bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2025–08–31
sixty-six papers selected by
Viktor Korolchuk, Newcastle University
  1. Two specific interactions of GATE16 with TRPML3 and RAB33B regulate autophagy.
  2. Identification of organelle-specific autophagy regulators from tandem CRISPR screens.
  3. Deacetylation of ATG16L1 is required for LC3-associated lysosomal microautophagy.
  4. Spatio-temporal processes in autophagosome-lysosome fusion.
  5. Structural basis for the dynamic regulation of mTORC1 by amino acids.
  6. Cell type-specific autophagy in human leukocytes: signatures of aging, sex, and nutrient restriction.
  7. The TXNIP-mTOR-Autophagy axis in diabetic kidney disease: mechanistic insights and therapeutic implications.
  8. Nutrient sensing receptor GPRC6A regulates mTORC1 signaling and Tau biology.
  9. PRMT1 (protein arginine methyltransferase 1) is essential for neuromuscular junction and mitochondrial homeostasis via mitophagy regulation.
  10. A chaperone-proteasome-based fragmentation machinery is essential for aggrephagy.
  11. Novel Role of the Epstein-Barr Virus Encoded Deubiquitinating Enzyme (BPLF1) in mTOR-Mediated Cell Growth and Proliferation Pathways.
  12. Interplay of Oxidative Stress, Autophagy, and Rubicon in Ovarian Follicle Dynamics: Orchestrating Ovarian Aging.
  13. YTHDF proteins and m6A-RNA clients undergo autophagic turnover during contact inhibition.
  14. The role of mitophagy in perioperative neurocognitive disorder: from mechanisms to implications.
  15. LC3 and GABARAP independent autophagy of misfolded procollagen in mouse osteoblasts.
  16. Putative PINK1/Parkin activators lower the threshold for mitophagy by sensitizing cells to mitochondrial stress.
  17. Unc-51-like kinase 1 (ULK1) regulates bacterial ubiquitylation and p62 recruitment during xenophagic clearance of Listeria monocytogenes.
  18. Alpha-Mangostin Alleviates Mitochondrial Damage and Autophagy Dysregulation in the MPP+ Cellular Model of Parkinson's Disease.
  19. Unveiling the impact of non-coding RNAs on virus-induced cellular autophagy: roles and research advances.
  20. Regulation of autophagy by a tRNA-derived fragment.
  21. Porphyromonas gingivalis hijacks mitophagy and lysosomal function to persist in endothelial cells.
  22. Arabidopsis MACP2 contributes to autophagy induction by modulating starvation-induced reactive oxygen species homeostasis.
  23. Ridaifen derivatives function as potent lysosomotropic agents, depending on their basic side chains.
  24. Soma-localized Rab39 inhibits synaptic autophagy by controlling trafficking of Atg9 vesicles.
  25. Lysosomal polyamine storage upon ATP13A2 loss impairs β-glucocerebrosidase via altered lysosomal pH and electrostatic hydrolase-lipid interactions.
  26. CDK5 Inhibits Synphilin-1 Ubiquitination and Basal Mitophagy: Implications for Parkinson's Disease.
  27. Episodic transport of protein aggregates achieves a positive size selectivity in aggresome formation.
  28. Endocytosis is essential for cysteine-deprivation-induced ferroptosis.
  29. Liver CYP4A autophagic lysosomal degradation: A major role for the autophagic receptor SQSTM1/p62 through an uncommon target interaction site.
  30. Impact of O-GlcNAcylation Elevation on Mitophagy and Glia in the Dentate Gyrus.
  31. Jolkinolide B Activates Mitophagy to Exhibit Anti-pancreatic Cancer Activity and Alleviate Cognitive Deficits in Alzheimer's Disease.
  32. SQSTM1/p62 drives radiosensitivity in cervical cancer via autophagy-independent mechanisms.
  33. PARP7 is a proteotoxic stress sensor that labels proteins for degradation.
  34. LYVAC/PDZD8 is a lysosomal vacuolator.
  35. Piezo1 regulates autophagy in HT22 hippocampal neurons through the Ca2+/Calpain and Calcineurin/TFEB signaling pathways.
  36. CHIP protects lysosomes from CLN4 mutant-induced membrane damage.
  37. ACSS2-TFEB axis acts as a critical regulator of the autophagic machinery in head and neck squamous cell carcinoma.
  38. DHX8 regulates degradation of RNA by RNautophagy.
  39. Modulation of Autophagy by Ursolic and Betulinic Acids: Distinct Cytotoxic and Membrane-Disruption in Malignant and Nonmalignant Cells.
  40. Autophagy in mycobacterial infections: molecular mechanisms, host-pathogen interactions, and therapeutic opportunities.
  41. Camellia japonica Flower Extract and the Active Constituent Hyperoside Repair DNA Damage Through FUNDC1-Mediated Mitophagy Pathway for Skin Anti-Aging.
  42. Mitochondrial quality control in diabetes mellitus and complications: molecular mechanisms and therapeutic strategies.
  43. Non-coding RNAs regulate autophagy in kidney disease: friend or foe?
  44. Rho kinase isoforms in neurodegeneration: from cellular functions to therapeutic targets.
  45. ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits in mice.
  46. MiRNA-loaded MSC exosomes restore autophagy flux for acute pancreatitis therapy.
  47. How to control synaptic autophagy from the neuronal soma.
  48. Dual-key cooperatively activated DNA regulator for controlling mitochondria-lysosome interactions.
  49. Elevated levels of Letm1 drives mitochondrial dysfunction and cardiomyocyte stress-mediated apoptosis in cultured cardiomyocytes.
  50. Mitochondrial Extracellular Vesicles: A Novel Approach to Mitochondrial Quality Control.
  51. New perspectives on molecular mechanisms underlying exercise-induced benefits in Parkinson's disease.
  52. Cathepsins in Neurological Diseases.
  53. Genome-wide in vivo CRISPR screens identify GATOR1 complex as a tumor suppressor in Myc-driven lymphoma.
  54. Mitophagy Regulators as Novel Targets in Sepsis-Induced Myocardial Dysfunction.
  55. Atractylenolide III Mitigates Alzheimer's Disease by Enhancing Autophagy via the YY1-TFEB Pathway.
  56. Inhibition of Atg13-mediated autophagy enhances the anti-osteoclastogenic effect of sirolimus by counteracting its pro-autophagic activity.
  57. The hereditary spastic paraplegia type 21 (SPG21) protein is a RAB7A effector that promotes mTORC1-catalyzed TFEB phosphorylation and cytoplasmic retention.
  58. Decoding phospho-regulation and flanking regions in autophagy-associated short linear motifs.
  59. Mitochondrial proteins as biomarkers of cellular senescence and age-associated diseases.
  60. Cancer as a failed response to renegade mitochondria.
  61. Neuroprotective Effects of Phosphodiesterase Inhibitors on Sestrin-2 (SESN2) Expression and Autophagy in Alzheimer's Disease Model.
  62. Quantitative imaging of lipid transport in mammalian cells.
  63. Parkin, a key player in Parkinson's disease pathogenesis: A review.
  64. Complex Conformational Interplay for Parkin Activation is Revealed by 19F NMR Spectroscopy.
  65. A protein tunnel helps stressed lysosomes swell.
  66. Targeting Lipophagy in Liver Diseases: Impact on Oxidative Stress and Steatohepatitis.
  1. Sci Rep. 2025 Aug 25. 15(1): 31244
    Two specific interactions of GATE16 with TRPML3 and RAB33B regulate autophagy.
    Jiwoo Park, Areum Choi, Jin Kwon, Suzi Choi, Yun Min Park, Hyun Jin Kim.
      ATG8s are essential for autophagy as they recruit various machinery to autophagic structures. We previously reported that the intracellular Ca2+ channel TRPML3 specifically interacts with the mammalian ATG8 homolog GATE16, but not LC3B to increase autophagy. However, the underlying mechanism and the role of this specific interaction remain unclear. Here, we report that single amino acid motifs in GATE16 and TRPML3 determine the specificity of this interaction and its function in autophagy. We also discovered that RAB33B, a Golgi-resident small GTPase, functionally interacts with TRPML3 in autophagy and contains an LC3-interacting region (LIR) motif. Surprisingly, RAB33B specifically interacted with GATE16, but not with other ATG8s through an LIR motif, and disrupting this LIR motif inhibited autophagy. Upon induction of autophagy, RAB33B was recruited from the Golgi to the phagophore in an LIR-dependent manner, enhancing the interaction between RAB33B and TRPML3 while promoting autophagy. These results suggest that specific interactions involving GATE16 play a crucial role in autophagy by recruiting TRPML3 and RAB33B, forming protein complexes at the phagophore to promote autophagosome formation.
    Keywords:  ATG8; Autophagy; GATE16; RAB33B; TRPML3
    DOI:  https://doi.org/10.1038/s41598-025-16951-0
  2. J Cell Biol. 2025 Oct 06. pii: e202405138. [Epub ahead of print]224(10):
    Identification of organelle-specific autophagy regulators from tandem CRISPR screens.
    Truc T Losier, Karyn E King, Maxime W C Rousseaux, Ryan C Russell.
      Autophagy is a conserved degradative process that promotes cellular homeostasis under stress conditions. Under nutrient starvation, autophagy is nonselective, promoting indiscriminate breakdown of cytosolic components. Conversely, selective autophagy is responsible for the specific turnover of damaged organelles. We hypothesized that selective autophagy may be regulated by signaling pathways distinct from those controlling starvation-induced autophagy, thereby promoting organelle turnover. To address this question, we conducted kinome-wide CRISPR screens to identify distinct signaling pathways responsible for the regulation of basal autophagy, starvation-induced autophagy, and two types of selective autophagy, ER-phagy and pexophagy. These parallel screens identified both known and novel autophagy regulators, some common to all conditions and others specific to selective autophagy. More specifically, CDK11A and NME3 were further characterized to be selective ER-phagy regulators. Meanwhile, PAN3 and CDC42BPG were identified as an activator and inhibitor of pexophagy, respectively. Collectively, these datasets provide the first comparative description of the kinase signaling that defines the regulation of selective autophagy and bulk autophagy.
    DOI:  https://doi.org/10.1083/jcb.202405138
  3. Autophagy. 2025 Aug 28. 1-15
    Deacetylation of ATG16L1 is required for LC3-associated lysosomal microautophagy.
    Qian Wang, Wei Wan, Hongtao Zhang, Tianhua Zhou, Han-Ming Shen, Pingtong Huang, Wei Liu.
      Microautophagy is a selective cellular process in which endolysosomes directly engulf cytoplasmic cargo through membrane invagination. The regulatory mechanisms governing microautophagy remain poorly understood. Here, we identified the deacetylation of ATG16L1 as a critical regulator of LC3-associated lysosomal microautophagy. We demonstrate that ATG16L1 acetylation is dynamically controlled by the acetyltransferase KAT2B and the deacetylase HDAC3. Under lysosomal osmotic stress or glucose deprivation, HDAC3-mediated deacetylation of ATG16L1 within its WD40 domain promotes its interaction with V-ATPase, facilitating ATG16L1 recruitment to lysosomal membranes. While dispensable for macroautophagy, this post-translational modification is essential for LC3 lipidation on lysosomes and enables lysosomal recovery, including the restoration of lysosomal size and degradative capacity following stress. Our results reveal a key role for ATG16L1 deacetylation in driving LC3-associated microautophagy to maintain lysosomal homeostasis.
    Keywords:  ATG16L1; Acetylation; LC3 lipidation; LC3-associated microautophagy; V-ATPase; lysosome
    DOI:  https://doi.org/10.1080/15548627.2025.2551669
  4. Med Rev (2021). 2025 Aug;5(4): 297-317
    Spatio-temporal processes in autophagosome-lysosome fusion.
    Shizuo Liu, Huan Yan, Jiajie Diao, Shen Zhang, Qing Zhong.
      Macroautophagy/autophagy is a lysosome-dependent degradation process involved in cellular energy metabolism, recycling and quality control. Autophagy is a highly dynamic and precisely regulated process, which contains four major steps: autophagic membrane initiation and cargo recognition, autophagosome formation, autophagosome-lysosome fusion and lysosomal degradation. During the terminal phase of autophagy, the merging of the autophagosome and lysosome membranes is critical for the effective breakdown of sequestered cargoes. However, the participated molecules and the interplay among them have not been fully uncovered. The spatiotemporal property of these molecules is crucial for maintaining the orderly fusion of autophagosomes and lysosomes, otherwise it may lead to fusion disorders. In this article, we tend to summarize the molecules mediating autophagosome-lysosome fusion into two categories: effector molecules and regulatory molecules. The effector molecules are soluble N-ethylmaleimide-sensitive factor attachment protein receptor and tethering proteins, and the latter category contains phosphatidylinositol, Rab GTPases and ATG8-family proteins. The spatio-temporal properties of these autophagosome-lysosome fusion mediating molecules will be featured in this review.
    Keywords:  autophagosome-lysosome fusion; autophagy; sensitive factor attachment protein receptor; syntaxin 17
    DOI:  https://doi.org/10.1515/mr-2024-0095
  5. Nature. 2025 Aug 20.
    Structural basis for the dynamic regulation of mTORC1 by amino acids.
    Max L Valenstein, Maximilian Wranik, Pranav V Lalgudi, Karen Y Linde-Garelli, Yuri Choi, Raghu R Chivukula, David M Sabatini, Kacper B Rogala.
      The mechanistic target of rapamycin complex 1 (mTORC1) anchors a conserved signalling pathway that regulates growth in response to nutrient availability1-5. Amino acids activate mTORC1 through the Rag GTPases, which are regulated by GATOR, a supercomplex consisting of GATOR1, KICSTOR and the nutrient-sensing hub GATOR2 (refs. 6-9). GATOR2 forms an octagonal cage, with its distinct WD40 domain β-propellers interacting with GATOR1 and the leucine sensors Sestrin1 and Sestrin2 (SESN1 and SESN2) and the arginine sensor CASTOR1 (ref. 10). The mechanisms through which these sensors regulate GATOR2 and how they detach from it upon binding their cognate amino acids remain unknown. Here, using cryo-electron microscopy, we determined the structures of a stabilized GATOR2 bound to either Sestrin2 or CASTOR1. The sensors occupy distinct and non-overlapping binding sites, disruption of which selectively impairs the ability of mTORC1 to sense individual amino acids. We also resolved the apo (leucine-free) structure of Sestrin2 and characterized the amino acid-induced structural rearrangements within Sestrin2 and CASTOR1 that trigger their dissociation from GATOR2. Binding of either sensor restricts the dynamic WDR24 β-propeller of GATOR2, a domain essential for nutrient-dependent mTORC1 activation. These findings reveal the allosteric mechanisms that convey amino acid sufficiency to GATOR2 and the ensuing structural changes that lead to mTORC1 activation.
    DOI:  https://doi.org/10.1038/s41586-025-09428-7
  6. Autophagy Rep. 2025 ;4(1): 2543560
    Cell type-specific autophagy in human leukocytes: signatures of aging, sex, and nutrient restriction.
    Linh Vp Dang, Timothy J Sargeant.
      Macroautophagy (referred to here as autophagy) is thought to play a critical role in aging and age-related disease, making it a priority for development of targeted human therapies. We developed a flow cytometry-based method to measure autophagic flux in 19 subpopulations from whole blood, using chloroquine (CQ) to inhibit lysosomal degradation, and the autophagy protein MAP1LC3B (microtubule associated protein 1 light chain 3 beta) isoform II/LC3B-II to measure autophagic flux (the acquisition and degradation of autophagic cargo over time). Autophagic flux varies by cell type and is higher in whole blood compared with RPMI culture media. Basal autophagic flux shows sex- and age-specific variations. Further, monocytes, but not T cells, respond robustly to amino acid starvation by increasing autophagy, with older individuals exhibiting stronger responses, particularly in non-classical monocytes. These findings underscore the importance of cell type-specific autophagy measurements to understand the effects of aging, sex and nutrition, to develop targeted interventions for age-related diseases.
