bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2025–02–09
63 papers selected by
Viktor Korolchuk, Newcastle University
  1. Multifaceted roles of the ATG8 protein family in plant autophagy: from autophagosome biogenesis to cargo recognition.
  2. Regulatory Mechanisms and Therapeutic Implications of Lysosomal Dysfunction in Alzheimer's Disease.
  3. Impairment of proteasome-associated deubiquitinating enzyme Uchl5/UBH-4 affects autophagy.
  4. Sustained induction of autophagy enhances survival during prolonged starvation in newt cells.
  5. Development and validation of a sensitive sandwich ELISA against human PINK1.
  6. The cholesterol metabolite 25-hydroxycholesterol suppresses porcine deltacoronavirus via lipophagy inhibition and mTORC1 modulation.
  7. TOLLIP inhibits the replication of PEDV by autophagic degradation of Nsp9.
  8. Chikusetsu saponin IVa attenuates aging by improving autophagy and mitophagy.
  9. CaMKIIβ Ca2+ptures ER signals to initiate autophagosome biogenesis.
  10. The autophagy component LC3 regulates lymphocyte adhesion via LFA1 transport in response to outside-in signaling.
  11. Chaperone-mediated autophagy contributes to chromosomal stability by controlling TTC28 degradation.
  12. Targeting secretory autophagy in solid cancers: mechanisms, immune regulation and clinical insights.
  13. Cannabidiol-Induced Autophagy Ameliorates Tau Protein Clearance.
  14. Mec1-mediated Atg9 phosphorylation regulates the PAS recruitment of Atg9 vesicles upon energy stress.
  15. Flavivirus NS2A orchestrates reticulophagy to enhance viral pathogenicity.
  16. Cardioprotective Effects of Adiponectin-Stimulated Autophagy.
  17. A quantitative ultrastructural timeline of nuclear autophagy reveals a role for dynamin-like protein 1 at the nuclear envelope.
  18. Autophagy and the peroxisome proliferator-activated receptor signaling pathway: A molecular ballet in lipid metabolism and homeostasis.
  19. Evidence for cytoprotective autophagy in response to HER2-targeted monoclonal antibodies.
  20. Unravelling a mechanistic link between mitophagy defect, mitochondrial malfunction, and apoptotic neurodegeneration in Mucopolysaccharidosis VII.
  21. Calcium-mediated regulation of mitophagy: implications in neurodegenerative diseases.
  22. Vascular Contractility Relies on Integrity of Progranulin Pathway: Insights Into Mitochondrial Function.
  23. An overview of the value of mTOR inhibitors to the treatment of epilepsy: the evidence to date.
  24. VANGL2 alleviates inflammatory bowel disease by recruiting the ubiquitin ligase MARCH8 to limit NLRP3 inflammasome activation through OPTN-mediated selective autophagy.
  25. Pharmacological activation of TRPML1 enhances autophagy regulating hypertonicity and TGF-β-induced EMT in proximal tubular epithelial cells.
  26. Tetramethylpyrazine attenuates sodium arsenite-induced acute kidney injury by improving the autophagic flux blockade via a YAP1-Nrf2-p62-dependent mechanism.
  27. Rapamycin ameliorates inflammatory pain via recovery of autophagy flux mediated by mammalian target of rapamycin (mTOR) signaling pathway in the rat spinal cord.
  28. Illuminating cholesterol-mTORC1 signaling: LYCHOS in focus.
  29. Fibrinogen degradation products exacerbate alpha-synuclein aggregation by inhibiting autophagy via downregulation of Beclin1 in multiple system atrophy.
  30. Sodium pump subunit NKAα1 protects against diabetic endothelial dysfunction by inhibiting ferroptosis through the autophagy-lysosome degradation of ACSL4.
