bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2025–05–11
sixty-five papers selected by
Viktor Korolchuk, Newcastle University
  1. Niemann Pick C1 mistargeting disrupts lysosomal cholesterol homeostasis contributing to neurodegeneration in a Batten disease model.
  2. mTOR inhibitors in targeting autophagy and autophagy-associated signaling for cancer cell death and therapy.
  3. Autophagy in cancer and protein conformational disorders.
  4. NDP52 and its emerging role in pathogenesis.
  5. Mitochondrial fatty acid oxidation dysfunction impairs autophagic flux through ATP deficiency-caused lysosomal pH abnormity.
  6. Reduced Palmitoylation of SQSTM1/p62 in Huntington Disease Is Associated With Impaired Autophagy.
  7. ER-to-lysosome-associated degradation.
  8. SNX10 at the crossroad of endocytosis and piecemeal mitophagy.
  9. Rapamycin exerts neuroprotective effects by inhibiting FKBP12 instead of mTORC1 in the mouse model of Parkinson's disease.
  10. Unconventional secretion of PARK7 requires lysosomal delivery via chaperone-mediated autophagy and specialized SNARE complex.
  11. Stress and autophagy.
  12. Key Mechanisms in Lysosome Stability, Degradation and Repair.
  13. TRIM22 functions as a scaffold protein for autophagy initiation.
  14. A Ginsenoside Composition Ameliorated Aβ and Tau Aggregation via Autophagy Lysosome Pathway.
  15. Kinome screening identifies integrated stress response kinase EIF2AK1/HRI as a negative regulator of PINK1 mitophagy signaling.
  16. MoSec13 combined with MoGcn5b modulates MoAtg8 acetylation and regulates autophagy in Magnaporthe oryzae.
  17. mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery.
  18. Reticulon-dependent ER-phagy mediates adaptation to heat stress in C. elegans.
  19. Deacetylation of ANXA2 by SIRT2 desensitizes hepatocellular carcinoma cells to donafenib via promoting protective autophagy.
  20. Biased regulation of protein synthesis and hypoxic death by a conditional raptor mutation.
  21. Nucleophagy: A two-step exit with the help of an outsider.
  22. Selenium corrects dysregulated mitophagy and lipophagy in obesity-related acute pancreatitis through the GPX1-Mfn2-PLIN2 axis.
  23. Hypoxia impairs autophagy of cardiomyocytes via p38/MAPK/MAP4 pathway.
  24. p97/VCP is required for piecemeal autophagy of aggresomes.
  25. Mitochondrial viscosity, oxidative stress and autophagy responsive fluorescent Zn(II) complex for monitoring non-alcoholic fatty liver disease.
  26. NSP6 of SARS-CoV-2 Dually Regulates Autophagic-Lysosomal Degradation.
  27. Lymphatic endothelial mTORC1 instructs metabolic and developmental signaling during lymphangiogenesis.
  28. AlphaFold2 SLiM screen for LC3-LIR interactions in autophagy.
  29. Valine acts as an early biomarker and exacerbates pathological cardiac hypertrophy by impairing mitochondrial quality control.
  30. Inhibition of autophagy by Atg7 knockdown enhances chemosensitivity in gemcitabine/paclitaxel-resistant pancreatic cancer MIAPaCa2 cells.
  31. PLA2G15 is a BMP hydrolase and its targeting ameliorates lysosomal disease.
  32. mTOR-mediated nutrient sensing and oxidative stress pathways regulate autophagy: a key mechanism for traditional Chinese medicine to improve diabetic kidney disease.
  33. Promoting Secretion of Pathological Tau Species Using an Induced Proximity Platform That Engages the Autophagy Pathway.
  34. Roles of class III phosphatidylinositol 3-kinase, Vps34, in phagocytosis, autophagy, and endocytosis in retinal pigmented epithelium.
  35. p.Phe508del-CFTR Trafficking: A Protein Quality Control Perspective Through UPR, UPS, and Autophagy.
  36. Methylmercury Chloride Exposure Affects Oocyte Maturation Through AMPK/mTOR-Mediated Mitochondrial Autophagy.
  37. Muscle peripheral circadian clock drives nocturnal protein degradation via raised Ror/Rev-erb balance and prevents premature sarcopenia.
  38. Sinularin induces autophagy-dependent cell death by activating ULK1 and enhancing FOXO3-ATG4A axis in prostate cancer cells.
  39. Chimeric deubiquitinase engineering reveals structural basis for specific inhibition of the mitophagy regulator USP30.
  40. Conditional Overexpression of Neuritin in Supporting Cell Protects Cochlear Hair Cell and Delays Age-Related Hearing Loss by Enhancing Autophagy.
  41. Intermittent time-restricted eating may increase autophagic flux in humans: an exploratory analysis.
  42. Mitochondria and Endoplasmic Reticulum Contact Site as a Regulator of Proteostatic Stress Responses in Neurodegenerative Diseases.
  43. Role of Branched-Chain Amino Acid Catabolism in the Regulation of Adipocyte Metabolism.
  44. Lysosomal Ion Channels and Transporters: Recent Findings, Therapeutic Potential, and Technical Approaches.
  45. Autophagy Regulates Putative Anion Transporter 1 Expression in Intestinal Epithelial Cells.
  46. PLM-ATG: Identification of Autophagy Proteins by Integrating Protein Language Model Embeddings with PSSM-Based Features.
  47. Autophagy-independent role of ATG9A vesicles as carriers for galectin-9 secretion.
  48. Beclin-1-Dependent Autophagy Protects Perivascular Adipose Tissue Function from Hyperaldosteronism Effects.
  49. Trends and research focus on autophagy in Alzheimer's disease (2003-2023): A bibliometric study.
  50. PINK1-dependent NFKB signaling contributes to amyloid pathology in Alzheimer disease.
  51. Biochemical investigation of LC3/GABARAP-ligand interaction as an important quality measure for LC3/GABARAP-targeting small molecules: addendum to the guidelines (4th edition).
  52. Exosomes, autophagy, and cancer: A complex triad.
  53. mTORC2 is crucial for regulating the recombinant Mycobacterium tuberculosis CFP-10 protein-induced phagocytosis in macrophages.
  54. Phase separation in mitochondrial fate and mitochondrial diseases.
  55. STING-∆C, a novel splice isoform of STING, inhibits DNA virus-induced innate immunity and autophagy.
  56. PERK/Sestrin2 Signaling Pathway Mediated Autophagy Regulates Human Cardiomyocytes Apoptosis Induced by Traffic-Related PM2.5 and Diverse Constituents.
  57. Parkin mediates the mitochondrial dysfunction through mRpL18.
  58. Lysosomal EGFR functions as a GEF for Rheb.
  59. Sestrin2 is a central regulator of mitochondrial stress responses in disease and aging.
  60. OTUD4 inhibits ferroptosis by stabilizing GPX4 and suppressing autophagic degradation to promote tumor progression.
  61. Uncovering a key enzyme opens possible therapeutic avenues for lysosomal diseases.
  62. Tie-2 regulates endothelial morphological responses to shear stress by FOXO1-triggered autophagy.
  63. Calpain1 inhibition enhances autophagy-lysosomal pathway and ameliorates tubulointerstitial fibrosis in Nephronophthisis.
  64. Autophagy and extracellular vesicles mediate cisplatin resistance in oral squamous cell carcinoma with LC3B-II as a potential non-invasive biomarker.
  65. PDRN prevents SIRT1 degradation by attenuating autophagy during skin aging.
  1. Sci Adv. 2025 May 09. 11(19): eadr5703
    Niemann Pick C1 mistargeting disrupts lysosomal cholesterol homeostasis contributing to neurodegeneration in a Batten disease model.
    Abhilash P Appu, Maria B Bagh, Nisha Plavelil, Avisek Mondal, Tamal Sadhukhan, Satya P Singh, Neil J Perkins, Aiyi Liu, Anil B Mukherjee.
      Neurodegeneration is a devastating manifestation in most lysosomal storage disorders (LSDs). Loss-of-function mutations in CLN1, encoding palmitoyl-protein thioesterase-1 (PPT1), cause CLN1 disease, a devastating neurodegenerative LSD that has no curative treatment. Numerous proteins in the brain require dynamic S-palmitoylation (palmitoylation-depalmitoylation) for trafficking to their destination. Although PPT1 depalmitoylates S-palmitoylated proteins and its deficiency causes CLN1 disease, the underlying pathogenic mechanism has remained elusive. We report that Niemann-Pick C1 (NPC1), a polytopic membrane protein mediating lysosomal cholesterol egress, requires dynamic S-palmitoylation for trafficking to the lysosome. In Cln1-/- mice, Ppt1 deficiency misroutes NPC1-dysregulating lysosomal cholesterol homeostasis. Along with this defect, increased oxysterol-binding protein (OSBP) promotes cholesterol-mediated activation of mechanistic target of rapamycin C1 (mTORC1), which inhibits autophagy contributing to neurodegeneration. Pharmacological inhibition of OSBP suppresses mTORC1 activation, rescues autophagy, and ameliorates neuropathology in Cln1-/- mice. Our findings reveal a previously unrecognized role of CLN1/PPT1 in lysosomal cholesterol homeostasis and suggest that suppression of mTORC1 activation may be beneficial for CLN1 disease.
    DOI:  https://doi.org/10.1126/sciadv.adr5703
  2. Biochim Biophys Acta Rev Cancer. 2025 May 06. pii: S0304-419X(25)00084-8. [Epub ahead of print] 189342
    mTOR inhibitors in targeting autophagy and autophagy-associated signaling for cancer cell death and therapy.
    Prakash Kumar Senapati, Kewal Kumar Mahapatra, Amruta Singh, Sujit Kumar Bhutia.
      The mechanistic target of rapamycin (mTOR) is a protein kinase that plays a central regulatory switch to control multifaceted cellular processes, including autophagy. As a nutrient sensor, mTOR inhibits autophagy by phosphorylating and inactivating key regulators, including ULK1, Beclin-1, UVRAG, and TFEB, preventing autophagy initiation and lysosomal biogenesis. It also suppresses autophagy-related protein expression, prioritizing growth over cellular recycling. Under nutrient deprivation, mTORC1 activity decreases, allowing autophagy to restore cellular homeostasis. Hyperautophagic activities lead to autophagic cell death; sometime after the point of no return, the cell goes for non-apoptotic, non-necrotic cell death i.e., Autosis. In cancer, the crosstalk between autophagy and mTOR is context-dependent, driving either cell survival or autophagy-dependent cell death. Using mTOR inhibitors, autophagic cell death can be induced to regulate cell growth, and proliferation is a potential therapeutic option for cancer treatment. mTOR inhibitors are broadly categorized into two types, i.e., natural and synthetic mTOR inhibitors. Although several studies in preclinical and clinical trials of various synthetic mTOR inhibitors are now in focus for cancer therapies, limited work has been done to explore autophagic cell death-inducing mTOR inhibitors. In addition, many natural mTOR inhibitors display better efficacy over synthetic mTOR inhibitors due to their lower toxicity, biocompatibility, and potential to overcome drug resistance, highlighting the current status of mTOR inhibitors in inducing autophagic cell death for cancer treatment.
    Keywords:  Autophagic cell death; Autophagy; Cancer therapy; mTOR inhibitors; mTOR signaling
    DOI:  https://doi.org/10.1016/j.bbcan.2025.189342
  3. FEBS Lett. 2025 May 08.
    Autophagy in cancer and protein conformational disorders.
    Sergio Attanasio.
      Autophagy is a catabolic process by which cells maintain cellular homeostasis through the degradation of dysfunctional cytoplasmic components, such as toxic misfolded proteins and damaged organelles, within the lysosome. It is a multistep process that is tightly regulated by nutrient, energy, and stress-sensing mechanisms. Autophagy plays a pivotal role in various biological processes, including protein and organelle quality control, defense against pathogen infections, cell metabolism, and immune surveillance. As a result, autophagy dysfunction is linked to a variety of pathological conditions. The role of autophagy in cancer is complex and dynamic. Depending on the context, autophagy can have both tumor-suppressive and pro-tumorigenic effects. In contrast, its role is more clearly defined in protein conformational disorders, where autophagy serves as a mechanism to reduce toxic protein aggregation, thereby improving cellular homeostasis. Because autophagy-based therapies hold promising potential for the treatment of cancer and protein conformational disorders, this review will highlight the latest findings and advancements in these areas.
    Keywords:  RAS‐ and RAF‐induced cancer; alpha‐1 antitrypsin deficiency; autophagy; autophagy inhibitors; clinical trials; neurodegenerative disorders; pancreatic ductal adenocarcinoma; protein misfolding; proteinopathies
    DOI:  https://doi.org/10.1002/1873-3468.70061
  4. Cell Death Dis. 2025 May 03. 16(1): 359
    NDP52 and its emerging role in pathogenesis.
    Krenare Bruqi, Flavie Strappazzon.
      Autophagy is a pro-survival process that regulates the degradation and renewal of cellular components, making it a crucial mechanism for cellular homeostasis. There are selective forms of autophagy that are specific to a number of substrates, such as pathogens (bacteria or viruses), protein aggregates or excess/damaged organelles. These processes involve as key players autophagy receptors, that link the cargo to be degraded to the autophagic machinery. Among them, NDP52 (also known as CALCOCO2) has been described to act as a "bridge" between the autophagy machinery and (1) damaged mitochondria in the mitophagy process; (2) pathogens during xenophagy or (3) proteins in the process of aggrephagy. The aim of this review is to summarize the major functions of NDP52, and to highlight the existence of two human NDP52 variants that have been described as risk or protective factors for Crohn's disease or Multiple Sclerosis and Alzheimer's disease patients, respectively. As these three diseases share common pathological features that lead to inflammation, such as mitochondria or gut microbiota dysfunctions, but also pathogenic infections, it seems clear that NDP52 could be a key player at the crossroad by acting indirectly on inflammation, and therefore a potential target for clinical applications and benefits.
    DOI:  https://doi.org/10.1038/s41419-025-07668-z
  5. J Nutr Biochem. 2025 May 02. pii: S0955-2863(25)00106-8. [Epub ahead of print] 109943
    Mitochondrial fatty acid oxidation dysfunction impairs autophagic flux through ATP deficiency-caused lysosomal pH abnormity.
    Yan-Yu Zhang, Ze-Dong Lv, Mai Wang, Jun-Xian Wang, Samwel Mchele Limbu, Fang Qiao, Li-Qiao Chen, Mei-Ling Zhang, Yuan Luo, Zhen-Yu Du.
      Autophagy, a pivotal lysosomal degradation process, plays crucial roles in cellular homeostasis and energy metabolism. Mitochondrial fatty acid oxidation (FAO), a key mitochondrial function, is crucial for energy production. Generally, mitochondrial dysfunction exerts negative effects on autophagy, but the regulatory role of mitochondrial FAO dysfunction on the autophagic process remains unclear. The present study aimed to elucidate the role and mechanism of mitochondrial FAO in regulating autophagy process. We used Nile tilapia (Oreochromis niloticus) as a model and inhibited mitochondrial FAO by dietary mildronate feeding or knocking down carnitine palmitoyltransferase 1a. We found that mitochondrial FAO inhibition enhanced autophagy initiation and lysosomal proliferation accompanied by decreased autophagy degradation activity due to lysosomal acidification abnormity. Moreover, mitochondrial FAO inhibition decreased adenosine triphosphate (ATP) production and elevated adenosine monophosphate (AMP)/ATP promoted autophagy initiation via the AMP-activated protein kinase-serine/threonine kinase 1 pathway. Furthermore, mitochondrial FAO inhibition upregulated peroxisome proliferator-activated receptor alpha and retinoid X receptor alpha protein expression, which promoted transcription factor EB mRNA and its protein expression. Meanwhile, mitochondrial FAO inhibition led to lysosomal alkalinization, which is due to a pH increase caused by v-ATPase V1/V0 imbalance and ATP deficiency from mitochondrial dysfunction. Collectively, our results highlight the role of mitochondrial FAO in maintaining lysosomal homeostasis and autophagic flux through stabilizing lysosomal acidification.
