protein TMED9 in secretory pathway homeostasis.
    Benjamin S Roberts, Prasanna Satpute-Krishnan.
      The secretory pathway is an intracellular highway for the vesicular transport of newly synthesized proteins that spans the endoplasmic reticulum (ER), Golgi, lysosomes and the cell surface. A variety of cargo receptors, chaperones, and quality control proteins maintain the smooth flow of cargo along this route. Among these is vesicular transport protein TMED9, which belongs to the p24/transmembrane emp24 domain (TMED) family of proteins, and is expressed across vertebrate species. The TMED family is comprised of structurally-related type I transmembrane proteins with a luminal N-terminal Golgi-dynamics domain, a luminal coiled-coil domain, a transmembrane domain and a short cytosolic C-terminal tail that binds COPI and COPII coat proteins. TMED9, like other members of the TMED family, was first identified as an abundant constituent of the COPI and COPII coated vesicles that mediate traffic between the ER and the Golgi. TMED9 is typically purified in hetero-oligomers together with TMED family members, suggesting that it may function as part of a complex. Recently, TMED family members have been discovered to play various roles in secretory pathway homeostasis including secreted protein processing, quality control and degradation of misfolded proteins, and post-Golgi trafficking. In particular, TMED9 has been implicated in autophagy, lysosomal sorting, viral replication and cancer, which we will discuss in this Mini-Review.
    Keywords:  COP Coatomer; Golgi; autophagy; cargo receptor; endoplasmic reticulum; p24 family; secretory pathway homeostasis; transmembrane emp24 domain
    DOI:  https://doi.org/10.3389/fcell.2022.1096899
  48. Front Biosci (Landmark Ed). 2023 Jan 10. 28(1): 6
    Lipophagy: Molecular Mechanisms and Implications in Hepatic Lipid Metabolism.
    Sai Feng, Zeao Sun, Xiao Jia, Lingyun Li, Yijian Wu, Chengyu Wu, Ligen Lin, Jingxin Liu, Bin Zeng.
      The liver is the most significant metabolic organ in the body and plays an important role in lipid metabolism. Liver lipid metabolism disorders cause hepatic diseases such as hepatitis, hepatic cirrhosis, and hepatoma. Autophagy is a process of generating energy and building blocks by degrading redundant or damaged proteins and organelles. Thus, it helps in the maintenance of cellular homeostasis. Recent discoveries revealed that lipophagy plays a vital role in hepatic cellular homeostasis and lipid metabolism. Its imbalance is always associated with the perturbation of lipid metabolism in the liver. This article reviewed the molecular mechanisms involved in lipophagy and the interaction between lipophagy and hepatic lipid metabolism. Increasing evidence suggests that lipophagy is an effective method to resolve liver diseases.
    Keywords:  autophagy; lipid metabolism; lipophagy; liver
    DOI:  https://doi.org/10.31083/j.fbl2801006
  49. Int J Biochem Cell Biol. 2023 Jan 27. pii: S1357-2725(23)00015-8. [Epub ahead of print] 106376
    Chlamydia psittaci inclusion membrane protein CPSIT_0842 induces macrophage apoptosis through MAPK/ERK-mediated autophagy.
    Yanru Huang, Sijia Li, Siqin He, Yumeng Li, Qingzhi He, Yimou Wu.
      Chlamydia psittaci is a multi-host zoonotic pathogen, which mainly infects poultry and inflicts an appreciable economic burden on the livestock farming industry. C. psittaci inclusion membrane proteins are uniquely positioned at the host-pathogen interface and are important virulence proteins. We have previously confirmed that Incs regulate host cell survival to help Chlamydia sp. evade host-cell-mediated defense mechanisms. However, the role of the Inc, CPSIT_0842, in the regulation of cell death following the establishment of persistent C. psittaci infection remains unknown. This study explored the effect of CPSIT_0842 on the crosstalk between the autophagic and apoptotic pathways in macrophages. Results showed that CPSIT_0842 initiated autophagy and blocked autophagic flux in human macrophages, as indicated by autophagy-related protein LC3-II, Beclin-1, and p62 upregulation, autophagosome accumulation, and lysosomal protein LAMP1 diminution. We also showed that the disruption of autophagic flux had a regulatory effect on CPSIT_0842-induced apoptosis. Moreover, the suppression of autophagy initiation by 3-methyladenine attenuated CPSIT_0842-induced apoptosis. By contrast, the induction of autophagic flux by rapamycin did not significantly affect CPSIT_0842-induced apoptosis. Taken together, these findings demonstrate that CPSIT_0842 induced macrophage apoptosis by initiating incomplete autophagy through the MAPK/ERK/mTOR signaling pathway, which may be instrumental to the ability of C. psittaci to evade the host innate immune response and establish persistent infection. The improved understanding of the autophagic and cell death pathways triggered upon bacterial inclusion will likely help in the development of novel treatment strategies for chlamydia infection.
