bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2023–12–24
78 papers selected by
Viktor Korolchuk, Newcastle University
  1. MORG1 limits mTORC1 signaling by inhibiting Rag GTPases.
  2. Lysosomal microautophagy: an emerging dimension in mammalian autophagy.
  3. S-acylation regulates SQSTM1/p62-mediated selective autophagy.
  4. Differential Regulation of TFEB-Induced Autophagy during Mtb Infection and Starvation.
  5. The yeast dynamin-like GTPase Vps1 mediates Atg9 transport to the phagophore assembly site in Saccharomyces cerevisiae.
  6. VWCE modulates amino acid-dependent mTOR signaling and coordinates with KICSTOR to recruit GATOR1 to the lysosomes.
  7. Abnormal Cholesterol Metabolism and Lysosomal Dysfunction Induce Age-Related Hearing Loss by Inhibiting mTORC1-TFEB-Dependent Autophagy.
  8. Viruses and autophagy: bend, but don't break.
  9. Autophagy-dependent ferroptosis in infectious disease.
  10. The autophagy of stress granules.
  11. Generation of inducible mitophagy mice.
  12. The lipid flippase Drs2 regulates anterograde transport of Atg9 during autophagy.
  13. Mitochondrial quality control via organelle and protein degradation.
  14. The function of ER-phagy receptors is regulated through phosphorylation-dependent ubiquitination pathways.
  15. NDP52 mediates an antiviral response to hepatitis B virus infection through Rab9-dependent lysosomal degradation pathway.
  16. Mitochondrial quality control pathways sense mitochondrial protein import.
  17. Erbin accelerates TFEB-mediated lysosome biogenesis and autophagy and alleviates sepsis-induced inflammatory responses and organ injuries.
  18. Wait, can you remind me just why we need another journal focused on autophagy?
  19. Mec1-Rad53 Signaling Regulates DNA Damage-Induced Autophagy and Pathogenicity in Candida albicans.
  20. Atg15 is a vacuolar phospholipase that disintegrates organelle membranes.
  21. An Overview of Golgi Membrane-Associated Degradation (GOMED) and Its Detection Methods.
  22. Autophagy supports PDGFRA-dependent brain tumor development by enhancing oncogenic signaling.
  23. SLC16a6, mTORC1, and Autophagy Regulate Ketone Body Excretion in the Intestinal Cells.
  24. A lipid membrane-centric role of the SQSTM1/p62 body during autophagosome formation.
  25. Pib2 is a cysteine sensor involved in TORC1 activation in Saccharomyces cerevisiae.
  26. Autophagic dysfunction and gut microbiota dysbiosis cause chronic immune activation in a Drosophila model of Gaucher disease.
  27. PAK inhibitor FRAX486 decreases the metastatic potential of triple-negative breast cancer cells by blocking autophagy.
  28. Nutrient signaling: Starvation flips a phosphoinositide switch on lysosomal catabolism.
  29. A novel viral regulatory network for autophagy induction: Respiratory Syncytial Virus NS2 protein regulates autophagy by modulating BECN1 ISGylation and protein stability.
  30. The link between inhibition of PI3K signaling, induction of autophagy, and elimination of organelles to form the lens organelle-free zone.
  31. Fluvastatin prevents lung metastasis in triple-negative breast cancer by triggering autophagy via the RhoB/PI3K/mTOR pathway.
  32. Aggregation of E121K mutant D-amino acid oxidase and ubiquitination-mediated autophagy mechanisms leading to amyotrophic lateral sclerosis.
  33. Recent advances of vacuolar protein-sorting 34 inhibitors targeting autophagy.
  34. Unveiling autophagy and aging through time-resolved imaging of lysosomal polarity with a delayed fluorescent emitter.
  35. Cholesteryl Hemiazelate Present in Cardiovascular Disease Patients Causes Lysosome Dysfunction in Murine Fibroblasts.
  36. Quinolinic acid impairs mitophagy promoting microglia senescence and poor healthspan in C. elegans: a mechanism of impaired aging process.
  37. A novel mechanism of PHB2-mediated mitophagy participating in the development of Parkinson's disease.
  38. Autophagy as an innate immunity response against pathogens: a Tango dance.
  39. Mitochondrial Quality Control via Mitochondrial Unfolded Protein Response (mtUPR) in Ageing and Neurodegenerative Diseases.
  40. Hyperactive mTORC1 in lung mesenchyme induces endothelial cell dysfunction and pulmonary vascular remodeling.
  41. The Role of mTOR in Doxorubicin-Altered Cardiac Metabolism: A Promising Therapeutic Target of Natural Compounds.
  42. Identification of a Dual Autophagy and REV-ERB Inhibitor with in Vivo Anticancer Efficacy.
  43. Niemann-Pick Disease Type C (NPDC) by Mutation of NPC1 and NPC2: Aberrant Lysosomal Cholesterol Trafficking and Oxidative Stress.
  44. Host autophagy is exploited by the intracellular parasite Toxoplasma gondii to enhance amino acids levels.
  45. Disruption of Mitophagy Flux through the PARL-PINK1 Pathway by CHCHD10 Mutations or CHCHD10 Depletion.
  46. Autophagy of OTUD5 destabilizes GPX4 to confer ferroptosis-dependent kidney injury.
  47. Lnc-HIBADH-4 Regulates Autophagy-Lysosome Pathway in Amyotrophic Lateral Sclerosis by Targeting Cathepsin D.
  48. Neuron-targeted overexpression of caveolin-1 alleviates diabetes-associated cognitive dysfunction via regulating mitochondrial fission-mitophagy axis.
  49. Autophagy as a dual-faced host response to viral infections.
  50. Memories of heat: autophagy and Golgi recovery.
  51. Pharmacological targets at the lysosomal autophagy-NLRP3 inflammasome crossroads.
  52. D-Mannose reduces cellular senescence and NLRP3/GasderminD/IL-1β-driven pyroptotic uroepithelial cell shedding in the murine bladder.
  53. Impaired Autophagic Clearance with a Gain-of-Function Variant of the Lysosomal Cl-/H+ Exchanger ClC-7.
  54. Dual targeting agent Thiotert inhibits the progression of glioblastoma by inducing ER stress-dependent autophagy.
  55. NUAK1 coordinates growth factor-dependent activation of mTORC2 and Akt signaling.
  56. GSK-3β as a potential coordinator of anabolic and catabolic pathways in hepatitis C virus insulin resistance.
  57. Genetically encoded caspase sensor and RFP-LC3 for temporal analysis of apoptosis-autophagy.
  58. Signaling Pathways Involved in Manganese-Induced Neurotoxicity.
  59. Glucose-mediated mitochondrial reprogramming by cholesterol export at TM4SF5-enriched mitochondria-lysosome contact sites.
  60. The mechanism of macroautophagy: The movie.
  61. ATG8f Interacts with Chilli Veinal Mottle Virus 6K2 Protein to Limit Virus Infection.
  62. Defective autophagy contributes to bupivacaine-induced aggravation of painful diabetic neuropathy in db/db mice.
  63. FBXL4 mutation-caused mitochondrial DNA depletion syndrome is driven by BNIP3/BNIP3L-dependent excessive mitophagy.
  64. Editorial: Deciphering and targeting the mTOR pathway in hematologic malignancies.
  65. The Molecular Logic of Gtr1/2 and Pib2 Dependent TORC1 Regulation in Budding Yeast.
  66. Novel insights into the regulatory role of N6-methyladenosine methylation modified autophagy in sepsis.
  67. The cGAS-STING signaling pathway is modulated by urolithin A.
  68. Fingolimod exerts neuroprotection by regulating S1PR1 mediated BNIP3-PINK1-Parkin dependent mitophagy in rotenone induced mouse model of Parkinson's disease.
  69. Autophagy inhibition suppresses Newcastle disease virus-induced cell death by inhibiting viral replication in human breast cancer cells.
  70. Impaired autophagy in the lower airways and lung parenchyma in stable COPD.
  71. Inhibition of LRRK2 kinase activity rescues deficits in striatal dopamine physiology in VPS35 p.D620N knock-in mice.
  72. AoRab7A interacts with AoVps35 and AoVps41 to regulate vacuole assembly, trap formation, conidiation, and functions of proteasomes and ribosomes in Arthrobotrys oligospora.
  73. Apolipoprotein A-1 accelerated liver regeneration through regulating autophagy via AMPK-ULK1 pathway.
  74. Lysosomal membrane transporter purification and reconstitution for functional studies.
  75. Cellular stress responses as modulators of drug cytotoxicity in pharmacotherapy of glioblastoma.
  76. Pyrotinib and chrysin synergistically potentiate autophagy in HER2-positive breast cancer.
  77. The role of mitochondrial quality control in chronic obstructive pulmonary disease.
  78. Amino acid availability governs mTOR ubiquitination.
  1. Mol Cell. 2023 Dec 11. pii: S1097-2765(23)00968-1. [Epub ahead of print]
    MORG1 limits mTORC1 signaling by inhibiting Rag GTPases.
    Yakubu Princely Abudu, Athanasios Kournoutis, Hanne Britt Brenne, Trond Lamark, Terje Johansen.
      Autophagy, an important quality control and recycling process vital for cellular homeostasis, is tightly regulated. The mTORC1 signaling pathway regulates autophagy under conditions of nutrient availability and scarcity. However, how mTORC1 activity is fine-tuned during nutrient availability to allow basal autophagy is unclear. Here, we report that the WD-domain repeat protein MORG1 facilitates basal constitutive autophagy by inhibiting mTORC1 signaling through Rag GTPases. Mechanistically, MORG1 interacts with active Rag GTPase complex inhibiting the Rag GTPase-mediated recruitment of mTORC1 to the lysosome. MORG1 depletion in HeLa cells increases mTORC1 activity and decreases autophagy. The autophagy receptor p62/SQSTM1 binds to MORG1, but MORG1 is not an autophagy substrate. However, p62/SQSTM1 binding to MORG1 upon re-addition of amino acids following amino acid's depletion precludes MORG1 from inhibiting the Rag GTPases, allowing mTORC1 activation. MORG1 depletion increases cell proliferation and migration. Low expression of MORG1 correlates with poor survival in several important cancers.
    Keywords:  MORG1; Rag GTPases; WD-domain repeat protein; autophagy; mTORC1; p62/SQSTM1
    DOI:  https://doi.org/10.1016/j.molcel.2023.11.023
  2. Trends Cell Biol. 2023 Dec 15. pii: S0962-8924(23)00238-6. [Epub ahead of print]
    Lysosomal microautophagy: an emerging dimension in mammalian autophagy.
    Yoshihiko Kuchitsu, Tomohiko Taguchi.
      Autophagy is a self-catabolic process through which cellular components are delivered to lysosomes for degradation. There are three types of autophagy, i.e., macroautophagy, chaperone-mediated autophagy (CMA), and microautophagy. In macroautophagy, a portion of the cytoplasm is wrapped by the autophagosome, which then fuses with lysosomes and delivers the engulfed cytoplasm for degradation. In CMA, the translocation of cytosolic substrates to the lysosomal lumen is directly across the limiting membrane of lysosomes. In microautophagy, lytic organelles, including endosomes or lysosomes, take up a portion of the cytoplasm directly. Although macroautophagy has been investigated extensively, microautophagy has received much less attention. Nonetheless, it has become evident that microautophagy plays a variety of cellular roles from yeast to mammals. Here we review the very recent updates of microautophagy. In particular, we focus on the feature of the degradative substrates and the molecular machinery that mediates microautophagy.
    Keywords:  ESCRT complex; K63-linked ubiquitination; lysosome; microautophagy; vacuole
    DOI:  https://doi.org/10.1016/j.tcb.2023.11.005
  3. Autophagy. 2023 Dec 20.
    S-acylation regulates SQSTM1/p62-mediated selective autophagy.
    Xue Huang, Lu Liu, Jia Yao, Changhai Lin, Tingxiu Xiang, Aimin Yang.
      Macroautophagy/autophagy is a highly conserved metabolic process that degrades intracellular components and recycles bioenergetic substrates. SQSTM1/p62 (sequestosome 1) is a classical autophagy receptor that participates in selective autophagy to eliminate abnormal intracellular components and recycle bioenergetic substrates. In autophagy, SQSTM1 recruits ubiquitinated substrates to form SQSTM1 droplets and delivers these cargoes to phagophores, the precursors to autophagosomes. Recently, we reported a previously unidentified SQSTM1 S-acylation, which is catalyzed by S-acyltransferase ZDHHC19 and reversed by LYPLA1/APT1. S-acylation of SQSTM1 enhances the affinity of SQSTM1 droplets with the phagophore membrane, thereby promoting efficient autophagic degradation of ubiquitinated substrates. Our study uncovers the role of the S-acylation-deacylation cycle in regulating SQSTM1-mediated selective autophagy.
    Keywords:  Autophagosome; SQSTM1; s-acylation; selective autophagy
    DOI:  https://doi.org/10.1080/15548627.2023.2297623
  4. Microorganisms. 2023 Dec 08. pii: 2944. [Epub ahead of print]11(12):
    Differential Regulation of TFEB-Induced Autophagy during Mtb Infection and Starvation.
    Richa Dwivedi, Piyush Baindara.
      Through the promotion of phagolysosome formation, autophagy has emerged as a crucial mechanism to eradicate intracellular Mycobacterium tuberculosis (Mtb). A cell-autonomous host defense mechanism called lysosome biogenesis and autophagy transports cytoplasmic cargos and bacterial phagosomes to lysosomes for destruction during infection. Similar occurrences occurred in stressful or starvation circumstances and led to autophagy, which is harmful to the cell. It is interesting to note that under both hunger and infection states, the transcription factor EB (TFEB) acts as a master regulator of lysosomal activities and autophagy. This review highlighted recent research on the multitier regulation of TFEB-induced autophagy by a variety of host effectors and Mtb sulfolipid during Mtb infection and starvation. In general, the research presented here sheds light on how lysosome biogenesis and autophagy are differentially regulated by the TFEB during Mtb infection and starvation.
    Keywords:  Mycobacterium tuberculosis; TFEB; autophagy; host-directed therapies; infection; starvation
    DOI:  https://doi.org/10.3390/microorganisms11122944
  5. Autophagy Rep. 2023 Aug 17. 2(1): 2247309
    The yeast dynamin-like GTPase Vps1 mediates Atg9 transport to the phagophore assembly site in Saccharomyces cerevisiae.
    Yan Hu, Fulvio Reggiori.
      Macroautophagy/autophagy is a degradative pathway that plays an important role in maintaining cellular homeostasis in eukaryotes. During autophagy, cisternal compartments called phagophores are generated to sequester intracellular components; these structures mature into autophagosomes, which deliver the cargo into lysosomes/vacuoles for degradation. Numerous autophagy-related (Atg) proteins are part of the core machinery that mediates autophagosome biogenesis. Atg9, a lipid scramblase and the only multispanning transmembrane protein among the core Atg machinery, traffics between cytoplasmic reservoirs and the phagophore assembly site (PAS) to provide membranes, recruit other Atg proteins and rearrange lipids on the phagophore membrane. However, the factors mediating Atg9 trafficking remain to be fully understood. In our recent study, we found that the yeast dynamin-like GTPase Vps1 (vacuolar protein sorting 1) is involved in autophagy and is important for Atg9 transport to the PAS. Moreover, we showed that Vps1 function in autophagy requires its GTPase and oligomerization activities. Interestingly, specific mutations in DNM2 (dynamin 2), one of the human homologs of Vps1 that have been linked with specific human diseases such as microcytic anemia and Charcot-Marie-Tooth, also impairs Atg9 transport to the PAS, suggesting that a defect in autophagy may underlay the pathophysiology of these severe human pathologies.
    Keywords:  Autophagosome; DNM2; Saccharomyces cerevisiae; autophagy; phagophore; traffic
    DOI:  https://doi.org/10.1080/27694127.2023.2247309
  6. Nat Commun. 2023 Dec 20. 14(1): 8464
    VWCE modulates amino acid-dependent mTOR signaling and coordinates with KICSTOR to recruit GATOR1 to the lysosomes.
    Tianyu Zhao, Yuanyuan Guan, Chenchen Xu, Dong Wang, Jialiang Guan, Ying Liu.
      The mechanistic target of rapamycin complex 1 (mTORC1) is a crucial regulator of cell growth. It senses nutrient signals and adjusts cellular metabolism accordingly. Deregulation of mTORC1 has been associated with metabolic diseases, cancer, and aging. Amino acid signals are transduced to mTORC1 through sensor proteins and two protein complexes named GATOR1 and GATOR2. In this study, we identify VWCE (von Willebrand factor C and EGF domains) as a negative regulator of amino acid-dependent mTORC1 signaling. Knockdown of VWCE promotes mTORC1 activity even in the absence of amino acids. VWCE interacts with the KICSTOR complex to facilitate the recruitment of GATOR1 to the lysosomes. Bioinformatic analysis reveals that expression of VWCE is reduced in prostate cancer. More importantly, overexpression of VWCE inhibits the development of prostate cancer. Therefore, VWCE may serve as a potential therapeutic target for the treatment of prostate cancers.