    Keywords:  autophagy; fatty acid oxidation inhibition; lysosome; mitochondrial dysfunction; vacuolar ATPase
    DOI:  https://doi.org/10.1016/j.jnutbio.2025.109943
  6. FASEB J. 2025 May 15. 39(9): e70549
    Reduced Palmitoylation of SQSTM1/p62 in Huntington Disease Is Associated With Impaired Autophagy.
    F Abrar, M C Davies, Y Alshehabi, A Kumar, A Dang, Y T N Nguyen, J Collins, N S Caron, J S Choudhary, S S Sanders, M O Collins, M R Hayden, D D O Martin.
      Disruption of autophagy has emerged as a common feature in many neurodegenerative diseases. Autophagy is a membrane-dependent pathway that requires many key regulators to quickly localize on and off membranes during induction, promoting membrane fusion. Previously, our bioinformatic approaches have shown that autophagy and Huntington disease (HD) are enriched in palmitoylated proteins. Palmitoylation involves the reversible addition of long-chain fatty acids to promote membrane binding. Herein, we show that inhibition of palmitoylation regulates the abundance of several key regulators of autophagy and leads to a partial block of autophagic flux. We confirm that the autophagy receptor SQSTM1/p62 (sequestosome 1) is palmitoylated and directed to the lysosome. Importantly, we report that SQSTM1 palmitoylation is significantly reduced in HD patient and mouse model brains. This finding reveals a novel mechanism contributing to the generation of empty autophagosomes previously seen in HD models and patient-derived cells.
    DOI:  https://doi.org/10.1096/fj.202401781R
  7. Curr Biol. 2025 May 05. pii: S0960-9822(25)00384-7. [Epub ahead of print]35(9): R320-R322
    ER-to-lysosome-associated degradation.
    Maurizio Molinari.
      Maurizio Molinari introduces ER-to-lysosome-associated degradation - the autophagic and non-autophagic pathways that deliver ERAD-resistant misfolded proteins to the lysosome for degradation to maintain cellular proteostasis.
    DOI:  https://doi.org/10.1016/j.cub.2025.03.068
  8. Autophagy. 2025 May 06. 1-3
    SNX10 at the crossroad of endocytosis and piecemeal mitophagy.
    Laura Trachsel-Moncho, Benan John Mathai, Chiara Veroni, Anne Simonsen.
      Mitophagy targets damaged or dysfunctional mitochondria for lysosomal degradation. While canonical mitophagy pathways target the whole mitochondria for lysosomal degradation, it has become clear that selected mitochondrial components can be targeted for lysosomal degradation via other pathways, such as piecemeal mitophagy or mitochondria-derived vesicles. In a recent study, we identified the PX domain-containing endosomal protein SNX10 as a negative modulator of piecemeal mitophagy. Endosomal SNX10-positive vesicles dynamically interact with mitochondria and acquire selected mitochondrial proteins upon hypoxia. Zebrafish larvae lacking Snx10 show elevated Cox-IV degradation, increased levels of reactive oxygen species (ROS), and ROS-dependent neuronal death.
    Keywords:  SNX10; endosomal sorting; mitophagy; oxidative stress; zebrafish
    DOI:  https://doi.org/10.1080/15548627.2025.2499641
  9. Neuropharmacology. 2025 May 07. pii: S0028-3908(25)00210-2. [Epub ahead of print] 110504
    Rapamycin exerts neuroprotective effects by inhibiting FKBP12 instead of mTORC1 in the mouse model of Parkinson's disease.
    Zeyan Zhang, Ziyue Shen, Shiming Xie, Junyu Li, Zeyu Zhang, Sheng Zhang, Bo Peng, Qianchu Huang, Mingtao Li, Shanshan Ma, Qiaoying Huang.
      Parkinson's disease (PD), characterized by the selective loss of nigral dopaminergic neurons, is a common neurodegenerative disorder for which effective disease-modifying therapies remain unavailable. Rapamycin, a clinical immunosuppressant used for decades, has demonstrated neuroprotective effects in various animal models of neurological diseases, including PD. These effects are believed to be mediated through the inhibition of mammalian target of rapamycin (mTOR) complex 1 (mTORC1) signaling, with rapamycin binding to FKBP12. However, recent studies have suggested that mTOR activation can be neuroprotective in degenerating dopaminergic neurons, presenting a paradox to the neuroprotective mechanism of rapamycin via mTORC1 inhibition. In this study, we showed that mTORC1 signaling was inactivated in nigral dopaminergic neurons in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of PD. Notably, the optimal neuroprotective dose of rapamycin did not inhibit mTORC1 signaling nor restore autophagy defects in nigral dopaminergic neurons of MPTP-treated male C57BL/6 mice. Furthermore, acute Raptor knockout in dopaminergic neurons, which abolishes mTORC1 activity, did not diminish rapamycin's neuroprotective effects, suggesting that its protection is independent of mTORC1 inhibition. Importantly, rapamycin is also a potent inhibitor of FKBP12, a peptidyl-prolyl cis-trans isomerase highly expressed in the brain. Selective knockdown of FKBP12 in nigral dopaminergic neurons confers neuroprotective effects comparable to that of rapamycin, with no synergism observed when the two are combined. Collectively, our results indicate that rapamycin exerts neuroprotective effects in parkinsonian mice through inhibition of FKBP12 rather than mTORC1 signaling. These findings suggest that FKBP12 may serve as a novel target for disease-modifying therapies in PD.
    Keywords:  FKBP12; Parkinson’s disease; mTORC1; neuroprotection; rapamycin
    DOI:  https://doi.org/10.1016/j.neuropharm.2025.110504
  10. Proc Natl Acad Sci U S A. 2025 May 13. 122(19): e2414790122
    Unconventional secretion of PARK7 requires lysosomal delivery via chaperone-mediated autophagy and specialized SNARE complex.
    Biplab Kumar Dash, Yasuomi Urano, Yuichiro Mita, Yuki Ashida, Ryoma Hirose, Noriko Noguchi.
      PARK7/DJ-1, a redox-sensitive protein implicated in neurodegeneration, cancer, and inflammation, exhibits increased secretion under stress. We previously demonstrated that, as a leaderless protein, PARK7 relies on an unconventional autophagy pathway for stress-induced secretion. The current study delves deeper into the mechanisms governing PARK7 secretion under oxidative stress triggered by the neurotoxin 6-hydroxydopamine (6-OHDA). Here, we revealed that 6-OHDA-induced autophagic flux is critical for PARK7 secretion. Downregulation of syntaxin 17 (STX17), a SNARE protein crucial for autophagosome-lysosome fusion and cargo degradation, hindered PARK7 secretion. Likewise, impairing lysosomal function with bafilomycin A1 (BafA1) or chloroquine (CQ) diminished PARK7 release, highlighting the importance of functional lysosomes, potentially in the form of secretory autolysosomes, in PARK7 release. We also found that 6-OHDA appeared to promote the unfolding of PARK7, allowing its selective recognition by the chaperone HSPA8 via KFERQ-like motifs, leading to PARK7 translocation to the lysosomal membrane through LAMP2 via chaperone-mediated autophagy (CMA). Additionally, a dedicated SNARE complex comprising Qabc-SNAREs (STX3/4, VTI1B, and STX8) and R-SNARE SEC22B mediates the fusion of PARK7-containing autolysosomes with the plasma membrane, facilitating the extracellular release of PARK7. Hence, this study uncovers a mechanism where 6-OHDA-induced autophagic flux drives the unconventional secretion of PARK7, involving CMA for PARK7 translocation to lysosomes and specialized SNARE complexes for membrane fusion events.
    Keywords:  PARK7/DJ-1; SNAREs; chaperone-mediated autophagy; secretory autolysosome; unconventional secretion
    DOI:  https://doi.org/10.1073/pnas.2414790122
  11. Nat Neurosci. 2025 May 08.
    Stress and autophagy.
    Leonie Welberg.
      
    DOI:  https://doi.org/10.1038/s41593-025-01969-4
  12. Mol Cell Biol. 2025 May 09. 1-13
    Key Mechanisms in Lysosome Stability, Degradation and Repair.
    Rui Zhang, Marc A Vooijs, Tom Gh Keulers.
      Lysosomes are organelles that play pivotal roles in macromolecule digestion, signal transduction, autophagy, and cellular homeostasis. Lysosome instability, including the inhibition of lysosomal intracellular activity and the leakage of their contents, is associated with various pathologies, including cancer, neurodegenerative diseases, inflammatory diseases and infections. These lysosomal-related pathologies highlight the significance of factors contributing to lysosomal dysfunction. The vulnerability of the lysosomal membrane and its components to internal and external stimuli make lysosomes particularly susceptible to damage. Cells are equipped with mechanisms to repair or degrade damaged lysosomes to prevent cell death. Understanding the factors influencing lysosome stabilization and damage repair is essential for developing effective therapeutic interventions for diseases. This review explores the factors affecting lysosome acidification, membrane integrity, and functional homeostasis and examines the underlying mechanisms of lysosomal damage repair. In addition, we summarize how various risk factors impact lysosomal activity and cell fate.
    Keywords:  ESCRT; Lysosome stabilization; ROS; lipid peroxidation; lysophagy; lysosomal membrane permeabilization
    DOI:  https://doi.org/10.1080/10985549.2025.2494762
  13. Anim Cells Syst (Seoul). 2025 ;29(1): 296-311
    TRIM22 functions as a scaffold protein for autophagy initiation.
    Hyungsun Park, Hansol Heo, Yeongseo Song, Myung Shin Lee, Yebin Cho, Jae-Seon Lee, Jaerak Chang, Seongju Lee.
      Tripartite motif (TRIM) family proteins are increasingly recognized as important regulators of autophagy under various physiological and pathological conditions. TRIM22 has been previously shown to mediate autophagosome-lysosome fusion, but its potential role in earlier stages of autophagy remained unexplored. In this study, we investigated the function of TRIM22 in autophagy initiation. Overexpression of TRIM22 increased LC3-II levels and enhanced autophagic flux without affecting mTOR and AMPK activity. We found that TRIM22 interacts with components of both the ULK1 complex and the class III PI3K complex through distinct domains, recruiting them into punctate structures that represent autophagosome formation sites. Domain mapping revealed that the SPRY domain mediates interactions with ATG13 and FIP200, while the N-terminal region interacts with ULK1 and ATG101. The B-box domain of TRIM22 was identified as crucial for its interaction with Beclin-1, a key component of the class III PI3K complex. Deletion of this domain impaired the ability of TRIM22 to assemble the class III PI3K complex and induce autophagic flux. Interestingly, competitive binding assays revealed that Beclin-1 and PLEKHM1 bind to the same region of TRIM22, suggesting a mechanism for coordinating different stages of autophagy. The Alzheimer's disease-associated TRIM22 variant R321K maintained autophagy initiation function in both cell lines and primary neurons. These findings demonstrate that TRIM22 acts as a scaffold protein to promote autophagy initiation, in addition to its previously described role in autophagosome-lysosome fusion. Our study provides new insights into the molecular mechanisms by which TRIM proteins regulate multiple stages of the autophagy process.
    Keywords:  Autophagy; Beclin-1; Class III PI3K complex; TRIM22; ULK1 complex
    DOI:  https://doi.org/10.1080/19768354.2025.2498926
  14. Mol Neurobiol. 2025 May 06.
    A Ginsenoside Composition Ameliorated Aβ and Tau Aggregation via Autophagy Lysosome Pathway.
    Chengmu Zhao, Juan Yue, Yu Xie, Bo Liu, Shuaishuai Xu, Dejuan Zhi, Dongsheng Wang.
      Alzheimer's disease (AD) is a complex neurodegenerative disorder characterized by the abnormal deposition of amyloid-beta (Aβ) peptides and neurofibrillary tangles (NFTs). Ginsenosides, the primary active constituents in ginseng, exhibit potential in combating AD. In our previous work, the ginsenoside SumI was demonstrated to have superior anti-AD activity compared to other ginsenosides when used alone. This study revealed that SumI effectively decreased the lysosomal pH, promoted autophagosome formation, increased autophagic flux, and facilitated the transport of misfolded proteins to lysosomes for degradation in Caenorhabditis elegans. SumI activated the HLH-30 transcription factor by triggering a lipid-catabolic response akin to starvation. bec-1 RNAi significantly abrogated the anti-AD effect of SumI. Our findings indicate that SumI mitigated protein aggregation by activating the autophagy-lysosome pathway in C. elegans and provide scientific evidence that ginsenoside composition could be a potential therapeutic agent for treating or preventing AD.
    Keywords:  Alzheimer’s disease; Autophagosomes; Autophagy; Ginsenoside composition; Starvation-like effect
    DOI:  https://doi.org/10.1007/s12035-025-05017-x
  15. Sci Adv. 2025 May 09. 11(19): eadn2528
    Kinome screening identifies integrated stress response kinase EIF2AK1/HRI as a negative regulator of PINK1 mitophagy signaling.
    Pawan K Singh, Shalini Agarwal, Ilaria Volpi, Léa P Wilhelm, Giada Becchi, Andrew Keenlyside, Thomas Macartney, Rachel Toth, Adrien Rousseau, Glenn R Masson, Ian G Ganley, Miratul M K Muqit.
      Loss-of-function mutations in the PINK1 kinase lead to early-onset Parkinson's disease (PD). PINK1 is activated by mitochondrial damage to phosphorylate ubiquitin and Parkin, triggering mitophagy. PINK1 also indirectly phosphorylates Rab GTPases, such as Rab8A. Using an siRNA library targeting human Ser/Thr kinases in HeLa cells, we identified EIF2AK1 [heme-regulated inhibitor (HRI) kinase], a branch of the integrated stress response (ISR), as a negative regulator of PINK1. EIF2AK1 knockdown enhances mitochondrial depolarization-induced PINK1 stabilization and phosphorylation of ubiquitin and Rab8A. These results were confirmed in SK-OV-3, U2OS, and ARPE-19 cells. Knockdown of DELE1, an activator of EIF2AK1, produced similar effects. Notably, the ISR inhibitor ISRIB also enhanced PINK1 activation. In human cells with mito-QC mitophagy reporters, EIF2AK1 knockdown or ISRIB treatment increased PINK1-dependent mitophagy without affecting deferiprone-induced mitophagy. These findings suggest that the DELE1-EIF2AK1 ISR pathway is a negative regulator of PINK1-dependent mitophagy. Further evaluation in PD-relevant models is needed to assess the therapeutic potential of targeting this pathway.