    Keywords:  CPSIT-0842; Chlamydia psittaci; MAPK/ERK pathway; apoptosis; incomplete autophagy
    DOI:  https://doi.org/10.1016/j.biocel.2023.106376
  50. Cell Chem Biol. 2023 Jan 24. pii: S2451-9456(23)00023-5. [Epub ahead of print]
    Targeting VPS41 induces methuosis and inhibits autophagy in cancer cells.
    Yue Liu, Yong Sun, Yuliang Xu, Ting Dong, Lilin Qian, Hongbo Zheng, Yun Gao, Zhaojun Chu, Xiaojie Fu, Hanrui Zhang, Feng Xie, Chunyang Zhang, Yajie Tang, Hongxiang Lou.
      The homotypic fusion and vacuole protein sorting (HOPS) complex mediates membrane trafficking involved in endocytosis, autophagy, lysosome biogenesis, and phagocytosis. Defects in HOPS subunits are associated with various forms of cancer, but their potential as drug targets has rarely been examined. Here, we identified vacuolar protein sorting-associated protein 41 homolog (VPS41), a subunit of the HOPS complex, as a target of methyl 2,4-dihydroxy-3-(3-methyl-2-butenyl)-6-phenethylbenzoate (DMBP), a natural small molecule with preferable anticancer activity. DMBP induced methuosis and inhibited autophagic flux in cancer cells by inhibiting the function of VPS41, leading to the restrained fusion of late endosomes and autophagosomes with lysosomes. Moreover, DMBP effectively inhibited metastasis in a mouse metastatic melanoma model. Collectively, the current work revealed that targeting VPS41 would provide a valuable method of inhibiting cancer proliferation through methuosis.
    Keywords:  HOPS complex; VPS41; autophagy; cytoplasmic vacuolization; liverworts; methuosis; micropinocytosis
    DOI:  https://doi.org/10.1016/j.chembiol.2023.01.002
  51. Exp Mol Med. 2023 Feb 01.
    TRPV1 regulates ApoE4-disrupted intracellular lipid homeostasis and decreases synaptic phagocytosis by microglia.
    Chenfei Wang, Jia Lu, Xudong Sha, Yu Qiu, Hongzhuan Chen, Zhihua Yu.
      Although the ε4 allele of the apolipoprotein E (ApoE4) gene has been established as a genetic risk factor for many neurodegenerative diseases, including Alzheimer's disease, the mechanism of action remains poorly understood. Transient receptor potential vanilloid 1 (TRPV1) was reported to regulate autophagy to protect against foam cell formation in atherosclerosis. Here, we show that ApoE4 leads to lipid metabolism dysregulation in microglia, resulting in enhanced MHC-II-dependent antigen presentation and T-cell activation. Lipid accumulation and inflammatory reactions were accelerated in microglia isolated from TRPV1flox/flox; Cx3cr1cre-ApoE4 mice. We showed that metabolic boosting by treatment with the TRPV1 agonist capsaicin rescued lipid metabolic impairments in ApoE4 neurons and defects in autophagy caused by disruption of the AKT-mTOR pathway. TRPV1 activation with capsaicin reversed ApoE4-induced microglial immune dysfunction and neuronal autophagy impairment. Capsaicin rescued memory impairment, tau pathology, and neuronal autophagy in ApoE4 mice. Activation of TRPV1 decreased microglial phagocytosis of synapses in ApoE4 mice. TRPV1 gene deficiency exacerbated recognition memory impairment and tau pathology in ApoE4 mice. Our study suggests that TRPV1 regulation of lipid metabolism could be a therapeutic approach to alleviate the consequences of the ApoE4 allele.