    DOI:  https://doi.org/10.1038/s41467-023-44241-8
  7. Int J Mol Sci. 2023 Dec 15. pii: 17513. [Epub ahead of print]24(24):
    Abnormal Cholesterol Metabolism and Lysosomal Dysfunction Induce Age-Related Hearing Loss by Inhibiting mTORC1-TFEB-Dependent Autophagy.
    Yun Yeong Lee, Jungho Ha, Young Sun Kim, Sivasubramanian Ramani, Siung Sung, Eun Sol Gil, Oak-Sung Choo, Jeong Hun Jang, Yun-Hoon Choung.
      Cholesterol is a risk factor for age-related hearing loss (ARHL). However, the effect of cholesterol on the organ of Corti during the onset of ARHL is unclear. We established a mouse model for the ARHL group (24 months, n = 12) and a young group (6 months, n = 12). Auditory thresholds were measured in both groups using auditory brainstem response (ABR) at frequencies of 8, 16, and 32 kHz. Subsequently, mice were sacrificed and subjected to histological analyses, including transmission electron microscopy (TEM), H&E, Sudan Black B (SBB), and Filipin staining, as well as biochemical assays such as IHC, enzymatic analysis, and immunoblotting. Additionally, mRNA extracted from both young and aged cochlea underwent RNA sequencing. To identify the mechanism, in vitro studies utilizing HEI-OC1 cells were also performed. RNA sequencing showed a positive correlation with increased expression of genes related to metabolic diseases, cholesterol homeostasis, and target of rapamycin complex 1 (mTORC1) signaling in the ARHL group as compared to the younger group. In addition, ARHL tissues exhibited increased cholesterol and lipofuscin aggregates in the organ of Corti, lateral walls, and spiral ganglion neurons. Autophagic flux was inhibited by the accumulation of damaged lysosomes and autolysosomes. Subsequently, we observed a decrease in the level of transcription factor EB (TFEB) protein, which regulates lysosomal biosynthesis and autophagy, together with increased mTORC1 activity in ARHL tissues. These changes in TFEB and mTORC1 expression were observed in a cholesterol-dependent manner. Treatment of ARHL mice with atorvastatin, a cholesterol synthesis inhibitor, delayed hearing loss by reducing the cholesterol level and maintaining lysosomal function and autophagy by inhibiting mTORC1 and activating TFEB. The above findings were confirmed using stress-induced premature senescent House Ear Institute organ of Corti 1 (HEI-OC1) cells. The findings implicate cholesterol in the pathogenesis of ARHL. We propose that atorvastatin could prevent ARHL by maintaining lysosomal function and autophagy by inhibiting mTORC1 and activating TFEB during the aging process.
    Keywords:  age-related hearing loss; autophagy; hearing loss; lysosome biogenesis; mTORC1; transcription factor
    DOI:  https://doi.org/10.3390/ijms242417513
  8. Nat Rev Microbiol. 2023 Dec 15.
    Viruses and autophagy: bend, but don't break.
    Alagie Jassey, William T Jackson.
      Autophagy is a constitutive cellular process of degradation required to maintain homeostasis and turn over spent organelles and aggregated proteins. For some viruses, the process can be antiviral, degrading viral proteins or virions themselves. For many other viruses, the induction of the autophagic process provides a benefit and promotes viral replication. In this Review, we survey the roles that the autophagic pathway plays in the replication of viruses. Most viruses that benefit from autophagic induction block autophagic degradation, which is a 'bend, but don't break' strategy initiating but limiting a potentially antiviral response. In almost all cases, it is other effects of the redirected autophagic machinery that benefit these viruses. This rapid mechanism to generate small double-membraned vesicles can be usurped to shape membranes for viral genome replication and virion maturation. However, data suggest that autophagic maintenance of cellular homeostasis is crucial for the initiation of infection, as viruses have evolved to replicate in normal, healthy cells. Inhibition of autophagic degradation is important once infection has initiated. Although true degradative autophagy is probably a negative for most viruses, initiating nondegradative autophagic membranes benefits a wide variety of viruses.
    DOI:  https://doi.org/10.1038/s41579-023-00995-y
  9. J Transl Int Med. 2023 Dec;11(4): 355-362
    Autophagy-dependent ferroptosis in infectious disease.
    Jiarou Li, Hongliang Wang.
      Autophagy is the initial defense response of the host against pathogens. Autophagy can be either non-selective or selective. It selectively targets the degradation of autophagic substrates through the sorting and transportation of autophagic receptor proteins. However, excessive autophagy activity will trigger cell death especially ferroptosis, which was characterized by the accumulation of lipid peroxide and free iron. Several certain types of selective autophagy degrade antioxidant systems and ferritin. Here, we summarized the latest researches of autophagy in infection and discuss the regulatory mechanisms and signaling pathways of autophagy-dependent ferroptosis.
    Keywords:  autophagy; ferroptosis; infectious disease; selective autophagy; sepsis
    DOI:  https://doi.org/10.2478/jtim-2023-0099
  10. FEBS Lett. 2023 Dec 15.
    The autophagy of stress granules.
    Laura Ryan, David C Rubinsztein.
      Our understanding of stress granule (SG) biology has deepened considerably in recent years, and with this, increased understanding of links has been made between SGs and numerous neurodegenerative diseases. One of the proposed mechanisms by which SGs and any associated protein aggregates may become pathological is based upon defects in their autophagic clearance, and so the precise processes governing the degradation of SGs are important to understand. Mutations and disease-associated variants implicated in amyotrophic lateral sclerosis, Huntington's disease, Parkinson's disease and frontotemporal lobar dementia compromise autophagy, whilst autophagy-inhibiting drugs or knockdown of essential autophagy proteins result in the persistence of SGs. In this review, we will consider the current knowledge regarding the autophagy of SG.
    Keywords:  P62; amyotrophic lateral sclerosis; autophagy; granulophagy; neurodegeneration; proteostasis; stress granules; valosin-containing protein
    DOI:  https://doi.org/10.1002/1873-3468.14787
  11. Genes Cells. 2023 Dec 22.
    Generation of inducible mitophagy mice.
    Toshiyuki Nishiji, Atsushi Hoshino, Yuki Uchio, Satoaki Matoba.
      Mitophagy is programmed selective autophagy of mitochondria and is important for mitochondrial quality control and cellular homeostasis. Mitochondrial dysfunction and impaired mitophagy are closely associated with various diseases, including heart failure and diabetes. To better understand the pathophysiological role of mitophagy, we generated doxycycline-inducible mitophagy mice using a synthetic mitophagy adaptor protein consisting of an outer mitochondrial membrane targeting sequence and an engineered LIR. To evaluate the activation of mitophagy upon doxycycline treatment, we also generated mitophagy reporter mito-QC mice in which mitochondria tandemly express mCherry and GFP, and only GFP signals are lost in acidic lysosomes subjected to mitophagy. With the ROSA26 promoter-driven rtTA, mitophagy was observed at least in heart, liver, and skeletal muscle. We investigated the relationship between mitophagy activation and pressure overload heart failure or high fat diet-induced obesity. Unexpectedly, we were unable to confirm the protective effect of mitophagy in these two pathological models. Further titration of the level of mitophagy induction is required to demonstrate the potency of the protective effects of mitophagy in disease models.
    Keywords:  bioengineering; heart failure; mitophagy
    DOI:  https://doi.org/10.1111/gtc.13091
  12. Autophagy Rep. 2022 Aug 09. 1(1): 345-367
    The lipid flippase Drs2 regulates anterograde transport of Atg9 during autophagy.
    Franziska Kriegenburg, Wouter Huiting, Fleur van Buuren-Broek, Emma Zwilling, Ralph Hardenberg, Muriel Mari, Claudine Kraft, Fulvio Reggiori.
      Macroautophagy/autophagy is a conserved catabolic pathway during which cellular material is sequestered within newly formed double-membrane vesicles called autophagosomes and delivered to the lytic compartment of eukaryotic cells for degradation. Autophagosome biogenesis depends on the core autophagy-related (Atg) machinery, and involves a massive supply and remodelling of membranes. To gain insight into the lipid remodelling mechanisms during autophagy, we have systematically investigated whether lipid flippases are required for this pathway in the yeast Saccharomyces cerevisiae. We found that the flippase Drs2, which transfers phosphatidylserine and phosphatidylethanolamine from the lumenal to the cytosolic leaflet of the limiting membrane at the trans-Golgi network, is required for normal progression of autophagy. We also show that Drs2 is important for the trafficking of the core Atg protein Atg9. Atg9 is a transmembrane protein important for autophagosome biogenesis and its anterograde transport from its post-Golgi reservoirs to the site of autophagosome formation is severely impaired in the absence of Drs2. Thus, our results identify a novel autophagy player and highlight that membrane asymmetry regulates early autophagy steps.
    Keywords:  Aminophospholipid; Atg protein; autophagosome; flippase; lipid asymmetry; phagophore; phagophore assembly site
    DOI:  https://doi.org/10.1080/27694127.2022.2104781
  13. J Biochem. 2023 Dec 15. pii: mvad106. [Epub ahead of print]
    Mitochondrial quality control via organelle and protein degradation.
    Koji Yamano, Hiroki Kinefuchi, Waka Kojima.
      Mitochondria are essential eukaryotic organelles that produce ATP as well as synthesize various macromolecules. They also participate in signaling pathways such as the innate immune response and apoptosis. These diverse functions are performed by >1000 different mitochondrial proteins. Although mitochondria are continuously exposed to potentially damaging conditions such as reactive oxygen species, proteases/peptidases localized in different mitochondrial sub-compartments, termed mitoproteases, maintain mitochondrial quality and integrity. In addition to processing incoming precursors and degrading damaged proteins, mitoproteases also regulate metabolic reactions, mitochondrial protein half-lives, and gene transcription. Impaired mitoprotease function is associated with various pathologies. In this review, we highlight recent advances in our understanding of mitochondrial quality control regulated by autophagy, ubiquitin-proteasomes, and mitoproteases.
    Keywords:  autophagy; mitophagy; peptidase; protease; ubiquitin
    DOI:  https://doi.org/10.1093/jb/mvad106
  14. Nat Commun. 2023 Dec 15. 14(1): 8364
    The function of ER-phagy receptors is regulated through phosphorylation-dependent ubiquitination pathways.
    Rayene Berkane, Hung Ho-Xuan, Marius Glogger, Pablo Sanz-Martinez, Lorène Brunello, Tristan Glaesner, Santosh Kumar Kuncha, Katharina Holzhüter, Sara Cano-Franco, Viviana Buonomo, Paloma Cabrerizo-Poveda, Ashwin Balakrishnan, Georg Tascher, Koraljka Husnjak, Thomas Juretschke, Mohit Misra, Alexis González, Volker Dötsch, Paolo Grumati, Mike Heilemann, Alexandra Stolz.
      Selective autophagy of the endoplasmic reticulum (ER), known as ER-phagy, is an important regulator of ER remodeling and essential to maintain cellular homeostasis during environmental changes. We recently showed that members of the FAM134 family play a critical role during stress-induced ER-phagy. However, the mechanisms on how they are activated remain largely unknown. In this study, we analyze phosphorylation of FAM134 as a trigger of FAM134-driven ER-phagy upon mTOR (mechanistic target of rapamycin) inhibition. An unbiased screen of kinase inhibitors reveals CK2 to be essential for FAM134B- and FAM134C-driven ER-phagy after mTOR inhibition. Furthermore, we provide evidence that ER-phagy receptors are regulated by ubiquitination events and that treatment with E1 inhibitor suppresses Torin1-induced ER-phagy flux. Using super-resolution microscopy, we show that CK2 activity is essential for the formation of high-density FAM134B and FAM134C clusters. In addition, dense clustering of FAM134B and FAM134C requires phosphorylation-dependent ubiquitination of FAM134B and FAM134C. Treatment with the CK2 inhibitor SGC-CK2-1 or mutation of FAM134B and FAM134C phosphosites prevents ubiquitination of FAM134 proteins, formation of high-density clusters, as well as Torin1-induced ER-phagy flux. Therefore, we propose that CK2-dependent phosphorylation of ER-phagy receptors precedes ubiquitin-dependent activation of ER-phagy flux.
    DOI:  https://doi.org/10.1038/s41467-023-44101-5
  15. Nat Commun. 2023 Dec 19. 14(1): 8440
    NDP52 mediates an antiviral response to hepatitis B virus infection through Rab9-dependent lysosomal degradation pathway.
    Shuzhi Cui, Tian Xia, Jianjin Zhao, Xiaoyu Ren, Tingtao Wu, Mireille Kameni, Xiaoju Guo, Li He, Jingao Guo, Aléria Duperray-Susini, Florence Levillayer, Jean-Marc Collard, Jin Zhong, Lifeng Pan, Frédéric Tangy, Pierre-Olivier Vidalain, Dongming Zhou, Yaming Jiu, Mathias Faure, Yu Wei.
      Autophagy receptor NDP52 triggers bacterial autophagy against infection. However, the ability of NDP52 to protect against viral infection has not been established. We show that NDP52 binds to envelope proteins of hepatitis B virus (HBV) and triggers a degradation process that promotes HBV clearance. Inactivating NDP52 in hepatocytes results in decreased targeting of viral envelopes in the lysosome and increased levels of viral replication. NDP52 inhibits HBV at both viral entry and late replication stages. In contrast to NDP52-mediated bacterial autophagy, lysosomal degradation of HBV envelopes is independent of galectin 8 and ATG5. NDP52 forms complex with Rab9 and viral envelope proteins and links HBV to Rab9-dependent lysosomal degradation pathway. These findings reveal that NDP52 acts as a sensor for HBV infection, which mediates a unique antiviral response to eliminate the virus. This work also suggests direct roles for autophagy receptors in other lysosomal degradation pathways than canonical autophagy.
    DOI:  https://doi.org/10.1038/s41467-023-44201-2
  16. Trends Endocrinol Metab. 2023 Dec 15. pii: S1043-2760(23)00243-6. [Epub ahead of print]
    Mitochondrial quality control pathways sense mitochondrial protein import.
    Laurie P Lee-Glover, Timothy E Shutt.
      Mitochondrial quality control (MQC) mechanisms are required to maintain a functional proteome, which enables mitochondria to perform a myriad of important cellular functions from oxidative phosphorylation to numerous other metabolic pathways. Mitochondrial protein homeostasis begins with the import of over 1000 nuclear-encoded mitochondrial proteins and the synthesis of 13 mitochondrial DNA-encoded proteins. A network of chaperones and proteases helps to fold new proteins and degrade unnecessary, damaged, or misfolded proteins, whereas more extensive damage can be removed by mitochondrial-derived vesicles (MDVs) or mitochondrial autophagy (mitophagy). Here, focusing on mechanisms in mammalian cells, we review the importance of mitochondrial protein import as a sentinel of mitochondrial function that activates multiple MQC mechanisms when impaired.
    Keywords:  mitochondria; mitochondrial protein import; mitochondrial quality control; mitochondrial unfolded protein response; mitochondrial-derived vesicles; mitophagy
    DOI:  https://doi.org/10.1016/j.tem.2023.11.004
  17. J Transl Med. 2023 Dec 17. 21(1): 916
    Erbin accelerates TFEB-mediated lysosome biogenesis and autophagy and alleviates sepsis-induced inflammatory responses and organ injuries.
    Qing Fang, Guoqing Jing, Ying Zhang, Hongyu Wang, Huan Luo, Yun Xia, Qiyan Jin, Yuping Liu, Jing Zuo, Cheng Yang, Xiaodong Zhang, Shi Liu, Xiaojing Wu, Xuemin Song.
      Mounting attention has been focused on defects of the autophagy-lysosomal pathway in sepsis, however, the precise mechanisms governing the autophagy-lysosomal process in sepsis are poorly known. We have previously reported that Erbin deficiency aggravated the inflammatory response and organ injuries caused by sepsis. In the present study, we found that Erbin knockout impaired the autophagy process in both muramyl dipeptide (MDP)-induced bone marrow-derived macrophages (BMDMs) and sepsis mouse liver and lung, as detected by the accumulation of LC3-II and SQSTM1/p62, and autophagosomes. Pretreatment with autophagy inhibitor chloroquine (CQ) further aggravated inflammatory response and organ injuries in vivo and in vitro sepsis model. We also observed that the impaired lysosomal function mediated autophagic blockade, as detected by the decreased expression of ATP6V, cathepsin B (CTSB) and LAMP2 protein. Immunoprecipitation revealed that the C-terminal of Erbin (aa 391-964) interacts with the N-terminal of transcription factor EB (TFEB) (aa 1-247), and affects the stability of TFEB-14-3-3 and TFEB-PPP3CB complexes and the phosphorylation status of TFEB, thereby promote the nucleus translocation of TFEB and the TFEB target genes transcription. Thus, our study suggested that Erbin alleviated sepsis-induced inflammatory responses and organ injuries by rescuing dysfunction of the autophagy-lysosomal pathway through TFEB-14-3-3 and TFEB-PPP3CB pathway.
    Keywords:  Autophagy; Erbin; Lysosome; Sepsis; TFEB
    DOI:  https://doi.org/10.1186/s12967-023-04796-y
  18. Autophagy Rep. 2022 Mar 17. 1(1): 1-4
    Wait, can you remind me just why we need another journal focused on autophagy?
    Daniel J Klionsky, Fulvio Reggiori.