    DOI:  https://doi.org/10.1126/sciadv.adn2528
  16. Autophagy. 2025 May 09. 1-18
    MoSec13 combined with MoGcn5b modulates MoAtg8 acetylation and regulates autophagy in Magnaporthe oryzae.
    Hui Qian, Ming-Hua Wu, Wen-Hui Zhao, Xue-Ming Zhu, Li-Xiao Sun, Jian-Ping Lu, Daniel J Klionsky, Fu-Cheng Lin, Xiao-Hong Liu.
      Macroautophagy/autophagy is an evolutionarily conserved cellular degradation process that is crucial for cellular homeostasis in Magnaporthe oryzae. However, the precise regulatory mechanisms governing autophagy in this organism remain unclear. In this study, we found a multiregional localization of MoSec13 to the vesicle membrane, endoplasmic reticulum, nucleus, and perinucleus. MoSec13 negatively regulated autophagy through specific amino acid residues in its own WD40 structural domain by interacting with MoAtg7 and MoAtg8. We also found that the histone acetyltransferase MoGcn5b mediated the acetylation of MoAtg8 and regulated autophagy activity. Subsequently, we further determined that MoSec13 regulated the acetylation status of MoAtg8 by controlling the interaction between MoGcn5b and MoAtg8 in the nucleus. In addition, MoSec13 maintained lipid homeostasis by controlling TORC2 activity. This multilayered integration establishes MoSec13 as an essential node within the autophagic regulatory network. Our findings fill a critical gap in understanding the role of Sec13 in autophagy of filamentous fungi and provide a molecular foundation for developing new therapeutic strategies against rice blast fungus.ABBREVIATIONS BFA: brefeldin A; BiFC: bimolecular fluorescence complementation; CM: complete medium; CMAC: 7-amino-4-chloromethylcoumarin; Co-IP: co-immunoprecipitation; COPII: coat complex II; GFP: green fluorescent protein; HPH: hygromycin phosphotransferase; MM-N: nitrogen-starvation conditions; NPC: nuclear pore complex; PAS: phagophore assembly site; PE: phosphatidylethanolamine; UPR: unfolded protein response.
    Keywords:  Autophagy; Gcn5b; Magnaporthe oryzae; Sec13; TORC2
    DOI:  https://doi.org/10.1080/15548627.2025.2499289
  17. Nat Commun. 2025 May 06. 16(1): 4201
    mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery.
    Julia Hermann, Toman Borteçen, Robert Kalis, Alexander Kowar, Catarina Pechincha, Vivien Vogt, Martin Schneider, Dominic Helm, Jeroen Krijgsveld, Fabricio Loayza-Puch, Johannes Zuber, Wilhelm Palm.
      Synthesizing the cellular proteome is a demanding process that is regulated by numerous signaling pathways and RNA modifications. How precisely these mechanisms control the protein synthesis machinery to generate specific proteome subsets remains unclear. Here, through genome-wide CRISPR screens we identify genes that enable mammalian cells to adapt to inactivation of the kinase mechanistic target of rapamycin complex 1 (mTORC1), the central driver of protein synthesis. When mTORC1 is inactive, enzymes that modify tRNAs at wobble uridines (U34-enzymes), Elongator and Ctu1/2, become critically essential for cell growth in vitro and in tumors. By integrating quantitative nascent proteomics, steady-state proteomics and ribosome profiling, we demonstrate that the loss of U34-enzymes particularly impairs the synthesis of ribosomal proteins. However, when mTORC1 is active, this biosynthetic defect only mildly affects steady-state protein abundance. By contrast, simultaneous suppression of mTORC1 and U34-enzymes depletes cells of ribosomal proteins, globally inhibiting translation. Thus, mTORC1 cooperates with tRNA U34-enzymes to sustain the protein synthesis machinery and support the high translational requirements of cell growth.
    DOI:  https://doi.org/10.1038/s41467-025-59185-4
  18. Curr Biol. 2025 May 02. pii: S0960-9822(25)00457-9. [Epub ahead of print]
    Reticulon-dependent ER-phagy mediates adaptation to heat stress in C. elegans.
    Claudia Serot, Vincent Scarcelli, Alexandre Pouget, Céline Largeau, Audrey Sagot, Kenza El-Hachami, Denis Dupuy, Emmanuel Culetto, Christophe Lefebvre, Renaud Legouis.
      The selective degradation of endoplasmic reticulum (ER) by autophagy, named ER-phagy, promotes the recovery of ER homeostasis after stress. Depending on the ER stress, different types of ER-phagy involve various selective autophagy receptors. In this study, we report a macroER-phagy induced by the fragmentation of tubular ER in response to acute heat stress. We identified a novel ER-phagy receptor encoded by the reticulon long isoform RET-1d. RET-1d is mainly expressed in the nervous system and the epidermis and colocalizes with the ubiquitin-like autophagy protein LGG-1/GABARAP during heat-stress-induced autophagy. Two LC3-interacting region (LIR) motifs in the long intrinsically disordered region of RET-1d mediate its interaction with the LGG-1 protein. The specific depletion of the RET-1d isoform or the mutations of the LIRs resulted in a defective ER-phagy and a decrease in the capacity of animals to adapt to heat stress. Our data revealed a RET-1d- and LGG-1-dependent ER-phagy mechanism that takes place in neurons and epidermis and participates in the adaptation of C. elegans to heat stress.
    Keywords:  ER stress; LGG-1/Gabarap; LIR motif; RET-1 isoforms; autophagosomes; autophagy; development; endoplasmic reticulum; locomotion; neuron
    DOI:  https://doi.org/10.1016/j.cub.2025.04.028
  19. Cell Death Differ. 2025 May 03.
    Deacetylation of ANXA2 by SIRT2 desensitizes hepatocellular carcinoma cells to donafenib via promoting protective autophagy.
    Liangbo Sun, Meng He, Dong Liu, Meihua Shan, Lingxi Chen, Mingzhen Yang, Xufang Dai, Jie Yao, Tao Li, Yan Zhang, Yang Zhang, Li Xiang, An Chen, Yingxue Hao, Fengtian He, Haojun Xiong, Jiqin Lian.
      Hepatocellular carcinoma (HCC) is one of the most lethal forms of cancer globally. HCC cells frequently undergo macroautophagy, also known as autophagy, which can lead to tumor progression and chemotherapy resistance. Annexin A2 (ANXA2) has been identified as a potential therapeutic target in HCC and is involved in the regulation of autophagic process. Here, we for the first time showed that ANXA2 deacetylation plays a crucial role in donafenib-induced autophagy. Mechanistically, donafenib increased SIRT2 activity via triggering both SIRT2 dephosphorylation and deacetylation by respectively downregulating cyclin E/CDK and p300. Moreover, elevation of SIRT2 activity by donafenib caused ANXA2 deacetylation at K81/K206 sites, leading to a reduction of the binding between ANXA2 and mTOR, which resulted in a decrease of mTOR phosphorylation and activity, and ultimately promoted protective autophagy and donafenib insensitivity in HCC cells. Additionally, ANXA2 deacetylation at K81/K206 sites was positively correlated with poor prognosis in HCC patients. Meanwhile, we found that selective inhibition of SIRT2 increased the sensitivity of donafenib in HCC cells by strengthening ANXA2 acetylation. In summary, this study reveals that donafenib induces protective autophagy and decreases its sensitivity in HCC cells through enhancing SIRT2-mediated ANXA2 deacetylation, which suggest that targeting ANXA2 acetylation/deacetylation may be a promising strategy for improving the sensitivity of donafenib in HCC treatment.
    DOI:  https://doi.org/10.1038/s41418-025-01499-3
  20. Curr Biol. 2025 May 01. pii: S0960-9822(25)00504-4. [Epub ahead of print]
    Biased regulation of protein synthesis and hypoxic death by a conditional raptor mutation.
    Chun-Ling Sun, Cong Xu, Omar Itani, Elyse L Christensen, Harshitha Vijay, Jessica Ho, Abraham Correa-Medina, Christian B Klingler, Neal D Mathew, Stephane Flibotte, Ian R Humphreys, Diego Delgadillo Rubalcaba, Alison E Ritter, Muriel Desbois, Brock Grill, C Michael Crowder.
      Mechanistic target of rapamycin (mTOR) functions in mTOR complex 1 (mTORC1) with raptor to match metazoan metabolism to available nutrients to regulate multiple cellular, physiological, and pathological processes. Hypoxic cellular injury is influenced by the mTORC1 pathway, but whether its activity promotes or prevents injury is unclear, and which mTORC1-regulated mechanisms control hypoxic injury are obscure. Here, we report the discovery of a hypoxia-resistant, temperature-sensitive raptor mutant in an unbiased forward mutagenesis screen in C. elegans. This raptor mutant is both hypoxia resistant and long lived at intermediate temperatures, while unable to develop at higher temperatures. Temperature-shift experiments show that the conditional hypoxia resistance can be induced in the raptor mutant immediately prior to the hypoxic insult. At these intermediate temperatures, the raptor mutation selectively reduces protein synthesis without affecting autophagy, and epistasis experiments implicate mTOR-targeted translation regulators as components of the hypoxia resistance mechanism. Using the conditional developmental arrest phenotype in a selection for suppressors of raptor loss of function, we isolated multiple second-site raptor missense mutants, whose mutated residue is predicted to interact with RagA, a raptor-binding protein. These suppressor mutations restore normal protein synthesis, hypoxic sensitivity, and lifespan and thereby implicate raptor-RagA interactions as critical to these biological processes.
    Keywords:  C. elegans; anoxia; autophagy; cell death; conditional mutant; mTOR; mTORC1; metabolism; rapamycin; translation
    DOI:  https://doi.org/10.1016/j.cub.2025.04.040
  21. Curr Biol. 2025 May 05. pii: S0960-9822(25)00359-8. [Epub ahead of print]35(9): R342-R344
    Nucleophagy: A two-step exit with the help of an outsider.
    Georgios Konstantinidis, Nektarios Tavernarakis.
      Maintenance of nuclear surveillance and quality control is paramount to a cell's long-term survival and function. A new study reveals how nucleophagy achieves the selective recycling of nuclear components via the autophagic pathway in the cytoplasm without compromising the integrity of the nuclear envelope.
    DOI:  https://doi.org/10.1016/j.cub.2025.03.043
  22. Biochem Biophys Res Commun. 2025 Apr 28. pii: S0006-291X(25)00630-8. [Epub ahead of print]768 151916
    Selenium corrects dysregulated mitophagy and lipophagy in obesity-related acute pancreatitis through the GPX1-Mfn2-PLIN2 axis.
    Peiyu Han, Xiaoyu Ma, Yuqiu Ge, Hongbo Ren, Yu Wu.
      The incidence of acute pancreatitis (AP) has been on the rise in recent years. Obesity, a significant contributor to AP, increases the risk of AP and promotes disease progression, leading to adverse outcomes. Mitophagy and lipophagy are two main types of selective autophagy in AP and obesity, but their contribution to comorbidity in obesity-related AP (OB-AP) remains unknown. This study demonstrated that OB-AP exhibited more severe pancreatic injury than AP in vivo and in vitro. We found that the balance between mitophagy and lipophagy was disrupted, with a significant increase in mitophagy and a corresponding significant decrease in lipophagy. Mechanistically, overexpression of selenoprotein glutathione peroxidase 1 (GPX1) stabilized mitofusin 2 (Mfn2) protein, promoting the interaction between Mfn2 and perilipin 2 (PLIN2), and thereby attenuating excessive mitophagy and increasing lipophagy. Selenium supplementation improved pancreatic autophagy homeostasis in OB-AP through increasing GPX1 expression, thereby reducing disease severity. Notably, OB-AP patients exhibited lower selenium levels than healthy individuals. In conclusion, selenium supplementation enhanced GPX1 expression, corrected the imbalance between mitophagy and lipophagy, and mitigated disease severity in OB-AP through the GPX1-Mfn2-PLIN2 axis, and therefore has therapeutic potential in OB-AP.
    Keywords:  Glutathione peroxidase 1; Lipophagy; Mitophagy; Obesity-related acute pancreatitis; Selenium
    DOI:  https://doi.org/10.1016/j.bbrc.2025.151916
  23. Burns. 2025 Apr 18. pii: S0305-4179(25)00140-8. [Epub ahead of print]51(5): 107511
    Hypoxia impairs autophagy of cardiomyocytes via p38/MAPK/MAP4 pathway.
    Nuo Chen, Qiongfang Ruan, Siyu Zhang, Zhigang Chu, Weiguo Xie.
       BACKGROUND: Myocardial hypoxia occurs in severe burns and may cause severe cardiac dysfunction, in which the blockage of the autophagy flux plays an important role. Previous studies indicates that the p38/MAPK pathway is involved in regulating the microtubule structure by regulating MAP4 phosphorylation, and the microtubule structure affects the autophagy. However, as a complex degradation process, how autophagy is specifically affected by microtubules remains unknown. An in-depth understanding of hypoxia-related autophagy disorders is critical for the treatment of myocardial injury.
    METHODS: Cardiomyocytes (CMs) were isolated from the ventricles of neonatal Sprague-Dawley rats and cultured in an incubator filled with 1 % O2, 5 % CO2, and 94 % N2. SB203580 and MKK6 (Glu) recombinant adenovirus were used to specifically inhibit and activate the p38/MAPK pathway, respectively. The adeno-associated viruses (AAVs) encoding MAP4 gene and MAP4 siRNA were used to up-regulate and down-regulate the expression of MAP4, respectively. After infection of cells with AAV encoding GFP-LC3 fusion proteins, the number of green spots under fluorescence microscopy shows the quantity of autophagosomes. Western blots access the expression of LC3-II, LC3-I and p62. The ratio of LC3-II to LC3-I (LC3-II/I) tells the quantity of autophagosomes, and the expression of p62 indicates the extent of autophagosome degradation. Cell Counting Kit 8 was used to detect cell viability. Rapamycin was used to recover the autophagy.
    RESULTS: Hypoxia reduced the viability of cardiomyocytes, in which the quantity of autophagosomes is increased, while the degradation is reduced, and the p38/MAPK pathway is activated. Activation of the p38/MAPK pathway could block the autophagy pathway. The phosphorylation of MAP4 did not affect the quantity of autophagosomes, but hindered its degradation. The p38/MAPK pathway could regulate the phosphorylation of MAP4. Finally, when the autophagy pathway was restored, cell viability has partially recovered.
    CONCLUSIONS: Hypoxia regulates the phosphorylation of MAP4 through the p38/MAPK pathway, thereby hindering the degradation of autophagosomes, rather than the quantity, blocking autophagic flux and ultimately affecting cell viability.
    Keywords:  Autophagy; Cardiomyocytes; Hypoxia; Microtubule-associated protein
    DOI:  https://doi.org/10.1016/j.burns.2025.107511
  24. Nat Commun. 2025 May 07. 16(1): 4243
    p97/VCP is required for piecemeal autophagy of aggresomes.
    Maria Körner, Paul Müller, Hirak Das, Felix Kraus, Timo Pfeuffer, Sven Spielhaupter, Silke Oeljeklaus, Christina Schülein-Völk, J Wade Harper, Bettina Warscheid, Alexander Buchberger.