    DOI:  https://doi.org/10.1038/s12276-023-00935-z
  52. Exp Mol Med. 2023 Feb 01.
    Chemical mimetics of the N-degron pathway alleviate systemic inflammation by activating mitophagy and immunometabolic remodeling.
    Prashanta Silwal, Young Jae Kim, Yoon Jee Lee, In Soo Kim, Sang Min Jeon, Taylor Roh, Jin Kyung Kim, Min Joung Lee, Jun Young Heo, Doo Sin Jo, Sang-Hee Lee, Dong-Hyung Cho, Jin Man Kim, Yong Tae Kwon, Eun-Kyeong Jo.
      The Arg/N-degron pathway, which is involved in the degradation of proteins bearing an N-terminal signal peptide, is connected to p62/SQSTM1-mediated autophagy. However, the impact of the molecular link between the N-degron and autophagy pathways is largely unknown in the context of systemic inflammation. Here, we show that chemical mimetics of the N-degron Nt-Arg pathway (p62 ligands) decreased mortality in sepsis and inhibited pathological inflammation by activating mitophagy and immunometabolic remodeling. The p62 ligands alleviated systemic inflammation in a mouse model of lipopolysaccharide (LPS)-induced septic shock and in the cecal ligation and puncture model of sepsis. In macrophages, the p62 ligand attenuated the production of proinflammatory cytokines and chemokines in response to various innate immune stimuli. Mechanistically, the p62 ligand augmented LPS-induced mitophagy and inhibited the production of mitochondrial reactive oxygen species in macrophages. The p62 ligand-mediated anti-inflammatory, antioxidative, and mitophagy-activating effects depended on p62. In parallel, the p62 ligand significantly downregulated the LPS-induced upregulation of aerobic glycolysis and lactate production. Together, our findings demonstrate that p62 ligands play a critical role in the regulation of inflammatory responses by orchestrating mitophagy and immunometabolic remodeling.
    DOI:  https://doi.org/10.1038/s12276-023-00929-x
  53. PNAS Nexus. 2022 Sep;1(4): pgac192
    An explanation of how mutant and wild-type mitochondria might stably co-exist in inherited mitochondrial diseases.
    Axel Kowald, Felix P Kemeth, Tom B L Kirkwood.
      Mitochondria are cellular organelles of crucial relevance for the survival of metazoan organisms. Damage to the mitochondrial DNA can give rise to a variety of mitochondrial diseases and is thought also to be involved in the aging process. The fate of mtDNA mutants is controlled by their synthesis as well as degradation and mathematical models can help to better understand this complex interplay. We present here a model that combines a replicative advantage for mtDNA mutants with selective degradation enabled by mitochondrial fission and fusion processes. The model not only shows that the cell has efficient means to deal with (many) types of mutants but, surprisingly, also predicts that under certain conditions a stable co-existence of mutant and wild-type mtDNAs is possible. We discuss how this new finding might explain how mitochondria can be at the heart of processes with such different phenotypes as mitochondrial diseases and aging.
    Keywords:  aging; mathematical model; mitochondrial disease
    DOI:  https://doi.org/10.1093/pnasnexus/pgac192
  54. Trends Endocrinol Metab. 2023 Jan 28. pii: S1043-2760(23)00012-7. [Epub ahead of print]
    mTORC1 syndrome (TorS): unified paradigm for diabetes/metabolic syndrome.
    Jacob Bar-Tana.