      Well, because you ask that question, we are going to attempt to explain exactly why we do indeed need another journal focused on autophagy. If you are reading this far, you presumably know what "autophagy" means, so we do not have to impress upon you the importance of this topic, and how autophagic dysfunction is associated with numerous diseases in humans (okay, we felt compelled to slip that in anyway). Nor do we think that you need to be introduced to the journal Autophagy, which is just starting its eighteenth year and publishes papers on pretty much any topic; at least any topic that is connected to autophagy, which, after all, means pretty much any topic, if you get our drift. So, if Autophagy has done so well and serves such an important purpose, why do we need another journal? To find the answer, read on.
    Keywords:  Acceptance rate; expansion; new journal; not all topics are equal; the bar to publish; we feel your pain
    DOI:  https://doi.org/10.1080/27694127.2022.2034253
  19. J Fungi (Basel). 2023 Dec 09. pii: 1181. [Epub ahead of print]9(12):
    Mec1-Rad53 Signaling Regulates DNA Damage-Induced Autophagy and Pathogenicity in Candida albicans.
    Jiawen Du, Yixuan Dong, Wenjie Zuo, Ying Deng, Hangqi Zhu, Qilin Yu, Mingchun Li.
      DNA damage activates the DNA damage response and autophagy in C. albicans; however, the relationship between the DNA damage response and DNA damage-induced autophagy in C. albicans remains unclear. Mec1-Rad53 signaling is a critical pathway in the DNA damage response, but its role in DNA damage-induced autophagy and pathogenicity in C. albicans remains to be further explored. In this study, we compared the function of autophagy-related (Atg) proteins in DNA damage-induced autophagy and traditional macroautophagy and explored the role of Mec1-Rad53 signaling in regulating DNA damage-induced autophagy and pathogenicity. We found that core Atg proteins are required for these two types of autophagy, while the function of Atg17 is slightly different. Our results showed that Mec1-Rad53 signaling specifically regulates DNA damage-induced autophagy but has no effect on macroautophagy. The recruitment of Atg1 and Atg13 to phagophore assembly sites (PAS) was significantly inhibited in the mec1Δ/Δ and rad53Δ/Δ strains. The formation of autophagic bodies was obviously affected in the mec1Δ/Δ and rad53Δ/Δ strains. We found that DNA damage does not induce mitophagy and ER autophagy. We also identified two regulators of DNA damage-induced autophagy, Psp2 and Dcp2, which regulate DNA damage-induced autophagy by affecting the protein levels of Atg1, Atg13, Mec1, and Rad53. The deletion of Mec1 or Rad53 significantly reduces the ability of C. albicans to systematically infect mice and colonize the kidneys, and it makes C. albicans more susceptible to being killed by macrophages.
    Keywords:  Atg1; Atg13; Candida albicans; DNA damage-induced autophagy; Mec1-Rad53 signaling; autophagosome biogenesis
    DOI:  https://doi.org/10.3390/jof9121181
  20. Cell Rep. 2023 Dec 15. pii: S2211-1247(23)01579-6. [Epub ahead of print] 113567
    Atg15 is a vacuolar phospholipase that disintegrates organelle membranes.
    Yasunori Watanabe, Yurina Iwasaki, Kyoka Sasaki, Chie Motono, Kenichiro Imai, Kuninori Suzuki.
      Atg15 (autophagy-related 15) is a vacuolar phospholipase essential for the degradation of cytoplasm-to-vacuole targeting (Cvt) bodies and autophagic bodies, hereinafter referred to as intravacuolar/intralysosomal autophagic compartments (IACs), but it remains unknown if Atg15 directly disrupts IAC membranes. Here, we show that the recombinant Chaetomium thermophilum Atg15 lipase domain (CtAtg15(73-475)) possesses phospholipase activity. The activity of CtAtg15(73-475) was markedly elevated by limited digestion. We inserted the human rhinovirus 3C protease recognition sequence and found that cleavage between S159 and V160 was important to activate CtAtg15(73-475). Our molecular dynamics simulation suggested that the cleavage facilitated conformational change around the active center of CtAtg15, resulting in an exposed state. We confirmed that CtAtg15 could disintegrate S. cerevisiae IAC in vivo. Further, both mitochondria and IAC of S. cerevisiae were disintegrated by CtAtg15. This study suggests Atg15 plays a role in disrupting any organelle membranes delivered to vacuoles by autophagy.
    Keywords:  CP: Cell biology; autophagosome; autophagy; autophagy-related 15; cytoplasm-to-vacuole targeting; molecular dynamics simulation; organelle membrane; phospholipase; phospholipid; vacuole; yeast
    DOI:  https://doi.org/10.1016/j.celrep.2023.113567
  21. Cells. 2023 Dec 11. pii: 2817. [Epub ahead of print]12(24):
    An Overview of Golgi Membrane-Associated Degradation (GOMED) and Its Detection Methods.
    Hajime Tajima Sakurai, Satoko Arakawa, Hirofumi Yamaguchi, Satoru Torii, Shinya Honda, Shigeomi Shimizu.
      Autophagy is a cellular mechanism that utilizes lysosomes to degrade its own components and is performed using Atg5 and other molecules originating from the endoplasmic reticulum membrane. On the other hand, we identified an alternative type of autophagy, namely, Golgi membrane-associated degradation (GOMED), which also utilizes lysosomes to degrade its own components, but does not use Atg5 originating from the Golgi membranes. The GOMED pathway involves Ulk1, Wipi3, Rab9, and other molecules, and plays crucial roles in a wide range of biological phenomena, such as the regulation of insulin secretion and neuronal maintenance. We here describe the overview of GOMED, methods to detect autophagy and GOMED, and to distinguish GOMED from autophagy.
    Keywords:  GOMED; Golgi; ULK1; autophagy
    DOI:  https://doi.org/10.3390/cells12242817
  22. Dev Cell. 2023 Dec 08. pii: S1534-5807(23)00621-4. [Epub ahead of print]
    Autophagy supports PDGFRA-dependent brain tumor development by enhancing oncogenic signaling.
    Joanne E Simpson, Morwenna T Muir, Martin Lee, Catherine Naughton, Nick Gilbert, Steven M Pollard, Noor Gammoh.
      Autophagy is a conserved cellular degradation process. While autophagy-related proteins were shown to influence the signaling and trafficking of some receptor tyrosine kinases, the relevance of this during cancer development is unclear. Here, we identify a role for autophagy in regulating platelet-derived growth factor receptor alpha (PDGFRA) signaling and levels. We find that PDGFRA can be targeted for autophagic degradation through the activity of the autophagy cargo receptor p62. As a result, short-term autophagy inhibition leads to elevated levels of PDGFRA but an unexpected defect in PDGFA-mediated signaling due to perturbed receptor trafficking. Defective PDGFRA signaling led to its reduced levels during prolonged autophagy inhibition, suggesting a mechanism of adaptation. Importantly, PDGFA-driven gliomagenesis in mice was disrupted when autophagy was inhibited in a manner dependent on Pten status, thus highlighting a genotype-specific role for autophagy during tumorigenesis. In summary, our data provide a mechanism by which cells require autophagy to drive tumor formation.
    Keywords:  PDGFRA; PTEN; RTK; autophagy; cancer; endocytosis; glioblastoma; signaling
    DOI:  https://doi.org/10.1016/j.devcel.2023.11.023
  23. Biology (Basel). 2023 Nov 26. pii: 1467. [Epub ahead of print]12(12):
    SLC16a6, mTORC1, and Autophagy Regulate Ketone Body Excretion in the Intestinal Cells.
    Takashi Uebanso, Moeka Fukui, Chisato Naito, Takaaki Shimohata, Kazuaki Mawatari, Akira Takahashi.
      Ketone bodies serve several functions in the intestinal epithelium, such as stem cell maintenance, cell proliferation and differentiation, and cancer growth. Nevertheless, there is limited understanding of the mechanisms governing the regulation of intestinal ketone body concentration. In this study, we elucidated the factors responsible for ketone body production and excretion using shRNA-mediated or pharmacological inhibition of specific genes or functions in the intestinal cells. We revealed that a fasting-mimicked culture medium, which excluded glucose, pyruvate, and glutamine, augmented ketone body production and excretion in the Caco2 and HT29 colorectal cells. This effect was attenuated by glucose or glutamine supplementation. On the other hand, the inhibition of the mammalian target of rapamycin complex1 (mTORC1) recovered a fraction of the excreted ketone bodies. In addition, the pharmacological or shbeclin1-mediated inhibition of autophagy suppressed ketone body excretion. The knockdown of basigin, a transmembrane protein responsible for targeting monocarboxylate transporters (MCTs), such as MCT1 and MCT4, suppressed lactic acid and pyruvic acid excretion but increased ketone body excretion. Finally, we found that MCT7 (SLC16a6) knockdown suppressed ketone body excretion. Our findings indicate that the mTORC1-autophagy axis and MCT7 are potential targets to regulate ketone body excretion from the intestinal epithelium.
    Keywords:  autophagy; intestinal cell; ketone body; mTORC1; solute carrier family 16 member 6: SLC16a6 (MCT7)
    DOI:  https://doi.org/10.3390/biology12121467
  24. Autophagy. 2023 Dec 19.
    A lipid membrane-centric role of the SQSTM1/p62 body during autophagosome formation.
    Jinpei Zhang, Xintong He, Na Mi.
      The phase separated SQSTM1/p62 body drives the formation of autophagosomes during macroautophagy/autophagy. However, the underlying mechanism by which the SQSTM1/p62 body acts during this process remains less understood. Recently, we reported that the SQSTM1/p62 body can work as a nucleation center to recruit local membrane sources for the expanding phagophore. Proteomics analysis reveals membrane vesicle-related components as important constituents of the SQSTM1/p62 body. ATG9- and ATG16L1-positive vesicles are recruited by the SQSTM1/p62 body as initial membrane sources of phagophores. ATG2 promotes the lipid transfer and vesicle fusion to further expand the membrane architecture of the initial phagophore. The lipid composition and content within the SQSTM1/p62 body is significantly affected by ATG2. The SQSTM1/p62 body also regulates the proper positioning and abundance of ATG9-positive vesicles. Furthermore, by spatially gathering ULK1 and membrane-anchored class III phosphatidylinositol (PtdIns) 3-kinase complexes, the SQSTM1/p62 body acts a local reaction platform to generate PtdIns-3-phosphate (PtdIns3P) to accelerate autophagosome maturation. These findings highlight a lipid membrane gathering model of the multifaceted SQSTM1/p62 body when driving autophagosome formation.
    Keywords:  ATG2; ATG9; autophagy; lipid; membrane; p62
    DOI:  https://doi.org/10.1080/15548627.2023.2297622
  25. Cell Rep. 2023 Dec 20. pii: S2211-1247(23)01611-X. [Epub ahead of print]43(1): 113599
    Pib2 is a cysteine sensor involved in TORC1 activation in Saccharomyces cerevisiae.
    Qingzhong Zeng, Yasuhiro Araki, Takeshi Noda.
      Target of rapamycin complex 1 (TORC1) is a master regulator that monitors the availability of various amino acids to promote cell growth in Saccharomyces cerevisiae. It is activated via two distinct upstream pathways: the Gtr pathway, which corresponds to mammalian Rag, and the Pib2 pathway. This study shows that Ser3 was phosphorylated exclusively in a Pib2-dependent manner. Using Ser3 as an indicator of TORC1 activity, together with the established TORC1 substrate Sch9, we investigated which pathways were employed by individual amino acids. Different amino acids exhibited different dependencies on the Gtr and Pib2 pathways. Cysteine was most dependent on the Pib2 pathway and increased the interaction between TORC1 and Pib2 in vivo and in vitro. Moreover, cysteine directly bound to Pib2 via W632 and F635, two critical residues in the T(ail) motif that are necessary to activate TORC1. These results indicate that Pib2 functions as a sensor for cysteine in TORC1 regulation.
    Keywords:  CP: Molecular biology; Cysteine; Pib2; TORC1; mTORC1
    DOI:  https://doi.org/10.1016/j.celrep.2023.113599
  26. PLoS Genet. 2023 Dec;19(12): e1011063
    Autophagic dysfunction and gut microbiota dysbiosis cause chronic immune activation in a Drosophila model of Gaucher disease.
    Magda L Atilano, Alexander Hull, Catalina-Andreea Romila, Mirjam L Adams, Jacob Wildfire, Enric Ureña, Miranda Dyson, Jorge Ivan-Castillo-Quan, Linda Partridge, Kerri J Kinghorn.
      Mutations in the GBA1 gene cause the lysosomal storage disorder Gaucher disease (GD) and are the greatest known genetic risk factors for Parkinson's disease (PD). Communication between the gut and brain and immune dysregulation are increasingly being implicated in neurodegenerative disorders such as PD. Here, we show that flies lacking the Gba1b gene, the main fly orthologue of GBA1, display widespread NF-kB signalling activation, including gut inflammation, and brain glial activation. We also demonstrate intestinal autophagic defects, gut dysfunction, and microbiome dysbiosis. Remarkably, modulating the microbiome of Gba1b knockout flies, by raising them under germ-free conditions, partially ameliorates lifespan, locomotor and immune phenotypes. Moreover, we show that modulation of the immune deficiency (IMD) pathway is detrimental to the survival of Gba1 deficient flies. We also reveal that direct stimulation of autophagy by rapamycin treatment achieves similar benefits to germ-free conditions independent of gut bacterial load. Consistent with this, we show that pharmacologically blocking autophagosomal-lysosomal fusion, mimicking the autophagy defects of Gba1 depleted cells, is sufficient to stimulate intestinal immune activation. Overall, our data elucidate a mechanism whereby an altered microbiome, coupled with defects in autophagy, drive chronic activation of NF-kB signaling in a Gba1 loss-of-function model. It also highlights that elimination of the microbiota or stimulation of autophagy to remove immune mediators, rather than prolonged immunosuppression, may represent effective therapeutic avenues for GBA1-associated disorders.
    DOI:  https://doi.org/10.1371/journal.pgen.1011063
  27. Br J Cancer. 2023 Dec 18.
    PAK inhibitor FRAX486 decreases the metastatic potential of triple-negative breast cancer cells by blocking autophagy.
    Liang Lyu, Haiyan Li, Kefeng Lu, Shu Jiang, Huihui Li.
       BACKGROUND: Triple-negative breast cancer (TNBC) is a unique breast cancer subtype with a high risk of metastasis and recurrence and a poor prognosis. Epithelial-mesenchymal transition (EMT) endows epithelial cells with the ability to move to distant sites, which is essential for the metastasis of TNBC to organs, including the lung. Autophagy, an intracellular degradation process that involves formation of double-layered lipid autophagosomes that transport cytosolic cargoes into lysosomes via autophagosome-lysosome fusion, is involved in various diseases, including cancer and neurodegenerative, metabolic, cardiovascular, and infectious diseases. The relationship between autophagy and cancer has become relatively clear. However, research on pharmacological drugs that block cancer EMT by targeting autophagy is still in the initial stages. Therefore, the re-evaluation of old drugs for their potential in blocking both autophagy and EMT was conducted.
    METHODS: More than 2000 small molecule chemicals were screened for dual autophagy/EMT inhibitors, and FRAX486 was identified as the best candidate inhibitor of autophagy/EMT. The functions of FRAX486 in TNBC metastasis were detected by CCK-8, migration and wound healing assays. The effects of FRAX486 on autophagy and its target PAK2 were determined by immunoblotting, immunofluorescence, immunoprecipitation analysis and transmission electron microscopy. The findings were validated in mouse models.
    RESULTS: Here, we report that FRAX486, a potent P21-activated kinase 2 (PAK2) inhibitor, facilitates TNBC suppression both in vitro and in vivo by blocking autophagy. Mechanistically, FRAX486 inhibits autophagy in TNBC cells by targeting PAK2, leading to the ubiquitination and proteasomal degradation of STX17, which mediates autophagosome-lysosome fusion. The inhibition of autophagy by FRAX486 causes upregulation of the epithelial marker protein E-cadherin and thus suppresses the migration and metastasis of TNBC cells.
    CONCLUSIONS: The effects of FRAX486 on TNBC metastasis suppression were verified to be dependent on PAK2 and autophagy inhibition. Together, our results provide a molecular basis for the application of FRAX486 as a potential treatment for inhibiting the metastasis of TNBC.
    DOI:  https://doi.org/10.1038/s41416-023-02523-4
  28. Curr Biol. 2023 Dec 18. pii: S0960-9822(23)01489-6. [Epub ahead of print]33(24): R1289-R1291
    Nutrient signaling: Starvation flips a phosphoinositide switch on lysosomal catabolism.
    Michal J Nagiec, John Blenis.
      Lysosomes are highly dynamic organelles that rapidly respond to changes in cellular nutrient status. A new study identifies a phosphoinositide switch that dictates lysosome function during nutrient starvation.
    DOI:  https://doi.org/10.1016/j.cub.2023.10.066
  29. Autophagy Rep. 2022 ;1(1): 219-222
    A novel viral regulatory network for autophagy induction: Respiratory Syncytial Virus NS2 protein regulates autophagy by modulating BECN1 ISGylation and protein stability.
    Kim Chiok, Santanu Bose.