    Keywords:  Aging; LC3B-II; PBMCs; autophagic flux; autophagy; nutrition; sex
    DOI:  https://doi.org/10.1080/27694127.2025.2543560
  7. Mol Biol Rep. 2025 Aug 21. 52(1): 839
    The TXNIP-mTOR-Autophagy axis in diabetic kidney disease: mechanistic insights and therapeutic implications.
    Qi Zhu, Xiaodan Wu, Yunhua Di, Lv Liu, Yu Liu.
      Diabetic kidney disease (DKD) remains a prevalent complication of diabetes mellitus and a leading cause of end-stage renal disease. A growing body of evidence highlights the central role of the thioredoxin-interacting protein (TXNIP)-mTOR-autophagy axis in the pathogenesis of DKD. Chronic hyperglycemia significantly induces TXNIP expression, triggering oxidative stress, inflammasome activation, and mitochondrial dysfunction in renal cells. TXNIP directly promotes activation of the mammalian target of rapamycin (mTOR) complex 1 (mTORC1), which consequently impairs autophagic flux, leading to accumulation of damaged organelles and proteins, cellular hypertrophy, and fibrosis. Restoration of autophagy via inhibition of TXNIP or mTOR signaling pathways alleviates these pathological changes in various DKD models. Specifically, genetic or pharmacological suppression of TXNIP attenuates oxidative injury, reduces inflammasome activation, and restores autophagic activity. Similarly, mTOR inhibitors such as rapamycin have demonstrated substantial renoprotective effects through reactivation of autophagy and reduction of renal fibrosis. Furthermore, combined targeting of TXNIP and mTOR presents a promising therapeutic strategy that may synergistically restore autophagic homeostasis with reduced side effects. This review synthesizes recent mechanistic insights into the interplay between TXNIP, mTOR signaling, and autophagy dysregulation in DKD and discusses potential therapeutic interventions. Ultimately, understanding and therapeutically targeting the TXNIP-mTOR-autophagy axis could offer new opportunities for effective clinical management of diabetic kidney disease.
    Keywords:  Autophagy dysregulation; Diabetic kidney disease; MTOR signaling; TXNIP; Therapeutic targeting
    DOI:  https://doi.org/10.1007/s11033-025-10946-w
  8. Neurobiol Dis. 2025 Aug 21. pii: S0969-9961(25)00270-0. [Epub ahead of print] 107054
    Nutrient sensing receptor GPRC6A regulates mTORC1 signaling and Tau biology.
    Chao Ma, Kelsey Campbell, Andrii Kovalenko, Leslie A Sandusky-Beltran, Huimin Liang, Jerry B Hunt, John Calahatian, Mani Kallupurackal, Shalini Pandey, Muskan Vasisht, Mallory Watler, Zainuddin Quadri, Camilla Michalski, Margaret Fahnestock, Athanasios Papangelis, Daniel Sejer Pedersen, Trond Ulven, Kevin Nash, Maj-Linda B Selenica, Dave Morgan, Paula C Bickford, Daniel C Lee.
      Tauopathies, including Alzheimer's disease (AD), comprise microtubule-associated protein tau aggregates that cause neuronal cell death and clinical cognitive decline. Reducing overall tau abundance remains a central strategy for therapeutics; however, no disease-modifying treatment exists to date. One principal pathway for balancing cellular proteostasis includes the mechanistic target of rapamycin complex 1 (mTORC1) signaling. Recently, arginine emerged as one of the primary amino acids to activate mTORC1 through several intracellular arginine sensors and an extracellular arginine receptor, namely the G protein-coupled receptor (GPCR) family C, group 6, member A (GPRC6A). Human AD brains were previously reported with elevated mTORC1 signaling; however, it is unclear whether arginine sensing and signaling to mTORC1 plays a role in tauopathies. Herein, we examined arginine sensing associated with mTORC1 signaling in the human AD and animal models of tauopathy. We found that human AD brains maintained elevated levels of arginine sensors with potential uncoupling of arginine sensing pathways. Furthermore, we observed increased GPRC6A and arginine in the brain, accompanied by increased mTORC1 signaling and decreased autophagy in a mouse model of tauopathy (Tau PS19). We also discovered that both supplementing arginine and overexpressing GPRC6A in cell culture models could independently activate mTORC1 and promote tau accumulation. In addition, we found that suppressing GPRC6A signaling by either genetic reduction or pharmacological antagonism reduced tau accumulation, phosphorylation, and oligomerization. Overall, these findings uncover the crucial role of arginine sensing pathways in deregulating mTORC1 signaling in tauopathies and identify GPRC6A as a promising target for future therapeutics in tauopathies and other proteinopathies. SIGNIFICANCE STATEMENT: Tauopathies, including Alzheimer's disease (AD), accumulate pathogenic tau protein inclusions that potentially contribute to the hyperactive mechanistic target of rapamycin complex 1 (mTORC1) signaling and eventually cause neuronal cell death. Here, we presented novel findings that AD and animal models of tauopathy maintained increased expression of arginine sensors and uncoupling of arginine sensing associated with mTORC1 signaling. We investigated the role of a putative extracellular arginine and basic L-amino acid sensing G protein-coupled receptor (GPCR) family C, group 6, member A (GPRC6A) in activating mTORC1 and accelerating pathogenic tau phenotypes in several cell models. Additionally, we showed that genetic repression or antagonism of GPRC6A signaling provides a novel therapeutic target for tauopathies and other proteinopathies.
    Keywords:  Alzheimer's disease; Arginine metabolism; Arginine sensors; Autophagy; GPCR; Proteinopathies; Tau PS19
    DOI:  https://doi.org/10.1016/j.nbd.2025.107054
  9. Autophagy. 2025 Sep 01. 1-18
    PRMT1 (protein arginine methyltransferase 1) is essential for neuromuscular junction and mitochondrial homeostasis via mitophagy regulation.
    Ju-Hyeon Bae, Chang-Lim You, Yideul Jeong, June Kim, Jinwoo Lee, Hyeon-Ju Jeong, Hyebeen Kim, Tuan Anh Vuong, Youngdae Gwon, Gyu-Un Bae, Jong-Sun Kang.
      The neuromuscular junction (NMJ) is essential for transmitting neural stimulus to muscles, triggering muscle contraction. Mitochondria are enriched in NMJ to support the energy needs required for neuromuscular function and stability. Thus, maintaining mitochondrial homeostasis through the clearance of damaged mitochondria, a process known as mitophagy, is vital for preserving neuromuscular health. Here, we highlight the crucial role of muscle PRMT1 in maintaining NMJ and mitochondrial homeostasis via mitophagy regulation. PRMT1 is distinctively expressed in myofibers, accumulating in the postsynaptic area, with its levels upregulated in denervated muscles. PRMT1-ablated muscles displayed disrupted NMJs and an accumulation of abnormal mitochondria, accompanied by increased mitochondrial oxidative stress. Additionally, prmt1 depletion in muscles specifically impaired TBK1 (TANK binding kinase 1)-OPTN (optineurin)-mediated mitophagy. Overall, our findings suggest that PRMT1 plays a critical role in maintaining NMJ and mitochondrial health by regulating selective mitophagy through TBK1-OPTN.Abbreviations: ADMA: asymmetric arginine dimethylation; BTX: α-bungarotoxin; EDL: extensor digitorum longus; FDB: flexor digitorum brevis; GAS: gastrocnemius; NMJ: Neuromuscular junction; Mko: mice with muscle-specific prmt1 ablation; MTOR: mechanistic target of rapamycin kinase; OPTN: optineurin; PRMT1: protein arginine methyltransferase 1; SA: sodium arsenate; SNI: sciatic nerve crush injury; Sol: soleus; SQSTM1/p62: sequestosome 1; TBK1: TANK binding kinase 1; TOMM20: translocase of outer mitochondrial membrane 20; TA: tibialis anterior; VDAC1: voltage dependent anion channel 1.
    Keywords:  Mitophagy; PRMT1; TBK1; neuromuscular junction; skeletal muscle
    DOI:  https://doi.org/10.1080/15548627.2025.2551477
  10. Nat Cell Biol. 2025 Aug 27.
    A chaperone-proteasome-based fragmentation machinery is essential for aggrephagy.
    Mario Mauthe, Nicole van de Beek, Muriel Mari, Giel Korsten, Parisa Nobari, Kennith B Castelino, Eduardo P de Mattos, Ibtisam Ouhida, Jesse L Dijkstra, Sabine Schipper-Krom, Laura R de la Ballina, Monja R Mueller, Anne Simonsen, Mark S Hipp, Lukas C Kapitein, Harm H Kampinga, Fulvio Reggiori.
      Perturbations in protein quality control lead to the accumulation of misfolded proteins and protein aggregates, which can compromise health and lifespan. One key mechanism eliminating protein aggregates is aggrephagy, a selective type of autophagy. Here we reveal that fragmentation is required before autophagic clearance of various types of amorphous aggregates. This fragmentation requires both the 19S proteasomal regulatory particle and the DNAJB6-HSP70-HSP110 chaperone module. These two players are also essential for aggregate compaction that leads to the clustering of the selective autophagy receptors, which initiates the autophagic removal of the aggregates. We also found that the same players delay the formation of disease-associated huntingtin inclusions. This study assigns a novel function to the 19S regulatory particle and the DNAJB6-HSP70-HSP110 module, and uncovers that aggrephagy entails a piecemeal process, with relevance for proteinopathies.
    DOI:  https://doi.org/10.1038/s41556-025-01747-1
  11. Viruses. 2025 Aug 20. pii: 1139. [Epub ahead of print]17(8):
    Novel Role of the Epstein-Barr Virus Encoded Deubiquitinating Enzyme (BPLF1) in mTOR-Mediated Cell Growth and Proliferation Pathways.
    Rachel Mund, Sage L Atkins, Anwen Cao, Aminatou Diallo, Christopher B Whitehurst.
      Epstein-Barr Virus (EBV) is a causative agent of infectious mononucleosis and is strongly associated with Burkitt lymphoma, Hodgkin lymphoma, and nasopharyngeal carcinoma. EBV encodes a deubiquitinating enzyme, BPLF1, which is important for infectious virus production, B-cell immortalization, and tumorigenesis. To elucidate BPLF1's role, an affinity-based mass spectrometry screen was performed, which suggested that BPLF1 and mTOR interact. mTOR, a critical mediator within cellular signaling cascades and oncogenesis, exists in two distinct complexes: mTOR Complex 1 (mTORC1) and mTOR Complex 2 (mTORC2). Here, we show that BPLF1 has direct deubiquitinating (DUB) activity on mTOR, removing both K48- and K63-ubiquitin linkages. Additionally, WT BPLF1 decreased mTORC1 localization to the lysosome and decreased the phosphorylation of mTORC1 downstream effectors, 4E-BP1 and S6K1. BPLF1 also had DUB activity on Raptor and Rictor, which have both been shown to preferentially cause the formation of mTORC2 over mTORC1 when not ubiquitinated. Immunoprecipitation of mTOR shows decreased mTORC1 formation in the presence of WT BPLF1. Importantly, treatment with rapamycin, an mTORC1 inhibitor, increased infectious virus production, while JR-AB2-011, an mTORC2 inhibitor, reduced infectious virus production. Taken together, these data demonstrate that BPLF1's effect on the mTOR signaling cascade regulates cellular and viral processes during EBV infectivity and replication.
    Keywords:  BPLF1; DUB; EBV; Epstein-Barr Virus; deubiquitinating enzyme; mTOR; mTORC1
    DOI:  https://doi.org/10.3390/v17081139
  12. Antioxidants (Basel). 2025 Jul 27. pii: 919. [Epub ahead of print]14(8):
    Interplay of Oxidative Stress, Autophagy, and Rubicon in Ovarian Follicle Dynamics: Orchestrating Ovarian Aging.
    Kiyotaka Yamada, Masami Ito, Haruka Nunomura, Takashi Nishigori, Atsushi Furuta, Mihoko Yoshida, Akemi Yamaki, Kanto Shozu, Ippei Yasuda, Sayaka Tsuda, Tomoko Shima, Akitoshi Nakashima.
      Organ functions generally decline with age, but the ovary is a prototypical organ that undergoes functional loss over time. Autophagy plays a crucial role in maintaining organ homeostasis, and age-related upregulation of the autophagy inhibitor protein, Rubicon, has been linked to cellular and tissue dysfunction. This review describes how granulosa cell autophagy supports follicular growth and oocyte selection and maturation by regulating cellular energy metabolism and protein quality control. We then introduce the role of selective autophagy, including mitophagy or lipophagy, in steroidogenesis and cellular remodeling during luteinization. In aged ovaries, Rubicon accumulation suppresses autophagic flux, leading to diminished oxidative-stress resilience and enhanced DNA damage. Moreover, impaired autophagy drives the accumulation of ATP citrate lyase, which correlates with poor oocyte quality and reduced ovarian reserve. Following fertilization, oocytes further upregulate autophagy to provide the energy required for blastocyst transition. Conversely, in infertility-related disorders, such as premature ovarian insufficiency, endometriosis, and polycystic ovary syndrome, either deficient or excessive autophagy contributes to disease pathogenesis. Both autophagy inhibitors (e.g., Rubicon) and activators (e.g., Beclin1) could be emerging as promising biomarkers for assessing ovarian autophagy status. Therapeutically, Rubicon inhibition by trehalose in aged ovaries and autophagy suppression by agents such as hydroxychloroquine in polycystic ovary syndrome and endometriosis hold potential. Establishing robust methods to evaluate ovarian autophagy will be essential for translating these insights into targeted treatments.
    Keywords:  autophagy; granulosa cells; ovarian aging; oxidative stress; rubicon
    DOI:  https://doi.org/10.3390/antiox14080919
  13. Cell Rep. 2025 Aug 23. pii: S2211-1247(25)00959-3. [Epub ahead of print]44(9): 116188
    YTHDF proteins and m6A-RNA clients undergo autophagic turnover during contact inhibition.
    Hung Ho-Xuan, Astrid Bruckmann, Lautaro Natali, Cristian Prieto-Garcia, Jan F M Stuke, Lorene Brunello, Alexandre Vicente, Alexander Pfab, Hagen Wesseling, Sara Cano-Franco, Anshu Khatri, Simone Larivera, Pablo Sanz-Martinez, Benjamin de la Cruz-Thea, Anne-Claire Jacomin, Jan Prochazka, Regina Feederle, Volker Dötsch, Radislav Sedlacek, Gerhard Hummer, Stefanie Kaiser, Ivan Dikic, Melina M Musri, Gunter Meister, Alexandra Stolz.
      The YTHDF protein family plays a critical role in cancer development by recognizing and regulating the stability of N6-methyladenosine (m6A)-modified RNA. Here, we reveal an autophagy-dependent mechanism controlling YTHDF protein levels. Using contact inhibition as a cellular model system, we show YTHDF proteins to be rapidly degraded, coinciding with increased autophagy and decreased mTOR activity. Upon pharmacological mTOR inhibition, YTHDF2 is also downregulated via lysosomal degradation. YTHDF2 selectively interacts with the autophagy modifier GABARAP L2 through LC3-interacting region (LIR) motifs in its unstructured N- and C-terminal regions. Autophagic YTHDF2 downregulation results in the co-degradation of its bound m6A-modified RNA clients. While YTHDF depletion induces cell death in contact-inhibition-deficient HCT116 cancer cells, contact-inhibited MRC5 and RPE1 cells remain unaffected. Our findings uncover a regulatory pathway that governs YTHDF protein stability with significant implications for cancer biology and cell fate determination and suggest the existence of an autophagy-mediated degradation pathway for m6A-modified RNA.
    Keywords:  CP: Cell biology; RNA binding; YTHDF; cancer; cellular homeostasis; contact inhibition; lysosomal degradation; m6A; selective autophagy
    DOI:  https://doi.org/10.1016/j.celrep.2025.116188
  14. Neuroscience. 2025 Aug 18. pii: S0306-4522(25)00868-1. [Epub ahead of print]584 160-165
    The role of mitophagy in perioperative neurocognitive disorder: from mechanisms to implications.