      'Glucolipotoxicity' and 'insulin resistance' are claimed to drive type 2 diabetes (T2D) and the non-glycemic diseases of the metabolic syndrome (MetS) (obesity, dyslipidemia, hypertension). In line with that, glycemic and/or insulin control are considered to be primary goal in treating T2D/MetS. However, recent standard-of-care (SOC) treatments of T2D, initially designed to control T2D hyperglycemia, appear now to alleviate the cardio-renal and non-glycemic diseases of T2D/MetS independently of glucose lowering and insulin resistance, and in non-T2D patients altogether, calling for an alternative unifying pathophysiology/treatment paradigm for T2D/MetS. This opinion article proposes to replace the current 'glucolipotoxic/insulin-resistance' paradigm of T2D/MetS with an 'mammalian target of rapamycin complex 1 (mTORC1) syndrome' (TorS) paradigm, implying an exhaustive cohesive disease entity driven by an upstream hyperactive mTORC1, and which includes diabetic hyperglycemia, diabetic dyslipidemia, hypertension, diabetic macrovascular and microvascular disease, non-alcoholic fatty liver disease, some cancers, neurodegeneration, polycystic ovary syndrome (PCOS), psoriasis, and others. The TorS paradigm may account for the insulin-resistant glycemic context of TorS, combined with response to insulin of the non-glycemic diseases of TorS. The TorS paradigm may account for the efficacy of current antidiabetic SOC treatments in diabetic and nondiabetic patients. Most importantly, the TorS paradigm may generate novel treatments for TorS.
    Keywords:  diabetes; mTORC1; metabolic syndrome
    DOI:  https://doi.org/10.1016/j.tem.2023.01.001
  55. J Neuroinflammation. 2023 Feb 02. 20(1): 21
    TNEA therapy promotes the autophagic degradation of NLRP3 inflammasome in a transgenic mouse model of Alzheimer's disease via TFEB/TFE3 activation.
    Wenjia Lin, Zhao Li, Guangfeng Liang, Runjin Zhou, Xiaoyan Zheng, Rongrong Tao, Qingwei Huo, Chengfu Su, Min Li, Nenggui Xu, Chunzhi Tang, Ju-Xian Song.
       BACKGROUND: The impairment in the autophagy-lysosomal pathway (ALP) and the activation of NLR family pyrin domain containing 3 (NLRP3) inflammasome represent two molecular events leading to neurodegeneration and neuroinflammation in Alzheimer's disease (AD), a devastating neurodegenerative disorder without a cure. Previously we demonstrated the cognitive-enhancing effect of a combined electroacupuncture (EA) therapy termed TNEA in a transgenic mouse model of AD, involving activation of transcription factor EB (TFEB), a master regulator of ALP. However, whether and how TNEA inhibits NLRP3 inflammasome via TFEB-mediated ALP in AD remains to be investigated.
    METHODS: 5xFAD mice overexpressing amyloid-β (Aβ) were treated with TNEA or EA on its composing acupoints (GB13 and GV24). The changes in the signaling pathways regulating NLRP3 inflammasome, the association of NLRP3 inflammasome with ALP, and the roles of TFEB/TFE3 in mice brains were determined by immunoblots, immunohistochemistry and AAV-mediated knockdown assays.
    RESULTS: TNEA inhibits the activation of NLRP3 inflammasome and the release of active interleukin 1β (IL1B) in the hippocampi of 5xFAD mice. Mechanistically, TNEA promoted the autophagic degradation of inflammasome components via activating both TFEB and TFE3 by modulating kinases including AMPK and AKT. The composing acupoints in TNEA showed synergistic effects on regulating these molecular events and memory improvement.
    CONCLUSION: Our findings suggest that TNEA attenuates AD-associated memory impairment via promoting TFEB/TFE3-mediated autophagic clearance of Aβ and NLRP3 inflammasome, and partially reveal the molecular basis of combined acupoints therapy originated from ancient wisdom.
    Keywords:  Alzheimer’s disease; Autophagy; Electroacupuncture; NLRP3 inflammasome; Transcription factor EB
    DOI:  https://doi.org/10.1186/s12974-023-02698-w
  56. EMBO J. 2023 Jan 30. e111614
    TSC2 regulates tumor susceptibility to TRAIL-mediated T-cell killing by orchestrating mTOR signaling.
    Chun-Pu Lin, Joleen J H Traets, David W Vredevoogd, Nils L Visser, Daniel S Peeper.