      Respiratory syncytial virus, or RSV, is a leading cause of viral pneumonia and bronchiolitis in children and other susceptible populations. RSV infection dysregulates the immune response leading to exaggerated inflammation in the airway. Among other responses, RSV induces macroautophagy/autophagy, a key process that regulates immune response during infection. We investigated the molecular mechanisms underlying RSV-induced autophagy and showed that the RSV nonstructural NS2 protein promotes autophagy using a dual mechanism. First, NS2 interacts with and stabilizes the autophagy regulator BECN1 (beclin 1), augmenting its intracellular availability for autophagy induction. Second, NS2 interferes with BECN1 ISGylation, thus restricting the intracellular pool of the anti-autophagy ISGylated form of BECN1. Thus, the viral protein (i.e., NS2)-autophagy-ISGylation axis represents a yet unknown regulatory network for viruses. As many viruses induce autophagy that shapes virus-associated immune responses including inflammation, exploring viral protein-autophagy-ISGylation regulatory networks can aid in developing interventions to curb exaggerated immune responses such as inflammation for treating virus-associated inflammatory diseases.
    Keywords:  Autophagy; Beclin1; ISGylation; NS2; dysregulation; proteasomal degradation; respiratory syncytial virus
    DOI:  https://doi.org/10.1080/27694127.2022.2076769
  30. Autophagy Rep. 2022 ;1(1): 238-241
    The link between inhibition of PI3K signaling, induction of autophagy, and elimination of organelles to form the lens organelle-free zone.
    A Sue Menko.
      
    Keywords:  AKT; PI3K; autophagy; development; differentiation; lens; nuclei; organelle free zone (OFZ); organelles; signaling
    DOI:  https://doi.org/10.1080/27694127.2022.2080315
  31. Exp Cell Res. 2023 Dec 18. pii: S0014-4827(23)00444-5. [Epub ahead of print] 113893
    Fluvastatin prevents lung metastasis in triple-negative breast cancer by triggering autophagy via the RhoB/PI3K/mTOR pathway.
    Wen-Huan Xu, Ting Zhang, Yunhai Zhou, Yong Mao.
      Triple-negative breast cancer is more common among younger than older women and is associated with the poorest survival outcomes of all breast cancer types. Fluvastatin inhibits tumour progression and induces the autophagy of breast cancer cells; however, the role of autophagy in fluvastatin-induced inhibition of breast cancer metastasis is unknown. Therefore, this study aimed to determine this mechanism. The effect of fluvastatin on human hormone receptor-negative breast cancer cells was evaluated in vitro via migration and wound healing assays, western blotting, and morphological measurements, as well as in vivo using a mouse xenograft model. Chloroquine, a prophylactic medication used to prevent malaria in humans was used as an autophagy inhibitor. We found that fluvastatin administration effectively prevented the migration/invasion of triple-negative breast cancer cells, an effect that was largely dependent on the induction of autophagy. Administration of the autophagy inhibitor chloroquine prevented the fluvastatin-induced suppression of lung metastasis in the nude mouse model. Furthermore, fluvastatin increased Ras homolog family member B (RhoB) expression, and the autophagy and anti-metastatic activity induced by fluvastatin were predominantly dependent on the regulation of RhoB through the protein kinase B-mammalian target of rapamycin (Akt-mTOR) signaling pathway. These results suggest that fluvastatin inhibits the metastasis of triple-negative breast cancer cells by modulating autophagy via the up regulation of RhoB through the AKT-mTOR signaling pathway. Fluvastatin may be a promising therapeutic option for patients with triple-negative breast cancer.
    Keywords:  Autophagy; Fluvastatin; Metastasis; RhoB; Triple-negative breast cancer
    DOI:  https://doi.org/10.1016/j.yexcr.2023.113893
  32. J Neurol Sci. 2023 Dec 17. pii: S0022-510X(23)02307-9. [Epub ahead of print]456 122845
    Aggregation of E121K mutant D-amino acid oxidase and ubiquitination-mediated autophagy mechanisms leading to amyotrophic lateral sclerosis.
    Upma Dave, Priyam Narain, Dibyakanti Mishra, James Gomes.
      Amyotrophic Lateral Sclerosis (ALS) is a terminal adult-onset neuromuscular disorder. Our group has been studying this illness and previously reported novel mutations and rare mutations in a study using next-generation sequencing of DNA samples from Indian ALS patients. In this paper, we focus on the E121K mutation in the DAO gene to understand how it leads to ALS. Our experiments in SH-SY5Y cells indicate that the E121K mutation results in the accumulation of mutant protein aggregates, a change in cell morphology, and the death of neuronal cells. These protein aggregates get ubiquitinated and cause an imbalance in autophagy regulation. We observed an increase in the cellular concentrations of p62, OPTN, and LC3II. Through confocal microscopy studies, we show that the binding of p62 with ubiquitinated aggregates and its recruitment to LC3II mediates autophagosome generation. These relative changes in the key partners in autophagy increase cell death in cells harboring the E121K mutation and is a probable mechanism leading to ALS.
    Keywords:  ALS; Aggregation; Autophagy; DAO mutation; Ubiquitination
    DOI:  https://doi.org/10.1016/j.jns.2023.122845
  33. Bioorg Chem. 2023 Dec 19. pii: S0045-2068(23)00700-9. [Epub ahead of print]143 107039
    Recent advances of vacuolar protein-sorting 34 inhibitors targeting autophagy.
    Long Chen, Tian Gao, Pijun Zhou, Wenxuan Xia, Hong Yao, Shengtao Xu, Jinyi Xu.
      Autophagy is a ubiquitous pathological/physiological antioxidant cellular reaction in eukaryotic cells. Vacuolar protein sorting 34 (Vps34 or PIK3C3), which plays a crucial role in autophagy, has received much attention. As the only Class III phosphatidylinositol-3 kinase in mammals, Vps34 participates in vesicular transport, nutrient signaling and autophagy. Dysfunctionality of Vps34 induces carcinogenesis, and abnormal autophagy mediated by dysfunction of Vps34 is closely related to the pathological progression of various human diseases, which makes Vps34 a novel target for tumor immunotherapy. In this review, we summarize the molecular mechanisms underlying macroautophagy, and further discuss the structure-activity relationship of Vps34 inhibitors that have been reported in the past decade as well as their potential roles in anticancer immunotherapy to better understand the antitumor mechanism underlying the effects of these inhibitors.
    Keywords:  Autolysosome; Autophagy; Mechanism; Tumor immunotherapy; Vps34 inhibitors
    DOI:  https://doi.org/10.1016/j.bioorg.2023.107039
  34. Chem Sci. 2023 Dec 20. 15(1): 102-112
    Unveiling autophagy and aging through time-resolved imaging of lysosomal polarity with a delayed fluorescent emitter.
    Subhadeep Das, Abhilasha Batra, Subhankar Kundu, Rati Sharma, Abhijit Patra.
      Detecting the lysosomal microenvironmental changes like viscosity, pH, and polarity during their dynamic interorganelle interactions remains an intriguing area that facilitates the elucidation of cellular homeostasis. The subtle variation of physiological conditions can be assessed by deciphering the lysosomal microenvironments during lysosome-organelle interactions, closely related to autophagic pathways leading to various cellular disorders. Herein, we shed light on the dynamic lysosomal polarity in live cells and a multicellular model organism, Caenorhabditis elegans (C. elegans), through time-resolved imaging employing a thermally activated delayed fluorescent probe, DC-Lyso. The highly photostable and cytocompatible DC-Lyso rapidly labels the lysosomes (within 1 min of incubation) and exhibits red luminescence and polarity-sensitive long lifetime under the cellular environment. The distinct variation in the fluorescence lifetime of DC-Lyso suggests an increase in local polarity during the lysosomal dynamics and interorganelle interactions, including lipophagy and mitophagy. The lifetime imaging analysis reveals increasing lysosomal polarity as an indicator for probing the successive development of C. elegans during aging. The in vivo microsecond timescale imaging of various cancerous cell lines and C. elegans, as presented here, therefore, expands the scope of delayed fluorescent emitters for unveiling complex biological processes.
    DOI:  https://doi.org/10.1039/d3sc02450d
  35. Cells. 2023 Dec 13. pii: 2826. [Epub ahead of print]12(24):
    Cholesteryl Hemiazelate Present in Cardiovascular Disease Patients Causes Lysosome Dysfunction in Murine Fibroblasts.
    Elizeth Lopes, Gisela Machado-Oliveira, Catarina Guerreiro Simões, Inês S Ferreira, Cristiano Ramos, José Ramalho, Maria I L Soares, Teresa M V D Pinho E Melo, Rosa Puertollano, André R A Marques, Otília V Vieira.
      There is growing evidence supporting the role of fibroblasts in all stages of atherosclerosis, from the initial phase to fibrous cap and plaque formation. In the arterial wall, as with macrophages and vascular smooth muscle cells, fibroblasts are exposed to a myriad of LDL lipids, including the lipid species formed during the oxidation of their polyunsaturated fatty acids of cholesteryl esters (PUFA-CEs). Recently, our group identified the final oxidation products of the PUFA-CEs, cholesteryl hemiesters (ChE), in tissues from cardiovascular disease patients. Cholesteryl hemiazelate (ChA), the most prevalent lipid of this family, is sufficient to impact lysosome function in macrophages and vascular smooth muscle cells, with consequences for their homeostasis. Here, we show that the lysosomal compartment of ChA-treated fibroblasts also becomes dysfunctional. Indeed, fibroblasts exposed to ChA exhibited a perinuclear accumulation of enlarged lysosomes full of neutral lipids. However, this outcome did not trigger de novo lysosome biogenesis, and only the lysosomal transcription factor E3 (TFE3) was slightly transcriptionally upregulated. As a consequence, autophagy was inhibited, probably via mTORC1 activation, culminating in fibroblasts' apoptosis. Our findings suggest that the impairment of lysosome function and autophagy and the induction of apoptosis in fibroblasts may represent an additional mechanism by which ChA can contribute to the progression of atherosclerosis.
    Keywords:  atherosclerosis; autophagy and apoptosis; cholesteryl hemiazelate; cholesteryl hemiesters; lysosome dysfunction; mouse embryonic fibroblasts
    DOI:  https://doi.org/10.3390/cells12242826
  36. Biol Direct. 2023 Dec 20. 18(1): 86
    Quinolinic acid impairs mitophagy promoting microglia senescence and poor healthspan in C. elegans: a mechanism of impaired aging process.
    Anjila Dongol, Xi Chen, Peng Zheng, Zehra Boz Seyhan, Xu-Feng Huang.
      Senescent microglia are a distinct microglial phenotype present in aging brain that have been implicated in the progression of aging and age-related neurodegenerative diseases. However, the specific mechanisms that trigger microglial senescence are largely unknown. Quinolinic acid (QA) is a cytotoxic metabolite produced upon abnormal activation of microglia. Brain aging and age-related neurodegenerative diseases have an elevated concentration of QA. In the present study, we investigated whether QA promotes aging and aging-related phenotypes in microglia and C. elegans. Here, we demonstrate for the first time that QA, secreted by abnormal microglial stimulation, induces impaired mitophagy by inhibiting mitolysosome formation and consequently promotes the accumulation of damaged mitochondria due to reduced mitochondrial turnover in microglial cells. Defective mitophagy caused by QA drives microglial senescence and poor healthspan in C. elegans. Moreover, oxidative stress can mediate QA-induced mitophagy impairment and senescence in microglial cells. Importantly, we found that restoration of mitophagy by mitophagy inducer, urolithin A, prevents microglial senescence and improves healthspan in C. elegans by promoting mitolysosome formation and rescuing mitochondrial turnover inhibited by QA. Thus, our study indicates that mitolysosome formation impaired by QA is a significant aetiology underlying aging-associated changes. QA-induced mitophagy impairment plays a critical role in neuroinflammation and age-related diseases. Further, our study suggests that mitophagy inducers such as urolithin A may offer a promising anti-aging strategy for the prevention and treatment of neuroinflammation-associated brain aging diseases.
    Keywords:  Aging; Microglia; Mitochondria; Mitolysosome; Mitophagy; Neuroinflammation; Quinolinic acid; Senescence
    DOI:  https://doi.org/10.1186/s13062-023-00445-y
  37. Neural Regen Res. 2024 Aug 01. 19(8): 1828-1834
    A novel mechanism of PHB2-mediated mitophagy participating in the development of Parkinson's disease.
    Yongjiang Zhang, Shiyi Yin, Run Song, Xiaoyi Lai, Mengmeng Shen, Jiannan Wu, Junqiang Yan.
      JOURNAL/nrgr/04.03/01300535-202408000-00037/figure1/v/2023-12-16T180322Z/r/image-tiff Endoplasmic reticulum stress and mitochondrial dysfunction play important roles in Parkinson's disease, but the regulatory mechanism remains elusive. Prohibitin-2 (PHB2) is a newly discovered autophagy receptor in the mitochondrial inner membrane, and its role in Parkinson's disease remains unclear. Protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK) is a factor that regulates cell fate during endoplasmic reticulum stress. Parkin is regulated by PERK and is a target of the unfolded protein response. It is unclear whether PERK regulates PHB2-mediated mitophagy through Parkin. In this study, we established a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced mouse model of Parkinson's disease. We used adeno-associated virus to knockdown PHB2 expression. Our results showed that loss of dopaminergic neurons and motor deficits were aggravated in the MPTP-induced mouse model of Parkinson's disease. Overexpression of PHB2 inhibited these abnormalities. We also established a 1-methyl-4-phenylpyridine (MPP+)-induced SH-SY5Y cell model of Parkinson's disease. We found that overexpression of Parkin increased co-localization of PHB2 and microtubule-associated protein 1 light chain 3, and promoted mitophagy. In addition, MPP+ regulated Parkin involvement in PHB2-mediated mitophagy through phosphorylation of PERK. These findings suggest that PHB2 participates in the development of Parkinson's disease by interacting with endoplasmic reticulum stress and Parkin.
    DOI:  https://doi.org/10.4103/1673-5374.389356
  38. FEBS Lett. 2023 Dec 15.
    Autophagy as an innate immunity response against pathogens: a Tango dance.
    Milton O Aguilera, Laura R Delgui, Fulvio Reggiori, Patricia S Romano, María I Colombo.
      Intracellular infections as well as changes in the cell nutritional environment are main events that trigger cellular stress responses. One crucial cell response to stress conditions is autophagy. During the last 30 years, several scenarios involving autophagy induction or inhibition over the course of an intracellular invasion by pathogens have been uncovered. In this review, we will present how this knowledge was gained by studying different microorganisms. We intend to discuss how the cell, via autophagy, tries to repel these attacks with the objective of destroying the intruder, but also how some pathogens have developed strategies to subvert this. These two fates can be compared with a Tango, a dance originated in Buenos Aires, Argentina, in which the partner dancers are in close connection. One of them is the leader, embracing and involving the partner, but the follower may respond escaping from the leader. This joint dance is indeed highly synchronized and controlled, perfectly reflecting the interaction between autophagy and microorganism.
    Keywords:  ATG; LC3; LAP; autophagy; intracellular microorganisms; invading bacteria; parasites; viruses
    DOI:  https://doi.org/10.1002/1873-3468.14788
  39. Biomolecules. 2023 Dec 13. pii: 1789. [Epub ahead of print]13(12):
    Mitochondrial Quality Control via Mitochondrial Unfolded Protein Response (mtUPR) in Ageing and Neurodegenerative Diseases.
    Paula Cilleros-Holgado, David Gómez-Fernández, Rocío Piñero-Pérez, Jose Manuel Romero-Domínguez, Diana Reche-López, Alejandra López-Cabrera, Mónica Álvarez-Córdoba, Manuel Munuera-Cabeza, Marta Talaverón-Rey, Alejandra Suárez-Carrillo, Ana Romero-González, Jose Antonio Sánchez-Alcázar.
      Mitochondria play a key role in cellular functions, including energy production and oxidative stress regulation. For this reason, maintaining mitochondrial homeostasis and proteostasis (homeostasis of the proteome) is essential for cellular health. Therefore, there are different mitochondrial quality control mechanisms, such as mitochondrial biogenesis, mitochondrial dynamics, mitochondrial-derived vesicles (MDVs), mitophagy, or mitochondrial unfolded protein response (mtUPR). The last item is a stress response that occurs when stress is present within mitochondria and, especially, when the accumulation of unfolded and misfolded proteins in the mitochondrial matrix surpasses the folding capacity of the mitochondrion. In response to this, molecular chaperones and proteases as well as the mitochondrial antioxidant system are activated to restore mitochondrial proteostasis and cellular function. In disease contexts, mtUPR modulation holds therapeutic potential by mitigating mitochondrial dysfunction. In particular, in the case of neurodegenerative diseases, such as primary mitochondrial diseases, Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), Amyotrophic Lateral Sclerosis (ALS), or Friedreich's Ataxia (FA), there is a wealth of evidence demonstrating that the modulation of mtUPR helps to reduce neurodegeneration and its associated symptoms in various cellular and animal models. These findings underscore mtUPR's role as a promising therapeutic target in combating these devastating disorders.