    Shuai Gao, Jiaqiang Wang, Jiawei Chen.
      Perioperative neurocognitive disorder (PND) is a significant neurological complication in aging perioperativepatients, seriously impacting their postoperative recovery and cognition as well as quality of life. The occurrence of PND is closely related to various factors, including neuroinflammation and oxidative stress, while the exact mechanism is still unknown. Mitophagy is a specialized form of autophagy and maintains cellular homeostasis by selectively degrading damaged and dysfunctional mitochondria, serving as a crucial quality control mechanism to ensure the mitochondrial network's integrity and functionality. Mitophagy has been proved to be involved in the onset and progression of major neurodegenerative diseases, such as Parkinson's disease and Alzheimer's disease. Recently, findings indicated that mitophagy may also play critical roles in the pathogenesis of PND, and the mechanisms may involve ubiquitin-dependent pathways (such as the PINK1/Parkin pathway) and non-ubiquitin-dependent pathways (such as the BNIP3/FUNDC1 pathway). Studies indicated that the PINK1/Parkin pathway is impaired in the animal PND models. In contrast, the BNIP3/ FUNDC1 pathway is neuroprotective by promoting mitophagy under stress conditions such as hypoxia. In addition, abnormal Tau protein aggregation and ferroptosis are correlated with mitophagy and PND in animal studies. In this review, we focused on the role and detailed mechanism of mitophagy in the occurrence and development of PND, as well as on possible potential targets involving mitophagy modulation.
    Keywords:  Cognitive function; Ferroptosis; Mitophagy; Perioperative neurocognitive disorder (PND); Signal pathway; Tau protein
    DOI:  https://doi.org/10.1016/j.neuroscience.2025.08.028
  15. Autophagy. 2025 Aug 24.
    LC3 and GABARAP independent autophagy of misfolded procollagen in mouse osteoblasts.
    Elena Makareeva, Shakib Omari, Anna M Roberts-Pilgrim, Laura Gorrell, Bella Radant, Muthulakshmi Sellamani, Edward L Mertz, Basma Khoury, Kenneth Kozloff, Sergey Leikin.
      Bone synthesis should depend on autophagy because over 10% of type I procollagen (PC1) - a heterotrimer of COL1A1 and COL1A2 chains and the precursor of the main bone matrix molecule - is misfolded and rerouted from osteoblast endoplasmic reticulum (ER) to lysosomes. However, osteoblast-specific macroautophagy knockouts in mice have produced only mild bone effects. To reconcile these observations, we compared how hypomorphic expression and a conditional knockout (cKO) of Atg5 - encoding a protein required for autophagosome formation - affected Col1a2G610C/+ versus wild-type Col1a2+/+ osteoblasts in vivo and in vitro. The Gly610-to-Cys substitution (G610C) in the triple helical region of the COL1A2/proα2(I) chain increases PC1 misfolding, causing its accumulation in the ER, cell stress, and osteoblast malfunction. Because autophagy reroutes misfolded PC1 from the ER to lysosomes, disruption of PC1 autophagy should significantly increase osteoblast malfunction and bone pathology in Col1a2G610C/+ mice. Nonetheless, the present study revealed only minor effects of the atg5 cKO on osteoblast function and bone formation in the Col1a2G610C/+ mice, like in Col1a2+/+ controls. The cKO did not reduce the autophagy flux of misfolded G610C or wild-type PC1 in primary osteoblast cultures, even though the LC3 and GABARAP lipidation and therefore autophagosome formation were disrupted. Live-cell imaging in atg5 cKO osteoblasts demonstrated that PC1 was efficiently delivered to lysosomes without LC3 via ER exit site (ERES) microautophagy. Taken together, these observations indicate that LC3- and GABARAP-independent ERES microautophagy is the primary pathway of misfolded procollagen degradation in osteoblasts both in culture and in vivo.
    Keywords:  ATG5; ER exit site; ERES microautophagy; G610C mutation; bone; osteogenesis imperfecta
    DOI:  https://doi.org/10.1080/15548627.2025.2551478
  16. Sci Adv. 2025 Aug 29. 11(35): eady0240
    Putative PINK1/Parkin activators lower the threshold for mitophagy by sensitizing cells to mitochondrial stress.
    William M Rosencrans, Ryan W Lee, Logan McGraw, Ian Horsburgh, Ting-Yu Wang, Baiyi Quan, Diana Huynh, Jennifer A Johnston, David C Chan, Tsui-Fen Chou.
      The PINK1/Parkin pathway targets damaged mitochondria for degradation via mitophagy. Genetic evidence implicates impaired mitophagy in Parkinson's disease, making its pharmacological enhancement a promising therapeutic strategy. Here, we characterize two mitophagy activators: a novel Parkin activator, FB231, and the reported PINK1 activator MTK458. Both compounds lower the threshold for mitochondrial toxins to induce PINK1/Parkin-mediated mitophagy. However, global proteomics revealed that FB231 and MTK458 independently induce mild mitochondrial stress, resulting in impaired mitochondrial function and activation of the integrated stress response, effects that result from PINK1/Parkin-independent off-target activities. We find that these compounds impair mitochondria by distinct mechanisms and synergistically decrease mitochondrial function and cell viability in combination with classical mitochondrial toxins. Our findings support a model whereby weak or "silent" mitochondrial toxins potentiate other mitochondrial stressors, enhancing PINK1/Parkin-mediated mitophagy. These insights highlight important considerations for therapeutic strategies targeting mitophagy activation in Parkinson's disease.
    DOI:  https://doi.org/10.1126/sciadv.ady0240
  17. mSphere. 2025 Aug 25. e0030825
    Unc-51-like kinase 1 (ULK1) regulates bacterial ubiquitylation and p62 recruitment during xenophagic clearance of Listeria monocytogenes.
    J S Ribeiro, M S Siqueira, T S M Farias, T D P Spinasse, P L O Correia, R M Ribeiro, F M Bastos de Oliveira, L A M Carneiro, L H Travassos.
      Autophagy is an essential cellular homeostatic process that also serves as an innate immune mechanism against intracellular bacterial pathogens through a highly selective form of autophagy known as xenophagy. Despite advances in understanding how bacteria are targeted for autophagic degradation, the specific regulatory mechanisms that drive the initial steps and ensure bacterial selection remain incompletely defined. Our study uncovers a pivotal role for Unc-51-like kinase 1 (ULK1) in the xenophagic clearance of the intracellular bacterial pathogen Listeria monocytogenes. We observed that ULK1 is essential for the efficient ubiquitylation of bacteria and subsequent recruitment of the autophagic adaptor protein p62 to the bacterial surface. Furthermore, we show that the impact of ULK1 deficiency in these early events-reduction in bacterial ubiquitylation, followed by impaired p62 targeting, results in diminished formation of bacteria-targeted autophagosomes. Notably, phosphorylation of p62 at the S409 residue, which is known to be dependent on ULK1 to enhance its affinity for ubiquitin, is necessary for the recruitment of p62 to the bacterial surface and adequate bacterial clearance, highlighting the regulatory role of ULK1 in this process. These findings unveil a previously unrecognized function of ULK1 in modulating early xenophagy steps, contributing to the autophagic control of intracellular pathogens. Our findings offer new perspectives into the manipulation of ULK1 activity for therapeutic interventions against infectious diseases.IMPORTANCEAutophagy is a vital process in eukaryotic cells that enables them to digest intracellular components, helping them respond to various stresses, including starvation, the accumulation of dysfunctional organelles, and infections. While the autophagic flux has been extensively studied over the past few decades, some key mechanisms remain poorly understood. Our research aimed to clarify one such mechanism: how the autophagic machinery specifically targets intracellular bacteria. We identified a novel role for the protein ULK1 in this process, demonstrating that ULK1 is essential for tagging bacteria with ubiquitin within the cell and recruiting the protein p62. These are critical steps for adequate bacterial clearance. Our results underscore the pivotal role of ULK1 in initiating the cellular defense against bacterial infections. Our findings could pave the way for new therapeutic strategies to enhance the body's capacity to combat bacterial infections.
    Keywords:  Listeria monocytogenes; ULK1; autophagy; bacterial clearance; host-microbe interactions; infection; innate immunity; p62; ubiquitination; xenophagy
    DOI:  https://doi.org/10.1128/msphere.00308-25
  18. Adv Pharmacol Pharm Sci. 2025 ;2025 5567858
    Alpha-Mangostin Alleviates Mitochondrial Damage and Autophagy Dysregulation in the MPP+ Cellular Model of Parkinson's Disease.
    Korede Jacob Abraham, Permphan Dharmasaroja.
      Alpha-mangostin (α-M), a xanthone derivative with known antioxidative properties, has demonstrated a protective effect on neurons under oxidative stress, a key factor in the pathogenesis of Parkinson's disease (PD). However, its impact on mitochondrial integrity and autophagy in PD remains insufficiently understood. Therefore, the present study aimed to investigate the role of α-M in regulating defective mitochondrial proteins and its influence on the mTOR pathway, both of which are critical in the regulation of autophagy. This study investigated the effects of α-M pretreatment on 1-methyl-4-phenylpyridinium (MPP+)-induced neurotoxicity in SH-SY5Y dopaminergic neurons. MPP+, a mitochondrial complex I inhibitor, significantly reduced the expression of mitochondrial proteins NDUFS3 and TIMM23, induced mitochondrial damage, and triggered excessive autophagy, as evidenced by elevated LC3-II/LC3-I ratio and phospho-Beclin-1 expression. These changes were accompanied by dysregulation of the mTOR signaling pathway, including increased phosphorylation of mTOR and suppression of its downstream effector p70S6K. α-M pretreatment restored NDUFS3 and TIMM23 levels, preserved mitochondrial morphology and membrane potential, and reduced autophagy activation by mitigating MPP+-induced LC3B accumulation and Beclin-1 activation. Additionally, α-M restored balance in the mTOR signaling pathway by reducing mTOR phosphorylation and restoring p70S6K activity, counteracting the autophagic dysregulation caused by MPP+. Importantly, α-M exhibited no toxicity under normal conditions, indicating its protective effects are context-dependent and activated only during cellular stress. These findings highlight the potential of α-M as a therapeutic agent for PD, providing neuroprotection through its targeted modulation of mitochondrial proteins and mTOR signaling that regulates autophagy.
    Keywords:  MPP+; alpha-mangostin; autophagy; mTOR; mitochondria; p70S6K
    DOI:  https://doi.org/10.1155/adpp/5567858
  19. Front Microbiol. 2025 ;16 1632425
    Unveiling the impact of non-coding RNAs on virus-induced cellular autophagy: roles and research advances.
    Ming Yu, Ying Yi, Honglin Yang, Yi Zhang.
      Autophagy is the process by which cells degrade and recycle damaged organelles and macromolecules by forming autophagosomes. This process is closely related to the maintenance of cellular homeostasis, ontogeny, and the occurrence and development of various diseases. Non-coding RNAs (ncRNAs) are a class of RNA molecules that do not encode proteins but play crucial roles in regulating gene expression. Numerous studies have demonstrated that ncRNAs are involved in regulating autophagy, and accumulating scientific evidence suggests that ncRNAs play an essential role in virus-induced cellular autophagy. ncRNAs affect autophagy by participating in the autophagy regulatory network, mediating the transcriptional and post-transcriptional regulation of autophagy-related genes. This review aims to explore the role of ncRNAs in autophagy induced by viral infection and analyze the relevant molecular regulatory mechanisms underlying autophagy. By examining the content above, we speculate that targeted regulation of ncRNAs can affect autophagy induced upon viral infection, thereby achieving antiviral effects and host cell protection.
    Keywords:  autophagy; non-coding RNAs; regulatory mechanism; viral infection; virology
    DOI:  https://doi.org/10.3389/fmicb.2025.1632425
  20. Nat Rev Nephrol. 2025 Aug 26.
    Regulation of autophagy by a tRNA-derived fragment.
    Susan J Allison.
      
    DOI:  https://doi.org/10.1038/s41581-025-01001-9
  21. Front Cell Infect Microbiol. 2025 ;15 1613366
    Porphyromonas gingivalis hijacks mitophagy and lysosomal function to persist in endothelial cells.
    Cheng Zheng, Jianmin Huang, Shengming Xu, Bin Lu, Hanxin Que, Tianhao Chen, Yubo Hou, Linlin He, Xia Fan, Fa-Ming Chen, Yi Wang, Hui Deng.
       Introduction: The direct infection of endothelial cells by Porphyromonas gingivalis (P. gingivalis), a keystone periodontal pathogen, has been implicated in the development of atherosclerosis. While non-selective autophagy facilitates its intracellular persistence in endothelial cells, the role of selective autophagy in this process remains unclear. This study investigated whether P. gingivalis hijacks mitophagy and lysosomes to persist in endothelial cells.
    Methods: Human aortic endothelial cells (HAECs) were infected with P. gingivalis for 24 h. Mitophagy was detected by Western Blotting (WB), immunofluorescence, and transmission electron microscopy. Lysosomal function was assessed by acridine orange staining, lysosensor staining, and WB. The effects of mitophagy and lysosomes on P. gingivalis intracellular survival were evaluated by antibiotic protection assays and SYTO-9 staining.
    Results: Our data demonstrated that P. gingivalis initiates PTEN-induced putative kinase 1 (PINK1)-Parkin-mediated mitophagy in HAECs, leading to increased formation of autophagosomes and mitophagosomes, but disrupted autophagy/mitophagy flux. This blockage of autophagy/mitophagy flux was linked to lysosomal dysfunction, characterized by increased lysosome number, lysosomal membrane permeabilization, disruption of the lysosomal acidic environment, and decreased enzymatic activity. Additionally, antibiotic protection assays and SYTO-9 staining further revealed that P. gingivalis promotes its intracellular survival in endothelial cells by initiating mitophagy and impairing lysosomal function. Furthermore, the mitophagy activator decreased the co-localization of P. gingivalis with microtubule-associated protein 1 light chain 3 (LC3)-p62, LC3-NDP52, and lysosomal-associated membrane protein 1 (LAMP1), suggesting that P. gingivalis-initiated mitophagy inhibited xenophagosome formation and autophagosome/xenophagosome-lysosome fusion.
    Conclusion: Our findings reveal that P. gingivalis may promote its intracellular survival in endothelial cells by initiating PINK1-Parkin-mediated mitophagy and impairing lysosomal function, thereby suppressing xenophagosome formation and xenophagic degradation. This study provides new insights into the mechanisms by which P. gingivalis persists in endothelial cells and its potential role in atherosclerosis progression.
    Keywords:  Porphyromonas gingivalis; endothelial cells; lysosomal function; mitophagy; xenophagy
    DOI:  https://doi.org/10.3389/fcimb.2025.1613366
  22. Adv Biotechnol (Singap). 2025 Aug 20. 3(3): 25
    Arabidopsis MACP2 contributes to autophagy induction by modulating starvation-induced reactive oxygen species homeostasis.
    Ying Zhou, Xue Zhang, Tiancong Qi, Zi-Han Wang, Yao Wang, Lin-Na Wang, Yong-Lun Zeng, Hanjie He, Liwen Jiang, Daoxin Xie, Shi Xiao, Lu-Jun Yu, Qin-Fang Chen.