      Resistance to cancer immunotherapy continues to impair common clinical benefit. Here, we use whole-genome CRISPR-Cas9 knockout data to uncover an important role for Tuberous Sclerosis Complex 2 (TSC2) in determining tumor susceptibility to cytotoxic T lymphocyte (CTL) killing in human melanoma cells. TSC2-depleted tumor cells had disrupted mTOR regulation following CTL attack, which was associated with enhanced cell death. Wild-type tumor cells adapted to CTL attack by shifting their mTOR signaling balance toward increased mTORC2 activity, circumventing apoptosis, and necroptosis. TSC2 ablation strongly augmented tumor cell sensitivity to CTL attack in vitro and in vivo, suggesting one of its functions is to critically protect tumor cells. Mechanistically, TSC2 inactivation caused elevation of TRAIL receptor expression, cooperating with mTORC1-S6 signaling to induce tumor cell death. Clinically, we found a negative correlation between TSC2 expression and TRAIL signaling in TCGA patient cohorts. Moreover, a lower TSC2 immune response signature was observed in melanomas from patients responding to immune checkpoint blockade. Our study uncovers a pivotal role for TSC2 in the cancer immune response by governing crosstalk between TSC2-mTOR and TRAIL signaling, aiding future therapeutic exploration of this pathway in immuno-oncology.
    Keywords:  T-cell sensitivity; TRAIL; TSC2; mTOR; tumor cells
    DOI:  https://doi.org/10.15252/embj.2022111614
  57. Res Sq. 2023 Jan 10. pii: rs.3.rs-2320717. [Epub ahead of print]
    Post-fast refeeding enhances intestinal stem cell-mediated regeneration and tumourigenesis through mTORC1-dependent polyamine synthesis.
    Shinya Imada, Heaji Shin, Saleh Khawaled, Sven Meckelmann, Charles Whittaker, Renan Correa, Dikshant Pradhan, Gizem Calibasi, Luiza Nascentes Nascentes, Gabriele Allies, Pia Wittenhofer, Oliver Schmitz, Jatin Roper, Marco Vinolo, Chia-Wei Cheng, Alpaslan Tasdogan, Ã-Mer Yilmaz.
      For more than a century, fasting regimens have improved health, lifespan, and tissue regeneration in diverse organisms, including humans. However, how fasting and post-fast refeeding impact adult stem cells and tumour formation has yet to be explored in depth. Here, we demonstrate that post-fast refeeding increases intestinal stem cell (ISC) proliferation and tumour formation: Post-fast refeeding augments the regenerative capacity of Lgr5+ intestinal stem cells (ISCs), and loss of the tumour suppressor Apc in ISCs under post-fast refeeding leads to a higher tumour incidence in the small intestine and colon than in the fasted or ad libitum (AL) fed states. This demonstrates that post-fast refeeding is a distinct state. Mechanistically, we discovered that robust induction of mTORC1 in post-fast-refed ISCs increases protein synthesis via polyamine metabolism to drive these changes, as inhibition of mTORC1, polyamine metabolite production, or protein synthesis abrogates the regenerative or tumourigenic effects of post-fast refeeding. Thus, fast-refeeding cycles must be carefully considered when planning diet-based strategies for regeneration without increasing cancer risk, as post-fast refeeding leads to a burst not only in stem cell-driven regeneration but also in tumourigenicity.
    DOI:  https://doi.org/10.21203/rs.3.rs-2320717/v1
  58. Front Cell Dev Biol. 2022 ;10 963389
    Skeletal diseases caused by mutations in PTH1R show aberrant differentiation of skeletal progenitors due to dysregulation of DEPTOR.
    Fabiana Csukasi, Michaela Bosakova, Tomas Barta, Jorge H Martin, Jesus Arcedo, Maya Barad, Gustavo A Rico-Llanos, Jennifer Zieba, Jose Becerra, Pavel Krejci, Ivan Duran, Deborah Krakow.