      Metazoan cells adapt to the exhaustion of protein quality control (PQC) systems by sequestering aggregation-prone proteins in large, pericentriolar structures termed aggresomes. Defects in both aggresome formation and clearance affect proteostasis and have been linked to neurodegenerative diseases, but aggresome clearance pathways are still underexplored. Here we show that aggresomes comprising endogenous proteins are cleared via selective autophagy requiring the cargo receptor TAX1BP1. TAX1BP1 proximitomes reveal the presence of various PQC systems at aggresomes, including Hsp70 chaperones, the 26S proteasome, and the ubiquitin-selective unfoldase p97/VCP. While Hsp70 and p97/VCP with its cofactors UFD1-NPL4 and FAF1 play key roles in aggresome disassembly, the 26S proteasome is dispensable. We identify aggresomal client proteins that are degraded via different routes, in part in a p97/VCP-dependent manner via aggrephagy. Upon acute inhibition of p97/VCP, aggresomes fail to disintegrate and cannot be incorporated into autophagosomes despite the presence of factors critical for aggrephagosome formation, including p62/SQSTM1, TAX1BP1, and WIPI2. We conclude that the p97/VCP-mediated removal of ubiquitylated aggresomal clients is essential for the disintegration and subsequent piecemeal autophagy of aggresomes.
    DOI:  https://doi.org/10.1038/s41467-025-59556-x
  25. Spectrochim Acta A Mol Biomol Spectrosc. 2025 Apr 29. pii: S1386-1425(25)00625-0. [Epub ahead of print]340 126319
    Mitochondrial viscosity, oxidative stress and autophagy responsive fluorescent Zn(II) complex for monitoring non-alcoholic fatty liver disease.
    Yu Zhang, Ya-Ping Wang, Hui-Li Sun, Xiao-Dong Zhang, Shao-Qi Guan, Mei Pan.
      Accumulating evidence highlights the critical role of dysfunctional mitochondrial quality control in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). However, there is limited information available regarding of viscosity-related cellular metabolic processes of NAFLD. To address this, we developed a novel viscosity-sensitive fluorescent metal Zn(II) complex, LIFM-ZY-1, for monitoring viscosity changes with one-photon (OP) and two-photon (TP) fluorescence. It could effectively track cellular oxidative stress induced by lipotoxicity with viscosity changes, as reflected by viscosity changes in the OP/TP channel. Besides, LIFM-ZY-1 was capable of detecting non-selective mitophagy triggered by starvation in real time and selective mitophagy induced by autophagy drug rapamycin. Moreover, LIFM-ZY-1 successfully monitored the deterioration and therapeutic outcome of NAFLD mice with changing viscosity induced by overeating and autophagy drug empagliflozin. Overall, our findings demonstrated the potential of LIFM-ZY-1 as a valuable tool for real time monitoring NAFLD treatment through viscosity, oxidative stress and autophagy changes, offering valuable insights into the underlying biological processes and potential therapeutic strategies for NAFLD.
    Keywords:  Metabolic processes; NAFLD; TP fluorescence; Viscosity changes; Zinc (II) complex
    DOI:  https://doi.org/10.1016/j.saa.2025.126319
  26. Int J Mol Sci. 2025 Apr 14. pii: 3699. [Epub ahead of print]26(8):
    NSP6 of SARS-CoV-2 Dually Regulates Autophagic-Lysosomal Degradation.
    Haijiao Zhang, Jianying Chang, Ren Sheng.
      The pandemic of coronavirus disease 2019 (COVID-19), brought about by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has significantly impacted public health and the economy. A fundamental aspect of addressing this virus lies in elucidating the mechanisms through which it induces disease. Our study reveals that Non-structural protein 6 (NSP6) of SARS-CoV-2 promotes the initiation of autophagy by activating Beclin1. In the later stage of autophagy, however, NSP6 causes a blockage in the autophagy-lysosome degradation via the inhibition of Mucolipin 1 (MLN1). The single nucleotide polymorphism (SNP) L37F in NSP6, which is associated with asymptomatic infection, similarly enhances the initiation of autophagy but displays a reduced ability to impede lysosome-dependent degradation. In summary, we demonstrated the dual-regulation mechanism of NSP6 in autophagy, which may be one of the reasons for targeting cellular autophagy to induce viral pathogenesis. This finding may provide promising new directions for future research and clinical interventions.
    Keywords:  Beclin1; COVID-19; MLN1; NSP6; SARS-CoV-2; autophagy–lysosome degradation
    DOI:  https://doi.org/10.3390/ijms26083699
  27. Dev Cell. 2025 May 02. pii: S1534-5807(25)00250-3. [Epub ahead of print]
    Lymphatic endothelial mTORC1 instructs metabolic and developmental signaling during lymphangiogenesis.
    Fei Han, Summer Simeroth, Jie Zhu, Irma Gryniuk, Atul Pranay, Weiqing Chen, Yuan Wang, Yuanyuan Cai, Zhiyuan Shen, Guangyu Wang, Courtney T Griffin, Lijun Xia, Pengchun Yu.
      The lymphatic vasculature comprises lymphatic capillaries and collecting vessels. To support lymphatic development, lymphatic endothelial cells (LECs) utilize nutrients to fuel lymphangiogenic processes. Meanwhile, LECs maintain constant prospero homeobox 1 (PROX1) expression critical for lymphatic specification. However, molecular mechanisms orchestrating nutrient metabolism while sustaining PROX1 levels in LECs remain unclear. Here, we show that loss of RAPTOR, an indispensable mechanistic target of rapamycin complex 1 (mTORC1) component, downregulates PROX1 and impairs lymphatic capillary growth and differentiation of collecting lymphatics in mice. Mechanistically, mTORC1 inhibition in mouse and human LECs causes Myc reduction, which decreases hexokinase 2 (HK2) and glutaminase (GLS), inhibiting glycolysis and glutaminolysis. Myc or HK2/GLS ablation impedes lymphatic capillary and collecting vessel formation. Interestingly, mTORC1 regulation of PROX1 is independent of Myc-HK2/GLS signaling. Moreover, genetic interaction analysis indicates that Myc and PROX1 play crucial roles in mTORC1-regulated lymphatic development. Collectively, our findings identify mTORC1 as a key regulator of metabolic programs and PROX1 expression during lymphangiogenesis.
    Keywords:  Myc; PROX1; glutaminase; glutaminolysis; glycolysis; hexokinase 2; lymphangiogenesis; lymphatic endothelial cell; lymphatic vessel; mTORC1
    DOI:  https://doi.org/10.1016/j.devcel.2025.04.012
  28. Autophagy. 2025 May 04. 1-21
    AlphaFold2 SLiM screen for LC3-LIR interactions in autophagy.
    Jan Felix Maximilian Stuke, Gerhard Hummer.
      In selective macroautophagy/autophagy, cargo recruitment is mediated by MAP1LC3/LC3-interacting regions (LIRs)/Atg8-family interacting motifs (AIMs) in the cargo or cargo receptor proteins. The binding of these motifs to LC3/Atg8 proteins at the phagophore membrane is often modulated by post-translational modifications, especially phosphorylation. As a challenge for computational LIR predictions, sequences may contain the short canonical (W/F/Y)XX(L/I/V) motif without being functional. Conversely, LIRs may be formed by non-canonical but functional sequence motifs. AlphaFold2 has proven to be useful for LIR predictions, even if some LIRs are missed and proteins with thousands of residues reach the limits of computational feasibility. We present a fragment-based approach to address these limitations. We find that fragment length and phosphomimetic mutations modulate the interactions predicted by AlphaFold2. Systematic fragment screening for a range of target proteins yields structural models for interactions that AlphaFold2 and AlphaFold3 fail to predict for full-length targets. We provide guidance on fragment choice, sequence tuning, LC3 isoform effects, and scoring for optimal LIR screens. Finally, we also test the transferability of this general framework to SUMO-SIM interactions, another type of protein-protein interaction involving short linear motifs (SLiMs).Abbreviations: 2-HP-LIR: ncLIR binding either or both HPs with non-canonical residues; AIM: Atg8-family interacting motif; ap. LIR: antiparallel LIR; A.t.; Arabidopsis thaliana; AT5G06830/C53 (A.t.): CDK5RAP3-like protein; Atg8/ATG8: autophagy related 8, in yeast and plants, respectively; ATG8CL: ATG8C-like of Solanum tuberosum (potato); ATG8E: ATG8e of A.t.; Av. num. of contacts: average number of heavy atom contacts; BCL2: BCL2 apoptosis regulator; BNIP3: BCL2 interacting protein 3; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CALR: calreticulin; can. LIR: canonical LIR; CDF: cumulative distribution function; CDK5RAP3/C53 (H.s.): CDK5 regulatory subunit associated protein 3; [DE]W[DE]-LIR: TRIM5-like ncLIR; DSK2A: ubiquitin domain-containing protein DSK2a; FUNDC1: FUN14 domain containing 1; GABARAP: GABA type A receptor-associated protein; HP0/1/2: hydrophobic pocket 0/1/2; HP0-LIR: ncLIR engaging HP0; H.s.; Homo sapiens; lcLIR: low-confidence LIR (ncLIR not similar to previously characterized ncLIRs); LDS: LIR-docking site; LIR: LC3-interacting region; LO score: length-weighted fraction of occurrence score; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MD: molecular dynamics; MEFV/pyrin: MEFV innate immunity regulator, pyrin; minPAE: minimum PAE; MSA: multiple sequence alignment; ncLIR: non-canonical LIR; NPC: nuclear pore complex; Nup159: nucleoporin 159; NUP214: nucleoporin 214; OPTN: optineurin; other@LDS: other interaction proximal to the LIR-docking site; PAE: predicted aligned error; PDCD6IP: programmed cell death 6 interacting protein; PDF: probability distribution function; pLDDT: predicted local-distance difference test; PLEKHM1: pleckstrin homology and RUN domain containing M1; PTM: post-translational modification; sAIM: shuffled AIM (ncLIR with shuffled motif); seq.: sequence; SIM: SUMO-interacting motif; SLiM: short linear motif; SMN1/SMN: survival of motor neuron 1, telomeric; ST: phosphomimetic; STBD1: starch binding domain 1; STK3: serine/threonine kinase 3; SUMO: small ubiquitin like modifier; TBC1D2/TBC1D2A: TBC1 domain family member 2; TEX264: testis expressed 264, ER-phagy receptor; TRIM5/TRIM5α: tripartite motif-containing protein 5; UDS: UIM-docking site; UIM: ubiquitin-interacting motif; UIMC1/RAP80: ubiquitin interaction motif containing 1; ULK1: unc-51 like autophagy activating kinase 1; ULK2: unc-51 like autophagy activating kinase 2; WT: wild type.
    Keywords:  AIM; Atg8; SUMO-SIM interaction; phosphorylation; prediction; selective autophagy receptor
    DOI:  https://doi.org/10.1080/15548627.2025.2493999
  29. Atherosclerosis. 2025 Apr 26. pii: S0021-9150(25)00114-5. [Epub ahead of print]405 119216
    Valine acts as an early biomarker and exacerbates pathological cardiac hypertrophy by impairing mitochondrial quality control.
    Hongyu Kuang, Dan Li, Yunlin Chen, Hongmi Zou, Fang Li, Zhiyan Gong, Yuxiang Long, Hao Zhou, Huaan Du, Yuehui Yin.
       OBJECTIVE: Pathological cardiac hypertrophy is an independent risk factor for heart failure (HF). Early identification and timely treatment are crucial for significantly delaying the progression of HF.
    METHODS: Targeted amino acid metabolomics and RNA sequencing (RNA-seq) were combined to explore the underlying mechanism. In vitro, H9c2 cells were stimulated with angiotensin II (Ang II) or were incubated with extra valine after Ang II stimulation. The branched chain alpha-ketoate dehydrogenase kinase (Bckdk) inhibitor 3,6-dichlorobenzo[b]thiophene-2-carboxylic acid (BT2) and rapamycin were utilized to confirm the role of the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway in this process.
    RESULTS: A significant accumulation of valine was detected within hypertrophic hearts from spontaneously hypertensive rats (SHR). When branched chain amino acid (BCAA) degradation was increased by BT2, the most pronounced decrease was observed in the valine level (Δ = 0.185 μmol/g, p < 0.001), and cardiac hypertrophy was ameliorated. The role of imbalanced mitochondrial quality control (MQC), including the suppression of mitophagy and excessive mitochondrial fission, was revealed in myocardial hypertrophy. In vitro, high concentrations of valine exacerbated cardiomyocyte hypertrophy stimulated by Any II, resulting in the accumulation of impaired mitochondria and respiratory chain dysfunction. BT2, rapamycin, and mitochondrial division inhibitor 1 (Mdivi-1) all ameliorated MQC imbalance, mitochondrial damage and oxidative stress in hypertensive models with high valine concentration.
    CONCLUSION: Valine exacerbated pathological cardiac hypertrophy by causing a MQC imbalance, probably as an early biomarker for cardiac hypertrophy under chronic hypertension.
    Keywords:  Branched chain amino acids; Cardiac hypertrophy; Mitophagy; Oxidative stress; Valine
    DOI:  https://doi.org/10.1016/j.atherosclerosis.2025.119216
  30. J Biochem. 2025 May 07. pii: mvaf022. [Epub ahead of print]
    Inhibition of autophagy by Atg7 knockdown enhances chemosensitivity in gemcitabine/paclitaxel-resistant pancreatic cancer MIAPaCa2 cells.
    Yudai Kudo, Kotaro Hirota, Honoka Tsuzuki, Shinya Kawano, Tomofumi Saka, Riri Hayashi, Yuta Yoshino, Akira Ikari, Satoshi Endo.
      The 5-year survival rate for pancreatic cancer is extremely low, at approximately 12%, primarily because most patients present with advanced and unresectable tumors. Chemotherapy regimens, such as gemcitabine (GEM) plus paclitaxel (PTX) and FOLFIRINOX, are standard treatments; however, resistance to these therapies remains a major challenge. Autophagy has been implicated in this resistance. Both the Atg8 and Atg12 conjugation systems are essential for autophagosome maturation, and the ubiquitin-like protein activator Atg7 plays an essential role in these systems. This study investigated the effects of Atg7 knockdown on GEM/PTX sensitivity in GEM/PTX-resistant pancreatic cancer MIAPaCa2 (GP-R) cells. GP-R cells exhibited reduced sensitivity to GEM/PTX, increased expression of autophagy-related factors, and elevated basal autophagy compared to parental cells. Atg7 knockdown in GP-R cells effectively inhibited both basal and GEM/PTX-induced autophagy, significantly increased total and mitochondrial reactive oxygen species (ROS), and led to the induction of apoptotic cell death. These findings suggest that autophagy inhibition via Atg7 knockdown enhances GEM/PTX sensitivity in GP-R cells. In conclusion, targeting Atg7 to inhibit autophagy may be a promising approach to improving the efficacy of GEM/PTX therapy in pancreatic cancer.
    Keywords:  Atg7; Autophagy; anticancer drug resistance; pancreatic cancer
    DOI:  https://doi.org/10.1093/jb/mvaf022
  31. Nature. 2025 May 07.
    PLA2G15 is a BMP hydrolase and its targeting ameliorates lysosomal disease.
    Kwamina Nyame, Jian Xiong, Hisham N Alsohybe, Arthur P H de Jong, Isabelle V Peña, Ricardo de Miguel, Thijn R Brummelkamp, Guido Hartmann, Sebastian M B Nijman, Matthijs Raaben, Judith A Simcox, Vincent A Blomen, Monther Abu-Remaileh.