      In plants, autophagy is a conserved recycling system essential for development and stress responses by targeting cellular components for massive degradation in the vacuole. Our previous work suggested that autophagy contributes to Arabidopsis (Arabidopsis thaliana) stress responses by modulating NADPH-oxidase-mediated reactive oxygen species (ROS) homeostasis; however, the molecular link between extracellular ROS and autophagy remains unknown. We performed a yeast two-hybrid screen to identify components involved in autophagy, using the central autophagy component ATG8e as a bait. We identified MEMBRANE ATTACK COMPLEX/PERFORIN-LIKE 2 (MACP2) as an interactor of ATG8e via its the ATG8-interacting motif and confirmed this interaction by co-immunoprecipitation and bimolecular fluorescence complementation assays. MACP2-overexpressing lines showed enhanced sensitivity to nutritional starvation, accelerated leaf senescence, and increased hydrogen peroxide (H2O2) levels, resembling the phenotypes of atg mutants defective in autophagy. Conversely, macp2 knockouts exhibited diminished starvation-induced H2O2 accumulation and attenuated autophagosome formation and fully suppressed the starvation-hypersensitive phenotypes of the atg5-1 mutant. In particular, MACP2 was degraded through the autophagy machinery during prolonged starvation, suggesting a feedback regulatory mechanism for maintaining MACP2 homeostasis. Our findings suggest that MACP2 acts as a key regulator in autophagy induction by controlling influx of extracellular H2O2 in Arabidopsis.
    Keywords:   Arabidopsis; MACP2; ROS; Autophagy
    DOI:  https://doi.org/10.1007/s44307-025-00078-4
  23. Eur J Pharmacol. 2025 Aug 20. pii: S0014-2999(25)00836-2. [Epub ahead of print]1005 178082
    Ridaifen derivatives function as potent lysosomotropic agents, depending on their basic side chains.
    Yuta Semba, Kyoka Komukai, Eri Murata, Fumi Sato, Amane Yoneoka, Takatsugu Murata, Hidesuke Fukazawa, Isamu Shiina, Shunsuke Takahashi, Yukitoshi Nagahara.
      Autophagy plays a key role in cellular homeostasis, but dysregulated autophagy can lead to resistance to chemotherapeutic agents. The Ridaifen (RID) compound series comprises structural analogues of tamoxifen that exhibit more potent anticancer activity and have been implicated in modulating autophagy. Here, we investigated how the RID compounds interact with autophagy and explored the factors contributing to their enhanced cytotoxicity. We synthesized RID derivatives containing varying numbers of basic side chains and evaluated their intracellular behavior. We assessed cell viability using an MTT assay and determined lysosomal pH by flow cytometry. To visualize the subcellular distribution of the RID derivative, we employed a fluorescent dye‒conjugated form of the compound. Additionally, we monitored autophagic and apoptotic markers through immunoblotting. RID-B demonstrated potent lysosomal neutralization and inhibited autophagic flux near its half-maximal inhibitory concentration. This neutralization led to the accumulation of insoluble SQSTM1-containing aggregates, implicating proteotoxic stress in apoptosis. Confocal imaging revealed proton-dependent lysosomal localization of RID-B, followed by partial cytoplasmic translocation. Notably, co-treatment with bafilomycin A1 reduced RID-B‒induced apoptosis, underscoring lysosomal dysfunction initiated apoptotic signaling. Analyses across multiple RID derivatives showed a correlation among the number of basic side chains, lysosomal neutralization, and between lysosomal neutralization and cytotoxicity. Our findings indicate that basic side chains markedly enhance lysosomotropic behavior, enabling sustained autophagy inhibition and apoptosis induction. By revealing a strong link between lysosomal neutralization and proteotoxic cell death, the results suggest that modified tamoxifen analogues, such as RID-B, may offer a promising strategy to overcome autophagy-related drug resistance in cancer therapy.
    Keywords:  Anti-cancer compound; Autophagy; Lysosomotropic agents; Ridaifen
    DOI:  https://doi.org/10.1016/j.ejphar.2025.178082
  24. EMBO J. 2025 Aug 21.
    Soma-localized Rab39 inhibits synaptic autophagy by controlling trafficking of Atg9 vesicles.
    Ayse Kilic, Gokhan Ozturan, Dirk Vandekerkhove, Sabine Kuenen, Jef Swerts, Esther Muñoz Pedrazo, Carles Calatayud Aristoy, Abril Escamilla Ayala, Nikky Corthout, Pablo Hernández Varas, Stéphane Plaisance, Valerie Uytterhoeven, Eliana Nachman, Patrik Verstreken.
      Presynaptic terminals can be located far from the neuronal cell body and are thought to independently regulate protein and organelle turnover. Autophagy is a critical process for maintaining proteostasis, and its synaptic dysregulation is associated with neurodegenerative diseases. In this work, we report a soma-centered mechanism that regulates autophagy-controlled protein turnover at distant presynaptic terminals in Drosophila. We show that a central component of this system is Rab39, whose human homolog RAB39B is mutated in Parkinson's disease. Although Rab39 is localized in the soma, its loss of function or a human pathogenic mutation causes increased autophagy at presynaptic terminals, resulting in faster synaptic protein turnover and dopaminergic synapse degeneration. Using a large-scale unbiased genetic modifier screen, we identified genes encoding cytoskeletal and axonal organizing proteins, including Shortstop (Shot), as suppressors of synaptic autophagy. We demonstrate that active Rab39 selectively controls Shot- and Unc104/KIF1A-mediated delivery of autophagy-related Atg9-positive vesicles to synapses. Our findings suggest that Rab39-mediated trafficking in the soma orchestrates a cross-compartmental mechanism that regulates the levels of autophagy at synapses.
    Keywords:   Drosophila ; Genetic Suppressor Screen; Parkinson’s Disease; Rab39; Synaptic Autophagy
    DOI:  https://doi.org/10.1038/s44318-025-00536-8
  25. Cell Rep. 2025 Aug 22. pii: S2211-1247(25)00950-7. [Epub ahead of print]44(9): 116179
    Lysosomal polyamine storage upon ATP13A2 loss impairs β-glucocerebrosidase via altered lysosomal pH and electrostatic hydrolase-lipid interactions.
    Madhuja Samaddar, Gabriel A Fitzgerald, Ann Hong Nguyen, Sonnet S Davis, Shourya Jain, Jian Guo, Nicholas E Propson, Bettina van Lengerich, Yajuan Shi, Srijana Balasundar, Lionel Rougé, Jamal Alkabsh, Anil Rana, Julie Yi, Marcus Y Chin, Isabel A Becerra, Annie Arguello, Brian M Fox, Todd Logan, Jung H Suh, Anastasia G Henry, Gilbert Di Paolo.
      ATP13A2 is an endolysosomal polyamine transporter mutated in several neurodegenerative conditions involving lysosomal defects, including Parkinson's disease (PD). While polyamines are polybasic and polycationic molecules that play pleiotropic cellular roles, their specific impact on lysosomal health is unknown. Here, we demonstrate lysosomal polyamine accumulation in ATP13A2 knockout (KO) cell lines and human induced pluripotent stem cell (iPSC)-derived neurons. Primary polyamine storage caused secondary storage of lysosomal anionic phospholipid bis(monoacylglycero)phosphate (BMP) and an age-dependent increase in the β-glucocerebrosidase (GCase) substrate glucosylsphingosine in Atp13a2 KO brains. Polyamine accumulation inhibited lysosomal GCase activity in cells, and this was reversed by lysosome reacidification or BMP supplementation. A liposome-based GCase assay utilizing physiological substrates demonstrated dose-dependent inhibition of BMP-stimulated GCase activity by polyamines, in part via a pH-independent, electrostatics-based mechanism. Therefore, excess polyamine compromises lysosomes by disrupting pH and electrostatic interactions between GCase and BMP that enable efficient substrate hydrolysis, potentially clarifying pathogenic mechanisms and suggesting convergence on PD-relevant pathways.
    Keywords:  CP: Neuroscience; Kufor-Rakeb syndrome; P-type ATPase; Parkinson’s disease; glucocerebrosidase; glycosphingolipid; lysosomal storage disorder; neuronal ceroid lipofuscinosis; polyamine; spermine
    DOI:  https://doi.org/10.1016/j.celrep.2025.116179
  26. Int J Mol Sci. 2025 Aug 20. pii: 8048. [Epub ahead of print]26(16):
    CDK5 Inhibits Synphilin-1 Ubiquitination and Basal Mitophagy: Implications for Parkinson's Disease.
    Mor Savyon, Eyal Avraham, Ankit Kumar Shah, Haya Hamza, Raymonde Szargel, Fatimah Abd Elghani, Malik Farhoud, Michal Toren-Hershkoviz, Nicole Pavoncello, Sofia Zaer, Rina Bandopadhyay, Hazem Safory, Simone Engelender.
      Parkinson's disease (PD) is characterized by the loss of dopaminergic neurons in the substantia nigra and the presence of α-synuclein-positive inclusions known as Lewy bodies. Synphilin-1 is a protein of unknown function that interacts with α-synuclein and has been shown to exhibit cytoprotective effects in both in vitro and in vivo models. In this study, we investigated whether synphilin-1 is phosphorylated by pathological CDK5 and explored the consequences of this modification. Pathological activation of CDK5 occurs mainly through its association with the calpain-cleaved protein p25. Although CDK5 inhibition protects against neurodegeneration in pharmacological PD models, we now show that p25 levels are increased in PD brains. Furthermore, we demonstrate that CDK5, in conjunction with p25, directly phosphorylates synphilin-1, mainly at serine 566. This phosphorylation reduces synphilin-1's interaction with SIAH1, leading to reduced ubiquitination and subsequent accumulation. We also observed that CDK5-phosphorylated synphilin-1 exhibits a reduced ability to interact with PINK1 and to promote basal levels of mitophagy. Consistent with these findings, the phosphorylation-mimicking synphilin-1 S566E shows decreased translocation to mitochondria, and synphilin-1 levels are reduced in the mitochondria of PD brains compared to age-matched controls. Finally, synphilin-1 S566E promotes retraction of neuronal processes. Taken together, our results suggest that phosphorylation by CDK5 disrupts synphilin-1's interactions with its protein partners, rendering it more toxic and impairing its ability to support mitophagy and maintain neuronal process homeostasis. We hypothesize that phosphorylation of synphilin-1 by CDK5 may contribute to the pathogenesis of PD.
    Keywords:  CDK5; Parkinson’s disease; mitophagy; neurodegeneration; neuronal processes; synphilin-1; ubiquitination
    DOI:  https://doi.org/10.3390/ijms26168048
  27. Nat Commun. 2025 Aug 22. 16(1): 7852
    Episodic transport of protein aggregates achieves a positive size selectivity in aggresome formation.
    Rui Fang, Luolan Bai, Bert M Verheijen, Boyan Li, Kevin Dong, Joao A Paulo, Mengying Zhou, Yi-Chi Chu, Yuyu Song, Michael Y Sherman, Steven Gygi, Christine M Field, Timothy J Mitchison, Ying Lu.
      Eukaryotic cells direct toxic misfolded proteins to various quality control pathways based on their chemical properties and aggregation status. Aggregated proteins are targeted to selective autophagy or specifically sequestered into the "aggresome", a perinuclear inclusion at the microtubule-organizing center (MTOC). However, the mechanism for selective aggresome recruitment remains unclear. To investigate this process, here we reconstitute MTOC-directed aggregate transport in Xenopus laevis egg extract using AgDD, a chemically inducible aggregation system. High-resolution single-particle tracking reveals that dynein-mediated aggregate transport is highly episodic, with average velocity positively correlating with aggregate size. Mechanistic modeling suggests that recurrent formation of the dynein transport complex biases larger aggregates towards active transport, compensating for the slowdown due to viscosity. Both episodic transport and positive size selectivity are conferred by aggresome-specific dynein adapters. Coupling an aggresome adapter to polystyrene beads recapitulates positive size selectivity in transport, while recruiting conventional dynein adapters to protein aggregates perturbs aggresome formation and reverses the size selectivity.
    DOI:  https://doi.org/10.1038/s41467-025-62751-5
  28. Mol Cell. 2025 Aug 19. pii: S1097-2765(25)00656-2. [Epub ahead of print]
    Endocytosis is essential for cysteine-deprivation-induced ferroptosis.
    Xuesong Liu, Zechuan Zhao, Zhixuan Bian, Fahad A Benthani, Yingying Hu, Deguang Liang, Xuejun Jiang.
      Ferroptosis is a form of cell death caused by iron-dependent phospholipid peroxidation and subsequent membrane rupture. Autophagic degradation of the iron-storage protein ferritin promotes ferroptosis by increasing cytosolic bioactive iron, presumably explaining how lysosomal inhibitors suppress ferroptosis. Surprisingly, we found that lysosomal inhibitors suppress cysteine-deprivation-induced (CDI) ferroptosis, even in autophagy-defective cells, and subsequently discovered that clathrin-mediated endocytosis (CME) of transferrin is essential for CDI ferroptosis. Blocking lysosomal proteolytic activity failed to inhibit ferroptosis, whereas disrupting endosomal acidification and eliminating the endocytic protein AP2M1 both impeded ferroptosis. Conversely, replenishing cellular iron with ferric ammonium citrate, but not with transferrin, restored CDI ferroptosis in endocytosis-deficient cells. Unexpectedly, abolishing endosomal acidification, CME, and the associated increase in cellular labile iron could not prevent ferroptosis triggered by direct inhibition of the ferroptosis-suppressing enzyme glutathione peroxidase-4 (GPX4). Together, this study reveals the essential role of endocytosis, specifically for CDI ferroptosis.
    Keywords:  AP2M1; GPX4; autophagy; cysteine deprivation; endocytosis; endosome; ferroptosis; iron; lysosome; transferrin
    DOI:  https://doi.org/10.1016/j.molcel.2025.08.006
  29. Mol Pharmacol. 2025 Jul 11. pii: S0026-895X(25)15321-2. [Epub ahead of print]107(9): 100061
    Liver CYP4A autophagic lysosomal degradation: A major role for the autophagic receptor SQSTM1/p62 through an uncommon target interaction site.
    Liang He, Doyoung Kwon, Michael J Trnka, Yi Liu, Jade Yang, Kathy H Li, Rheem A Totah, Eric F Johnson, Alma L Burlingame, Maria Almira Correia.
      The hepatic P450 hemoproteins CYPs 4A are typical N-terminally anchored type I endoplasmic reticulum (ER) proteins, inducible by many hypolipidemic drugs and peroxisome proliferators. They are engaged in the ω-/ω-1-oxidation of various fatty acids including arachidonic acid, prostaglandins, and leukotrienes and in the biotransformation of some therapeutic drugs. Because the proteolytic turnover of the mammalian liver CYPs 4A remains obscure, we have characterized it. We report that of these proteins, human CYP4A11 and mouse Cyp4a12a are preferential targets of the ER-lysosome-associated degradation. Consequently, these proteins are stabilized 2- to 3-fold both as 1%Triton X100-soluble and insoluble species in mouse hepatocytes and HepG2 cells deficient in the autophagic initiation ATG5 gene. Despite exhibiting surface microtubule-associated protein light chain 3-interacting regions that could target them directly to the autophagosome, they nevertheless interact intimately with the autophagic receptor SQSTM1/p62. Through structural deletion analyses and site-directed mutagenesis, we have identified the CYP4A-interacting p62 subdomain to lie between residues 170 and 233, which include its Traf6-binding and LIM-binding subdomains. Mice carrying a liver-specific genetic deletion of p62 residues 69-251 (p62Mut) that includes the CYP4A-interacting subdomain also exhibit Cyp4a-protein stabilization as 1% Triton X100-soluble and insoluble species. Consistently, p62Mut mouse liver microsomes exhibit 1.5- to 2-fold enhanced ω- and ω-1-arachidonic acid hydroxylation to its physiologically active metabolites 19 and 20-HETEs relative to the corresponding wild-type mouse liver microsomes. Collectively, our findings suggest that disruption of CYP4A ER-lysosome-associated degradation results in functionally active P450 protein stabilization and consequent proinflammatory metabolite generation along with insoluble CYP4A aggregates, which may contribute to pathological aggregates, ie, Mallory-Denk bodies/inclusions, hallmarks of many liver diseases. SIGNIFICANCE STATEMENT: Human CYP4A11 and mouse Cyp4a12a, liver P450 enzymes engaged in ω-/ω-1-oxidation of arachidonic acid, prostaglandins, and leukotrienes, are documented to physiologically turn over via endoplasmic reticulum-lysosome-associated autophagic degradation, which involves their intimate association with the autophagic receptor SQSTM1/p62. Genetic endoplasmic reticulum-lysosome-associated autophagic degradation disruption or deletion of their hepatic p62-interaction subdomain in mice results in Cyp4a-protein stabilization as functionally active solubilizable species with consequently enhanced proinflammatory 20-HETE arachidonate metabolite generation and insoluble Cyp4a aggregates, potential contributors to pathologic liver inclusions.