    Keywords:  ageing; mitochondria; mitochondrial biogenesis; mitochondrial diseases; mitochondrial dynamics; mitochondrial quality control mechanisms; mitochondrial unfolded protein response (mtUPR); mitophagy; neurodegenerative diseases; therapeutic target
    DOI:  https://doi.org/10.3390/biom13121789
  40. J Clin Invest. 2023 Dec 21. pii: e172116. [Epub ahead of print]
    Hyperactive mTORC1 in lung mesenchyme induces endothelial cell dysfunction and pulmonary vascular remodeling.
    Susan M Lin, Ryan Rue, Alexander R Mukhitov, Akansha Goel, Maria C Basil, Kseniya Obraztsova, Apoorva Babu, Slaven Crnkovic, Owen Ledwell, Laura T Ferguson, Joseph D Planer, Ana N Nottingham, Kanth Swaroop Vanka, Carly J Smith, Edward Cantu Iii, Grazyna Kwapiszewska, Edward E Morrisey, Jillian F Evans, Vera P Krymskaya.
      Lymphangioleiomyomatosis (LAM) is a progressive cystic lung disease caused by tuberous sclerosis complex 1/2 (TSC1/2) gene mutations in pulmonary mesenchymal cells resulting in activation of the mechanistic target of rapamycin complex 1 (mTORC1). A subset of LAM patients develops pulmonary vascular remodeling and pulmonary hypertension. Little, however, is known regarding how LAM cells communicate with endothelial cells (ECs) to trigger vascular remodeling. In end-stage LAM lung explants, we identified endothelial cell dysfunction characterized by increased proliferation, migration, defective angiogenesis, and dysmorphic endothelial tube network formation. To model LAM disease, we utilized an mTORC1 gain-of-function mouse model with a Tsc2 knock-out (Tsc2KO) specific to lung mesenchyme (Tbx4LME-CreTsc2fl/fl), similar to the mesenchyme specific genetic alterations seen in human disease. As early as 8 weeks of age, ECs from Tbx4LME-CreTsc2fl/fl mice exhibited marked transcriptomic changes despite absence of morphological changes to the distal lung microvasculature. In contrast, 1 year old Tbx4LME-CreTsc2fl/fl mice spontaneously developed pulmonary vascular remodeling with increased medial thickness. Single cell RNA-sequencing of 1 year old mouse lung identified paracrine ligands originating from Tsc2KO mesenchyme which can signal through receptors in arterial ECs. These ECs had transcriptionally altered genes including those in pathways associated with blood vessel remodeling. The proposed pathophysiologic mesenchymal ligand/ EC receptor crosstalk highlights the importance of an altered mesenchymal-EC axis in LAM and other hyperactive mTORC1-driven diseases. Since ECs in LAM patients and in Tbx4LME-CreTsc2fl/fl mice do not harbor TSC2 mutations, our study demonstrates that constitutively active mTORC1 lung mesenchymal cells orchestrate dysfunctional EC responses which contribute to pulmonary vascular remodeling.
    Keywords:  Cell Biology; Endothelial cells; Mouse models; Vascular Biology
    DOI:  https://doi.org/10.1172/JCI172116
  41. Cardiovasc Toxicol. 2023 Dec 18.
    The Role of mTOR in Doxorubicin-Altered Cardiac Metabolism: A Promising Therapeutic Target of Natural Compounds.
    Fatemeh Yarmohammadi, Mahvash Hesari, Dareuosh Shackebaei.
      Doxorubicin (DOX) is commonly used for the treatment of various types of cancer, however can cause serious side effects, including cardiotoxicity. The mechanisms involved in DOX-induced cardiac damage are complex and not yet fully understood. One mechanism is the disruption of cardiac metabolism, which can impair cardiac function. The mammalian target of rapamycin (mTOR) is a key regulator of cardiac energy metabolism, and dysregulation of mTOR signaling has been implicated in DOX-induced cardiac dysfunction. Natural compounds (NCs) have been shown to improve cardiac function in vivo and in vitro models of DOX-induced cardiotoxicity. This review article explores the protective effects of NCs against DOX-induced cardiac injury, with a focus on their regulation of mTOR signaling pathways. Generally, the modulation of mTOR signaling by NCs represents a promising strategy for decreasing the cardiotoxic effects of DOX.
    Keywords:  Autophagy; Cardiotoxicity; Doxorubicin; mTORC1; mTORC2
    DOI:  https://doi.org/10.1007/s12012-023-09820-7
  42. J Med Chem. 2023 Dec 20.
    Identification of a Dual Autophagy and REV-ERB Inhibitor with in Vivo Anticancer Efficacy.
    Martina Palomba, Donatella Vecchio, Giulia Allavena, Vito Capaccio, Claudia De Mei, Rita Scarpelli, Benedetto Grimaldi.
      The autophagy process appears as a promising target for anticancer interventions. Chloroquine (CQ) and its derivative hydroxychloroquine (HCQ) are the only FDA-approved autophagy flux inhibitors. Although diverse anticancer clinical trials are providing encouraging results, several limitations associated with the need of high dosage and long-term administration of these autophagy inhibitors are also emerging. We showed that the inhibition of REV-ERB, a nuclear receptor regulating circadian rhythm and metabolism, enhances CQ-mediated cancer cell death and identified a class of dual inhibitors of autophagy and REV-ERB displaying an in vitro anticancer activity against diverse tumor cells greatly higher than CQ. Herein, we describe our lead optimization strategy that led to the identification of compound 24 as a dual autophagy and REV-ERB inhibitor, showing improved potency in blocking autophagy, enhanced toxicity against cancer cells, optimal drug-like properties, and efficacy in a mouse xenograft model of melanoma as a single anticancer agent.
    DOI:  https://doi.org/10.1021/acs.jmedchem.3c01432
  43. Antioxidants (Basel). 2023 Nov 21. pii: 2021. [Epub ahead of print]12(12):
    Niemann-Pick Disease Type C (NPDC) by Mutation of NPC1 and NPC2: Aberrant Lysosomal Cholesterol Trafficking and Oxidative Stress.
    Dongun Lee, Jeong Hee Hong.
      Cholesterol trafficking is initiated by the endocytic pathway and transported from endo/lysosomes to other intracellular organelles. Deficiencies in cholesterol-sensing and binding proteins NPC1 and NPC2 induce accumulation in lysosomes and the malfunction of trafficking to other organelles. Each organelle possesses regulatory factors to induce cholesterol trafficking. The mutation of NPC1 and NPC2 genes induces Niemann-Pick disease type C (NPDC), which is a hereditary disease and causes progressive neurodegeneration, developmental disability, hypotonia, and ataxia. Oxidative stress induces damage in NPDC-related intracellular organelles. Although studies on the relationship between NPDC and oxidation are relatively rare, several studies have reported the therapeutic potential of antioxidants in treating NPDC. Investigating antioxidant drugs to relieve oxidative stress and cholesterol accumulation is suggested to be a powerful tool for developing treatments for NPDC. Understanding NPDC provides challenging issues in understanding the oxidative stress-lysosome metabolism of the lipid axis. Thus, we elucidated the relationship between complexes of intracellular organelles and NPDC to develop our knowledge and suggested potential antioxidant reagents for NPDC therapy.
    Keywords:  Niemann-Pick disease type C; cholesterol trafficking; lysosomal proteins; lysosomal storage disorders; oxidative stress
    DOI:  https://doi.org/10.3390/antiox12122021
  44. bioRxiv. 2023 Dec 08. pii: 2023.12.08.570852. [Epub ahead of print]
    Host autophagy is exploited by the intracellular parasite Toxoplasma gondii to enhance amino acids levels.
    Matthew D White, Rajendra K Angara, Leticia Torres Dias, Dhananjay D Shinde, Vinai C Thomas, Leonardo Augusto.
      Toxoplasma gondii, a widespread parasite, has the ability to infect nearly any nucleated cell in warm-blooded vertebrates. It is estimated that around 2 billion people globally have been infected by this pathogen. Although most healthy individuals can effectively control parasite replication, certain parasites may evade the immune response, establishing cysts in the brain that are refractory to the immune system and resistance to available drugs. For its chronic persistence in the brain, the parasite relies on host cells' nutrients, particularly amino acids and lipids. Therefore, understanding how latent parasites persist in the brain is crucial for identifying potential drug targets against chronic forms. While shielded within parasitophorous vacuoles (PVs) or cysts, Toxoplasma exploits the host endoplasmic reticulum (ER) metabolism to sustains its persistence in the brain, resulting in host neurological alterations. In this study, we demonstrate that T. gondii disrupts the host ER homeostasis, resulting in accumulation of unfolded protein with the host ER. The host counters this stress by initiating an autophagic pathway known as ER-phagy, which breaks down unfolded proteins into amino acids, promoting their recycling. Remarkably, the persistence of latent forms in cell culture as well as behavioral changes in mice caused by the latent infection could be successfully reversed by restricting the availability of various amino acids during T. gondi infection. Our findings unveil the underlying mechanisms employed by T. gondii to exploit host ER and lysosomal pathways, enhancing nutrient levels during infection. These insights provide new strategies for the treatment of toxoplasmosis.
    Importance: Intracellular parasites employ several mechanisms to manipulate the cellular environment, enabling them to persist in the host. Toxoplasma gondii , a single-celled parasite, possesses the ability to infect virtually any nucleated cell of warm-blooded vertebrates, including nearly 2 billion people worldwide. Unfortunately, existing treatments and immune responses are not entirely effective in eliminating the chronic persisting forms of the parasite. This study reveals that T. gondii induces the host's autophagic pathway to boost amino acid levels in infected cells. The depletion of amino acids, in turn, influences the persistence of the parasite's chronic forms, resulting in a reduction of neurological alterations caused by chronic infection in mice. Significantly, our investigation establishes the crucial role of host ER-phagy in the parasite's persistence within the host during latent infection.
    DOI:  https://doi.org/10.1101/2023.12.08.570852
  45. Cells. 2023 Dec 07. pii: 2781. [Epub ahead of print]12(24):
    Disruption of Mitophagy Flux through the PARL-PINK1 Pathway by CHCHD10 Mutations or CHCHD10 Depletion.
    Tian Liu, Liam Wetzel, Zexi Zhu, Pavan Kumaraguru, Viraj Gorthi, Yan Yan, Mohammed Zaheen Bukhari, Aizara Ermekbaeva, Hanna Jeon, Teresa R Kee, Jung-A Alexa Woo, David E Kang.
      Coiled-coil-helix-coiled-coil-helix domain-containing 10 (CHCHD10) is a nuclear-encoded mitochondrial protein which is primarily mutated in the spectrum of familial and sporadic amyotrophic lateral sclerosis (ALS)-frontotemporal dementia (FTD). Endogenous CHCHD10 levels decline in the brains of ALS-FTD patients, and the CHCHD10S59L mutation in Drosophila induces dominant toxicity together with PTEN-induced kinase 1 (PINK1), a protein critical for the induction of mitophagy. However, whether and how CHCHD10 variants regulate mitophagy flux in the mammalian brain is unknown. Here, we demonstrate through in vivo and in vitro models, as well as human FTD brain tissue, that ALS/FTD-linked CHCHD10 mutations (R15L and S59L) impair mitophagy flux and mitochondrial Parkin recruitment, whereas wild-type CHCHD10 (CHCHD10WT) normally enhances these measures. Specifically, we show that CHCHD10R15L and CHCHD10S59L mutations reduce PINK1 levels by increasing PARL activity, whereas CHCHD10WT produces the opposite results through its stronger interaction with PARL, suppressing its activity. Importantly, we also demonstrate that FTD brains with TAR DNA-binding protein-43 (TDP-43) pathology demonstrate disruption of the PARL-PINK1 pathway and that experimentally impairing mitophagy promotes TDP-43 aggregation. Thus, we provide herein new insights into the regulation of mitophagy and TDP-43 aggregation in the mammalian brain through the CHCHD10-PARL-PINK1 pathway.
    Keywords:  CHCHD10; PARL; PINK1; TDP-43; mitophagy
    DOI:  https://doi.org/10.3390/cells12242781
  46. Nat Commun. 2023 Dec 18. 14(1): 8393
    Autophagy of OTUD5 destabilizes GPX4 to confer ferroptosis-dependent kidney injury.
    Li-Kai Chu, Xu Cao, Lin Wan, Qiang Diao, Yu Zhu, Yu Kan, Li-Li Ye, Yi-Ming Mao, Xing-Qiang Dong, Qian-Wei Xiong, Ming-Cui Fu, Ting Zhang, Hui-Ting Zhou, Shi-Zhong Cai, Zhou-Rui Ma, Ssu-Wei Hsu, Reen Wu, Ching-Hsien Chen, Xiang-Ming Yan, Jun Liu.
      Ferroptosis is an iron-dependent programmed cell death associated with severe kidney diseases, linked to decreased glutathione peroxidase 4 (GPX4). However, the spatial distribution of renal GPX4-mediated ferroptosis and the molecular events causing GPX4 reduction during ischemia-reperfusion (I/R) remain largely unknown. Using spatial transcriptomics, we identify that GPX4 is situated at the interface of the inner cortex and outer medulla, a hyperactive ferroptosis site post-I/R injury. We further discover OTU deubiquitinase 5 (OTUD5) as a GPX4-binding protein that confers ferroptosis resistance by stabilizing GPX4. During I/R, ferroptosis is induced by mTORC1-mediated autophagy, causing OTUD5 degradation and subsequent GPX4 decay. Functionally, OTUD5 deletion intensifies renal tubular cell ferroptosis and exacerbates acute kidney injury, while AAV-mediated OTUD5 delivery mitigates ferroptosis and promotes renal function recovery from I/R injury. Overall, this study highlights a new autophagy-dependent ferroptosis module: hypoxia/ischemia-induced OTUD5 autophagy triggers GPX4 degradation, offering a potential therapeutic avenue for I/R-related kidney diseases.
    DOI:  https://doi.org/10.1038/s41467-023-44228-5
  47. Mol Neurobiol. 2023 Dec 22.
    Lnc-HIBADH-4 Regulates Autophagy-Lysosome Pathway in Amyotrophic Lateral Sclerosis by Targeting Cathepsin D.
    Jingxuan Huang, Yujiao Yu, Dejiang Pang, Chunyu Li, Qianqian Wei, Yangfan Cheng, Yiyuan Cui, Ruwei Ou, Huifang Shang.
      Amyotrophic lateral sclerosis (ALS) is the most prevalent and lethal class of severe motor neuron diseases (MND) with no efficacious treatment. The pathogenic mechanisms underlying ALS remain unclear. Nearly 90% of patients exhibit sporadic onset (sALS). Therefore, elucidating the pathophysiology of ALS is imperative. Long non-coding RNA (lncRNA) is a large class of non-coding RNAs that regulate transcription, translation, and post-translational processes. LncRNAs contribute to the pathogenesis of diverse neurodegenerative disorders and hold promise as targets for interference in the realm of neurodegeneration. However, the mechanisms of which lncRNAs are involved in ALS have not been thoroughly investigated. We identified and validated a downregulated lncRNA, lnc-HIBADH-4, in ALS which correlated with disease severity and overall survival. Lnc-HIBADH-4 acted as a "molecular sponge" regulating lysosomal function through the lnc-HIBADH-4/miR-326/CTSD pathway, thereby impacting autophagy-lysosome dynamics and the levels of cell proliferation and apoptosis. Therefore, this study discovered and revealed the role of lnc-HIBADH-4 in the pathogenesis of ALS. With further research, lnc-HIBADH-4 is expected to provide a new biomarker in the diagnosis and treatment of ALS.
    Keywords:  ALS; CTSD; Lnc-HIBADH-4; miR-326
    DOI:  https://doi.org/10.1007/s12035-023-03835-5
  48. Cell Commun Signal. 2023 Dec 15. 21(1): 357
    Neuron-targeted overexpression of caveolin-1 alleviates diabetes-associated cognitive dysfunction via regulating mitochondrial fission-mitophagy axis.
    Wenxin Tang, Chaoying Yan, Shuxuan He, Mengyu Du, Bo Cheng, Bin Deng, Shan Zhu, Yansong Li, Qiang Wang.
       BACKGROUND: Type 2 diabetes mellitus (T2DM) induced diabetes-associated cognitive dysfunction (DACD) that seriously affects the self-management of T2DM patients, is currently one of the most severe T2DM-associated complications, but the mechanistic basis remains unclear. Mitochondria are highly dynamic organelles, whose function refers to a broad spectrum of features such as mitochondrial dynamics, mitophagy and so on. Mitochondrial abnormalities have emerged as key determinants for cognitive function, the relationship between DACD and mitochondria is not well understood.
    METHODS: Here, we explored the underlying mechanism of mitochondrial dysfunction of T2DM mice and HT22 cells treated with high glucose/palmitic acid (HG/Pal) focusing on the mitochondrial fission-mitophagy axis with drug injection, western blotting, Immunofluorescence, and electron microscopy. We further explored the potential role of caveolin-1 (cav-1) in T2DM induced mitochondrial dysfunction and synaptic alteration through viral transduction.