      Lysosomes catabolize lipids and other biological molecules, maintaining cellular and organismal homeostasis. Bis(monoacylglycero)phosphate (BMP), a major lipid constituent of intralysosomal vesicles, stimulates lipid-degrading enzymes and is altered in various human conditions, including neurodegenerative diseases1,2. Although lysosomal BMP synthase was recently discovered3, the enzymes mediating BMP turnover remain elusive. Here we show that lysosomal phospholipase PLA2G15 is a physiological BMP hydrolase. We further demonstrate that the resistance of BMP to lysosomal hydrolysis arises from its unique sn2, sn2' esterification position and stereochemistry, as neither feature alone confers resistance. Purified PLA2G15 catabolizes most BMP species derived from cell and tissue lysosomes. Furthermore, PLA2G15 efficiently hydrolyses synthesized BMP stereoisomers with primary esters, challenging the long-held thought that BMP stereochemistry alone ensures resistance to acid phospholipases. Conversely, BMP with secondary esters and S,S stereoconfiguration is stable in vitro and requires acyl migration for hydrolysis in lysosomes. Consistent with our biochemical data, PLA2G15-deficient cells and tissues accumulate several BMP species, a phenotype reversible by supplementing wild-type PLA2G15 but not its inactive mutant. Targeting PLA2G15 reduces the cholesterol accumulation in fibroblasts of patients with Niemann-Pick disease type C1 and significantly ameliorates disease pathologies in Niemann-Pick disease type C1-deficient mice, leading to an extended lifespan. Our findings established the rules governing BMP stability in lysosomes and identified PLA2G15 as a lysosomal BMP hydrolase and a potential target for therapeutic intervention in neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s41586-025-08942-y
  32. Front Pharmacol. 2025 ;16 1578400
    mTOR-mediated nutrient sensing and oxidative stress pathways regulate autophagy: a key mechanism for traditional Chinese medicine to improve diabetic kidney disease.
    Liu Li, Junju Zou, Tongyi Zhou, Xiu Liu, Danni Tan, Qin Xiang, Rong Yu.
       Context: Autophagy plays a pivotal role in the pathogenesis of DKD, and the mechanistic target of rapamycin (mTOR) pathway, which regulates nutrient sensing and oxidative stress responses, is a key regulator of autophagy. Traditional Chinese Medicine (TCM) has garnered attention for its potential to treat DKD by modulating the mTOR signaling pathway, reducing oxidative stress, and restoring autophagic function.
    Objective: The objective of this study is to examine how mTOR-mediated regulation of nutrient sensing and oxidative stress impacts autophagy in DKD, and to explore how TCM modulates these pathways to improve the condition.
    Methods: A systematic review was conducted using PubMed, Web of Science, Wanfang Data, and China National Knowledge Infrastructure (CNKI), with the search extended to December 2024. The search subject terms included 'diabetic kidney disease,' 'Traditional Chinese Medicine,' 'mTOR,' 'nutrient sensing,' and 'oxidative stress.' Studies were rigorously screened by two investigators.
    Results: This review systematically examines the pathogenesis of mTOR-mediated nutrient sensing dysfunction and oxidative stress in DKD, highlighting their impact on autophagy. It further clarifies how these mechanisms are targeted by Chinese medicine in the treatment of DKD. The review summarizes the potential mechanisms by which TCM, including monomers (e.g., Astragaloside IV), individual botanical drugs (e.g., Dendrobium nobile Lindl.), and compound formulations (e.g., Tongluo Digui Decoction), regulate autophagy in DKD through pathways such as AMP-activated protein kinase (AMPK), mTOR, sirtuins (Sirt), and the phosphatidylinositol three kinase (PI3K)/Akt/mTOR signaling pathway. TCM compound formulas share a common foundational framework, with the majority being formulated based on therapeutic principles such as 'Yiqi', 'Yangyin', 'Tongluo', and 'Huashi'.
    Conclusion: TCM shows promise in treating DKD, with unique advantages in modulating key signaling pathways. However, the underlying mechanisms remain complex and warrant further investigation.
    Keywords:  autophagy; diabetic kidney disease; mTOR; mechanism; oxidative stress; sense of nutrition; traditional Chinese medicine
    DOI:  https://doi.org/10.3389/fphar.2025.1578400
  33. ACS Chem Neurosci. 2025 May 09.
    Promoting Secretion of Pathological Tau Species Using an Induced Proximity Platform That Engages the Autophagy Pathway.
    Yekaterina Kovalyova, Cesar De Leon, Alicja Krasowska-Zoladek, Sokreine Suon, Jacky Wong, Seth Young, Julien Lee Heberling, Laura Price, Raphaëlle Berger, Brian Magliaro, Yu-Shan Cheng, Andrea Peier, Deborah M Rothman, Abbas Walji, Sean Smith, Jacob Marcus, Xiaoqing Han, Marija Usenovic.
      Intracellular accumulation of aberrantly phosphorylated aggregated tau protein can contribute to neuronal dysfunction associated with many neurodegenerative diseases. Thus, removing such tau species is an attractive therapeutic hypothesis for these diseases. Targeted protein degradation (TPD) strategies leveraging the autophagy-lysosome pathway (ALP) are promising approaches to decrease protein aggregates by designating them for degradation. Here, we developed a novel heterobifunctional molecule, MRL828, combining a tau pathology-binding ligand and modified guanine moiety based on the autophagy-targeting chimaera technology to selectively designate aggregated tau proteins for clearance via the ALP. Surprisingly, the MRL828-dependent decrease in intracellular tau aggregates was dependent on the autophagosome, but not the lysosome. MRL828 treatment led to autophagosome-dependent secretion of oligomeric and phosphorylated tau species, suggesting a reduction of intracellular tau aggregates via secretory autophagy rather than degradation via the ALP. This work highlights a novel mechanism of action (MOA) of an ALP-based heterobifunctional molecule and a potential new strategy for the cellular removal of proteins of interest.
    Keywords:  aggregates; autophagy; neurodegenerative diseases; secretion; targeted protein degradation; tau
    DOI:  https://doi.org/10.1021/acschemneuro.5c00161
  34. iScience. 2025 May 16. 28(5): 112371
    Roles of class III phosphatidylinositol 3-kinase, Vps34, in phagocytosis, autophagy, and endocytosis in retinal pigmented epithelium.
    Feng He, Ralph M Nichols, Melina A Agosto, Theodore G Wensel.
      Phosphatidylinositol-3-phosphate (PI(3)P) is important for multiple functions of retinal pigmented epithelial (RPE) cells, but its functions in RPE have not been studied. In RPE from mouse eyes and in cultured human RPE cells, PI(3)P-enriched membranes include endosomes, the trans-Golgi network, phagosomes, and autophagophores. Mouse RPE cells lacking activity of the PI-3 kinase, Vps34, lack detectable PI(3)P and die prematurely. Phagosomes containing rod discs accumulate, as do membrane aggregates positive for autophagosome markers. These autophagy-related membranes recruit LC3/Atg8 without Vps34, but phagosomes do not. Vps34 loss leads to accumulation of lysosomes which do not fuse with phagosomes or membranes with autophagy markers. Thus, Vps34-derived PI(3)P is not needed for initiation of phagocytosis or endocytosis, nor for formation of membranes containing autophagy markers. In contrast, Vps34 and PI(3)P are essential for intermediate and later stages, including membrane fusion with lysosomes.
    Keywords:  Enzymology; Functional aspects of cell biology; Lipid; Membranes; Model organism
    DOI:  https://doi.org/10.1016/j.isci.2025.112371
  35. Int J Mol Sci. 2025 Apr 11. pii: 3623. [Epub ahead of print]26(8):
    p.Phe508del-CFTR Trafficking: A Protein Quality Control Perspective Through UPR, UPS, and Autophagy.
    Pascal Trouvé, Claude Férec.
      Cystic fibrosis (CF) is a genetic disease due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The most frequent mutation (p.Phe508del) results in a misfolded protein (p.Phe508del-CFTR) with an altered transport to the membrane of the cells via the conventional protein secretion (CPS) pathway. Nevertheless, it can use unconventional protein secretion (UPS). Indeed, p.Phe508del-CFTR forms a complex with GRASP55 to assist its direct trafficking from the endoplasmic reticulum to the plasma membrane. While GRASP55 is a key player of UPS, it is also a key player of stress-induced autophagy. In parallel, the unfolded protein response (UPR), which is activated in the presence of misfolded proteins, is tightly linked to UPS and autophagy through the key effectors IRE1, PERK, and ATF6. A better understanding of how UPS, UPR, and stress-induced autophagy interact to manage protein trafficking in CF and other conditions could lead to novel therapeutic strategies. By enhancing or modulating these pathways, it may be possible to increase p.Phe508del-CFTR surface expression. In summary, this review highlights the critical roles of UPS- and UPR-induced autophagy in managing protein transport, offering new perspectives for therapeutic approaches.
    Keywords:  autophagy; conventional protein secretion (CPS); cystic fibrosis (CF); p.Phe508del-CFTR; unconventional protein secretion (UPS); unfolded protein response (UPR)
    DOI:  https://doi.org/10.3390/ijms26083623
  36. Int J Mol Sci. 2025 Apr 11. pii: 3603. [Epub ahead of print]26(8):
    Methylmercury Chloride Exposure Affects Oocyte Maturation Through AMPK/mTOR-Mediated Mitochondrial Autophagy.
    Shengkui Hou, Caiyu Wang, Xin Ma, Jing Zhao, Jun Wang, Yi Fang, Hongyu Liu, He Ding, Jing Guo, Wenfa Lu.
      Mercury, a prevalent heavy metal, negatively impacts oocyte maturation. However, the exact mechanism by which methylmercury chloride (MMC) affects this process remains elusive. The present study found that MMC administration triggered meiotic failure in oocytes by disrupting cumulus cell expansion, leading to compromised spindle apparatus and altered chromosomal architecture, which are crucial for oocyte development. This disruption is characterized by abnormal microtubule organization and defective chromosome alignment. Additionally, MMC exposure caused oxidative stress-induced apoptosis due to mitochondrial dysfunction, as indicated by decreased mitochondrial membrane potential, mitochondrial content, mitochondrial DNA copy number, and adenosine triphosphate levels. Proteomic analysis identified 97 differentially expressed proteins, including P62, an autophagy marker. Our results confirmed that MMC induced autophagy, particularly through the hyperactivation of the mitochondrial autophagy to remove damaged and normal mitochondria. The mitochondrial reactive oxygen species (ROS) scavenger Mito-TEMPO alleviated oxidative stress and mitochondrial autophagy levels, suggesting that mitochondrial ROS initiates this autophagic response. Notably, MMC activates mitochondrial autophagy via the monophosphate-activated protein kinase (AMPK)/mammalian target of rapamycin (mTOR) signal pathway due to mitochondrial dysfunction. In vivo studies in mice revealed that MMC exposure decreased reproductive performance, attributed to excessive mitochondrial autophagy leading to reduced oocyte quality. Overall, these findings demonstrate that MMC exposure impairs oocyte maturation via the hyperactivation of mitochondrial autophagy induced by mitochondrial dysfunction.
    Keywords:  MMC; mitochondrial autophagy; oocyte; oxidative stress
    DOI:  https://doi.org/10.3390/ijms26083603
  37. Proc Natl Acad Sci U S A. 2025 May 13. 122(19): e2422446122
    Muscle peripheral circadian clock drives nocturnal protein degradation via raised Ror/Rev-erb balance and prevents premature sarcopenia.
    Jeffrey J Kelu, Simon M Hughes.
      How central and peripheral circadian clocks regulate protein metabolism and affect tissue mass homeostasis has been unclear. Circadian shifts in the balance between anabolism and catabolism control muscle growth rate in young zebrafish independent of behavioral cycles. Here, we show that the ubiquitin-proteasome system (UPS) and autophagy, which mediate muscle protein degradation, are each upregulated at night under the control of the muscle peripheral clock. Perturbation of the muscle transcriptional molecular clock disrupts nocturnal proteolysis, increases muscle growth measured over 12 h, and compromises muscle function. Mechanistically, the shifting circadian balance of Ror and Rev-erb regulates nocturnal UPS, autophagy, and muscle growth through altered TORC1 activity. Although environmental zeitgebers initially mitigate defects, lifelong muscle clock inhibition reduces muscle size and growth rate, accelerating aging-related loss of muscle mass and function. Circadian misalignment such as shift work, sleep deprivation, or dementia may thus unsettle muscle proteostasis, contributing to muscle wasting and sarcopenia.
    Keywords:  autophagy; circadian clock; mTOR; muscle; proteasome
    DOI:  https://doi.org/10.1073/pnas.2422446122
  38. Sci Rep. 2025 May 07. 15(1): 15875
    Sinularin induces autophagy-dependent cell death by activating ULK1 and enhancing FOXO3-ATG4A axis in prostate cancer cells.
    Xiang-Yu Meng, Yi Li, Ze-Jun Yan, Sha-Zhou Ye, Ke-Jie Wang, Jun-Feng Chen, Rui Yu, Qi Ma.
      Sinularin is a natural product extracted from soft coral and is shown to exhibit antitumor effects against multiple human cancers. We previously showed that Sinularin induces apoptotic cell death via stabilizing the FOXO3 protein in prostate cancer cells. In this study, we demonstrated that Sinularin triggers autophagy via two different mechanisms in prostate cancer cells. First, Sinularin reduced the S757 phosphorylation of ULK1 protein, which was mediated by mTOR, leading to ULK1 activation and autophagy initiation. Second, Sinularin enhanced the expression of autophagic protein ATG4A, which is the key regulator in the formation of autophagosome, through a FOXO3-dependent transcriptional mechanism. Next, we identified that ATG4A is a new target gene of the transcription factor FOXO3. Additionally, we also found that Sinularin-induced autophagy promoted survivin degradation and led to cell apoptosis. Taken together, these findings suggest that Sinularin induces prostate cancer cell autophagy by promoting autophagy initiation through activation of ULK1 and formation of autophagosome through the FOXO3-ATG4A pathway.
    Keywords:  Apoptosis; Autophagy; FOXO3; Prostate cancer; Sinularin
    DOI:  https://doi.org/10.1038/s41598-025-00909-3
  39. Nat Struct Mol Biol. 2025 May 05.
    Chimeric deubiquitinase engineering reveals structural basis for specific inhibition of the mitophagy regulator USP30.
    Nafizul Haque Kazi, Nikolas Klink, Kai Gallant, Gian-Marvin Kipka, Malte Gersch.
      The mitochondrial deubiquitinase ubiquitin-specific protease (USP) 30 negatively regulates PINK1-parkin-driven mitophagy. Whether enhanced mitochondrial quality control through inhibition of USP30 can protect dopaminergic neurons is currently being explored in a clinical trial for Parkinson's disease. However, the molecular basis for specific inhibition of USP30 by small molecules has remained elusive. Here we report the crystal structure of human USP30 in complex with a specific inhibitor, enabled by chimeric protein engineering. Our study uncovers how the inhibitor extends into a cryptic pocket facilitated by a compound-induced conformation of the USP30 switching loop. Our work underscores the potential of exploring induced pockets and conformational dynamics to obtain deubiquitinase inhibitors and identifies residues facilitating specific inhibition of USP30. More broadly, we delineate a conceptual framework for specific USP deubiquitinase inhibition based on a common ligandability hotspot in the Leu73 ubiquitin binding site and on diverse compound extensions. Collectively, our work establishes a generalizable chimeric protein-engineering strategy to aid deubiquitinase crystallization and enables structure-based drug design with relevance to neurodegeneration.