    Keywords:  Autophagic lysosomal degradation (ALD); Chemical crosslinking mass spectrometry (XLMS); Cytochromes P450; ER-lysosomal-associated degradation (ERLAD); Endoplasmic reticulum (ER)-associated degradation (ERAD); Sequestosome 1 (SQSTM-1/p62)
    DOI:  https://doi.org/10.1016/j.molpha.2025.100061
  30. J Neurochem. 2025 Aug;169(8): e70205
    Impact of O-GlcNAcylation Elevation on Mitophagy and Glia in the Dentate Gyrus.
    Joshua Kramer, Sarah Fu, Xiaosen Ouyang, Eric Rohwer, John C Chatham, Martin E Young, Victor Darley-Usmar, Jianhua Zhang.
      O-GlcNAcylation is a dynamic and reversible protein posttranslational modification of serine or threonine residues which modulates the activity of transcriptional and signaling pathways and controls cellular responses to metabolic and inflammatory stressors. We and others have shown that O-GlcNAcylation has the potential to regulate autophagy and mitophagy to play a critical role in mitochondrial quality control, but this has not been assessed in vivo in the brain. This is important since mitochondrial dysfunction contributes to the development of neurodegenerative diseases. We used mito-QC reporter mice to assess mitophagy in diverse cells in the dentate gyrus in response to pharmacological inhibition of O-GlcNAcase (OGA) with thiamet G which leads to elevation of protein O-GlcNAcylation. We demonstrate that mitophagy occurs predominantly in the GFAP-positive astrocytes and is significantly decreased in response to elevated O-GlcNAcylation. Furthermore, with increased O-GlcNAcylation, the levels of astrocyte markers GFAP and S100B, and the microglial cell marker IBA1, decreased in the dentate gyrus, while the levels of microglial cell marker TMEM119 were increased, indicating significant changes in glia homeostasis. These results provide strong evidence of the regulation of mitophagy and glia signatures by the O-GlcNAc pathway.
    Keywords:  O‐GlcNAc; astrocyte; hippocampus; microglia; mitophagy
    DOI:  https://doi.org/10.1111/jnc.70205
  31. Mol Cell Proteomics. 2025 Aug 25. pii: S1535-9476(25)00159-8. [Epub ahead of print] 101060
    Jolkinolide B Activates Mitophagy to Exhibit Anti-pancreatic Cancer Activity and Alleviate Cognitive Deficits in Alzheimer's Disease.
    Mingjie Gao, Weiyi Hu, Delan Meng, Pengju Yao, Siqi Yang, Yuanpeng Tong, Lei Wang, Ya Zhang, Qingsong Wang, Jianguo Ji, Wenyuan Zhu.
      Dysfunctional mitophagy leads to the pathological accumulation of damaged mitochondria, which is closely associated with the development of human diseases such as cancer and Alzheimer's disease. The identification of safer and more effective mitophagy regulators may provide a novel approach for treating mitochondrial diseases. Covalent-binding drugs have attracted substantial attention due to their high specificity, selectivity, and low resistance potential. In this study, we demonstrated that the natural epoxide compound jolkinolide B (JB) specifically induces mitophagy both in vitro and in vivo. Mass spectrometry analysis confirmed that JB directly binds to the outer mitochondrial membrane translocase protein TOM40, leading to autophagic cell death in pancreatic cancer. As a mitophagy enhancer, JB also ameliorates mitochondrial dysfunction and mitigates cognitive deficits in the 5×FAD mouse model of Alzheimer's disease. The findings indicate that JB selectively targets mitochondria to enhance mitophagy while exhibiting minimal toxicity in pancreatic cancer and Alzheimer's disease mouse models, highlighting its potential as a therapeutic agent for mitochondrial diseases.
    Keywords:  Alzheimer's disease; Jolkinolide B; Mitochondrial protein TOM40; Mitophagy enhancer; Pancreatic cancer
    DOI:  https://doi.org/10.1016/j.mcpro.2025.101060
  32. J Reprod Immunol. 2025 Aug 18. pii: S0165-0378(25)00211-6. [Epub ahead of print]171 104633
    SQSTM1/p62 drives radiosensitivity in cervical cancer via autophagy-independent mechanisms.
    Mihoko Yoshida, Haruka Nunomura, Atsushi Furuta, Kiyotaka Yamada, Ippei Yasuda, Kyoko Takemura, Sayaka Tsuda, Akemi Yamaki-Ushijima, Tomoko Shima, Ryohei Ogawa, Qing-Li Zhao, Jun-Ichi Saitoh, Koki Saito, Eiji Morita, Mitsuaki Okodo, Akitoshi Nakashima.
      Cervical cancer comprises squamous cell carcinomas (SCCs), which are generally radiosensitive; meanwhile, adenocarcinomas respond poorly to radiation. Here, we explored the role of selective autophagy receptors in modulating radiosensitivity across these subtypes. We found that SQSTM1/p62 was highly expressed in human papillomavirus (HPV)-positive SCC cell lines (HeLa, ME180) and clinical SCC specimens, but was low or undetectable in HPV-negative adenocarcinomas and the C33A cell line. Clonogenic assays confirmed that HPV-positive cells exhibited greater radiosensitivity than C33A. Upon irradiation, only HPV-positive cells showed upregulation of p62 and DNA-damage response proteins, whereas C33A cells did not. Treatment with autophagy inhibitors (bafilomycin A1 and chloroquine) further increased p62 levels in HPV-positive cells but not in HPV-negative cells. The sustained low p62 levels in C33A cells, regardless of autophagy inhibition, may represent a distinctive biomolecular feature of HPV-negative cervical cancer. Notably, overexpression of Atg4B to block autophagic flux without affecting p62 expression had no impact on radiosensitivity in either cell type, whereas pharmacologic inhibition of autophagy selectively enhanced radiation-induced cytotoxicity in HPV-positive cells. Conversely, siRNA-mediated knockdown of p62 in HPV-positive cells attenuated radiation-induced growth suppression. Together, these data indicate that p62 promotes radiosensitivity in HPV-positive cervical cancer through a mechanism distinct from classical autophagy. Therefore, p62 represents both a predictive biomarker for radiation response and a potential target for radiosensitization strategies in HPV-positive tumors, while its unresponsiveness in HPV-negative cancers suggests the need for alternative approaches in that context.
    Keywords:  Autophagy; Cervical cancer; HPV; Radiosensitivity; SQSTM1/p62
    DOI:  https://doi.org/10.1016/j.jri.2025.104633
  33. EMBO J. 2025 Aug 20.
    PARP7 is a proteotoxic stress sensor that labels proteins for degradation.
    Nonso J Ikenga, Jörg Vervoorts, Bernhard Lüscher, Roko Žaja, Karla L H Feijs-Žaja.
      ADP-ribosylation is a post-translational modification that plays a critical role in cellular stress responses. We have observed that during proteotoxic stress, cellular ADP-ribosylation increases, with ADP-ribosylated proteins accumulating in cytoplasmic foci containing ubiquitin and p62. During prolonged stress, these ADP-ribosylated proteins are transported to aggresomes and subsequently degraded via autophagy. In the absence of ubiquitination, ADP-ribosylated proteins become more prevalent and less soluble, indicating that ubiquitination is indispensable for this process. Upon inhibition of PARP7, accumulation of mono(ADP-ribosyl)ated proteins in response to proteotoxic stress is impeded. PARP7 turnover is very high under normal conditions; however, the protein becomes stabilised following proteotoxic stress and thereby forms an ideal proteotoxic stress sensor. Our findings imply that, contrary to the current paradigm, not all ADP-ribosylation may occur on specific sites to regulate specific protein characteristics. Instead, it may be rather promiscuous to enable efficient protein degradation or segregation to prevent irreversible damage caused by defective proteins.
    Keywords:  ADP-ribosylation; Macrodomain; PARP; Protein Degradation; Ubiquitination
    DOI:  https://doi.org/10.1038/s44318-025-00545-7
  34. Science. 2025 Aug 21. 389(6762): eadz0972
    LYVAC/PDZD8 is a lysosomal vacuolator.
    Haoxiang Yang, Jinrui Xun, Yajuan Li, Awishi Mondal, Bo Lv, Simon C Watkins, Lingyan Shi, Jay Xiaojun Tan.
      Lysosomal vacuolation is commonly found in many pathophysiological conditions, but its molecular mechanisms and functions remain largely unknown. Here, we show that the endoplasmic reticulum (ER)-anchored lipid transfer protein PDZ domain-containing 8 (PDZD8), which we propose to be renamed as lysosomal vacuolator (LYVAC), is a general mediator of lysosomal vacuolation. Using human cell lines, we found that diverse lysosomal vacuolation inducers converged on lysosomal osmotic stress, triggering LYVAC recruitment through multivalent interactions. Stress-induced lysosomal lipid signaling contributed to both the recruitment and activation of LYVAC. By directly sensing lysosomal phosphatidylserine and cholesterol, the lipid transfer domain of LYVAC mediated directional ER-to-lysosome lipid movement, leading to osmotic membrane expansion of lysosomes. These findings uncover an essential mechanism for lysosomal vacuolation with broad implications in pathophysiology.
    DOI:  https://doi.org/10.1126/science.adz0972
  35. PLoS One. 2025 ;20(8): e0330282
    Piezo1 regulates autophagy in HT22 hippocampal neurons through the Ca2+/Calpain and Calcineurin/TFEB signaling pathways.
    Yatong Wu, Yan Lu, Hao Zhang, Suhe Dong, Ziqing Zhang, Sinian Wang, Fengsheng Li, Shimin Yin.
       OBJECTIVE: To investigate the functional and molecular mechanisms by which Piezo1regulates HT-22 hippocampal neuronal autophagy, and to explore whether Piezo1 regulates hippocampal neuronal autophagy via the Ca2+/Calpain, CaMKKβ, or Calcineurin pathways.
    METHODS: The impacts of Piezo1 inhibition, activation and gene knockdown on the autophagy of HT22 neurons was investigated by Western blotting, PCR and immunofluorescence. The changes of intracellular calcium (Ca2+) concentration were also observed. To pinpoint the specific downstream Ca2+ signaling pathway by which Piezo1 modulates autophagy, the calcium chelator BAPTA-AM, the Calpain inhibitor PD151746, and the CaMKKβ inhibitor STO609 were employed either alone or in combination.
    RESULTS: Enhanced autophagy was observed when Piezo1 was activated using the agonist Yoda1, manifesting as increased release of autophagic vacuoles, enhanced LC3 II/LC3 I ratio, decreased p62 protein level, and elevated nuclear translocation and expression of the TFEB protein. ATG7 knockdown by ATG7 shRNA mitigated the effects of Yoda1 on LC3 II/LC3 I ratio and p62 protein levels. The Piezo1 inhibitor GsMTx4 partially reversed the autophagy caused by starvation in HT22 neurons while Yoda1 still activated autophagy in the presence of BDNF. Following Piezo1 knockdown, neuronal autophagy was decreased. Piezo1-induced autophagy was accompanied with an increased cytoplasmic concentration of Ca2+. The calcium chelator BAPTA-AM partly reversed Piezo1 activation-induced autophagy, which was also mitigated by blocking calcineurin/TFEB signaling or Calpain signaling.
    CONCLUSION: Piezo1 modulates the autophagy of HT-22 neurons by activating Ca2+/Calpain and Calcineurin/TFEB pathways.
    DOI:  https://doi.org/10.1371/journal.pone.0330282
  36. Nat Cell Biol. 2025 Aug 25.
    CHIP protects lysosomes from CLN4 mutant-induced membrane damage.
    Juhyung Lee, Natalie Chin, Jizhong Zou, Wan Nur Atiqah Binti Mazli, Michal Jarnik, Layla Saidi, Yue Xu, Eutteum Jeong, Jessica Suh, John Replogle, Michael E Ward, Juan S Bonifacino, Wei Zheng, Ling Hao, Yihong Ye.
      Understanding how cells mitigate lysosomal damage is critical for unravelling pathogenic mechanisms of lysosome-related diseases. Here we generate and characterize induced pluripotent stem cell (iPSC)-derived neurons (i3Neuron) bearing ceroid lipofuscinosis neuronal 4 (CLN4)-linked DNAJC5 mutations, which revealed extensive lysosomal abnormality in mutant neurons. In vitro membrane-damaging experiments establish lysosomal damages caused by lysosome-associated CLN4 mutant aggregates, as a critical pathogenic linchpin in CLN4-associated neurodegeneration. Intriguingly, in non-neuronal cells, a ubiquitin-dependent microautophagy mechanism downregulates CLN4 aggregates to counteract CLN4-associated lysotoxicity. Genome-wide CRISPR screens identify the ubiquitin ligase carboxyl terminus of Hsc70-interacting protein (CHIP) as a central microautophagy regulator that confers ubiquitin-dependent lysosome protection. Importantly, CHIP's lysosome protection function is transferrable: ectopic CHIP improves lysosomal function in CLN4 i3Neurons and effectively alleviates lipofuscin accumulation and cell death in a Drosophila CLN4 disease model. Our study establishes CHIP-mediated microautophagy as a key organelle guardian that preserves lysosome integrity, offering new insights into therapeutic development for lysosome-related neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s41556-025-01738-2
  37. Cell Death Dis. 2025 Aug 26. 16(1): 650
    ACSS2-TFEB axis acts as a critical regulator of the autophagic machinery in head and neck squamous cell carcinoma.
    Danhui Yin, Qian Yang, Shisheng Li, Yongchun Peng, Jianbo Zhang, Zuozhong Xie, Tengfei Fan.
      Head and neck squamous cell carcinoma (HNSCC) has a high rate of metastasis and recurrence, and poses a considerable threat to patient survival. Autophagy, an intracellular degradation pathway, plays a crucial role in tumor progression; however, the underlying mechanisms of action remain unclear. This study aimed to explore the role of the ACSS2-TFEB axis in the regulation of autophagy and its impact on HNSCC cell proliferation, migration, invasion, and lysosomal function. HNSCC tumor tissues and cell lines were analyzed for ACSS2 protein expression. The effects of the ACSS2 knockdown on cell proliferation, migration, invasion, and autophagic flux were also assessed. The interaction between ACSS2 and transcription factor EB (TFEB) and its influence on lysosomal function were also examined. In this study, we found that ACSS2 protein expression was significantly upregulated and correlated with metastasis and poor prognosis. ACSS2 knockdown inhibited the proliferation, migration, and invasion of HNSCC cells, and disrupted autophagy flux, primarily by impairing lysosomal function. Additionally, ACSS2 was found to sustain autophagic flux through TFEB activation, a key regulator of the autophagy-lysosome pathway. TFEB activation promotes lysosomal function and autophagic flux, thereby facilitating tumor cell growth and metastasis. This study elucidated the molecular mechanism by which ACSS2 enhances HNSCC cell proliferation and invasion via TFEB activation. The ACSS2-TFEB axis is a potential therapeutic target for HNSCC and provides a foundation for the development of targeted therapies.
    DOI:  https://doi.org/10.1038/s41419-025-07971-9
  38. Nucleic Acids Res. 2025 Aug 11. pii: gkaf801. [Epub ahead of print]53(15):
    DHX8 regulates degradation of RNA by RNautophagy.
    Ryohei Sakai, Eigo Takeda, Chihana Kabuta, Viorica Raluca Contu, Yuuki Fujiwara, Nobuhiro Fujikake, Tadafumi Hashimoto, Yoshinori Ohsumi, Tomohiro Kabuta.