      Alterations in the balance between skeletogenesis and adipogenesis is a pathogenic feature in multiple skeletal disorders. Clinically, enhanced bone marrow adiposity in bones impairs mobility and increases fracture risk, reducing the quality of life of patients. The molecular mechanism that underlies the balance between skeletogenesis and adipogenesis is not completely understood but alterations in skeletal progenitor cells' differentiation pathway plays a key role. We recently demonstrated that parathyroid hormone (PTH)/PTH-related peptide (PTHrP) control the levels of DEPTOR, an inhibitor of the mechanistic target of rapamycin (mTOR), and that DEPTOR levels are altered in different skeletal diseases. Here, we show that mutations in the PTH receptor-1 (PTH1R) alter the differentiation of skeletal progenitors in two different skeletal genetic disorders and lead to accumulation of fat or cartilage in bones. Mechanistically, DEPTOR controls the subcellular localization of TAZ (transcriptional co-activator with a PDZ-binding domain), a transcriptional regulator that governs skeletal stem cells differentiation into either bone and fat. We show that DEPTOR regulation of TAZ localization is achieved through the control of Dishevelled2 (DVL2) phosphorylation. Depending on nutrient availability, DEPTOR directly interacts with PTH1R to regulate PTH/PTHrP signaling or it forms a complex with TAZ, to prevent its translocation to the nucleus and therefore inhibit its transcriptional activity. Our data point DEPTOR as a key molecule in skeletal progenitor differentiation; its dysregulation under pathologic conditions results in aberrant bone/fat balance.
    Keywords:  DEPTOR; PTH signaling; TAZ; Wnt; osteogenesis; skeletal differentiation
    DOI:  https://doi.org/10.3389/fcell.2022.963389
  59. J Am Chem Soc. 2023 Feb 02.
    Molecular Engineering of pH-Responsive NIR Oxazine Assemblies for Evoking Tumor Ferroptosis via Triggering Lysosomal Dysfunction.
    Wei Li, Shulu Yin, Yang Shen, Haiyan Li, Lin Yuan, Xiao-Bing Zhang.
      Ferroptosis, a newly discovered form of regulated cell death, is emerging as a promising approach to tumor therapy. However, the spatiotemporal control of cell-intrinsic Fenton chemistry to modulate tumor ferroptosis remains challenging. Here, we report an oxazine-based activatable molecular assembly (PTO-Biotin Nps), which is capable of triggering the lysosomal dysfunction-mediated Fenton pathway with excellent spatiotemporal resolution via near-infrared (NIR) light to evoke ferroptosis. In this system, a pH-responsive NIR photothermal oxazine molecule was designed and functionalized with a tumor-targeting hydrophilic biotin-poly(ethylene glycol) (PEG) chain to engineer well-defined nanostructured assemblies within a single-molecular framework. PTO-Biotin Nps possesses a selective tropism to lysosome accumulation inside tumor cells, accommodated by its enhanced photothermal activity in the acidic microenvironment. Upon NIR light activation, PTO-Biotin Nps promoted lysosomal dysfunction and induced cytosolic acidification and impaired autophagy. More importantly, photoactivation-mediated lysosomal dysfunction via PTO-Biotin Nps was found to markedly enhance cellular Fenton reactions and evoke ferroptosis, thereby improving antitumor efficacy and mitigating systemic side effects. Overall, our study demonstrates that the molecular engineering approach of pH-responsive photothermal oxazine assemblies enables the spatiotemporal modulation of the intrinsic ferroptosis mechanism, offering a novel strategy for the development of metal-free Fenton inducers in antitumor therapy.
    DOI:  https://doi.org/10.1021/jacs.2c13222
  60. Chem Commun (Camb). 2023 Jan 25.
    Tracking endoplasmic reticulum viscosity during ferroptosis and autophagy using a molecular rotor probe.
    Akshay Silswal, Apurba Lal Koner.
      Ferroptosis is a unique non-apoptotic cell death process associated with endoplasmic reticulum (ER) stress-related diseases. We have designed and synthesized a far-red emitting and ER targetable viscosity-sensitive fluorophore to track ER-phagy. Furthermore, the ER viscosity alteration during the ferroptosis process was investigated via intensity and lifetime-based spectroscopy and microscopy.
    DOI:  https://doi.org/10.1039/d2cc06146e
  61. Mol Pain. 2023 Feb 02. 17448069231158289
    NFATc2-dependent Epigenetic Downregulation of the TSC2/Beclin-1 Pathway is Involved in Neuropathic Pain Induced by Oxaliplatin.
    Meng Liu, Jing-Wen Mai, De-Xing Luo, Guan-Xi Liu, Ting Xu, Wen-Jun Xin, Su-Yan Lin, Zhen-Yu Li.