    DOI:  https://doi.org/10.1038/s41594-025-01534-4
  40. Int J Mol Sci. 2025 Apr 14. pii: 3709. [Epub ahead of print]26(8):
    Conditional Overexpression of Neuritin in Supporting Cell Protects Cochlear Hair Cell and Delays Age-Related Hearing Loss by Enhancing Autophagy.
    Shanshan Wang, Shaowei Lv, Junhao Hu, Yunfan Shi, Yu Li, Jianyun Zhang, Xiaohua Tan, Rong Chen, Yu Hong.
      Age-related hearing loss (ARHL) is a highly prevalent, burdensome sensorineural hearing loss closely associated with impaired autophagic influx. Our previous studies revealed that neuritin, a neurotrophic factor primarily expressed in the central nervous system, could alleviate drug-induced damages in hair cells (HCs) and spiral ganglion neurons. However, its effects on ARHL and whether these effects are closely related to autophagy remain unclear. Using the Nrn1 knock-in mice and cultured cochlear basilar membrane (CBM) of the neonatal mouse, we show that neuritin could restore aging-associated hearing loss and alleviate senescence-associated damage in the cochlea. Overexpression of neuritin in support cells (SCs) alleviates the loss of cochlear HCs and nerve fibers, reducing the damage to spiral ganglion neurons and the shifts in ABR's high-frequency threshold. Furthermore, conditional overexpression of neuritin in SCs improves autophagic influx by upregulating the expression of microtubule-associated protein 1 light chain 3 type B (LCB3) protein and downregulating the expression of p21 protein. In cultured neonatal mouse CBM, neuritin administration significantly inhibits D-galactose-induced HC loss, cellular apoptosis, and ROS production and promotes autophagic influx. These effects were weakened when the autophagy inhibitor 3-MA was added. In summary, our results confirm the therapeutic potential of neuritin treatment for ARHL.
    Keywords:  LCB3; P21; age-related hearing loss; autophagy; hair cells; neuritin
    DOI:  https://doi.org/10.3390/ijms26083709
  41. J Physiol. 2025 May 09.
    Intermittent time-restricted eating may increase autophagic flux in humans: an exploratory analysis.
    Julien Bensalem, Xiao Tong Teong, Kathryn J Hattersley, Leanne K Hein, Célia Fourrier, Linh V P Dang, Sanjna Singh, Kai Liu, Gary A Wittert, Amy T Hutchison, Leonie K Heilbronn, Timothy J Sargeant.
      Autophagy slows age-related pathologies and is stimulated by nutrient restriction in animal studies. However, this has never been shown in humans. We measured autophagy using a physiologically relevant measure of autophagic flux (flux of MAP1LC3B isoform II/LC3B-II in peripheral blood mononuclear cells in the context of whole blood) in 121 humans with obesity who were randomised to standard care (SC, control condition), calorie restriction (CR) or intermittent fasting plus time-restricted eating (iTRE) for 6 months. While the differences in change from baseline between groups was not significant at 2 months, we observed a significant difference in change from baseline between iTRE compared to SC at 6 months (P = 0.04, post hoc analysis). This effect may be driven partly by a tendency for autophagy to decrease in the SC group. The difference in change from baseline between CR and SC was not significant. Uncorrected analysis of correlations showed a negative relationship between change in autophagy and change in blood triglycerides. Data on the specificity and performance of the methods used to measure human autophagy are also presented. This shows autophagy may be increased by intermittent nutrient restriction in humans. If so, this is a demonstration that nutrient restriction can be used to improve a primary hallmark of biological ageing and provides a mechanism for how fasting could delay the onset of age-related disease. KEY POINTS: Autophagy slows biological ageing, and dysfunction of autophagy has been implicated in age-related disease - an effective way of increasing autophagy in cells and animal models is nutrient restriction. However, the impact of different types of nutrient restriction on physiological autophagic flux in humans has not been extensively researched. Here we measure the effect of intermittent time-restricted eating (iTRE) and calorie restriction on physiological autophagic flux in peripheral blood mononuclear cells. After 6 months, there was a significant difference in change from baseline between the iTRE and the standard care control group, with flux being higher in the iTRE group at this timepoint. However, there was no significant increase from baseline within the iTRE group, showing that although autophagy may be modified by nutrient restriction in humans, further studies are required.
    Keywords:  autophagy; calorie restriction; fasting; human; intermittent fasting; time‐restricted eating
    DOI:  https://doi.org/10.1113/JP287938
  42. Bioessays. 2025 May 04. e70016
    Mitochondria and Endoplasmic Reticulum Contact Site as a Regulator of Proteostatic Stress Responses in Neurodegenerative Diseases.
    Seiji Watanabe, Koji Yamanaka.
      Recent evidence indicates that the mitochondria-endoplasmic reticulum (ER) contact site is a novel microdomain essential for cellular homeostasis. Various proteins are accumulated at the mitochondria-associated membrane (MAM), an ER subcomponent closely associated with the mitochondria, contributing to Ca2+ transfer to the mitochondria, lipid synthesis, mitochondrial fission/fusion, and autophagy. These functions are disrupted in the diseases, particularly in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and Alzheimer's disease. In this review, we summarize the disruption of protein homeostasis in various neurodegenerative diseases, present recent works on the mechanisms of MAM aberration, including ours mainly focused on ALS, and then discuss challenges and prospects for future MAM-targeted therapies in neurodegenerative diseases.
    Keywords:  mitochondria‐associated membranes; neurodegenerative diseases; protein homeostasis
    DOI:  https://doi.org/10.1002/bies.70016
  43. Endocrinology. 2025 May 08. pii: bqaf089. [Epub ahead of print]
    Role of Branched-Chain Amino Acid Catabolism in the Regulation of Adipocyte Metabolism.
    Haizhou Jiang, Feifan Guo, Fei Xiao.
      Adipocyte metabolism critically regulates systemic energy homeostasis, and its dysfunction contributes to obesity pathogenesis. Notably, elevated circulating branched-chain amino acid (BCAA) levels and impaired adipose tissue BCAA catabolism have been observed in both animal models and humans with obesity; however, the mechanisms underlying BCAA metabolism's regulation of adipocyte function remain incompletely understood. This review synthesizes recent advances in the roles of BCAA catabolic enzymes, their metabolites, and BCAAs themselves in modulating adipocyte metabolism, encompassing adipogenesis, lipid metabolism, and thermogenesis. Emerging evidence reveals that BCAA catabolism influences adipocyte metabolism through multiple pathways: by utilizing BCAAs as an energy substrate, and modulating signaling cascades via metabolites and unidentified mechanisms. Importantly, adipocyte BCAA catabolism directly impacts systemic BCAA clearance and plasma BCAA concentrations. Dietary interventions involving BCAA supplementation, restriction, or deprivation demonstrate diverse metabolic effects on adipocytes, mediated through key nutrient-sensing pathways including mammalian target of rapamycin complex 1 (mTORC1) and general control nonderepressible kinase 2 (GCN2)/activating transcription factor 4 (ATF4) signaling. We further discuss translational implications, evaluating therapeutic strategies targeting BCAA catabolism or dietary BCAA manipulation for obesity management. This review advances our understanding of amino acid metabolism's contribution to adipocyte function and obesity development.
    Keywords:  adipogenesis; adipose tissue; branched-chain amino acids; lipid metabolism; thermogenesis
    DOI:  https://doi.org/10.1210/endocr/bqaf089
  44. Bioelectricity. 2025 Mar;7(1): 29-57
    Lysosomal Ion Channels and Transporters: Recent Findings, Therapeutic Potential, and Technical Approaches.
    Artem Kondratskyi, Andre Bazzone, Markus Rapedius, Rocco Zerlotti, Bastien Masson, Nidish Ponath Sadanandan, Joanne L Parker, Alexandre Santinho, Marine Moutia, Abdou Rachid Thiam, Arlene Kemp, Fitzwilliam Seibertz, Nicoletta Murciano, Søren Friis, Nadine Becker, Alison Obergrussberger, Maria Barthmes, Cecilia George, Michael George, David Dalrymple, Bruno Gasnier, Simon Newstead, Christian Grimm, Niels Fertig.
      In recent years, there has been a growing interest in lysosomal ion channels and transporters due to their critical role in maintaining lysosomal function and their involvement in a variety of diseases, particularly lysosomal storage diseases, cancer, and neurodegenerative disorders. Recent advancements in research techniques, including manual and automated patch clamp (APC) electrophysiology, solid-supported membrane-based electrophysiology (SSME), and fluorescence-based ion imaging, have further enhanced our ability to investigate lysosomal ion channels and transporters in both physiological and pathological conditions, spurring drug discovery efforts. Several pharmaceutical companies are now developing therapies aimed at modulating these channels and transporters to improve lysosomal function in disease. Small molecules targeting channels like transient receptor potential mucolipin (TRPML) 1 and TMEM175, as well as drugs modulating lysosomal pH, are currently in preclinical and clinical development. This review provides an overview of the role of lysosomal ion channels and transporters in health and disease, highlights the cutting-edge techniques used to study them, and discusses the therapeutic potential of targeting these channels and transporters in the treatment of various diseases. Furthermore, in addition to summarizing recent discoveries, we contribute novel functional data on cystinosin, TRPML1, and two-pore channel 2 (TPC2), utilizing both SSME and APC approaches.
    Keywords:  APC; SSME; electrophysiology; ion channels; lysosome; patch clamp; pumps; transporters
    DOI:  https://doi.org/10.1089/bioe.2025.0010
  45. J Cell Mol Med. 2025 May;29(9): e70513
    Autophagy Regulates Putative Anion Transporter 1 Expression in Intestinal Epithelial Cells.
    Shubha Priyamvada, Dulari Jayawardena, Arivarasu N Anbazhagan, Anoop Kumar, Seema Saksena, Ravinder K Gill, Alip Borthakur, Waddah A Alrefai, Pradeep K Dudeja.
      Putative anion transporter 1 (PAT-1) is the key oxalate-secreting transporter in the intestine and therefore, maintaining its steady-state levels is critical for oxalate homeostasis. Autophagy is known to modulate the expression of intestinal solute transporters; however, its role in regulating PAT-1 has not been examined. Autophagy in Caco-2 cells was induced by either rapamycin treatment or by nutrient deprivation and assessed by conventional autophagy marker proteins. ATG7 (autophagy-related 7) protein expression was attenuated by ATG7-siRNA in Caco-2 cells or by utilising ATG7KO mice. PAT-1 protein levels in Caco-2 cells were significantly reduced by rapamycin or by nutrient deprivation at 48 and 72 h. Concomitantly, the LC3II/I ratio was increased, and p62 levels were significantly decreased, confirming the induction of autophagy. Nutrient deprivation for 6 h also caused a significant decrease in the surface levels of PAT-1. PAT-1 protein levels were increased by the siRNA-mediated ATG7 knockdown in Caco-2 cells and in the ileum of ATG7KO mice. In summary, Autophagy in intestinal epithelial cells modulates the basal levels of PAT-1 protein and may play a critical role in the maintenance of oxalate homeostasis.
    Keywords:  autophagy; intestine; post‐translational regulation; putative anion transporter 1
    DOI:  https://doi.org/10.1111/jcmm.70513
  46. Molecules. 2025 Apr 10. pii: 1704. [Epub ahead of print]30(8):
    PLM-ATG: Identification of Autophagy Proteins by Integrating Protein Language Model Embeddings with PSSM-Based Features.
    Yangying Wang, Chunhua Wang.
      Autophagy critically regulates cellular development while maintaining pathophysiological homeostasis. Since the autophagic process is tightly regulated by the coordination of autophagy-related proteins (ATGs), precise identification of these proteins is essential. Although current computational approaches have addressed experimental recognition's costly and time-consuming challenges, they still have room for improvement since handcrafted features inadequately capture the intricate patterns and relationships hidden in sequences. In this study, we propose PLM-ATG, a novel computational model that integrates support vector machines with the fusion of protein language model (PLM) embeddings and position-specific scoring matrix (PSSM)-based features for the ATG identification. First, we extracted sequence-based features and PSSM-based features as the inputs of six classifiers to establish baseline models. Among these, the combination of the SVM classifier and the AADP-PSSM feature set achieved the best prediction accuracy. Second, two popular PLM embeddings, i.e., ESM-2 and ProtT5, were fused with the AADP-PSSM features to further improve the prediction of ATGs. Third, we selected the optimal feature subset from the combination of the ESM-2 embeddings and AADP-PSSM features to train the final SVM model. The proposed PLM-ATG achieved an accuracy of 99.5% and an MCC of 0.990, which are nearly 5% and 0.1 higher than those of the state-of-the-art model EnsembleDL-ATG, respectively.
    Keywords:  autophagy proteins; position-specific scoring matrix; protein language model; support vector machine
    DOI:  https://doi.org/10.3390/molecules30081704
  47. Nat Commun. 2025 May 07. 16(1): 4259
    Autophagy-independent role of ATG9A vesicles as carriers for galectin-9 secretion.
    Wenting Zhang, Cuicui Ji, Xianghua Li, Tianlong He, Wei Jiang, Yukun Liu, Meiling Wu, Yunpeng Zhao, Xuechai Chen, Xiaoli Wang, Jian Li, Haolin Zhang, Juan Wang.
      Galectins play vital roles in cellular processes such as adhesion, communication, and survival, yet the mechanisms underlying their unconventional secretion remain poorly understood. This study identifies ATG9A, a core autophagy protein, as a key regulator of galectin-9 secretion via a mechanism independent of classical autophagy, secretory autophagy, or the LC3-dependent extracellular vesicle loading and secretion pathway. ATG9A vesicles function as specialized carriers, with the N-terminus of ATG9A and both carbohydrate recognition domains of galectin-9 being critical for the process. TMED10 mediates the incorporation of galectin-9 into ATG9A vesicles, which then fuse with the plasma membrane via the STX13-SNAP23-VAMP3 SNARE complex. Furthermore, ATG9A regulates the secretion of other proteins, including galectin-4, galectin-8, and annexin A6, but not IL-1β, galectin-3, or FGF2. This mechanism is potentially conserved across other cell types, including monocytic cells, which underscores its broader significance in unconventional protein secretion.
    DOI:  https://doi.org/10.1038/s41467-025-59605-5
  48. Am J Physiol Heart Circ Physiol. 2025 May 06.
    Beclin-1-Dependent Autophagy Protects Perivascular Adipose Tissue Function from Hyperaldosteronism Effects.
    Rafael M Costa, Ariane Bruder-Nascimento, Juliano V Alves, Wanessa M C Awata, Shubhnita Singh, Daniel Rodrigues, Thiago Bruder-Nascimento, Rita C Tostes.