      RNautophagy is an intracellular degradation pathway in which RNA is directly taken up by lysosomes. The cytoplasmic regions of the lysosomal membrane proteins, LAMP2C and SIDT2, can interact with consecutive guanine sequences in RNA, mediating the uptake of RNA during RNautophagy. RNautophagy has also been implicated in the clearance of expanded CAG-repeat mRNA and RNA foci associated with polyQ disease. However, the mechanisms of RNA uptake during RNautophagy remain unclear. Here, we screened for proteins that bind consecutive guanine sequences and identified RNA helicase DHX8 as a binding partner. DHX8 interacts with SIDT2 and is partially localized to the cytoplasmic side of the lysosomal membrane. We found that DHX8 regulates intracellular RNA degradation via SIDT2-dependent RNautophagy but not via macroautophagy. RNA binding, but not ATPase activity, of DHX8 is likely to be important for regulating RNA degradation. DHX8 also contributes to the clearance of pathogenic CAG repeat mRNA and RNA foci, and the levels of both soluble protein and insoluble high-molecular-weight aggregates of expanded polyQ tracts. Our findings provide insights into the mechanisms underlying the regulation of intracellular RNA degradation, autophagic pathways, and possibly the pathogenesis of repeat RNA-related disorders.
    DOI:  https://doi.org/10.1093/nar/gkaf801
  39. Cell Biol Int. 2025 Aug 23.
    Modulation of Autophagy by Ursolic and Betulinic Acids: Distinct Cytotoxic and Membrane-Disruption in Malignant and Nonmalignant Cells.
    Waleska Kerllen Martins, Tayana Mazin Tsubone, Chimara Emilia Nascimento Sanches, Cleidiane de Sousa Rocha, Ricardo Scarparo Navarro, Beatriz Simonsen Stolf, Susana Nogueira Diniz, Rosangela Itri, Mauricio S Baptista.
      Autophagy is a critical adaptive mechanism in tumor cells that promotes survival under stress, but when dysregulated, it may trigger programmed cell death. The pentacyclic triterpenoids betulinic acid (BA) and ursolic acid (UA) are structurally related compounds that modulate autophagy; however, comparative insights into their effects on nonmalignant and malignant cells, as well as model membranes, remain limited. Here, we investigated the distinct cellular outcomes induced by UA and BA in nonmalignant keratinocytes (HaCaT) and malignant cell lines (A549, HeLa, MCF7, MES-SA, PC3, SKMEL-25/28), as well as their interactions with mitochondrial membrane mimetics. At 20 μM, BA reduced HaCaT proliferation by 70%, while UA achieved only 30% inhibition. BA induced pronounced mitochondrial dysfunction (i.e., 60%), mitophagy activation, and autophagy-associated cell death linked to a lysosomal-mitochondrial stress axis. In contrast, UA induced lysosomal membrane permeabilization and the release of cathepsin B, resulting in ~50% cell death. In malignant cell lines, BA reduced viability to ~40%, whereas UA showed selective toxicity (53%-73% survival). Cotreatment with chloroquine enhanced UA's cytotoxicity by simulating BA-like lysosomal accumulation. Biophysical assays revealed differential membrane disruption profiles: BA permeabilized cardiolipin-rich membranes, while UA exerted milder surface-level effects. These findings illustrate how structurally similar triterpenoids exert divergent effects on cellular membranes, autophagic flux, and cell fate, offering a foundation for designing selective anticancer agents that target the lysosomal-mitochondrial axis.
    Keywords:  autophagy modulation; autophagy‐associated cell death; mimetic‐membrane models; mitochondrial–lysosomal stress axis; triterpenoids
    DOI:  https://doi.org/10.1002/cbin.70073
  40. Front Cell Infect Microbiol. 2025 ;15 1640647
    Autophagy in mycobacterial infections: molecular mechanisms, host-pathogen interactions, and therapeutic opportunities.
    Jinyan Li, Haibo Feng, Dechun Chen, Huanrong Zhang, Yi Liao.
      Mycobacteria pose significant global health burdens, with Mycobacterium tuberculosis complex causing tuberculosis-a leading infectious killer claiming over 1.25 million lives annually-and NTM driving pulmonary and ulcerative infections, particularly in immunocompromised populations. Autophagy, a conserved cellular degradation pathway, serves as a critical mechanism of host defense against mycobacteria by delivering bacteria to the lysosome. As a response, mycobacteria have evolved intricate strategies to subvert or exploit autophagy for survival. Consequently, autophagy exhibits a dichotomous role in mycobacterial infection: functioning as a protective mechanism of host while simultaneously serving as a virulence determinant hijacked by bacteria for their survival. This review synthesizes current insights into the molecular mechanisms mediating host-initiated autophagy during mycobacterial infection, as well as the bacterial strategies for subverting or hijacking autophagic pathways. While autophagy may be hijacked by mycobacteria, substantial evidence from numerous studies demonstrates that autophagy-activating agents may be beneficial in restricting mycobacteria infection, even with multidrug-resistant strains. This review also systematizes promising agents that enhance autophagy to improve bacterial clearance. By synthesizing the latest research findings, this article aims to enhance our understanding of the intricate relationship between autophagy and mycobacteria, paving the way for efficient host-directed therapies (HDTs) against this severely harmful pathogen.
    Keywords:  autophagy; host-directed therapy; host-pathogen interaction; molecular mechanism; mycobacterium
    DOI:  https://doi.org/10.3389/fcimb.2025.1640647
  41. Antioxidants (Basel). 2025 Aug 06. pii: 968. [Epub ahead of print]14(8):
    Camellia japonica Flower Extract and the Active Constituent Hyperoside Repair DNA Damage Through FUNDC1-Mediated Mitophagy Pathway for Skin Anti-Aging.
    Hongqi Gao, Jiahui Shi, Guangtao Li, Zhifang Lai, Yan Liu, Chanling Yuan, Wenjie Mei.
      Skin aging is closely related to mitochondrial dysfunction and cell cycle abnormalities, and developing intervention strategies targeting mitochondrial quality control is an important direction for anti-aging research. In this study, we investigated the anti-aging mechanism of Camellia japonica flower (CJF) extract and its active ingredient hyperoside based on a doxorubicin (DOX)-induced endogenous senescence model in human skin fibroblasts (HSFs). LC-MS proteomics analysis revealed that CJF extract and hyperoside specifically activated the FUNDC1-mediated mitochondrial autophagy pathway, significantly ameliorated the DOX-induced decrease in mitochondrial membrane potential and the accumulation of reactive oxygen species (ROS), and alleviated the cellular S-phase blockade and reversed the high expression of senescence-associated β-galactosidase (SA-β-gal). Further studies showed that the two cleared damaged mitochondria by enhancing mitochondrial autophagy and restoring cellular energy metabolism homeostasis while promoting type III collagen and elastin synthesis and repairing the expression of Claudin 1 related to skin barrier function. For the first time, the present study reveals the molecular mechanism of CJF extract in delaying skin aging by regulating the FUNDC1-dependent mitochondrial autophagy pathway, which provides a theoretical basis and a candidate strategy for developing novel anti-aging agents targeting mitochondrial quality control.
    Keywords:  Camellia japonica flower extract; DNA damage; FUNDC1-mediated mitophagy pathway; hyperoside; skin anti-aging
    DOI:  https://doi.org/10.3390/antiox14080968
  42. Cell Death Dis. 2025 Aug 27. 16(1): 652
    Mitochondrial quality control in diabetes mellitus and complications: molecular mechanisms and therapeutic strategies.
    Yanling Chen, Xun Liu, Yixuan Liu, Yujia Li, Dingxiang Li, Zhigang Mei, Yihui Deng.
      Diabetes mellitus (DM), a metabolic disease of globally health concern, is pathologically attributed to mitochondrial dysfunction, an essential component in disease progression. Mitochondrial quality control (MQC) acts as a critical defense mechanism for metabolic homeostasis, yet its implications in DM and its complications remain incompletely understood. This study thoroughly summarizes emerging evidence that delineates the molecular processes of MQC, with an emphasis on effector protein post-translational regulation, upstream signaling hubs, and interactions with other metabolic processes including ferroptosis and lipid metabolism. We highlight newly discovered processes involving mitochondrial-derived vesicles, licensed mitophagy, and mitocytosis that broaden the regulatory landscape of MQC, going beyond the traditionally recognized process including biogenesis, dynamics and mitophagy. MQC imbalance exacerbates insulin resistance, while impaired insulin signaling reciprocally compromises mitochondrial function, creating a vicious cycle of metabolic deterioration. Despite tissue-specific pathophysiology, diabetic complications exhibit identical MQC impairment including suppressed biogenesis, fission-fusion imbalance, and deficient mitophagy. Emerging therapies including clinical hypoglycemic agents and bioactive phytochemicals demonstrate therapeutic potential by restoring MQC. However, current strategies remain anchored to classical pathways, neglecting novel MQC mechanisms such as mitocytosis. Addressing this gap demands integration of cutting-edge MQC insights into drug discovery, particularly for compounds modulating upstream regulators. Future studies must prioritize mechanistic dissection of MQC novel targets and their translational relevance in halting metabolic collapse of diabetes progression. Since mitochondrial function is a cornerstone of metabolic restoration, synergizing precision MQC modulation with multi-target interventions, holds transformative potential for refine diabetic complications therapeutics.
    DOI:  https://doi.org/10.1038/s41419-025-07936-y
  43. Autophagy. 2025 Aug 24.
    Non-coding RNAs regulate autophagy in kidney disease: friend or foe?
    Yankun Li, Tongtong Ma, Xinhua Liang, Tingting Jin, Xingqi Zhao, Junmin Huang, Junfeng Hao, Huafeng Liu, Peng Wang.
      Macroautophagy/autophagy is a conserved cellular process that degrades misfolded proteins and damaged organelles to regulate cell survival and division. Normal levels of autophagy are observed in healthy kidney cells. In contrast, excessive or insufficient autophagy is observed during kidney disease progression. However, canonical treatments that regulate autophagy using chemical reagents may induce unexpected side effects in other organs. This necessitates the development of therapeutic approaches with fewer adverse effects. Non-coding RNAs, which are highly tissue-specific, regulate autophagy and accurately modulate the expression of related genes. This review presents evidence of the effects of non-coding RNAs on the progression of kidney diseases and their responses to treatment in vitro, in vivo, and in clinical trials. Our analyses and interpretations of key findings elucidate the pathogenesis of kidney diseases and explore potential new therapeutic approaches.
    Keywords:  circRNA; kidney disease; lncRNA; miRNA; precision medicine; therapeutic targets
    DOI:  https://doi.org/10.1080/15548627.2025.2551683
  44. Mol Biol Rep. 2025 Aug 26. 52(1): 846
    Rho kinase isoforms in neurodegeneration: from cellular functions to therapeutic targets.
    Chesta Shandilya, Shalini Mani.
      Mitochondria serve as an important cellular organelle for maintaining neurotransmission and synaptic plasticity in neuronal cells by playing a key role in ATP generation, maintaining calcium homeostasis, and regulating the levels of reactive oxygen species (ROS), etc. The regulation of the dynamic nature of mitochondria, including their fission, fusion, and removal of damaged mitochondria by mitophagy, is also very important for neuronal health. Abnormalities in mitochondrial processes, including but not limited to fission, fusion, and mitophagy, are known to be associated with numerous neurodegenerative diseases (NDDs), such as Parkinson's disease (PD), Alzheimer's disease (AD), Amyotrophic lateral sclerosis (ALS), and Huntington's disease (HD). In the recent past, the Rho kinase (ROCK) isoforms, particularly ROCK1 and ROCK2, have gained a lot of attention in NDDs, mainly for their role in regulating the dynamics of the mitochondria, mitophagy, and other cell signalling pathways. By adding phosphate groups to Drp1, ROCK1 is crucial in supporting excessive mitochondrial fission, causing the death of neuronal cells. On the other hand, ROCK2 inhibits Parkin-dependent mitophagy by inhibiting the PTEN protein, the activator of Parkin-dependent mitophagy. This impaired mitochondrial quality control via reduced mitophagic flux leads to oxidative stress and neuronal degeneration, the central pathological feature of NDDs. The inhibition of ROCK isoforms has shown great promise in neuroprotective effects, controlling the dynamics of mitochondria in neuronal cells, lowering inflammation, and improving motor and cognitive functions in preclinical models of different NDDs, indicating ROCK isoforms as an attractive therapeutic target in different NDDs. This review aims to highlight the therapeutic significance of targeting ROCK isoforms in different NDDs.
    Keywords:  Mitochondrial dynamics; Mitophagy; Neurodegenerative diseases; Neuroprotective; ROCK isoforms
    DOI:  https://doi.org/10.1007/s11033-025-10947-9
  45. Nat Commun. 2025 Aug 26. 16(1): 7951
    ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits in mice.
    Isadora Lenoel, Matthieu Ribon, Félicie Lorenc, Aurélien Diebold, Clementine E Philibert, David Robaldo, Manel Badsi, Julianne Perronnet, Julie Lameth, Felix Berriat, Hidemi Misawa, Marie Coutelier, Raphaelle Cassel, Nadège Sarrazin, Coline Jost-Mousseau, Delphine Bohl, Stéphanie Millecamps, Michel Mallat, David Brenner, Jochen H Weishaupt, Séverine Boillée, Christian S Lobsiger.
      TANK-Binding Kinase 1 (TBK1) is involved in autophagy and immune signaling. Dominant loss-of-function mutations in TBK1 have been linked to Amyotrophic Lateral Sclerosis (ALS), Fronto-temporal dementia (FTD), and ALS/FTD. However, pathogenic mechanisms remain unclear, particularly the cell-type specific disease contributions of TBK1 mutations. Here, we show that deleting Tbk1 from mouse motor neurons does not induce transcriptional stress, despite lifelong signs of autophagy deregulations. Conversely, Tbk1 deletion in microglia alters their homeostasis and reactive responses. In both spinal cord and brain, Tbk1 deletion leads to a pro-inflammatory, primed microglial signature with features of ageing and neurodegeneration. While it does not induce or modify ALS-like motor neuron damage, microglial Tbk1 deletion is sufficient to cause early FTD-like social recognition deficits. This phenotype is linked to focal microglial activation and T cell infiltration in the substantia nigra pars reticulata and pallidum. Our results reveal that part of TBK1-linked FTD disease originates from microglial dysfunction.
    DOI:  https://doi.org/10.1038/s41467-025-63211-w
  46. Front Immunol. 2025 ;16 1613716
    MiRNA-loaded MSC exosomes restore autophagy flux for acute pancreatitis therapy.
    Haojie Zeng, Tonghua Wu, Si Luo, Anxiang Zeng.
      Acute pancreatitis (AP) is an unpredictable and potentially fatal disease. Currently, it is believed that the pathological mechanism of AP is closely related to autophagy imbalance, abnormal activation of inflammatory signals, and impairments in cell damage repair. Autophagy exhibits a double-edged sword effect of "activation accompanied by flux impairment" in AP. In this article, a systematic review is conducted on how mesenchymal stem cells (MSCs) and their secreted exosomes deliver functional miRNAs, targeting and regulating pathways such as PI3K/AKT/mTOR to achieve multiple effects including anti-inflammation, regeneration promotion, and restoration of autophagy homeostasis, providing new strategies for AP treatment. Current research challenges focus on the standardization of exosome preparation, optimization of miRNA delivery efficiency, and long-term safety evaluation. Further elucidation of the "cell-vesicle-miRNA-target pathway" cascade network, combined with multi-omics technology to develop precise intervention programs, is needed to advance AP treatment from mechanistic exploration to clinical translation.
    Keywords:  acute pancreatitis; autophagy; exosomes; miRNA; signaling pathway
    DOI:  https://doi.org/10.3389/fimmu.2025.1613716
  47. EMBO J. 2025 Aug 21.
    How to control synaptic autophagy from the neuronal soma.
    Sheng Huang, Stephan J Sigrist.
      
    DOI:  https://doi.org/10.1038/s44318-025-00535-9
  48. Nat Commun. 2025 Aug 22. 16(1): 7811
    Dual-key cooperatively activated DNA regulator for controlling mitochondria-lysosome interactions.