      Neuropathic pain is a common dose-limiting side effect of oxaliplatin, which hampers the effective treatment of tumors. Here, we found that upregulation of transcription factor NFATc2 decreased the expression of Beclin-1, a critical molecule in autophagy, in the spinal dorsal horn, and contributed to neuropathic pain following oxaliplatin treatment. Meanwhile, manipulating autophagy levels by intrathecal injection of rapamycin (RAPA) or 3-methyladenine (3-MA) differentially altered mechanical allodynia in oxaliplatin-treated or naïve rats. Utilizing chromatin immunoprecipitation-sequencing (ChIP-seq) assay combined with bioinformatics analysis, we found that NFATc2 negatively regulated the transcription of tuberous sclerosis complex protein 2 (TSC2), which contributed to the oxaliplatin-induced Beclin-1 downregulation. Further assays revealed that NFATc2 regulated histone H4 acetylation and methylation in the TSC2 promoter site 1 in rats' dorsal horns with oxaliplatin treatment. These results suggested that NFATc2 mediated the epigenetic downregulation of the TSC2/Beclin-1 autophagy pathway and contributed to oxaliplatin-induced mechanical allodynia, which provided a new therapeutic insight for chemotherapy-induced neuropathic pain.
    Keywords:  Epigenetic regulation; NFATc2; Neuropathic pain; Oxaliplatin; Spinal dorsal horn
    DOI:  https://doi.org/10.1177/17448069231158289
  62. Aging Cell. 2023 Jan 31. e13788
    Age-dependent nuclear lipid droplet deposition is a cellular hallmark of aging in Caenorhabditis elegans.
    Konstantinos Palikaras, Meropi Mari, Christina Ploumi, Andrea Princz, George Filippidis, Nektarios Tavernarakis.
      Aging is the major risk factor for several life-threatening pathologies and impairs the function of multiple cellular compartments and organelles. Age-dependent deterioration of nuclear morphology is a common feature in evolutionarily divergent organisms. Lipid droplets have been shown to localize in most nuclear compartments, where they impinge on genome architecture and integrity. However, the significance of progressive nuclear lipid accumulation and its impact on organismal homeostasis remain obscure. Here, we implement non-linear imaging modalities to monitor and quantify age-dependent nuclear lipid deposition in Caenorhabditis elegans. We find that lipid droplets increasingly accumulate in the nuclear envelope, during aging. Longevity-promoting interventions, such as low insulin signaling and caloric restriction, abolish the rate of nuclear lipid accrual and decrease the size of lipid droplets. Suppression of lipotoxic lipid accumulation in hypodermal and intestinal nuclei is dependent on the transcription factor HLH-30/TFEB and the triglyceride lipase ATGL-1. HLH-30 regulates the expression of ATGL-1 to reduce nuclear lipid droplet abundance in response to lifespan-extending conditions. Notably, ATGL-1 localizes to the nuclear envelope and moderates lipid content in long-lived mutant nematodes during aging. Our findings indicate that the reduced ATGL-1 activity leads to excessive nuclear lipid accumulation, perturbing nuclear homeostasis and undermining organismal physiology, during aging.
    Keywords:  ATGL-1; HLH-30/TFEB; aging; lipid droplet; non-linear optical phenomena; nucleus
    DOI:  https://doi.org/10.1111/acel.13788
  63. Burns Trauma. 2023 ;11 tkac060
    Autophagy in the pathogenesis and therapeutic potential of post-traumatic osteoarthritis.
    Yunquan Gong, Song Li, Jinghui Wu, Tongyi Zhang, Shunzheng Fang, Daibo Feng, Xiaoqing Luo, Jing Yuan, Yaran Wu, Xiaojing Yan, Yan Zhang, Jun Zhu, Jiangyi Wu, Jiqin Lian, Wei Xiang, Zhenhong Ni.