      Background: Hyperaldosteronism (HA), characterized by excessive production of aldosterone (Aldo), contributes to cardiovascular damage and perivascular adipose tissue (PVAT) dysfunction. Previous studies have shown that Aldo can impair autophagy in various tissues. However, it remains unclear whether this impairment occurs specifically in PVAT and whether it involves disruption of autophagic flux through Beclin-1 (BCN1), a key regulator of autophagosome formation and maturation. We hypothesize that BCN1-dependent autophagy plays a protective role in PVAT by limiting inflammation and preserving its anti-contractile function in the context of HA. Methods: Male and female C57BL/6J (WT) and BCN1 knock-in mice, aged 10-12 weeks, underwent 14-day aldosterone infusion (600 μg/kg/day) using an osmotic mini-pump. Vascular function was assessed in PVAT-intact thoracic aortae, and blood pressure was monitored via radiotelemetry. Results: HA disrupted PVAT autophagic flux, leading to the accumulation of LC3II/I and p62 proteins and reduced BCN1 expression/activity. In WT mice, PVAT exhibited an anti-contractile effect, which was abolished by HA. In contrast, BCN1-knock-in mice were protected from this loss of PVAT function. HA also induced oxidative stress and inflammation in PVAT, as evidenced by increased ROS generation and elevated mRNA levels of TNF-α, IL-6, IL-1β, and IL-17. These pro-inflammatory and pro-oxidative changes were not observed in BCN1-knock-in mice, indicating preserved PVAT homeostasis. Furthermore, pharmacological induction of autophagy via spermidine and activation of BCN1 with TB peptide improved PVAT function in HA-treated WT mice. Lastly, BCN1-knock-in mice exhibited partial protection against HA-induced hypertension, highlighting the systemic vascular benefits of enhanced autophagic flux. Conclusions: In summary, our findings demonstrate that the activation of autophagy provides protection against HA-induced PVAT inflammation, dysfunction, and hypertension. Consequently, the activation of BCN1 could serve as a pharmacological strategy to prevent the harmful cardiovascular effects associated with HA.
    Keywords:  aldosterone; autophagy; beclin-1; perivascular adipose tissue
    DOI:  https://doi.org/10.1152/ajpheart.00829.2024
  49. J Alzheimers Dis. 2025 May 06. 13872877251336442
    Trends and research focus on autophagy in Alzheimer's disease (2003-2023): A bibliometric study.
    Tianyi Wang, Haochen Jiang, Ruwen Zheng, Chuchu Zhang, Xiumei Ma, Yi Liu.
      BackgroundAlzheimer's disease (AD) is characterized by amyloid-β plaques and tau aggregates, with autophagy dysfunction playing a key pathogenic role. While autophagy modulation shows therapeutic promise, comprehensive bibliometric analyses are lacking.ObjectiveThis study aims to map the research landscape of autophagy in AD through bibliometric analysis, identifying key trends, contributors, and emerging focus areas.MethodsWe analyzed 4018 publications (2003-2023) from Web of Science using VOSviewer and CiteSpace. Publication trends, influential authors, countries, institutions, and research hotspots were examined through co-occurrence, burst detection, and clustering analyses.ResultsAnnual publications have steadily increased, peaking in 2022. The US led in output and citations, with major contributions from the University of California and New York University. Ralph A. Nixon emerged as the most influential author. Early research (2003-2013) primarily focused on protein degradation mechanisms, whereas recent studies (2014-2023) emphasize mitochondrial dysfunction, apoptosis, and related pathways. Key evolving topics include endoplasmic reticulum stress and chaperone-mediated autophagy, with significant implications for therapeutic innovation.ConclusionsAutophagy plays a critical role in AD pathogenesis and represents a promising therapeutic target. Despite mechanistic advances, clinical translation remains challenging. Future research should prioritize multi-omics integration, drug delivery optimization, and managing risks associated with excessive autophagy activation. These findings provide valuable insights for developing novel AD therapies targeting autophagy.
    Keywords:  Alzheimer's disease; CiteSpace; VOSviewer; autophagy; bibliometrics
    DOI:  https://doi.org/10.1177/13872877251336442
  50. Autophagy. 2025 May 04. 1-17
    PINK1-dependent NFKB signaling contributes to amyloid pathology in Alzheimer disease.
    Fang Du, Qing Yu, Gang Hu, Chyuan-Sheng Lin, Shirley ShiDu Yan.
      Mitochondrial dysfunction plays a preponderant role in the development of Alzheimer disease (AD). We have demonstrated that activation of PINK1 (PTEN induced kinase 1)-dependent mitophagy ameliorates amyloid pathology, attenuates mitochondrial and synaptic dysfunction, and improves cognitive function. However, the underlying mechanisms remain largely unknown. Using a newly generated PINK1-AD transgenic mouse model and AD neuronal cell lines, we provide substantial evidence supporting the contribution of PINK1-mediated mitochondrial ROS (reactive oxygen species) and NFKB/NF-κB (nuclear factor kappa B) signaling to altering APP (amyloid beta precursor protein) processing and Aβ metabolism. Enhancing neuronal PINK1 is sufficient to suppress Aβ-induced activation of NFKB signal transduction in PINK1-overexpressed Aβ-AD mice and Aβ-producing neurons. Blocking PINK1-mediated NFKB activation inhibits activities of BACE1 (beta-secretase 1) and γ-secretase, which are key enzymes for cleavage of APP processing to produce Aβ. Conversely, loss or knockdown of PINK1 produces excessive ROS, along with increased phosphorylated NFKB1/p50 and RELA/p65 subunits, APP-related BACE1 and γ-secretase, and Aβ accumulation. Importantly, these detrimental effects were robustly blocked by the addition of scavenging PINK1 Aβ-induced mitochondrial ROS, leading to the suppression of NFKB activation, restoration of normal APP processing, and limitation of Aβ accumulation. Thus, our findings highlight a novel mechanism underlying PINK1-mediated modulation of Aβ metabolism via a ROS-NFKB-APP processing nexus. Activation of PINK1 signaling could be a potential therapeutic avenue for the early stages of AD by combining improving mitochondrial quality control with limiting amyloid pathology in AD.
    Keywords:  APP; Aβ metabolism; NFKB; PINK1; amyloid pathology; reactive oxygen species
    DOI:  https://doi.org/10.1080/15548627.2025.2463322
  51. Autophagy. 2025 May 09. 1-5
    Biochemical investigation of LC3/GABARAP-ligand interaction as an important quality measure for LC3/GABARAP-targeting small molecules: addendum to the guidelines (4th edition).
    Martin P Schwalm, Christopher Lenz, Krishna Saxena, Daniel J Klionsky, Ewgenij Proschak, Stefan Knapp.
      Targeted protein degradation (TPD) represents a new therapeutic modality that allows the targeting of proteins that are considered undruggable by conventional small molecules. While TPD approaches via the ubiquitin-proteasome system are well established and validated, additional degradation pathways still require rigorous characterization. Here, we focus on macroautophagy/autophagy tethering compounds, a class of small molecules, designed to recruit cargo to LC3/GABARAP proteins for subsequent autophagosome-dependent degradation. We provide guidance for the biophysical and structural characterization of small molecule modulators for studying LC3/GABARAP-ligand interactions. In addition, we discuss potential limitations of autophagy-based TPD systems and emphasize the need for rigorous quality control in the development of LC3/GABARAP-targeting small molecules.Abbreviations: DSF: differential scanning fluorimetry; FP: fluorescence polarization; FRET: Förster/fluorescence resonance energy transfer; HTRF: homogeneous time-resolved fluorescence; ITC: isothermal titration calorimetry; LIR: LC3-interacting region; MGs: molecular glues; NMR: nuclear magnetic resonance; PROTACs: PROteolysis-TArgeting Chimeras; SPR: surface plasmon resonance; TPD: targeted protein degradation; TR-FRET: time-resolved Förster/fluorescence resonance energy transfer; UPS: ubiquitin-proteasome system.
    Keywords:  ATTECs; AUTACs; Atg8; GABARAP; LC3
    DOI:  https://doi.org/10.1080/15548627.2025.2498506
  52. Int J Cancer. 2025 May 02.
    Exosomes, autophagy, and cancer: A complex triad.
    María Guerra-Andrés, Álvaro F Fernández, Tania Fontanil.
      Cancer remains one of the leading causes of death worldwide. Despite remarkable progress in prevention, diagnosis, and therapy, the incidence of certain types of cancer persists, urging the identification of clinically relevant biomarkers and the development of novel therapeutic strategies to improve clinical outcomes and overcome treatment resistance. Exosomes, small extracellular vesicles released by diverse types of cells, have attracted interest in biomedical research due to their potential as carriers for different treatments. Moreover, exosomes play a pivotal role in intercellular communication, modulating various cellular processes. One of those is autophagy, a pro-survival pathway that is essential for human cells. Even though autophagy is traditionally described as a catabolic route, its machinery is intricately involved in various cellular responses, including vesicle formation and secretion. In this regard, the link between autophagy and exosomes is complex, bidirectional, and highly dependent on the cellular context. Interestingly, both processes have been extensively implicated in cancer pathogenesis, highlighting their potential as therapeutic targets. This review updates our understanding of how exosomes can participate in cancer development and progression, with a specific focus on their influence on tumor growth, angiogenesis, and metastasis. Additionally, the interplay between these extracellular vesicles and autophagy is minutely reviewed and discussed, as we hypothesize that this crosstalk may hold valuable clues for biomarker discovery and the development of novel therapeutic strategies.
    Keywords:  angiogenesis; autophagy; cancer; exosomes; metastasis; tumor
    DOI:  https://doi.org/10.1002/ijc.35388
  53. BMC Immunol. 2025 May 09. 26(1): 36
    mTORC2 is crucial for regulating the recombinant Mycobacterium tuberculosis CFP-10 protein-induced phagocytosis in macrophages.
    Xian-Hui Huang, Yu Wang, Liu-Ying Wu, Ye-Lin Jiang, Ling-Jie Ma, Xiao-Feng Shi, Xing Wang, Meng-Meng Zheng, Lu Tang, Yong-Liang Lou, Dan-Li Xie.
      Mycobacterium tuberculosis (M. tuberculosis, Mtb) is a pathogenic bacterial species in the family Mycobacteriaceae and the causative agent of most cases of tuberculosis. Macrophages play essential roles in defense against invading pathogens, including M. tuberculosis. The study of M. tuberculosis-associated antigens is one of the hotspots of current research. The secreted proteins of M. tuberculosis, including early secretory antigen target 6 (ESTA6) and culture filtrate protein 10 (CFP-10), are crucial for the immunological diagnosis of tuberculosis. However, the relationship of CFP-10 alone with macrophages is still not well understood. In the present study, we report that the purified recombinant protein CFP-10 (rCFP-10) significantly enhanced the phagocytic capacity of murine macrophages. rCFP-10 induces both TNF-α and IL-6 production. Additionally, RNASeq analysis revealed that rCFP10 triggers multiple pathways involved with macrophage activation. Interestingly, neither mitochondrial reactive oxygen species nor lysosomal content had a significant difference treated with rCFP-10 in macrophages. Moreover, inhibition of the mammalian target of rapamycin (mTOR) activity was shown to significantly reverse the rCFP10-induced phagocytosis, various genes involved in lysosome acidification and TLR signaling. These findings highlight that the CFP-10 plays an essential role in the invasion of macrophages by M. tuberculosis, which is partly regulated by the mTORC2 signal pathway.
    Keywords:   Mycobacterium tuberculosis ; Culture filtrate protein 10; Mammalian target of Rapamycin complex 2; Phagocytosis
    DOI:  https://doi.org/10.1186/s12865-025-00715-6
  54. Proc Natl Acad Sci U S A. 2025 May 27. 122(21): e2422255122
    Phase separation in mitochondrial fate and mitochondrial diseases.
    Qingyi Chen, Sanqi An, Chuanlong Wang, Yanshuang Zhou, Xingguo Liu, Wenkai Ren.
      Mitochondria are central metabolic organelles that control cell fate and the development of mitochondrial diseases. Traditionally, phase separation directly regulates cell functions by driving RNA, proteins, or other molecules to concentrate into lipid droplets. Recent studies show that phase separation regulates cell functions and diseases through the regulation of subcellular organelles, particularly mitochondria. In fact, phase separation is involved in various mitochondrial activities including nucleoid assembly, autophagy, and mitochondria-related inflammation. Here, we outline the key mechanisms through which phase separation influences mitochondrial activities and the development of mitochondrial diseases. Insights into how phase separation regulates mitochondrial activities and diseases will help us develop interventions for related diseases.
    Keywords:  mitochondrial disease; mitochondrial dynamics; mitophagy; nucleoid assembly; phase separation
    DOI:  https://doi.org/10.1073/pnas.2422255122
  55. Int J Biol Macromol. 2025 May 02. pii: S0141-8130(25)04446-0. [Epub ahead of print] 143894
    STING-∆C, a novel splice isoform of STING, inhibits DNA virus-induced innate immunity and autophagy.
    Sheng-Nan Zheng, Jing Zhang, Tao Li, Cheng-Hao Li, Jian Deng, Jin-Xin Li, Pei-Hui Wang.
      Stimulator of interferon genes (STING) plays a critical role in the innate immune response to cytosolic DNA, primarily activating type I interferons (IFNs). Although alternative splicing is known to modulate immune pathways, the influence of STING splice isoforms requires further exploration. Here, we identified STING-∆C, a novel splice isoform of STING generated by retention of intron 6, resulting in a truncated C-terminus. While STING-∆C shares its N-terminal domain with full-length STING, it contains a unique C-terminal sequence. STING-∆C acts as a dominant negative regulator of cGAS-STING signaling pathway by suppressing cGAS-, 2'3'-cGAMP-, and STING-mediated activation of the IFN response. Gain- and loss-of-function experiments showed that STING-∆C inhibited IFN production in response to double-stranded DNA and DNA virus, including HSV-1 and HPV. Furthermore, STING-∆C promoted HSV-1 replication and reduces STING-induced autophagy. Mechanistically, STING-∆C interacts with full-length STING, preventing its oligomerization and assembly with TBK1, a vital component of the STING-TBK1-IRF3 signalsome. This interaction blocks IRF3 phosphorylation and nuclear translocation, thereby halting IFN production. STING-∆C thus represents a newly identified splice isoform that negatively regulates cGAS-STING signaling. These findings broaden our understanding of STING's regulatory mechanisms and may guide therapeutic strategies for autoimmune diseases and viral infections linked to excessive STING activation.
    Keywords:  HPV; STING-∆C; cGAS
    DOI:  https://doi.org/10.1016/j.ijbiomac.2025.143894
  56. Int J Mol Sci. 2025 Apr 17. pii: 3784. [Epub ahead of print]26(8):
    PERK/Sestrin2 Signaling Pathway Mediated Autophagy Regulates Human Cardiomyocytes Apoptosis Induced by Traffic-Related PM2.5 and Diverse Constituents.
    Jiayu Tian, Zeyu Niu, Huan Yang, Caihong Wang, Linlin Guan, Lifang Zhao, Dongxing Shi, Zhihong Zhang.