    Yang Xiao, Longyi Zhu, Songyuan Du, Xinyi Ge, Lequn Ma, Shengyuan Deng, Kewei Ren.
      Mitochondria-lysosome interactions are critical for maintaining cellular homeostasis. Although genetically encoded protein based optogenetic technique is developed to regulate such interactions, it still suffers from shortcomings including complicated operation and potential interference to organelle functions. Here, we present a fast, simple, biocompatible and programmable platform via activable DNA regulators to achieve spatiotemporal regulation of mitochondria-lysosome interactions in living cells. In our system, two locked DNA regulators, OK-MLIR and DK-MLIR, that can be respectively activated with UV light (One Key) as well as UV light and endogenous glutathione (Dual Keys), are modularly designed for modulating mitochondria-lysosome contacts. We show that these DNA regulators can be used for facilitating mitochondrial fission and autophagy. Moreover, the DK-MLIR enables selective and efficient manipulation of target cell migration and proliferation with highly temporal and spatial controllability. This programmable and modular design principle provides a platform for organelle interaction study, cellular regulation and precision therapy.
    DOI:  https://doi.org/10.1038/s41467-025-63040-x
  49. Cell Commun Signal. 2025 Aug 23. 23(1): 378
    Elevated levels of Letm1 drives mitochondrial dysfunction and cardiomyocyte stress-mediated apoptosis in cultured cardiomyocytes.
    Anushka Deshpande, Leo Weirauch, Tapan Kumar Baral, Marco Steier, Ankush Borlepawar, Manju Kumari, Lucia S Kilian, Karsten Richter, Elke Hammer, Derk Frank, Constanze Schmidt, Norbert Frey, Ashraf Y Rangrez.
       BACKGROUND: Cardiac ischemia, a predominant cause of heart failure, is marked by profound mitochondrial dysfunction, dysregulated ion homeostasis, and maladaptive cellular remodeling, all of which compromise cardiac performance. The mitochondrial inner membrane protein Leucine zipper-EF-hand containing Transmembrane Protein 1 (Letm1), implicated in Wolf-Hirschhorn Syndrome, is essential for mitochondrial function. Although genetic alterations in Letm1 are linked to cardiomyopathies, its specific contributions to cardiac pathophysiology, particularly in the context of ischemic heart disease, remain poorly defined. This study aims to elucidate the role of Letm1 in ischemic cardiac pathology and its mechanistic impact on cardiomyocyte function.
    METHODS: Letm1 expression was assessed in human and murine models of heart failure due to ischemic cardiomyopathy (ICM) and cardiac hypertrophy. Letm1 was overexpressed in neonatal rat ventricular cardiomyocytes, adult mouse cardiomyocytes, and human induced pluripotent stem cell (iPSC)-derived cardiomyocytes to study mitochondrial function (Seahorse assays), structural and molecular remodeling (fluorescence microscopy, transmission electron microscopy (TEM), qPCR, immunoblotting), transcriptomic/proteomic profiles, calcium handling and electrophysiology (patch-clamp), autophagic flux (Bafilomycin A1, LC3-RFP-GFP), and cell survival.
    RESULTS: Letm1 was markedly upregulated in ICM in both human and murine hearts, but unchanged in hypertrophic heart failure. Overexpression of Letm1 in cardiomyocytes resulted in profound mitochondrial dysfunction, including downregulation of oxidative phosphorylation (OXPHOS) genes, impaired membrane potential, reduced ATP output, increased proton leak, and elevated ROS levels. A metabolic shift toward glycolysis was observed, accompanied by reduced fatty acid oxidation. Electron microscopy revealed mitochondrial fragmentation, mitophagic vesicles, and sarcomeric disarray. Transcriptomic and proteomic analyses highlighted dysregulation of genes linked to mitochondrial organization, ion transport, and autophagy. Electrophysiologically, Letm1 reduced L-type Ca2+ current density and significantly shortened action potential duration, leading to impaired contractility. Letm1 overexpression activated upstream autophagy regulators (AMPK, ULK1) and enhanced LC3-II and p62 accumulation, but autophagic flux was impaired, as confirmed by LC3-RFP-GFP reporter and exacerbated by Bafilomycin A1 treatment. This dysregulated autophagy was coupled with mitochondrial stress, increased apoptosis (cleaved caspases), and reduced cardiomyocyte viability.
    CONCLUSION: This study indicates that Letm1 upregulation drives mitochondrial dysfunction, electrophysiology alterations, and activation of autophagy and apoptosis, culminating in cardiomyocyte injury in ischemic cardiomyopathy. By disrupting OXPHOS, calcium handling, and cell survival pathways, Letm1 contributes to ischemic remodeling and cardiac dysfunction. Targeting Letm1 presents a promising therapeutic strategy to alleviate ischemic damage and preserve cardiac function.
    Keywords:  Arrhythmias; Cardiomyocytes; Hypertrophy; Letm1; Mitochondrial metabolism
    DOI:  https://doi.org/10.1186/s12964-025-02378-7
  50. Biomolecules. 2025 Aug 08. pii: 1145. [Epub ahead of print]15(8):
    Mitochondrial Extracellular Vesicles: A Novel Approach to Mitochondrial Quality Control.
    Jie Kong, Rui Sun, Chengying Du, Yiyang Tang, Chengzhi Xie, Qian Li, Li Lin, Hongyan Wang.
      Mitochondria are central to cellular energy metabolism and play a key role in regulating important physiological processes, including apoptosis and oxidative stress. Mitochondrial quality control has recently garnered significant attention, with the underlying mechanisms traditionally considered to be mitophagy and its dynamics. Various studies have demonstrated that extracellular vesicles are crucial for the transmission of mitochondria and their components. These vesicles effectively transport mitochondria to target cells, facilitating intercellular material exchange and signal transmission, thereby enhancing cellular function and viability. This review explores the mechanisms of mitochondrial transfer through mitochondrial extracellular vesicles (MitoEVs), analyzes the novel roles of MitoEVs in mitochondrial quality control, and discusses their applications in disease treatment. We aim to provide new perspectives for future research and support the development of relevant therapeutic strategies.
    Keywords:  MitoEVs; extracellular vesicle; intercellular material exchange; mitochondria; mitochondrial quality control; signal transmission
    DOI:  https://doi.org/10.3390/biom15081145
  51. NPJ Parkinsons Dis. 2025 Aug 23. 11(1): 256
    New perspectives on molecular mechanisms underlying exercise-induced benefits in Parkinson's disease.
    Xingyue Chen, Guoxin Zhang, Miao Liu, Juanfeng He, Zhentao Zhang.
      Exercise offers neuroprotective benefits in Parkinson's disease (PD) by enhancing neurotrophic factors (e.g., BDNF, GDNF), improving mitochondrial function, reducing inflammation, and promoting autophagy. Irisin, a muscle-derived cytokine, links exercise to neuronal health by regulating mitochondria and mitigating oxidative stress. Notably, irisin may serve as a therapeutic target for patients unable to exercise. Thus, exercise is a promising non-pharmacological intervention warranting further research for novel PD therapies.
    DOI:  https://doi.org/10.1038/s41531-025-01113-w
  52. Int J Mol Sci. 2025 Aug 15. pii: 7886. [Epub ahead of print]26(16):
    Cathepsins in Neurological Diseases.
    Dominik Lewandowski, Mateusz Konieczny, Agata Różycka, Krzysztof Chrzanowski, Wojciech Owecki, Jan Kalinowski, Mikołaj Stepura, Paweł Jagodziński, Jolanta Dorszewska.
      Cathepsins, a family of lysosomal proteases, play critical roles in maintaining cellular homeostasis through protein degradation and modulation of immune responses. In the central nervous system (CNS), their functions extend beyond classical proteolysis, influencing neuroinflammation, synaptic remodeling, and neurodegeneration. Emerging evidence underscores the crucial role of microglial cathepsins in the pathophysiology of several neurological disorders. This review synthesizes current knowledge on the involvement of cathepsins in a spectrum of CNS diseases, including Parkinson's disease, Alzheimer's disease, multiple sclerosis, amyotrophic lateral sclerosis, epilepsy, Huntington's disease, and ischemic stroke. We highlight how specific cathepsins contribute to disease progression by modulating key pathological processes such as α-synuclein and amyloid-β clearance, tau degradation, lysosomal dysfunction, neuroinflammation, and demyelination. Notably, several cathepsins demonstrate both neuroprotective and pathogenic roles depending on disease context and expression levels. Additionally, the balance between cathepsins and their endogenous inhibitors, such as cystatins, emerges as a critical factor in CNS pathology. While cathepsins represent promising biomarkers and therapeutic targets, significant gaps remain in our understanding of their mechanistic roles across diseases. Future studies focusing on their regulation, substrate specificity, and interplay with genetic and epigenetic factors may yield novel strategies for early diagnosis and disease-modifying treatments in neurology.
    Keywords:  autophagy; cathepsins; neurodegenerative diseases; neuroinflammation; proteolysis
    DOI:  https://doi.org/10.3390/ijms26167886
  53. Nat Commun. 2025 Aug 21. 16(1): 7582
    Genome-wide in vivo CRISPR screens identify GATOR1 complex as a tumor suppressor in Myc-driven lymphoma.
    Margaret A Potts, Shinsuke Mizutani, Yexuan Deng, Srimayee Vaidyanathan, Keziah E Ting, Göknur Giner, Shruti Sridhar, Girija Shenoy, Yang Liao, Sarah T Diepstraten, Andrew J Kueh, Martin Pal, Geraldine Healey, Lin Tai, Zilu Wang, Christina König, Deeksha Kaloni, Lauren Whelan, Michael J G Milevskiy, Hannah D Coughlan, Giovanna Pomilio, Andrew H Wei, Jane E Visvader, Anthony T Papenfuss, Stephen Wilcox, Anand D Jeyasekharan, Wei Shi, Emily J Lelliott, Gemma L Kelly, Kristin K Brown, Andreas Strasser, Marco J Herold.
      Identifying tumor suppressor genes is predicted to inform on the development of novel strategies for cancer therapy. To identify new lymphoma driving processes that cooperate with oncogenic MYC, which is abnormally highly expressed in ~70% of human cancers, we use a genome-wide CRISPR gene knockout screen in Eµ-Myc;Cas9 transgenic hematopoietic stem and progenitor cells in vivo. We discover that loss of any of the GATOR1 complex components - NPRL3, DEPDC5, NPRL2 - significantly accelerates c-MYC-driven lymphoma development in mice. MYC-driven lymphomas lacking GATOR1 display constitutive mTOR pathway activation and are highly sensitive to mTOR inhibitors, both in vitro and in vivo. These findings identify GATOR1 suppression of mTORC1 as a tumor suppressive mechanism in MYC-driven lymphomagenesis and suggest an avenue for therapeutic intervention in GATOR1-deficient lymphomas through mTOR inhibition.
    DOI:  https://doi.org/10.1038/s41467-025-62615-y
  54. JACC Basic Transl Sci. 2025 Aug;pii: S2452-302X(25)00178-0. [Epub ahead of print]10(8): 101290
    Mitophagy Regulators as Novel Targets in Sepsis-Induced Myocardial Dysfunction.
    Katharina Friedrich, Kai Kappert.
      
    Keywords:  FUNDC1; c-FLIP; cardiac microcirculation; mitochondrial autophagy; sepsis-induced myocardial dysfunction (SIMD)
    DOI:  https://doi.org/10.1016/j.jacbts.2025.04.004
  55. Phytother Res. 2025 Aug 20.
    Atractylenolide III Mitigates Alzheimer's Disease by Enhancing Autophagy via the YY1-TFEB Pathway.
    Xiaowei Zhang, Shuang Chu, Yanli Huang, Zhonghua Li, Junying Song, Pan Wang, Yunfang Su, Zhenqiang Zhang, Zhishen Xie.
      Autophagy dysregulation serves as a significant pathogenic factor in Alzheimer's disease (AD), with transcription factor EB (TFEB) acting as a pivotal transcription factor that governs the process of autophagy. Atractylenolide III (AT-III), a terpenoid compound found in medicinal Atractylodes macrocephala Koidz, is well-known for its role in antioxidant and anti-inflammatory activities. The purpose of this study is to explore the beneficial impact of AT-III on AD pathology and identify the mechanisms involved. C. elegans CL4176, SH-SY5Y APPSWE, and APP/PS1 mice were used to investigate the efficacy and possible mechanism of AT-III on the treatment of AD. AT-III reduced amyloid protein (Aβ) deposition in C. elegans CL4176 heads, prolonged the paralysis time, and reduced Aβ levels in SH-SY5Y APPSWE cells. AT-III improved the learning and memory ability of APP/PS1 mice and decreased the deposition of Aβ plaques. Transcriptomics and experimental validation showed that AT-III stimulated transcription and translation of autolysosome-associated genes. AT-III enhanced co-localization of LC3 and LAMP2 with Aβ in APP/PS1 mice. Meanwhile, AT-III increased TFEB transcriptional activity, mRNA, and protein levels in the nucleus. Furthermore, AT-III enhanced the expression of Yin Yang 1 (YY1) protein, an upstream regulator of TFEB, and led to the stimulation of autophagy and lysosome biogenesis both in vivo and in vitro. The observed effects were reversed upon silencing YY1. AT-III may regulate the YY1-TFEB pathway, thereby restoring autophagy flux disturbances and ameliorating AD-related pathological changes and cognitive decline. This study provides a promising lead compound for intervention in AD.
    Keywords:   C. elegans ; Alzheimer's disease; Atractylenolide III; amyloid‐β; autophagy; cognitive impairment
    DOI:  https://doi.org/10.1002/ptr.70069
  56. Differentiation. 2025 Aug 23. pii: S0301-4681(25)00069-6. [Epub ahead of print]145 100902
    Inhibition of Atg13-mediated autophagy enhances the anti-osteoclastogenic effect of sirolimus by counteracting its pro-autophagic activity.
    Tingwei Gao, Jiankun Wang, Jiajia Wang, Xi Li, Zhanhao Xiao.
      Sirolimus can inhibit osteoclastogenesis. But sirolimus-activated autophagy is a favorable factor for osteoclastogenesis. This study aimed to explore the significance of autophagy in sirolimus-regulated osteoclastogenesis. Our results confirmed that sirolimus inhibited osteoclastic differentiation (including the number and size of osteoclasts as well as the expression of osteoclastic genes) and promotes osteoclast precursor (OCP) autophagy (including LC3 conversion and autophagosome/autolysosome formation). As expected, OCP autophagy (including LC3 conversion and LC3-puncta formation) promoted by sirolimus was reversed by autophagy inactivation with 3-MA or Atg13 silencing. Importantly, compared with single intervention of sirolimus, the combination of sirolimus and 3-MA or Atg13 silencing more effectively inhibited osteoclastic differentiation and OCP proliferation. In vivo experiments also demonstrated that the combination of sirolimus and Atg13-silencing adeno-associated viruses (AAVs) was more effective than sirolimus alone in improving decreased bone density and damaged bone microstructure (including Micro-CT imaging results, bone tissue parameters and trabecular area), and attenuating osteoclastic activity (including the abundance of osteoclasts in trabecular bones and the production of osteoclastic markers in serum) in ovariectomized (OVX) mice. In conclusion, repressing Atg13-related autophagy can effectively enhance the function of sirolimus in inhibiting osteoclastogenesis by counteracting its pro-autophagic activity. Therefore, the combination of sirolimus and Atg13-targeting therapy is expected to enhance the efficacy of sirolimus in ameliorating osteoclastic osteoporosis.
    Keywords:  Atg13; Autophagy; Osteoclast; Sirolimus; mTOR
    DOI:  https://doi.org/10.1016/j.diff.2025.100902
  57. Mol Biol Cell. 2025 Aug 20. mbcE25070346
    The hereditary spastic paraplegia type 21 (SPG21) protein is a RAB7A effector that promotes mTORC1-catalyzed TFEB phosphorylation and cytoplasmic retention.