      Autophagy, as a fundamental mechanism for cellular homeostasis, is generally involved in the occurrence and progression of various diseases. Osteoarthritis (OA) is the most common musculoskeletal disease that often leads to pain, disability and economic loss in patients. Post-traumatic OA (PTOA) is a subtype of OA, accounting for >12% of the overall burden of OA. PTOA is often caused by joint injuries including anterior cruciate ligament rupture, meniscus tear and intra-articular fracture. Although a variety of methods have been developed to treat acute joint injury, the current measures have limited success in effectively reducing the incidence and delaying the progression of PTOA. Therefore, the pathogenesis and intervention strategy of PTOA need further study. In the past decade, the roles and mechanisms of autophagy in PTOA have aroused great interest in the field. It was revealed that autophagy could maintain the homeostasis of chondrocytes, reduce joint inflammatory level, prevent chondrocyte death and matrix degradation, which accordingly improved joint symptoms and delayed the progression of PTOA. Moreover, many strategies that target PTOA have been revealed to promote autophagy. In this review,  we summarize the roles and mechanisms of autophagy in PTOA and the current strategies for PTOA treatment that depend on autophagy regulation, which may be beneficial for PTOA patients in the future.
    Keywords:  Autophagy; Noncoding RNAs; Post-traumatic osteoarthritis; mTOR
    DOI:  https://doi.org/10.1093/burnst/tkac060
  64. Toxicology. 2023 Jan 25. pii: S0300-483X(23)00019-7. [Epub ahead of print] 153434
    Dysregulation of the mTOR pathway by mechlorethamine.
    Trishaal Janardhanam Raghavendra Rao, Ganming Mao, Benedette J Cuffari, Blase Billack.
      Mechlorethamine (HN2) is a derivative of the chemical warfare agent sulfur mustard (SM) and cutaneous exposure to HN2 is associated with dermal-epidermal junction (DEJ) disruption (vesication). The primary purpose of the present study was to investigate the effect of HN2 on the mammalian target of rapamycin (mTOR) signaling pathway using an in vivo mouse ear vesicant model (MEVM). To this end, the ears of male C57BL/ 6J mice were exposed to a single topical dose of HN2 (100mM) or vehicle control (DMSO). Mice were then euthanized 30min, 1h or 24h following exposure. Mouse ear skin exposed to HN2 and biopsied 24h thereafter exhibited increased tissue expression of Raptor, an important member of the mTORC1 complex, relative to vehicle treated samples. HN2 reduced the downstream effectors phospho S6 (Ser 240/244) ribosomal protein and phospho 4E-BP1 (Thr 37/46) of the mTOR pathway in the epidermis at 30min, 1h and 24h following HN2 exposure but not in the dermis. These results support the hypothesis that HN2-mediated cutaneous toxicity involves dysregulation of the mTOR signaling pathway in the epidermis.
    Keywords:  mTOR; mechlorethamine; nitrogen mustard; phospho 4E-BP1; phospho S6 ribosomal protein; raptor
    DOI:  https://doi.org/10.1016/j.tox.2023.153434
  65. Bioessays. 2023 Jan 29. e2200160
    Mitochondrial protein import machinery conveys stress signals to the cytosol and beyond.
    Eirini Lionaki, Ilias Gkikas, Nektarios Tavernarakis.
      Mitochondria hold diverse and pivotal roles in fundamental processes that govern cell survival, differentiation, and death, in addition to organismal growth, maintenance, and aging. The mitochondrial protein import system is a major contributor to mitochondrial biogenesis and lies at the crossroads between mitochondrial and cellular homeostasis. Recent findings highlight the mitochondrial protein import system as a signaling hub, receiving inputs from other cellular compartments and adjusting its function accordingly. Impairment of protein import, in a physiological, or disease context, elicits adaptive responses inside and outside mitochondria. In this review, we discuss recent developments, relevant to the mechanisms of mitochondrial protein import regulation, with a particular focus on quality control, proteostatic and metabolic cellular responses, triggered upon impairment of mitochondrial protein import.
    Keywords:  metabolism; mitochondrial protein import; mitochondrial unfolded protein response; mitophagy; proteostasis
    DOI:  https://doi.org/10.1002/bies.202200160
  66. Front Mol Neurosci. 2023 ;16 1131002
    Editorial: mTOR pathway malfunctions in neurodevelopmental disorders.
    Xinqi Fang, Hong Jiang, Xiaobing Zhang, Longbo Zhang.
      
    Keywords:  epilepsy; genomics; mTOR; microbiota; neurodevelopmental disorders
    DOI:  https://doi.org/10.3389/fnmol.2023.1131002
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