      Although the strong causal association between PM2.5 and cardiovascular disease has been extensively studied, the latent molecular mechanisms have not been entirely explained. The objective of this research was to assess the cardiotoxicity of Traffic-related PM2.5 (TRPM2.5), water-soluble components (WSC), and water-insoluble components (WIC) in human cardiomyocytes (AC16) and to investigate the underlying molecular mechanisms. Endoplasmic reticulum stress (ERS), autophagy, and apoptosis were activated 24 h after exposure to total-TRPM2.5, WSC, or WIC. WIC was predominantly related to cardiotoxicity compared to WSC. Sestrin2 is an upstream molecule in several signaling pathways, including those involved in autophagy and apoptosis. In this study, we found that the knockdown of Protein Kinase RNA-like Endoplasmic Reticulum Kinase (PERK) suppressed the expression of PERK, Sestrin2, Caspase-12, Caspase-3, LC3, and p62 in TRPM2.5-treated AC16 cells. These results indicate that ERS participates in the activation of autophagy and apoptosis through the PERK/Sestrin2 pathway. We found that inhibiting autophagy with 3-methyladenine (3-MA) decreased the expression of autophagy-related factors and aggravated apoptosis. These observations suggest that protective autophagy was initiated. Finally, our findings provide valuable insights into the molecular mechanism by which ERS might regulate autophagy through the PERK/Sestrin2 signaling pathway, and protective autophagy may be activated to relieve TRPM2.5 and component-mediated apoptosis in AC16 cells.
    Keywords:  PERK/Sestrin2; apoptosis; autophagy; cardiotoxicity; traffic-related PM2.5
    DOI:  https://doi.org/10.3390/ijms26083784
  57. J Biol Chem. 2025 May 07. pii: S0021-9258(25)02057-5. [Epub ahead of print] 110208
    Parkin mediates the mitochondrial dysfunction through mRpL18.
    Xiuxiu Ti, Hui Zuo, Guochun Zhao, Yuwei Li, Minghui Du, Liwen Xu, Shengnan Li, Zhaoliang Shan, Yuxue Gao, Guangming Gan, Yan Wang, Qing Zhang.
      Loss of function of parkin leads to the mitochondrial dysfunction, which is closely related to Parkinson's disease. However, the in vivo mechanism is far from clear. One of the dogmas is that impaired Parkin causes dysfunction of mitophagy mediated by Pink1-Parkin axis. The other is that impaired Parkin causes Mfn accumulation which leads to mitochondrial dysfunction. Surprisingly, in Drosophila muscles, as reported, the first dogma is not applicable; for the second dogma, our study suggests that Parkin mediates the mitochondrial dysfunction through modulating mitochondrial morphology, which is determined by synergy of both Marf and mitochondrial protein mRpL18 got from our genome-wide screen, whose RNAi rescues parkin RNAi phenotype. Mechanistically, we found that impaired Parkin upregulated both the transcription and protein levels of mRpL18 dependent on its E3 ligase activity, causing the mRpL18 accumulation outside mitochondria. Consequently, cytosolic accumulated mRpL18 competitively bound Drp1, leading to the reduction of the binding of Drp1 to its receptor Fis1, which finally inhibited the mitochondrial fission and tipped the balance to mitochondrial hyperfusion, thereby affected the mitochondrial function. Taken together, our study suggests that impaired Parkin causes mitochondrial hyperfusion due to two reasons: (1) Parkin defect impairs Pink1-Parkin axis-mediated Marf degradation, which promotes mitochondrial fusion; (2) Parkin defect causes mRpL18 accumulation, which inhibits Drp1/Fis1-mediated mitochondrial fission. These two ways function together to drive Parkin-mediated mitochondrial hyperfusion. Therefore, knockdown of either marf or mRpL18 can prevent mitochondrial hyperfusion, leading to the rescue of Parkin defect-triggered fly wing phenotypes. Overall, our study unveils a new facet of how Parkin regulates mitochondrial morphology to affect mitochondrial function, which provides new insights for the understanding and treatment of Parkinson's disease.
    Keywords:  Drp1; Parkin; Parkinson's disease; mRpL18
    DOI:  https://doi.org/10.1016/j.jbc.2025.110208
  58. Cell Res. 2025 May 07.
    Lysosomal EGFR functions as a GEF for Rheb.
    Tao Hou, Peiqiang Yan, Hiroyuki Inuzuka, Wenyi Wei.
      
    DOI:  https://doi.org/10.1038/s41422-025-01126-3
  59. Ageing Res Rev. 2025 May 02. pii: S1568-1637(25)00108-4. [Epub ahead of print]109 102762
    Sestrin2 is a central regulator of mitochondrial stress responses in disease and aging.
    Ivo F Machado, Carlos M Palmeira, Anabela P Rolo.
      Mitochondria supply most of the energy for cellular functions and coordinate numerous cellular pathways. Their dynamic nature allows them to adjust to stress and cellular metabolic demands, thus ensuring the preservation of cellular homeostasis. Loss of normal mitochondrial function compromises cell survival and has been implicated in the development of many diseases and in aging. Although exposure to continuous or severe stress has adverse effects on cells, mild mitochondrial stress enhances mitochondrial function and potentially extends health span through mitochondrial adaptive responses. Over the past few decades, sestrin2 (SESN2) has emerged as a pivotal regulator of stress responses. For instance, SESN2 responds to genotoxic, oxidative, and metabolic stress, promoting cellular defense against stress-associated damage. Here, we focus on recent findings that establish SESN2 as an orchestrator of mitochondrial stress adaptation, which is supported by its involvement in the integrated stress response, mitochondrial biogenesis, and mitophagy. Additionally, we discuss the integral role of SESN2 in mediating the health benefits of exercise as well as its impact on skeletal muscle, liver and heart injury, and aging.
    Keywords:  Aging; Liver; Mitochondria; Mitohormesis; Muscle; Sestrin2
    DOI:  https://doi.org/10.1016/j.arr.2025.102762
  60. Cell Rep. 2025 May 06. pii: S2211-1247(25)00452-8. [Epub ahead of print]44(5): 115681
    OTUD4 inhibits ferroptosis by stabilizing GPX4 and suppressing autophagic degradation to promote tumor progression.
    Jinglian Chen, Chengqing Huang, Jiale Mei, Qiuhua Lin, Wenbo Chen, Jiali Tang, Xinjie Wei, Caixia Mo, Yueyan Zhang, Qi Zeng, Xianwei Mo, Weizhong Tang, Tao Luo.
      Ferroptosis, a regulated cell demise predicated on iron metabolism and lipid peroxidation, has increasingly become a focal point in oncological therapies. Nonetheless, its governance, particularly the role of deubiquitination, is not fully delineated. This investigation concentrates on the deubiquitinase OTUD4, scrutinizing its functional and molecular implications in ferroptosis within tumor cells. By engineering OTUD4 knockout cell lines via CRISPR-Cas9, we observed that these cells exhibit heightened sensitivity to ferroptosis inducers, augmenting ferroptotic cell death and robustly diminishing tumor growth both in vitro and in vivo. Mechanistically, OTUD4 not only sustains protein stability by directly deubiquitinating GPX4 but also impedes its degradation via RHEB-mediated autophagy, collectively stalling the ferroptosis pathway. In vivo assays substantiate that OTUD4 deletion, when combined with regorafenib, drastically reduces tumor proliferation, showcasing potent synergistic antitumor activity. This study pioneers the revelation of OTUD4's bifunctional role in modulating ferroptosis through deubiquitination and autophagy, underscoring its potential as a therapeutic target in oncology.
    Keywords:  CP: Cancer; CP: Molecular biology; GPX4; OTUD4; autophagy; ferroptosis; tumor
    DOI:  https://doi.org/10.1016/j.celrep.2025.115681
  61. Nature. 2025 May 07.
    Uncovering a key enzyme opens possible therapeutic avenues for lysosomal diseases.
      
    Keywords:  Cell biology; Diseases
    DOI:  https://doi.org/10.1038/d41586-025-01368-6
  62. PLoS One. 2025 ;20(5): e0322869
    Tie-2 regulates endothelial morphological responses to shear stress by FOXO1-triggered autophagy.
    Mana Ghanbarpour Houshangi, Keisuke Shirakura, Dietmar Vestweber.
       INTRODUCTION: Endothelial cells respond to flow-induced shear stress by morphological changes, a process which is important for vascular development and physiology. High laminar shear stress activates Tie-2 which supports endothelial junction integrity and protects against vascular leaks and the generation of atherosclerotic plaques.
    METHODS: We have examined the role of Tie-2 and FOXO1 in controlling vascular endothelial cell morphology under physiological shear stress. To address this, we exposed human umbilical vein endothelial cells (HUVECs) transfected with siRNA to 15 dyn/cm2 of shear stress for 24 hours. The resulting cells were analyzed by immunofluorescence staining.
    RESULTS: We found that shear stress-induced activation of Tie-2 is required for endothelial cell alignment and elongation in the direction of flow. Mechanistically, we found that FOXO1 is an essential target downstream of Tie-2, which becomes translocated from the nucleus into the cytosol. There, FOXO1 stimulates the formation of autophagosomes, and both FOXO1 and autophagy stimulation are needed for Tie-2-dependent cell alignment.
    CONCLUSION: In conclusion, laminar fluid shear stress stimulates a novel Tie-2-FOXO1-autophagy signaling axis which is required for endothelial cell alignment. This represents a new mechanism by which Tie-2 contributes to vascular protection under laminar shear stress.
    DOI:  https://doi.org/10.1371/journal.pone.0322869
  63. Mol Med. 2025 May 03. 31(1): 166
    Calpain1 inhibition enhances autophagy-lysosomal pathway and ameliorates tubulointerstitial fibrosis in Nephronophthisis.
    Dantong Li, Jinglan Zhang, Xinyu Su, Yichen Yang, Jiayong Lai, Xiaoya Wei, Huamu Chen, Yaqing Liu, Haiyan Wang, Liangzhong Sun.
       BACKGROUND: Nephronophthisis (NPH) is classified under the category of renal ciliopathies and is the most common genetic disease leading to renal failure in children. Early-onset and progressive renal tubulointerstitial fibrosis represents one of the most significant features, culminating in renal insufficiency. However, the molecular mechanism of tubulointerstitial fibrosis remains unclear. Previously, we constructed an NPH mouse model via CRISPR-Cas9. This mouse model demonstrated typical features of tubulointerstitial fibrosis. In this study, we aimed to explore the pathogenesis of tubulointerstitial fibrosis in NPH and identify early intervention targets in both the NPH models and patients.
    METHODS: In this study, transcriptome changes in mouse kidneys were analyzed through RNA sequencing to explore the molecular mechanisms of renal tubulointerstitial fibrosis in NPH. We found an increased abundance of calpain1 in both the NPH models and patients. Pathway enrichment analysis indicated autophagy-lysosomal pathway was altered in the NPH models. Western blot, immunofluorescence or immunohistochemical staining were used to verify the expression of calpain1. We also detected autophagy activities in NPH models by lysotracker staining and transmission electron microscopy (TEM). Epithelial or mesenchymal-specific markers and Masson's trichrome staining were used to detect the status of tubulointerstitial fibrosis. Furthermore, NPH models were treated with a calpain1 inhibitor to explore the role of calpain1 in autophagy-lysosomal pathway and tubulointerstitial fibrosis.
    RESULTS: The increased abundance of calpain1 impaired the autophagy-lysosomal pathway and induced tubulointerstitial fibrosis by promoting epithelial-to-mesenchymal transition. On the other hand, calpain1 inhibition could enhance the autophagy-lysosomal pathway and ameliorate the phenotypes of tubulointerstitial fibrosis in NPH models.
    CONCLUSIONS: Calpain1-mediated autophagy-lysosomal pathway disorder may be an important cause of tubulointerstitial fibrosis in NPH. Calpain1 may have therapeutic implications for renal tubulointerstitial fibrosis.
    Keywords:  Calpain1; Inherited kidney disease; Nephronophthisis; Renal ciliopathies; Renal tubulointerstitial fibrosis
    DOI:  https://doi.org/10.1186/s10020-025-01231-4
  64. Sci Rep. 2025 May 07. 15(1): 15945
    Autophagy and extracellular vesicles mediate cisplatin resistance in oral squamous cell carcinoma with LC3B-II as a potential non-invasive biomarker.
    Kar-Yan Su, Xin-Hui Khoo, Ian C Paterson, Bey-Hing Goh, Wai-Leng Lee.
      Drug resistance remains a critical challenge in cancer chemotherapy, particularly in oral squamous cell carcinoma (OSCC). Recent findings have highlighted the significant roles that autophagy and extracellular vesicles (EVs) play in contributing to chemoresistance. In previous studies, we demonstrated that EVs are essential in mediating cisplatin resistance in human OSCC cells. In this study, we sought to investigate the involvement of autophagy-related proteins in cisplatin resistance and their potential as non-invasive predictive biomarkers to enhance OSCC treatment strategies. Using bioinformatics analyses, we identified key autophagy-related proteins that may play a role in cisplatin resistance in OSCC cells. We then employed cisplatin-sensitive and -resistant OSCC cell models to investigate further the involvement of autophagy and EVs in drug resistance. The expression of the identified autophagy-related proteins was analyzed in OSCC cells and their EVs to explore their correlation with cisplatin resistance. Our bioinformatics analyses identified ATG12 and LC3B as potentially significant contributors to cisplatin resistance. Both autophagy and EVs were found to promote drug resistance in our OSCC cell models. Furthermore, we observed a positive correlation between cisplatin resistance and the expression of ATG12 and LC3B proteins in OSCC cells. Notably, LC3B-II expression was elevated in EVs derived from cisplatin-sensitive cells, suggesting its potential role in mediating resistance via EVs in OSCC. Our findings underscore the potential of LC3B-II as a non-invasive predictive biomarker for cisplatin resistance in OSCC. These results may pave the way for improved therapeutic strategies targeting drug resistance mechanisms in OSCC.
    Keywords:  Autophagy; Bioinformatics; Biomarkers; Drug resistance; Extracellular vesicles; Oral cancer
    DOI:  https://doi.org/10.1038/s41598-025-00703-1
  65. PLoS One. 2025 ;20(5): e0321005
    PDRN prevents SIRT1 degradation by attenuating autophagy during skin aging.
    Jingjing Chen, Fanshan Qiu, Jianfeng Shi, Wei Huang, Chenyu Zhao, Qianqian Han.
      Polydeoxyribonucleotide (PDRN) is a low molecular weight linear polyribonucleotide fragment derived from salmon sperm, known for its potential in tissue regeneration and anti-inflammatory applications. However, its specific function in cellular senescence is yet to be fully understood. Silent information regulator 1 (SIRT1), an NAD + -dependent deacetylase, plays a crucial role in regulating cellular aging and tumorigenesis. Notably, SIRT1 levels decrease with age in both mice and during cellular senescence, highlighting its significance in anti-aging processes. This study assessed the effects of PDRN on cellular aging induced by ultraviolet B (UVB) or hydrogen peroxide (H2O2) and investigated the mechanisms of its protective effects against aging at the cellular level. Our data demonstrated that PDRN treatment mitigated the decline in cell viability and inhibited cell aging when exposed to UVB or H2O2. Furthermore, PDRN ameliorated UVB-induced epidermal thickening in mouse skin. Mechanically, we found that PDRN treatment led to a reduction in nuclear autophagy and the formation of cytoplasmic stress granules by preventing the accumulation of damaged LC3 in the nuclear and inhibiting the degradation of SIRT1 and p62 in the cytoplasm during cellular senescence. In conclusion, PDRN exhibits antioxidant and anti-aging properties by diminishing autophagy and enhancing SIRT1 expression. These results suggest that PDRN has potential as a therapeutic compound for reducing skin aging induced by UVB or H2O2 through the modulation of SIRT1 levels.
    DOI:  https://doi.org/10.1371/journal.pone.0321005
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