    RESULTS: As previously reported, T2DM condition significantly prompted hippocampal mitochondrial fission, whereas mitophagy was blocked rather than increasing, which was accompanied by dysfunctional mitochondria and impaired neuronal function. By contrast, Mdivi-1 (mitochondrial division inhibitor) and urolithin A (mitophagy activator) ameliorated mitochondrial and neuronal function and thereafter lead to cognitive improvement by inhibiting excessive mitochondrial fission and giving rise to mitophagy, respectively. We have previously shown that cav-1 can significantly improve DACD by inhibiting ferroptosis. Here, we further demonstrated that cav-1 could not only inhibit mitochondrial fission via the interaction with GSK3β to modulate Drp1 pathway, but also rescue mitophagy through interacting with AMPK to activate PINK1/Parkin and ULK1-dependent signlings.
    CONCLUSIONS: Overall, our data for the first time point to a mitochondrial fission-mitophagy axis as a driver of neuronal dysfunction in a phenotype that was exaggerated by T2DM, and the protective role of cav-1 in DACD. Graphic Summary Illustration. In T2DM, excessive mitochondrial fission and impaired mitophagy conspire to an altered mitochondrial morphology and mitochondrial dysfunction, with a consequent neuronal damage, overall suggesting an unbalanced mitochondrial fission-mitophagy axis. Upon cav-1 overexpression, GSK3β and AMPK are phosphorylated respectively to activate Drp1 and mitophagy-related pathways (PINK1 and ULKI), ultimately inhibits mitochondrial fission and enhances mitophagy. In the meantime, the mitochondrial morphology and neuronal function are rescued, indicating the protective role of cav-1 on mitochondrial fission-mitophagy axis. Video Abstract.
    Keywords:  Caveolin-1; Diabetes-associated cognitive dysfunction; Mitochondrial fission; Mitophagy
    DOI:  https://doi.org/10.1186/s12964-023-01328-5
  49. Front Cell Infect Microbiol. 2023 ;13 1289170
    Autophagy as a dual-faced host response to viral infections.
    Huanjie Zhai, Tao Wang, Di Liu, Li Pan, Yuan Sun, Hua-Ji Qiu.
      Autophagy selectively degrades viral particles or cellular components, either facilitating or inhibiting viral replication. Conversely, most viruses have evolved strategies to escape or exploit autophagy. Moreover, autophagy collaborates with the pattern recognition receptor signaling, influencing the expression of adaptor molecules involved in the innate immune response and regulating the expression of interferons (IFNs). The intricate relationship between autophagy and IFNs plays a critical role in the host cell defense against microbial invasion. Therefore, it is important to summarize the interactions between viral infections, autophagy, and the host defense mechanisms against viruses. This review specifically focuses on the interactions between autophagy and IFN pathways during viral infections, providing a comprehensive summary of the molecular mechanisms utilized or evaded by different viruses.
    Keywords:  autophagy; interferons; viral infection; viral replication; viruses
    DOI:  https://doi.org/10.3389/fcimb.2023.1289170
  50. Trends Plant Sci. 2023 Dec 21. pii: S1360-1385(23)00394-1. [Epub ahead of print]
    Memories of heat: autophagy and Golgi recovery.
    Debora Goncalves Gouveia, João Antonio Siqueira, Adriano Nunes-Nesi, Wagner L Araújo.
      Fluctuations in temperature severely impact crop yield and trigger various plant response mechanisms. In a recent study, Zhou et al. discovered a non-canonical role of autophagy in mediating Golgi apparatus restoration after short-term heat stress (HS). Their results further suggest a critical, yet previously unknown, mechanism of autophagy-related (ATG)-8 in Golgi reassembly after HS.
    Keywords:  climate change; heat stress; stress response
    DOI:  https://doi.org/10.1016/j.tplants.2023.12.009
  51. Trends Pharmacol Sci. 2023 Dec 14. pii: S0165-6147(23)00257-2. [Epub ahead of print]
    Pharmacological targets at the lysosomal autophagy-NLRP3 inflammasome crossroads.
    Srinivasa Reddy Bonam, Dylan Mastrippolito, Philippe Georgel, Sylviane Muller.
      Many aspects of cell homeostasis and integrity are maintained by the nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) family pyrin domain-containing 3 (NLRP3) inflammasome. The NLRP3 oligomeric protein complex assembles in response to exogenous and endogenous danger signals. This inflammasome has also been implicated in the pathogenesis of a range of disease conditions, particularly chronic inflammatory diseases. Given that NLRP3 modulates autophagy, which is also a key regulator of inflammasome activity, excessive inflammation may be controlled by targeting this intersecting pathway. However, specific niche areas of NLRP3-autophagy interactions and their reciprocal regulatory mechanisms remain underexplored. Consequently, we lack treatment methods specifically targeting this pivotal axis. Here, we discuss the potential of such strategies in the context of autoimmune and metabolic diseases and propose some research avenues.
    Keywords:  NLRP3 inflammasome–autophagy regulation; drugs; low-grade systemic inflammation; lysosomal dysfunction
    DOI:  https://doi.org/10.1016/j.tips.2023.11.005
  52. Dev Cell. 2023 Dec 08. pii: S1534-5807(23)00615-9. [Epub ahead of print]
    D-Mannose reduces cellular senescence and NLRP3/GasderminD/IL-1β-driven pyroptotic uroepithelial cell shedding in the murine bladder.
    Chetanchandra S Joshi, Arnold M Salazar, Caihong Wang, Marianne M Ligon, Rayvanth R Chappidi, Bisiayo E Fashemi, Paul A Felder, Amy Mora, Sandra L Grimm, Cristian Coarfa, Indira U Mysorekar.
      Aging is a risk factor for disease via increased susceptibility to infection, decreased ability to maintain homeostasis, inefficiency in combating stress, and decreased regenerative capacity. Multiple diseases, including urinary tract infection (UTI), are more prevalent with age; however, the mechanisms underlying the impact of aging on the urinary tract mucosa and the correlation between aging and disease remain poorly understood. Here, we show that, relative to young (8-12 weeks) mice, the urothelium of aged (18-24 months) female mice accumulates large lysosomes with reduced acid phosphatase activity and decreased overall autophagic flux in the aged urothelium, indicative of compromised cellular homeostasis. Aged bladders also exhibit basal accumulation of reactive oxygen species (ROS) and a dampened redox response, implying heightened oxidative stress. Furthermore, we identify a canonical senescence-associated secretory phenotype (SASP) in the aged urothelium, along with continuous NLRP3-inflammasome- and Gasdermin-D-dependent pyroptotic cell death. Consequently, aged mice chronically exfoliate urothelial cells, further exacerbating age-related urothelial dysfunction. Upon infection with uropathogenic E. coli, aged mice harbor increased bacterial reservoirs and are more prone to spontaneous recurrent UTI. Finally, we discover that treatment with D-mannose, a natural bioactive monosaccharide, rescues autophagy flux, reverses the SASP, and mitigates ROS and NLRP3/Gasdermin/interleukin (IL)-1β-driven pyroptotic epithelial cell shedding in aged mice. Collectively, our results demonstrate that normal aging affects bladder physiology, with aging alone increasing baseline cellular stress and susceptibility to infection, and suggest that mannose supplementation could serve as a senotherapeutic to counter age-associated urothelial dysfunction.
    Keywords:  D-mannose; NLRP3; SASP; UTI; autophagy; pyroptosis; reactive oxygen species; senotherapeutic; uropathogenic E. coli
    DOI:  https://doi.org/10.1016/j.devcel.2023.11.017
  53. Biomolecules. 2023 Dec 15. pii: 1799. [Epub ahead of print]13(12):
    Impaired Autophagic Clearance with a Gain-of-Function Variant of the Lysosomal Cl-/H+ Exchanger ClC-7.
    Shroddha Bose, Cecilia de Heus, Mary E Kennedy, Fan Wang, Thomas J Jentsch, Judith Klumperman, Tobias Stauber.
      ClC-7 is a ubiquitously expressed voltage-gated Cl-/H+ exchanger that critically contributes to lysosomal ion homeostasis. Together with its β-subunit Ostm1, ClC-7 localizes to lysosomes and to the ruffled border of osteoclasts, where it supports the acidification of the resorption lacuna. Loss of ClC-7 or Ostm1 leads to osteopetrosis accompanied by accumulation of storage material in lysosomes and neurodegeneration. Interestingly, not all osteopetrosis-causing CLCN7 mutations from patients are associated with a loss of ion transport. Some rather result in an acceleration of voltage-dependent ClC-7 activation. Recently, a gain-of-function variant, ClC-7Y715C, that yields larger ion currents upon heterologous expression, was identified in two patients with neurodegeneration, organomegaly and albinism. However, neither the patients nor a mouse model that carried the equivalent mutation developed osteopetrosis, although expression of ClC-7Y715C induced the formation of enlarged intracellular vacuoles. Here, we investigated how, in transfected cells with mutant ClC-7, the substitution of this tyrosine impinged on the morphology and function of lysosomes. Combinations of the tyrosine mutation with mutations that either uncouple Cl- from H+ counter-transport or strongly diminish overall ion currents were used to show that increased ClC-7 Cl-/H+ exchange activity is required for the formation of enlarged vacuoles by membrane fusion. Degradation of endocytosed material was reduced in these compartments and resulted in an accumulation of lysosomal storage material. In cells expressing the ClC-7 gain-of-function mutant, autophagic clearance was largely impaired, resulting in a build-up of autophagic material.
    Keywords:  ClC-7; Ostm1; autophagy; chloride/proton exchange; endo-lysosomes; lysosomal storage disorder; osmotic pressure
    DOI:  https://doi.org/10.3390/biom13121799
  54. Biomed Pharmacother. 2023 Dec 14. pii: S0753-3322(23)01665-7. [Epub ahead of print]170 115867
    Dual targeting agent Thiotert inhibits the progression of glioblastoma by inducing ER stress-dependent autophagy.
    Jianhong Dong, Yiming Qian, Wei Zhang, Qian Wang, Mengxian Jia, Juanqing Yue, Ziwei Fan, Yuanyuan Jiang, Lipei Wang, Yongjie Wang, Zhihui Huang, Lushan Yu, Ying Wang.
      Glioblastoma (GBM) is the most aggressive and lethal type of tumor in the central nervous system, characterized by a high incidence and poor prognosis. Thiotert, as a novel dual targeting agent, has potential inhibitory effects on various tumors. Here, we found that Thiotert effectively inhibited the proliferation of GBM cells by inducing G2/M cell cycle arrest and suppressed the migratory ability in vitro. Furthermore, Thiotert disrupted the thioredoxin (Trx) system while causing cellular DNA damage, which in turn caused endoplasmic reticulum (ER) stress-dependent autophagy. Knockdown of ER stress-related protein ATF4 in U251 cells inhibited ER stress-dependent autophagy caused by Thiotert to some extent. Orthotopic transplantation experiments further showed that Thiotert had the same anti-GBM activity and mechanism as in vitro. Conclusively, these results suggest that Thiotert induces ER stress-dependent autophagy in GBM cells by disrupting redox homeostasis and causing DNA damage, which provides new insight for the treatment of GBM.
    Keywords:  Autophagy; DNA damage; ER stress; GBM; Thiotert; Trx system
    DOI:  https://doi.org/10.1016/j.biopha.2023.115867
  55. Cell Biosci. 2023 Dec 22. 13(1): 232
    NUAK1 coordinates growth factor-dependent activation of mTORC2 and Akt signaling.
    Mario Palma, Elizabeth Riffo, Alejandro Farias, Viviana Coliboro-Dannich, Luis Espinoza-Francine, Emilia Escalona, Roberto Amigo, José L Gutiérrez, Roxana Pincheira, Ariel F Castro.
       BACKGROUND: mTORC2 is a critical regulator of cytoskeleton organization, cell proliferation, and cancer cell survival. Activated mTORC2 induces maximal activation of Akt by phosphorylation of Ser-473, but regulation of Akt activity and signaling crosstalk upon growth factor stimulation are still unclear.
    RESULTS: We identified that NUAK1 regulates growth factor-dependent activation of Akt by two mechanisms. NUAK1 interacts with mTORC2 components and regulates mTORC2-dependent activation of Akt by controlling lysosome positioning and mTOR association with this organelle. A second mechanism involves NUAK1 directly phosphorylating Akt at Ser-473. The effect of NUAK1 correlated with a growth factor-dependent activation of specific Akt substrates. NUAK1 induced the Akt-dependent phosphorylation of FOXO1/3a (Thr-24/Thr-32) but not of TSC2 (Thr-1462). According to a subcellular compartmentalization that could explain NUAK1's differential effect on the Akt substrates, we found that NUAK1 is associated with early endosomes but not with plasma membrane, late endosomes, or lysosomes. NUAK1 was required for the Akt/FOXO1/3a axis, regulating p21CIP1, p27KIP1, and FoxM1 expression and cancer cell survival upon EGFR stimulation. Pharmacological inhibition of NUAK1 potentiated the cell death effect induced by Akt or mTOR pharmacological blockage. Analysis of human tissue data revealed that NUAK1 expression positively correlates with EGFR expression and Akt Ser-473 phosphorylation in several human cancers.
    CONCLUSIONS: Our results showed that NUAK1 kinase controls mTOR subcellular localization and induces Akt phosphorylation, demonstrating that NUAK1 regulates the growth factor-dependent activation of Akt signaling. Therefore, targeting NUAK1, or co-targeting it with Akt or mTOR inhibitors, may be effective in cancers with hyperactivated Akt signaling.
    Keywords:  Akt; Cancer signaling; Co-targeting; NUAK1; mTORC2
    DOI:  https://doi.org/10.1186/s13578-023-01185-2
  56. Intervirology. 2023 Dec 15.
    GSK-3β as a potential coordinator of anabolic and catabolic pathways in hepatitis C virus insulin resistance.
    F Blaine Hollinger, Gokul C Das.
       INTRODUCTION: Chronic HCV infection results in insulin resistance (IR) through interaction of pathways for glucose homeostasis, insulin signaling, and autophagy. Not known is how soon the pathways are activated, and how IR is related to the signals generated by catabolic and anabolic conditions occurring in infected cells. We have extended our studies to a cell culture system mimicking acute infection and to downstream pathways involving energy-sensor AMPK and nutrient-sensor mTOR that are active in catabolic and anabolic processes within the infected cells.
    METHODS: Huh7 liver cells were infected with HCV. We performed proteomics analysis of key proteins in infected cells by western blotting and IP experiments, with or without interferon-α exposure.
    RESULTS: We show that IRS-1 Ser312, Beclin-1, protein conjugate Atg12-Atg5 or GS Ser641 are upregulated early in infection by activating the same pathways utilized for persistent infection; Bcl-XL, an inhibitor of both autophagy and apoptosis, is present in a core-complex with IRS-1 Ser312 and Beclin-1 during progression of IR; AMPK level remains the same in infected cells where it is activated by phosphorylation at Thr172 concomitant with increased autophagy, a hallmark of catabolic conditions; an mTOR level that promotes anabolism is increased rather than decreased under an expanded autophagy; hypophosphorylation of translational repressor 4E-BP1 downstream of mTOR is suggestive of reduced protein synthesis; and β-catenin is upregulated but not phosphorylated suggesting indirectly our previous contention that its kinase, GSK-3β, is mostly in an inactive state.
    DISCUSSION/CONCLUSION: We report that in the development of IR following chronic infection, anabolic and catabolic pathways are activated early, and the metabolic interaction occurs possibly in a core-complex with IRS-1 Ser312, Beclin-1 and autophagy inhibitor BcL-XL. Induction of autophagy is usually controlled by a two-edged mechanism acting in opposition under anabolic and catabolic conditions by AMPK/mTOR/4E-BP1 pathways with GSK-3β mediated feed-back loops. However, we observed that an up-regulation of mTOR along with an up-regulation of AMPK caused by HCV infection is a deviation from the normal scenario described above which might be of therapeutic interest.
    DOI:  https://doi.org/10.1159/000535787
  57. Int J Biol Macromol. 2023 Dec 14. pii: S0141-8130(23)05706-9. [Epub ahead of print]257(Pt 2): 128807
    Genetically encoded caspase sensor and RFP-LC3 for temporal analysis of apoptosis-autophagy.
    Aneesh Chandrasekharan, Shivanshu Kumar Tiwari, Halikar Aman Munirpasha, Aswathy Sivasailam, Aparna Geetha Jayaprasad, Ashwathi Harikumar, T R Santhoshkumar.
      The balance between pro-death and pro-survival signaling determines the fate of cells under a variety of pathological and physiological conditions. The pro-cell death signaling, apoptosis, and survival singling, autophagy work in an integrated manner for maintaining cell integrity. Their altered balance drives pathological conditions such as cancer, inflammatory disorders, and neurodegenerative diseases. Dissecting complex crosstalk between autophagy and apoptosis requires simultaneous detection of both events at a single cell level with good temporal resolution in real-time. Here, we have used two distinct fluorescent-based probes of caspase activation and autophagy for generating such sensor cells. Cells stably expressing RFP-LC3 as an autophagy marker were further stably expressed with a FRET-based probe for caspase activation with a nuclear localization signal. The functional validation and live-cell imaging of the sensor cells using selected treatments revealed that stress that induces rapid cell death often fails to induce autophagy signaling, and slow cell death induction triggers simultaneous autophagy signaling with caspase activation. The real-time imaging revealed the time-dependent shift of cells towards caspase activation while autophagy is inhibited confirming basal autophagy confers survival against apoptosis under stress conditions. Confocal imaging also revealed that cells under 3D culture condition maintain increased autophagy over monolayer cultures. High-throughput adaptability of the system extends its application for the screening of compounds that cause caspase activation, autophagy, or both demonstrating the potential utility of the sensor probe for diverse biological applications.