    Jennifer M Kunselman, Chad D Williamson, Adriana E Golding, Rui Jia, Mira Sohn, Ryan K Dale, Juan S Bonifacino.
      Hereditary spastic paraplegia type 21 (SPG21) is an inherited neurological disorder caused by biallelic mutations in the SPG21 gene, which encodes a protein named SPG21 or maspardin. Herein, we report that the SPG21 protein localizes to endolysosomes through interaction with the GTP-bound form of RAB7A. Disease-associated SPG21 variants reduce expression of SPG21 and disrupt its endolysosomal localization in both non-neuronal cells and neurons. Consistent with this localization, functional dependency analysis links SPG21 to endolysosomal and mTORC1 signaling pathways. Biochemical studies reveal that SPG21 depletion does not affect phosphorylation of canonical mTORC1 substrates such as ULK1, S6K1, 4E-BP1, but reduces phosphorylation of the non-canonical mTORC1 substrate TFEB. This enhances nuclear localization of TFEB and expression of a subset of TFEB-target genes. We conclude that SPG21 acts as a RAB7A effector that promotes non-canonical mTORC1-catalyzed phosphorylation of TFEB, thereby suppressing its nuclear localization and transcriptional activity. These findings link SPG21 dysfunction to altered endolysosomal signaling, offering new insights into SPG21 pathogenesis.
    DOI:  https://doi.org/10.1091/mbc.E25-07-0346
  58. Commun Biol. 2025 Aug 20. 8(1): 1255
    Decoding phospho-regulation and flanking regions in autophagy-associated short linear motifs.
    Mattia Utichi, Oana N Antonescu, Valentina Sora, Henri-Baptiste Marjault, Matteo Tiberti, Emiliano Maiani, Matteo Lambrughi, Elena Papaleo.
      Short Linear Motifs (SLiMs) play a pivotal role in the interactions between intrinsically disordered proteins and their binding partners. SLiMs can undergo regulation through post-translational modifications, including phosphorylation. The flanking regions surrounding the core motifs also exert a crucial role for the interaction. While phosphorylation and flanking regions are known to influence SLiM function, the mechanistic basis of this regulation remains poorly understood. We integrate biomolecular simulations, in silico high-throughput mutational scans, and biophysical experiments to elucidate the phospho-regulation in SLiMs crucial for autophagy, i.e., the LC3 interacting regions (LIRs). We investigate the Optineurin LIR, which perfectly exemplifies a class of LIR with a complex interplay of phosphorylations and flanking regions. Here we show that specific phosphorylation events and flanking residues modulate binding to LC3 at the atomic level, and that disease-associated mutations alter these interactions in the phosphorylated context. Notably, we establish an approach based on Microfluidic Diffusional Sizing to investigate binding affinities of SLiMs to target proteins, complemented by Surface Plasmon Resonance, enabling precise measurements of dissociation constants and kinetics for a selection of variants. Our work provides a versatile toolkit to characterize phospho-regulated SLiMs, advancing the understanding of important cellular processes.
    DOI:  https://doi.org/10.1038/s42003-025-08399-9
  59. Aging (Albany NY). 2025 Aug 25. 17
    Mitochondrial proteins as biomarkers of cellular senescence and age-associated diseases.
    Anna Panfilova, Tatiana Zubareva, Ekaterina Mironova, Gianluigi Mazzoccoli, Maria Greta Pia Marasco, Sofya Balazovskaia, Peter Yablonsky, Igor Kvetnoy.
      Research in the field of mitochondrial biomarkers plays an important role in understanding the processes of cellular aging. Mitochondria are not only the energy centers of the cell, but also key regulators of signaling within the cell. They significantly affect the life and function of the cell. The aging process of cells is associated with various factors, including DNA damage, disruption of the cell cycle, changes in mitochondria, and problems with signal transmission. Mitochondrial dysfunction is a major contributor to cellular and organismal aging. As we age, there is an accumulation of dysfunctional mitochondria, leading to decreased efficiency of oxidative phosphorylation and increased production of reactive oxygen species. This review focuses on the main mitochondrial markers involved in the mechanisms of cell aging: DRP1, Prohibitin, Parkin, PINK1, MFF, VDAC, TOM. These signaling molecules are involved in mitochondrial fission and the mechanisms of mitochondria-dependent apoptosis, in the regulation of mitochondrial respiratory activity, ensuring the stability of the organization and copying of mitochondrial DNA, protecting cells from oxidative stress, in the process of autophagy of damaged mitochondria, in protective mechanisms during stress-induced mitochondrial dysfunction. Analysis of mitochondrial markers can provide valuable information about the state of cells and their functional significance at various stages of aging, which could promote our understanding of cellular aging mechanisms and developing corrective methods. These insights highlight mitochondrial proteins as potential therapeutic targets to combat age-related diseases.
    Keywords:  age-associated diseases; biomarkers; cellular senescence; mitochondria; mitochondrial proteins
    DOI:  https://doi.org/10.18632/aging.206305
  60. Exp Cell Res. 2025 Aug 20. pii: S0014-4827(25)00321-0. [Epub ahead of print]451(2): 114721
    Cancer as a failed response to renegade mitochondria.
    John Hartung.
      In 1948, before the word 'mitochondrion' gained common parlance in the lexicon of cell biologists, Cyril Darlington published The Plasmagene Theory of the Origin of Cancer without referring to mitochondria per se. Reconsideration of Darlington's theory is warranted today because discoveries about the extraordinary capacities of mitochondria - the organelles that house Darlington's "plasmagenes" - have grown exponentially. If Darlington was right, if intracellular competition between mutant and wild-type mitochondria is the first cause of cancer, it may be the case that a general cure for cancer will include injection of: (A) nanoparticles carrying wild-type mitochondrial genes, and (B) copious amounts of wild-type mitochondria.
    Keywords:  Apoptosis; Cancer; Evolution; Experiment; Heteroplasmic; Homoplasmic; Mitochondria; Mitochondrial transfer; Mitophagy; Reproductive competition; Reversible reaction
    DOI:  https://doi.org/10.1016/j.yexcr.2025.114721
  61. Cureus. 2025 Jul;17(7): e88449
    Neuroprotective Effects of Phosphodiesterase Inhibitors on Sestrin-2 (SESN2) Expression and Autophagy in Alzheimer's Disease Model.
    Gokhan Faikoglu, Kübra Saygisever-Faikoglu, Hande Ozbasak, Sedat Askin Ugur, Tugce Uskur, Ahmet Gökhan Akkan, Pelin Kelicen-Ugur, Sibel Ozyazgan.
       OBJECTIVE: Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline and the accumulation of amyloid-beta (Aβ) peptides. The neuroprotective protein sestrin-2 (SESN2) has been implicated in the cellular response to oxidative stress and autophagy, processes that are disrupted in AD. This study explores the effects of phosphodiesterase inhibitors (PDEIs) roflumilast (RF), rolipram (ROL), and tadalafil (TAD) on SESN2 expression and autophagy in Aβ25-35-treated hippocampal neuron (HT-22) cell cultures.
    METHODS: The HT-22 cells were exposed to 5 μM Aβ25-35 for 32 hours to induce AD-like pathology. Concurrently, cells were treated with PDEIs (ROL: 10 μM, TAD: 1.53 nM, RF: 5 μM). The SESN2, autophagy-related proteins (ATG5, beclin-1 (BECN1), LC3II), adenosine monophosphate-activated protein kinase (AMPK), and mTOR expression levels were analyzed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot techniques.
    RESULTS: The Aβ25-35 exposure significantly increased SESN2 expression and altered the levels of autophagy-related proteins, resulting in decreased active AMPK (phosphorylated (p)-AMPK) and increased active mTOR (phosphorylated (p)-mTOR). Treatment with PDEIs reduced the elevated SESN2 expression and modulated autophagy-related protein levels, enhancing ATG5, BECN1, and LC3II expression. The PDEIs also restored p-AMPK levels and reduced p-mTOR expression in Aβ25-35-treated cells.
    CONCLUSION: The PDEIs exhibit neuroprotective effects in an in vitro AD model by reducing SESN2 overexpression and modulating autophagy through the AMPK/mTOR pathway. These findings suggest that PDEIs could be potential therapeutic agents for AD, targeting SESN2 and autophagy pathways to mitigate neurodegenerative damage.
    Keywords:  alzheimer's disease; ampk; autophagy; mtor; phosphodiesterase inhibitors; sestrin-2
    DOI:  https://doi.org/10.7759/cureus.88449
  62. Nature. 2025 Aug 20.
    Quantitative imaging of lipid transport in mammalian cells.
    Juan M Iglesias-Artola, Kristin Böhlig, Kai Schuhmann, Katelyn C Cook, H Mathilda Lennartz, Milena Schuhmacher, Pavel Barahtjan, Cristina Jiménez López, Radek Šachl, Vannuruswamy Garikapati, Karina Pombo-Garcia, Annett Lohmann, Petra Riegerová, Martin Hof, Björn Drobot, Andrej Shevchenko, Alf Honigmann, André Nadler.
      Eukaryotic cells produce over 1,000 different lipid species that tune organelle membrane properties, control signalling and store energy1,2. How lipid species are selectively sorted between organelles to maintain specific membrane identities is largely unclear, owing to the difficulty of imaging lipid transport in cells3. Here we measured the retrograde transport and metabolism of individual lipid species in mammalian cells using time-resolved fluorescence imaging of bifunctional lipid probes in combination with ultra-high-resolution mass spectrometry and mathematical modelling. Quantification of lipid flux between organelles revealed that directional, non-vesicular lipid transport is responsible for fast, species-selective lipid sorting, in contrast to the slow, unspecific vesicular membrane trafficking. Using genetic perturbations, we found that coupling between energy-dependent lipid flipping and non-vesicular transport is a mechanism for directional lipid transport. Comparison of metabolic conversion and transport rates showed that non-vesicular transport dominates the organelle distribution of lipids, while species-specific phospholipid metabolism controls neutral lipid accumulation. Our results provide the first quantitative map of retrograde lipid flux in cells4. We anticipate that our pipeline for mapping of lipid flux through physical and chemical space in cells will boost our understanding of lipids in cell biology and disease.
    DOI:  https://doi.org/10.1038/s41586-025-09432-x
  63. Int J Biol Macromol. 2025 Aug 21. pii: S0141-8130(25)07591-9. [Epub ahead of print]323(Pt 1): 147034
    Parkin, a key player in Parkinson's disease pathogenesis: A review.
    Vidhi Malhotra, Jaoud Ansari, Sumaiya Khan, Nida Jamil Khan, Mohammad Shahid, Md Imtaiyaz Hassan, Asimul Islam.
      Neurodegenerative diseases are an assortment of chronic diseases affecting the central nervous system. The primary cause of these diseases is a persistent decline in neuronal function, which results in cerebral atrophy. Parkinson's disease is currently the second most prominent neurodegenerative disease and might be the most exacerbated one too. Currently, there are more than 6 million reported cases of Parkinson's disease globally, which will keep on rising. The emergence of typical symptoms is diagnosed at later stages of the disease, while the appearance of non-motor symptoms becomes quite common and easily observable. Parkinson's disease can be caused by mutations in both autosomal dominant and autosomal recessive genes. One primary reported cause of autosomal recessive Parkinson's disease is mutations in the Parkin. This protein is crucial for maintaining cellular homeostasis, which performs an essential role in the ubiquitin-proteasome system and aids in the removal of misfolded as well as aggregated proteins. The review provides a comprehensive overview of Parkin's pathological aspects, expression, insights into its structure, various functions performed by Parkin, post-translational modifications of Parkin, dysregulation, and therapeutic implications. Through a critical evaluation of several existing research and review papers, we observed various significant features of Parkin covered in this review.
    Keywords:  Neurodegenerative disease; Parkin; Post-translational modifications
    DOI:  https://doi.org/10.1016/j.ijbiomac.2025.147034
  64. J Mol Biol. 2025 Aug 19. pii: S0022-2836(25)00463-2. [Epub ahead of print] 169397
    Complex Conformational Interplay for Parkin Activation is Revealed by 19F NMR Spectroscopy.
    Elizabeth M Connelly, Gary S Shaw.
      Parkin is a 52 kDa RING-Between-RING E3 ligase that ubiquitinates proteins at the outer mitochondrial membrane in response to oxidative stress. Part of a neuroprotective pathway, over 100 mutations in the PRKN gene have been associated with Early Onset Parkinson's Disease. To be fully active parkin requires interaction with phosphorylated ubiquitin and phosphorylation of its N-terminal Ubl domain, both dependent on the PINK1 kinase. Along with recruitment of an E2 ∼ Ubiquitin conjugate these events form a ∼90 kDa complex, undergoing a series of conformational changes that regulate transthiolation of ubiquitin from the E2 enzyme to the catalytic domain in parkin (Rcat) prior to substrate labeling. Numerous crystal and NMR structures have captured snapshots of parkin activation and its catalytic mechanism, yet questions surrounding the relative abundance, timing and interplay of parkin conformations remain. Further, most studies use truncated versions of the E3 ligase that may hide details of conformational dependencies. To examine parkin through its activation cycle from inactive (autoinhibited) to E2 ∼ Ubiquitin binding states we incorporated 5-19F-tryptophan into the full-length enzyme and used 19F NMR spectroscopy to identify structural and dynamics changes. Using chemical shift perturbation and T2 analysis, we show that phosphorylation of parkin leads to a population of unbound and bound forms of the phosphorylated Ubl domain and that release of the catalytic Rcat domain is dependent upon E2 ∼ Ub conjugate binding. This study shows the unique abilities of 19F NMR spectroscopy to provide details of the structural rearrangements required for catalysis for the large E3 ligase parkin.
    Keywords:  NMR spectroscopy; conformational change; dynamics; protein structure; ubiquitination
    DOI:  https://doi.org/10.1016/j.jmb.2025.169397
  65. Science. 2025 Aug 21. 389(6762): 782-783
    A protein tunnel helps stressed lysosomes swell.
    Jennifer Lippincott-Schwartz.
      The endoplasmic reticulum donates lipids through a tunnel-like protein to help lysosomes expand.
    DOI:  https://doi.org/10.1126/science.aea5377
  66. Antioxidants (Basel). 2025 Jul 24. pii: 908. [Epub ahead of print]14(8):
    Targeting Lipophagy in Liver Diseases: Impact on Oxidative Stress and Steatohepatitis.
    Jin Seok Hwang, Trang Huyen Lai, Deok Ryong Kim.
      Metabolic dysfunction-associated steatotic liver disease (MASLD) encompasses a range of liver conditions, from simple hepatic steatosis to its more severe inflammatory form known as metabolic dysfunction-associated steatohepatitis (MASH). Despite its growing clinical significance and association with cirrhosis and cancer, there are currently few pharmacological treatments available for MASLD, highlighting the urgent need for new therapeutic strategies. This narrative review aims to elucidate the molecular mechanisms of lipophagy in MASLD progression, emphasizing how its dysfunction contributes to hepatic steatosis and lipotoxicity. We also explore the intersection of lipophagy failure with oxidative stress and inflammation in the liver, focusing on key signaling pathways, such as mTORC1 and AMPK, and discuss the therapeutic potential of targeting these pathways by systematically reviewing the literature from PubMed, Scopus, and Google Scholar databases. Recent studies suggest that lipophagy, the selective autophagic degradation of lipid droplets, is crucial for maintaining hepatic lipid homeostasis. Indeed, some vital components of the lipophagy machinery seem to be functionally inhibited in MASLD, resulting in the accumulation of intracellular triacylglycerol (TAG), lipotoxicity, and subsequent oxidative stress, all of which contribute to disease progression. In summary, impaired lipophagy is a central pathological mechanism in MASLD, making it an important therapeutic target. A deeper understanding of these mechanisms may offer new strategic insights for combating the progression of MASLD/MASH.
    Keywords:  MASH; MASLD; hepatic steatosis; lipophagy; lipotoxicity; metabolic dysfunction; oxidative stress
    DOI:  https://doi.org/10.3390/antiox14080908
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