    Keywords:  Apoptosis; Autophagy; Caspase sensor; Confocal imaging; High-throughput screening
    DOI:  https://doi.org/10.1016/j.ijbiomac.2023.128807
  58. Cells. 2023 Dec 14. pii: 2842. [Epub ahead of print]12(24):
    Signaling Pathways Involved in Manganese-Induced Neurotoxicity.
    Hong Cheng, Beatriz Ferrer Villahoz, Romina Deza Ponzio, Michael Aschner, Pan Chen.
      Manganese (Mn) is an essential trace element, but insufficient or excessive bodily amounts can induce neurotoxicity. Mn can directly increase neuronal insulin and activate insulin-like growth factor (IGF) receptors. As an important cofactor, Mn regulates signaling pathways involved in various enzymes. The IGF signaling pathway plays a protective role in the neurotoxicity of Mn, reducing apoptosis in neurons and motor deficits by regulating its downstream protein kinase B (Akt), mitogen-activated protein kinase (MAPK), and mammalian target of rapamycin (mTOR). In recent years, some new mechanisms related to neuroinflammation have been shown to also play an important role in Mn-induced neurotoxicity. For example, DNA-sensing receptor cyclic GMP-AMP synthase (cCAS) and its downstream signal efficient interferon gene stimulator (STING), NOD-like receptor family pyrin domain containing 3(NLRP3)-pro-caspase1, cleaves to the active form capase1 (CASP1), nuclear factor κB (NF-κB), sirtuin (SIRT), and Janus kinase (JAK) and signal transducers and activators of the transcription (STAT) signaling pathway. Moreover, autophagy, as an important downstream protein degradation pathway, determines the fate of neurons and is regulated by these upstream signals. Interestingly, the role of autophagy in Mn-induced neurotoxicity is bidirectional. This review summarizes the molecular signaling pathways of Mn-induced neurotoxicity, providing insight for further understanding of the mechanisms of Mn.
    Keywords:  autophagy; insulin-like growth factor (IGF); manganese; neurotoxicity; signaling pathway
    DOI:  https://doi.org/10.3390/cells12242842
  59. Cancer Commun (Lond). 2023 Dec 22.
    Glucose-mediated mitochondrial reprogramming by cholesterol export at TM4SF5-enriched mitochondria-lysosome contact sites.
    Ji Eon Kim, So-Young Park, Chulhwan Kwak, Yoonji Lee, Dae-Geun Song, Jae Woo Jung, Haesong Lee, Eun-Ae Shin, Yangie Pinanga, Kyung-Hee Pyo, Eun Hae Lee, Wonsik Kim, Soyeon Kim, Chang-Duck Jun, Jeanho Yun, Sun Choi, Hyun-Woo Rhee, Kwang-Hyeon Liu, Jung Weon Lee.
       BACKGROUND: Transmembrane 4 L six family member 5 (TM4SF5) translocates subcellularly and functions metabolically, although it is unclear how intracellular TM4SF5 translocation is linked to metabolic contexts. It is thus of interests to understand how the traffic dynamics of TM4SF5 to subcellular endosomal membranes are correlated to regulatory roles of metabolisms.
    METHODS: Here, we explored the metabolic significance of TM4SF5 localization at mitochondria-lysosome contact sites (MLCSs), using in vitro cells and in vivo animal systems, via approaches by immunofluorescence, proximity labelling based proteomics analysis, organelle reconstitution etc. RESULTS: Upon extracellular glucose repletion following depletion, TM4SF5 became enriched at MLCSs via an interaction between mitochondrial FK506-binding protein 8 (FKBP8) and lysosomal TM4SF5. Proximity labeling showed molecular clustering of phospho-dynamic-related protein I (DRP1) and certain mitophagy receptors at TM4SF5-enriched MLCSs, leading to mitochondrial fission and autophagy. TM4SF5 bound NPC intracellular cholesterol transporter 1 (NPC1) and free cholesterol, and mediated export of lysosomal cholesterol to mitochondria, leading to impaired oxidative phosphorylation but intact tricarboxylic acid (TCA) cycle and β-oxidation. In mouse models, hepatocyte Tm4sf5 promoted mitophagy and cholesterol transport to mitochondria, both with positive relations to liver malignancy.
    CONCLUSIONS: Our findings suggested that TM4SF5-enriched MLCSs regulate glucose catabolism by facilitating cholesterol export for mitochondrial reprogramming, presumably while hepatocellular carcinogenesis, recapitulating aspects for hepatocellular carcinoma metabolism with mitochondrial reprogramming to support biomolecule synthesis in addition to glycolytic energetics.
    Keywords:  cholesterol; fluorescent imaging; glucose catabolism; hepatocellular carcinogenesis; membrane contact sites; mitochondria function; mitophagy; oxidative phosphorylation; protein-protein interaction; tetraspanin
    DOI:  https://doi.org/10.1002/cac2.12510
  60. Autophagy Rep. 2022 Sep 14. 1(1): 414-417
    The mechanism of macroautophagy: The movie.
    Fulvio Reggiori, Patricia Boya, David da Costa, Zvulun Elazar, Eeva-Liisa Eskelinen, Judith Farrés, Sebastian Guettler, Claudine Kraft, Heinz Jungbluth, Ana Martinez, Etienne Morel, Ole Pless, Tassula Proikas-Cezanne, Anne Simonsen.
      This animated movie presents the mechanism of macroautophagy, hereafter autophagy, by showing the molecular features of the formation of autophagosomes, the hallmark organelle of this intracellular catabolic pathway. It is based on our current knowledge and it also illustrates how autophagosomes can recognize and eliminate selected cargoes.
    DOI:  https://doi.org/10.1080/27694127.2022.2096115
  61. Viruses. 2023 Nov 26. pii: 2324. [Epub ahead of print]15(12):
    ATG8f Interacts with Chilli Veinal Mottle Virus 6K2 Protein to Limit Virus Infection.
    Chenglong Ji, Jingya Zhou, Daoyong Yang, Bowen Yuan, Rongxia Tang, Yong Liu, Dehui Xi.
      Autophagy, as a conserved protein degradation pathway in plants, has also been reported to be intricately associated with antiviral defense mechanisms. However, the relationship between chilli veinal mottle virus (ChiVMV) and autophagy has not been investigated in the existing research. Here, we reveal that ChiVMV infection caused the accumulation of autophagosomes in infected Nicotiana benthamiana leaves and the upregulation of autophagy-related genes (ATGs). Moreover, the changes in gene expression were correlated with the development of symptoms. Treatment with autophagy inhibitors (3-MA or E-64D) could increase the infection sites and facilitate virus infection, whereas treatment with the autophagy activator (Rapamycin) limited virus infection. Then, ATG8f was identified to interact with ChiVMV 6K2 protein directly in vitro and in vivo. The silencing of ATG8f promoted virus infection, whereas the overexpression of ATG8f inhibited virus infection. Furthermore, the expression of 6K2-GFP in ATG8f- or ATG7-silenced plants was significantly higher than that in control plants. Rapamycin treatment reduced the accumulation of 6K2-GFP in plant cells, whereas treatment with the inhibitor of the ubiquitin pathway (MG132), 3-MA, or E-64D displayed little impact on the accumulation of 6K2-GFP. Thus, our results demonstrated that ATG8f interacts with the ChiVMV 6K2 protein, promoting the degradation of 6K2 through the autophagy pathway.
    Keywords:  6K2; ATG8f; ChiVMV; autophagy
    DOI:  https://doi.org/10.3390/v15122324
  62. Neuropharmacology. 2023 Dec 15. pii: S0028-3908(23)00404-5. [Epub ahead of print]245 109814
    Defective autophagy contributes to bupivacaine-induced aggravation of painful diabetic neuropathy in db/db mice.
    Keke Fan, Qinming Liao, Pengfei Yuan, Rui Xu, Zhongjie Liu.
      Current evidence suggests that hyperactivated or impaired autophagy can lead to neuronal death. The effect of local anesthetics on painful diabetic neuropathy (PDN) and the role of autophagy in the above pathological process remain unclear, warranting further studies. So, PDN models were established by assessing the paw withdrawal threshold (PWT) and paw withdrawal latency (PWL) in leptin gene-mutation (db/db) mice. Wild type (WT) and PDN mice received intrathecal 0.75% bupivacaine or/with intraperitoneal drug treatment (rapamycin or bafilomycin A1). Subsequently, the PWT and PWL were measured to assess hyperalgesia at 6 h, 24 h, 30 h, and 48 h after intrathecal bupivacaine. Also, sensory nerve conduction velocity (SNCV) and motor nerve conduction velocity (MNCV) were measured before and 48 h after intrathecal bupivacaine treatment. The spinal cord tissue of L4-L6 segments and serum were harvested to evaluate the change of autophagy, oxidative stress, oxidative injury, and apoptosis. We found that bupivacaine induced the activation of autophagy but did not affect the pain threshold, SNCV and MNCV in WT mice at predefined time points. Conversely, bupivacaine lowered autophagosome generation and degradation, slowed SNCV and aggravated spinal dorsal horn neuron oxidative injury and hyperalgesia in PDN mice. The autophagy activator (rapamycin) could decrease spinal dorsal horn neuron oxidative injury, alleviate the alterations in SNCV and hyperalgesia in bupivacaine-treated PDN mice. Meanwhile, the autophagy inhibitor (bafilomycin A1) could exacerbate spinal dorsal horn neuron oxidative injury, the alterations in SNCV and hyperalgesia in bupivacaine-treated PDN mice. Our results showed that bupivacaine could induce defective autophagy, slowed SNCV and aggravate spinal dorsal horn neuron oxidative injury and hyperalgesia in PDN mice. Restoring autophagy may represent a potential therapeutic approach against nerve injury in PDN patients with local anesthesia and analgesia.
    Keywords:  Anesthetic drugs; Autophagy; Bupivacaine; Diabetes mellitus; Neuropathic pain; Oxidative stress
    DOI:  https://doi.org/10.1016/j.neuropharm.2023.109814
  63. Trends Mol Med. 2023 Dec 19. pii: S1471-4914(23)00279-4. [Epub ahead of print]
    FBXL4 mutation-caused mitochondrial DNA depletion syndrome is driven by BNIP3/BNIP3L-dependent excessive mitophagy.
    Kun Gao, Xiayun Xu, Chenji Wang.
      Encephalomyopathic mitochondrial DNA (mtDNA) depletion syndrome 13 (MTDPS13) is an autosomal recessive disorder arising from biallelic F-box and leucine-rich repeat (LRR) protein 4 (FBXL4) gene mutations. Recent advances have shown that excessive BCL2 interacting protein 3 (BNIP3)/ BCL2 interacting protein 3 like (BNIP3L)-dependent mitophagy underlies the molecular pathogenesis of MTDPS13. Here, we provide an overview of these groundbreaking findings and discuss potential therapeutic strategies for this fatal disease.
    Keywords:  BNIP3/BNIP3L; FBXL4; MTDPS13; mitochondria; mitophagy; ubiquitination
    DOI:  https://doi.org/10.1016/j.molmed.2023.11.017
  64. Front Oncol. 2023 ;13 1293795
    Editorial: Deciphering and targeting the mTOR pathway in hematologic malignancies.
    Luca Lo Nigro.
      
    Keywords:  PI3 K/AKT; PTEN (phosphatase and tensin homolog deleted on chromosome 10); Rapalogs; acute leukemias; mTOR - mammalian target of rapamycin
    DOI:  https://doi.org/10.3389/fonc.2023.1293795
  65. bioRxiv. 2023 Dec 07. pii: 2023.12.06.570342. [Epub ahead of print]
    The Molecular Logic of Gtr1/2 and Pib2 Dependent TORC1 Regulation in Budding Yeast.
    Jacob H Cecil, Cristina M Padilla, Austin A Lipinski, Paul R Langlais, Xiangxia Luo, Andrew P Capaldi.
      The Target of Rapamycin kinase Complex I (TORC1) regulates cell growth and metabolism in eukaryotes. Previous studies have shown that, in Saccharomyces cerevisiae , nitrogen and amino acid signals activate TORC1 via the highly conserved small GTPases, Gtr1/2, and the phosphatidylinositol 3-phosphate binding protein, Pib2. However, it was unclear if/how Gtr1/2 and Pib2 cooperate to control TORC1. Here we report that this dual regulator system pushes TORC1 into three distinct signaling states: (i) a Gtr1/2 on, Pib2 on, rapid growth state in nutrient replete conditions; (ii) a Gtr1/2 off, Pib2 on, adaptive/slow growth state in poor-quality growth medium; and (iii) a Gtr1/2 off, Pib2 off, quiescent state in starvation conditions. We suggest that other signaling pathways work in a similar way, to drive a multi-level response via a single kinase, but the behavior has been overlooked since most studies follow signaling to a single reporter protein.
    DOI:  https://doi.org/10.1101/2023.12.06.570342
  66. Aging (Albany NY). 2023 Dec 18. 15
    Novel insights into the regulatory role of N6-methyladenosine methylation modified autophagy in sepsis.
    Cheng-Fei Bi, Jia Liu, Xiao-Dong Hu, Li-Shan Yang, Jun-Fei Zhang.
      Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection. It is characterized by high morbidity and mortality and one of the major diseases that seriously hang over global human health. Autophagy is a crucial regulator in the complicated pathophysiological processes of sepsis. The activation of autophagy is known to be of great significance for protecting sepsis induced organ dysfunction. Recent research has demonstrated that N6-methyladenosine (m6A) methylation is a well-known post-transcriptional RNA modification that controls epigenetic and gene expression as well as a number of biological processes in sepsis. In addition, m6A affects the stability, export, splicing and translation of transcripts involved in the autophagic process. Although it has been suggested that m6A methylation regulates the biological metabolic processes of autophagy and is more frequently seen in the progression of sepsis pathogenesis, the underlying molecular mechanisms of m6A-modified autophagy in sepsis have not been thoroughly elucidated. The present article fills this gap by providing an epigenetic review of the processes of m6A-modified autophagy in sepsis and its potential role in the development of novel therapeutics.
    Keywords:  autophagy; m6A methylation; sepsis
    DOI:  https://doi.org/10.18632/aging.205312
  67. Mech Ageing Dev. 2023 Dec 16. pii: S0047-6374(23)00123-9. [Epub ahead of print]217 111897
    The cGAS-STING signaling pathway is modulated by urolithin A.
    H B Madsen, J-H Park, X Chu, Y Hou, Z Li, L J Rasmussen, D L Croteau, V A Bohr, M Akbari.
      During aging, general cellular processes, including autophagic clearance and immunological responses become compromised; therefore, identifying compounds that target these cellular processes is an important approach to improve our health span. The innate immune cGAS-STING pathway has emerged as an important signaling system in the organismal defense against viral and bacterial infections, inflammatory responses to cellular damage, regulation of autophagy, and tumor immunosurveillance. These key functions of the cGAS-STING pathway make it an attractive target for pharmacological intervention in disease treatments and in controlling inflammation and immunity. Here, we show that urolithin A (UA), an ellagic acid metabolite, exerts a profound effect on the expression of STING and enhances cGAS-STING activation and cytosolic DNA clearance in human cell lines. Animal laboratory models and limited human trials have reported no obvious adverse effects of UA administration. Thus, the use of UA alone or in combination with other pharmacological compounds may present a potential therapeutic approach in the treatment of human diseases that involves aberrant activation of the cGAS-STING pathway or accumulation of cytosolic DNA and this warrants further investigation in relevant transgenic animal models.
    Keywords:  Autophagy; CGAS-STING; Endoplasmic reticulum; Inflammation; Urolithin A
    DOI:  https://doi.org/10.1016/j.mad.2023.111897
  68. Neurosci Lett. 2023 Dec 13. pii: S0304-3940(23)00555-4. [Epub ahead of print]820 137596
    Fingolimod exerts neuroprotection by regulating S1PR1 mediated BNIP3-PINK1-Parkin dependent mitophagy in rotenone induced mouse model of Parkinson's disease.
    Shruti Rajan, Anika Sood, Rachit Jain, Pushpa Tryphena Kamatham, Dharmendra Kumar Khatri.
      The motor impairments brought on by the loss of dopaminergic neurons in the substantia nigra are the most well-known symptoms of Parkinson's disease (PD). It is believed that dopaminergic neurons are especially vulnerable to mitochondrial malfunction. For the maintenance of mitochondrial integrity, selective autophagic removal of dysfunctional mitochondria via mitophagy primarily regulated by PINK1/Parkin pathway is essential. Moreover, newer studies also implicate the role of phospholipid metabolism, such as that of Sphingosine-1-phosphate (S1P) as a contributor to PD. S1P receptors have been reported to influence mitochondrial function in neurodegenerative diseases. Fingolimod (FTY720), an S1P receptor-1 modulator has been proven effective in PD but its regulation of mitophagy in PD is still elusive. In this study, the neuroprotective effect of FTY720 by modulating mitophagy, has been explored against rotenone (ROT) induced neurotoxicity in in-vivo. The animals were randomly divided into 5 groups namely, Normal Control (NC); Disease control (DC): ROT (1.5 mg/kg); Low dose (LD): ROT + FTY720 (0.5 mg/kg); High dose (HD): ROT + FTY720 (1 mg/kg) and Vehicle control (VC): 1 % DMSO. ROT was administered through i.p. and FTY720 through p.o. for 21 days. At the end of the study, various neurobehavioral studies (rotarod test and actimeter), western blot techniques, and immunofluorescence studies were performed. FTY720 restored the neurobehavioural functions and protein expression of PINK1, Parkin and BNIP3 in ROT-induced PD mice. The results obtained in our study suggest that FTY720 has a neuroprotective effect in ROT-induced mice model of PD via PINK1-Parkin mediated mitophagy.
    Keywords:  Fingolimod; Mitochondria; Mitophagy; Parkinson’s Disease; Rotenone
    DOI:  https://doi.org/10.1016/j.neulet.2023.137596
  69. Virology. 2023 Dec 07. pii: S0042-6822(23)00276-3. [Epub ahead of print]590 109957
    Autophagy inhibition suppresses Newcastle disease virus-induced cell death by inhibiting viral replication in human breast cancer cells.
    Megat Irfan Rozilah, Khatijah Yusoff, Suet Lin Chia, Saila Ismail.
      Newcastle disease virus (NDV) is an oncolytic virus which selectively replicates in cancer cells without harming normal cells. Autophagy is a cellular mechanism that breaks down unused cytoplasmic constituents into nutrients. In previous studies, autophagy enhanced NDV-induced oncolysis in lung cancer and glioma cells. However, the effect of autophagy inhibition on NDV-induced oncolysis in breast cancer cells remains unknown. This study aimed to examine the effect of autophagy inhibition on NDV-induced oncolysis in human breast cancer cells, MCF7. To inhibit autophagy, we knocked down the expression of the autophagy protein beclin-1 (BECN1) by short interfering RNA (siRNA). The cells were infected with the recombinant NDV strain AF2240 expressing green fluorescent protein. We found that NDV induced autophagy and knockdown of BECN1 significantly reduced the NDV-induced autophagy in MCF7 cells. Importantly, BECN1 knockdown significantly suppressed cell death by inhibiting viral replication, as observed at 24 h post infection. Overall, our data suggest that autophagy inhibition may not be a suitable strategy to enhance NDV oncolytic efficacy against breast cancer.
    Keywords:  Autophagy; Beclin-1; Breast cancer cells; Newcastle disease virus; Oncolytic virus
    DOI:  https://doi.org/10.1016/j.virol.2023.109957
  70. ERJ Open Res. 2023 Nov;pii: 00423-2023. [Epub ahead of print]9(6):
    Impaired autophagy in the lower airways and lung parenchyma in stable COPD.
    Stefano Levra, Umberto Rosani, Isabella Gnemmi, Paola Brun, Andrea Leonardi, Vitina Carriero, Francesca Bertolini, Bruno Balbi, Mirella Profita, Fabio Luigi Massimo Ricciardolo, Antonino Di Stefano.
       Background: There is increasing evidence of autophagy activation in COPD, but its role is complex and probably regulated through cell type-specific mechanisms. This study aims to investigate the autophagic process at multiple levels within the respiratory system, using different methods to clarify conflicting results reported so far.
    Methods: This cross-sectional study was performed on bronchial biopsies and peripheral lung samples obtained from COPD patients (30 and 12 per sample type, respectively) and healthy controls (25 and 22 per sample type, respectively), divided by smoking history. Subjects were matched for age and smoking history. We analysed some of the most important proteins involved in autophagosome formation, such as LC3 and p62, as well as some molecules essential for lysosome function, such as lysosome-associated membrane protein 1 (LAMP1). Immunohistochemistry was used to assess the autophagic process in both sample types. ELISA and transcriptomic analysis were performed on lung samples.
    Results: We found increased autophagic stimulus in smoking subjects, regardless of respiratory function. This was revealed by immunohistochemistry through a significant increase in LC3 (p<0.01) and LAMP1 (p<0.01) in small airway bronchiolar epithelium, alveolar septa and alveolar macrophages. Similar results were obtained in bronchial biopsy epithelium by evaluating LC3B (p<0.05), also increased in homogenate lung tissue using ELISA (p<0.05). Patients with COPD, unlike the others, showed an increase in p62 by ELISA (p<0.05). No differences were found in transcriptomics analysis.
    Conclusions: Different techniques, applied at post-transcriptional level, confirm that cigarette smoke stimulates autophagy at multiple levels inside the respiratory system, and that autophagy failure may characterise COPD.
    DOI:  https://doi.org/10.1183/23120541.00423-2023
  71. NPJ Parkinsons Dis. 2023 Dec 18. 9(1): 167
    Inhibition of LRRK2 kinase activity rescues deficits in striatal dopamine physiology in VPS35 p.D620N knock-in mice.
    Mengfei Bu, Jordan Follett, Isaac Deng, Igor Tatarnikov, Shannon Wall, Dylan Guenther, Melissa Maczis, Genevieve Wimsatt, Austen Milnerwood, Mark S Moehle, Habibeh Khoshbouei, Matthew J Farrer.
      Dysregulation of dopamine neurotransmission profoundly affects motor, motivation and learning behaviors, and can be observed during the prodromal phase of Parkinson's disease (PD). However, the mechanism underlying these pathophysiological changes remains to be elucidated. Mutations in vacuolar protein sorting 35 (VPS35) and leucine-rich repeat kinase 2 (LRRK2) both lead to autosomal dominant PD, and VPS35 and LRRK2 may physically interact to govern the trafficking of synaptic cargos within the endo-lysosomal network in a kinase-dependent manner. To better understand the functional role of VPS35 and LRRK2 on dopamine physiology, we examined Vps35 haploinsufficient (Haplo) and Vps35 p.D620N knock-in (VKI) mice and how their behavior, dopamine kinetics and biochemistry are influenced by LRRK2 kinase inhibitors. We found Vps35 p.D620N significantly elevates LRRK2-mediated phosphorylation of Rab10, Rab12 and Rab29. In contrast, Vps35 haploinsufficiency reduces phosphorylation of Rab12. While striatal dopamine transporter (DAT) expression and function is similarly impaired in both VKI and Haplo mice, that physiology is normalized in VKI by treatment with the LRRK2 kinase inhibitor, MLi-2. As a corollary, VKI animals show a significant increase in amphetamine induced hyperlocomotion, compared to Haplo mice, that is also abolished by MLi-2. Taken together, these data show Vps35 p.D620N confers a gain-of-function with respect to LRRK2 kinase activity, and that VPS35 and LRRK2 functionally interact to regulate DAT function and striatal dopamine transmission.
    DOI:  https://doi.org/10.1038/s41531-023-00609-7
  72. Microbiol Res. 2023 Dec 12. pii: S0944-5013(23)00275-6. [Epub ahead of print]280 127573
    AoRab7A interacts with AoVps35 and AoVps41 to regulate vacuole assembly, trap formation, conidiation, and functions of proteasomes and ribosomes in Arthrobotrys oligospora.
    Yingmei Zhu, Xuewei Yang, Na Bai, Qianqian Liu, Jinkui Yang.
      Rab GTPases regulate vesicle trafficking in organisms and play crucial roles in growth and development. Arthrobotrys oligospora is a ubiquitous nematode-trapping (NT) fungus, it can form elaborate traps to capture nematodes. Our previous study found that deletion of Aorab7A abolished the trap formation and sporulation. Here, we investigated the regulatory mechanism of AoRab7A using transcriptomic, biochemical, and phenotypic comparisons. Transcriptome analysis, yeast library screening, and yeast two-hybrid assay identified two vacuolar protein sorting (Vps) proteins, AoVps41 and AoVps35, as putative targets of AoRab7A. The deletion of Aovps41 and Aovps35 caused considerable defects in multiple phenotypic traits, such as conidiation and trap formation. We further found a close connection between AoRab7A and Vps proteins in vesicle-vacuole fusion, which triggered vacuolar fragmentation. Further transcriptome analysis showed that AoRab7A and AoVps35 play essential roles in many cellular processes and components including proteasomes, autophagy, fatty acid degradation, and ribosomes in A. oligospora. Furthermore, we verified that AoRab7A, AoVps41, and AoVps35 are involved in ribosome and proteasome functions. The absence of these proteins inhibited the biosynthesis of nascent proteins and enhanced ubiquitination. Our findings suggest that AoRab7A interacts with AoVps41 and AoVps35 to mediate vacuolar fusion and influence lipid droplet accumulation, autophagy, and stress response. These proteins are especially required for the conidiation and trap development of A. oligospora.
    Keywords:  Conidiation; Rab7A; Trap formation; Vacuolar protein sorting proteins; Vacuole assembly
    DOI:  https://doi.org/10.1016/j.micres.2023.127573
  73. Cell Mol Gastroenterol Hepatol. 2023 Dec 18. pii: S2352-345X(23)00217-5. [Epub ahead of print]
    Apolipoprotein A-1 accelerated liver regeneration through regulating autophagy via AMPK-ULK1 pathway.
    Zi Yi Wang, Rui Xiang Chen, Ji Fei Wang, Shuo Chen Liu, Xiao Xu, Tao Zhou, Yan An Lan Chen, Yao Dong Zhang, Xiang Cheng Li, Chang Xian Li.
       BACKGROUND & AIMS: Apolipoprotein A-1 (ApoA-1), the main apolipoprotein of high-density lipoprotein, has been well studied in the area of lipid metabolism and cardiovascular diseases. In this project, we intended to clarify the function and mechanism of ApoA-1 in liver regeneration.
    METHODS: 70% of partial hepatectomy was applied in male ApoA-1 knockout mice and wild-type mice to investigate the effects of ApoA-1 on liver regeneration. D-4F (ApoA-1 mimetic peptide), autophagy activator and AMPK activator were used to explore the mechanism of ApoA-1 on liver regeneration.
    RESULTS: We demonstrated that ApoA-1 levels were highly expressed during the early stage of liver regeneration. ApoA-1 deficiency greatly impaired liver regeneration after hepatectomy. Meanwhile, we found that ApoA-1 deficiency inhibited autophagy during liver regeneration. The activation of autophagy protected against ApoA-1 deficiency in inhibiting liver regeneration. Furthermore, ApoA-1 deficiency impaired autophagy through AMPK-ULK1 pathway, and AMPK activation significantly improved liver regeneration. The administration of D-4F could accelerated liver regeneration after hepatectomy.
    CONCLUSIONS: These findings suggested that ApoA-1 played an essential role in liver regeneration through promoting autophagy in hepatocytes via AMPK-ULK1 pathway. Our findings enriched the understanding of the underlying mechanism of liver regeneration and provided a potential therapeutic strategy for liver injury.
    Keywords:  AMPK pathway; ApoA-1; Autophagy; Liver regeneration
    DOI:  https://doi.org/10.1016/j.jcmgh.2023.12.004
  74. Mol Biol Cell. 2023 Dec 20. mbcE23060259
    Lysosomal membrane transporter purification and reconstitution for functional studies.
    Felichi Mae Arines, Aleksander Wielenga, Danielle Henn, Olive E Burata, Francisco Narro Garcia, Randy B Stockbridge, Ming Li.
      Lysosomes achieve their function through numerous transporters that import or export nutrients across their membrane. However, technical challenges in membrane protein overexpression, purification, and reconstitution hinder our understanding of lysosome transporter function. Here, we developed a platform to overexpress and purify the putative lysine transporter Ypq1 using a constitutive overexpression system in protease- and ubiquitination-deficient yeast vacuoles. Using this method, we purified and reconstituted Ypq1 into proteoliposomes and showed lysine transport function, supporting its role as a basic amino acid transporter on the vacuole membrane. We also found that the absence of lysine destabilizes purified Ypq1 and causes it to aggregate, consistent with its propensity to be downregulated in vivo upon lysine starvation. Our approach may be useful for the biochemical characterization of many transporters and membrane proteins to understand organellar transport and regulation.
    DOI:  https://doi.org/10.1091/mbc.E23-06-0259
  75. Biochim Biophys Acta Rev Cancer. 2023 Dec 14. pii: S0304-419X(23)00203-2. [Epub ahead of print]1879(1): 189054
    Cellular stress responses as modulators of drug cytotoxicity in pharmacotherapy of glioblastoma.
    Magdalena Kusaczuk, Elena Tovar Ambel, Monika Naumowicz, Guillermo Velasco.
      Despite the extensive efforts to find effective therapeutic strategies, glioblastoma (GBM) remains a therapeutic challenge with dismal prognosis of survival. Over the last decade the role of stress responses in GBM therapy has gained a great deal of attention, since depending on the duration and intensity of these cellular programs they can be cytoprotective or promote cancer cell death. As such, initiation of the UPR, autophagy or oxidative stress may either impede or facilitate drug-mediated cell killing. In this review, we summarize the mechanisms that regulate ER stress, autophagy, and oxidative stress during GBM development and progression to later discuss the involvement of these stress pathways in the response to different treatments. We also discuss how a precise understanding of the molecular mechanisms regulating stress responses evoked by different pharmacological agents could decisively contribute to the design of novel and more effective combinational treatments against brain malignancies.
    Keywords:  Autophagy; ER stress; Glioblastoma; Oxidative stress; Pharmacotherapy
    DOI:  https://doi.org/10.1016/j.bbcan.2023.189054
  76. Signal Transduct Target Ther. 2023 Dec 18. 8(1): 463
    Pyrotinib and chrysin synergistically potentiate autophagy in HER2-positive breast cancer.
    Xiaoxiao Liu, Xing Zhang, Zhiying Shao, Xiaorong Zhong, Xin Ding, Liang Wu, Jie Chen, Ping He, Yan Cheng, Kunrui Zhu, Dan Zheng, Jing Jing, Ting Luo.
      Human epidermal growth factor receptor 2 (HER2)-positive breast cancer (BC) has been the most challenging subtype of BC, consisting of 20% of BC with an apparent correlation with poor prognosis. Despite that pyrotinib, a new HER2 inhibitor, has led to dramatic improvements in prognosis, the efficacy of pyrotinib monotherapy remains largely restricted due to its acquired resistance. Therefore, identifying a new potential antitumor drug in combination with pyrotinib to amplify therapeutic efficacy is a pressing necessity. Here, we reported a novel combination of pyrotinib with chrysin and explored its antitumor efficacy and the underlying mechanism in HER2-positive BC. We determined that pyrotinib combined with chrysin yielded a potent synergistic effect to induce more evident cell cycle arrest, inhibit the proliferation of BT-474 and SK-BR-3 BC cells, and repress in vivo tumor growth in xenograft mice models. This may be attributed to enhanced autophagy induced by endoplasmic reticulum stress. Furthermore, the combined treatment of pyrotinib and chrysin induced ubiquitination and glucose-6-phosphate dehydrogenase (G6PD) degradation by upregulating zinc finger and BTB/POZ domain-containing family protein 16 (ZBTB16) in tumorigenesis of BC. Mechanistically, we identified that miR-16-5p was a potential upstream regulator of ZBTB16, and it showed a significant inverse correlation with ZBTB16. Inhibition of miR-16-5p overexpression by restoring ZBTB16 significantly potentiated the overall antitumor efficacy of pyrotinib combined with chrysin against HER2-positive BC. Together, these findings demonstrate that the combined treatment of pyrotinib and chrysin enhances autophagy in HER2-positive BC through an unrecognized miR-16-5p/ZBTB16/G6PD axis.
    DOI:  https://doi.org/10.1038/s41392-023-01689-w
  77. Lab Invest. 2023 Dec 15. pii: S0023-6837(23)00250-7. [Epub ahead of print] 100307
    The role of mitochondrial quality control in chronic obstructive pulmonary disease.
    Yu-Biao Liu, Jie-Ru Hong, Nan Jiang, Ling Jin, Wen-Jing Zhong, Chen-Yu Zhang, Hui-Hui Yang, Jia-Xi Duan, Yong Zhou.
      Chronic obstructive pulmonary disease (COPD) is a major cause of morbidity, mortality, and healthcare use worldwide with heterogeneous pathogenesis. Mitochondria, the powerhouses in cells responsible for oxidative phosphorylation and energy production, play essential roles in intracellular material metabolism, natural immunity, and cell death regulation. Therefore, it is crucial to address the urgent need for fine-tuning the regulation of mitochondrial quality to combat COPD effectively. Mitochondrial quality control (MQC) mainly refers to the selective removal of damaged or aging mitochondria and the generation of new mitochondria, which involves mitochondrial biogenesis, mitochondrial dynamics, mitophagy, etc. Mounting evidence suggests that mitochondrial dysfunction is a crucial contributor to the development and progression of COPD. This article mainly reviews the effects of MQC on COPD as well as their specific regulatory mechanisms. Finally, the therapeutic approaches of COPD via MQC are also illustrated.
    Keywords:  chronic obstructive pulmonary disease; mitochondrial biogenesis; mitochondrial dynamics; mitochondrial quality control; mitophagy
    DOI:  https://doi.org/10.1016/j.labinv.2023.100307
  78. Cell Res. 2023 Dec 15.
    Amino acid availability governs mTOR ubiquitination.
    Xiaoming Dai, Peiqiang Yan, Wenyi Wei.
      
    DOI:  https://doi.org/10.1038/s41422-023-00910-3
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