  31. Sex-specific and cell-type-specific changes in chaperone-mediated autophagy across tissues during aging.
  32. Glycogen synthase is required for heat shock-mediated autophagy induction in neuronal cells.
  33. Melatonin alleviates senile osteoporosis by regulating autophagy and enhancing fracture healing in aged mice.
  34. Role of Atg3, Atg5 and Atg12 in the crosstalk between apoptosis and autophagy in the posterior silk gland of Bombyx mori.
  35. Endoplasmic reticulum (ER) protein degradation by ER-associated degradation and ER-phagy.
  36. Microenvironment-Specific Enrichment Strategy Enables Lysosomal Proteomic Dynamics Analysis.
  37. Mitophagy is induced in human engineered heart tissue after simulated ischemia and reperfusion.
  38. Vacuolar Sts1 Degradation-Induced Cytoplasmic Proteasome Translocation Restores Cell Proliferation.
  39. Structural pathway for PI3-kinase regulation by VPS15 in autophagy.
  40. Triple-Target Inhibition of Cholinesterase, Amyloid Aggregation, and GSK3β to Ameliorate Cognitive Deficits and Neuropathology in the Triple-Transgenic Mouse Model of Alzheimer's Disease.
  41. METTL3 regulates autophagy of hypoxia-induced cardiomyocytes by targeting ATG7.
  42. Mitophagy in Neurodegenerative Diseases: Mechanisms of Action and the Advances of Drug Discovery.
  43. Aggregated proinsulin in pancreatic β-cells is degraded by the autophagy pathway.
  44. Autophagy induced by metabolic processes leads to solid tumor cell metastatic dormancy and recurrence.
  45. Unraveling the function of TSC1-TSC2 complex: implications for stem cell fate.
  46. Whole organism and tissue-specific analysis of pexophagy in Drosophila.
  47. Kinase Inhibitor-Induced Cell-Type Specific Vacuole Formation in the Absence of Canonical ATG5-Dependent Autophagy Initiation Pathway.
  48. Cellular senescence induced by cholesterol accumulation is mediated by lysosomal ABCA1 in APOE4 and AD.
  49. Aggregation-induced emission-twisted intramolecular charge transfer-activated fluorescent probe for analyzing mitochondrial viscosity in cells and zebrafish.
  50. USP14 is crucial for proteostasis regulation and α-synuclein degradation in human SH-SY5Y dopaminergic cells.
  51. The in vitro and in vivo skin-whitening activity of Ectoine through enhanced autophagy in melanocytes and keratinocytes and zebrafish model.
  52. VPS41 recruits biosynthetic LAMP-positive vesicles through interaction with Arl8b.
  53. Transmembrane Parkinson's Disease mutation of PINK1 leads to altered mitochondrial anchoring.
  54. GADD45α is a direct target of TFEB and contributes to tacrolimus-induced chronic nephrotoxicity.
  55. Autophagy inhibitor 3-methyladenine mitigates the severity of colitis in aged mice by inhibiting autophagy.
  56. Autophagy-dependent changes in alternative splicing bias translation toward inflammation in senescent cells.
  57. Inhibition of SQSTM1/p62 oligomerization and Keap1 sequestration by the Cullin-3 adaptor SHKBP1.
  58. The Batten disease gene Cln3 is required for the activation of intestinal stem cell during regeneration via JAK/STAT signaling in Drosophila.
  59. Novel TORC1 inhibitor Ecl1 is regulated by phosphorylation in fission yeast.
  60. Staphylococcus aureus induces mitophagy via the HDAC11/IL10 pathway to sustain intracellular survival.
  61. TRIM32 promotes neuronal ferroptosis by enhancing K63-linked ubiquitination and subsequent p62-selective autophagic degradation of GPX4.
  62. OSBP Participates in Neural Damage Repair by Regulating Lysosome Transport Under Oxidative Stress.
  63. Ibudilast Protects Retinal Bipolar Cells From Excitotoxic Retinal Damage and Activates the mTOR Pathway.
  1. J Mol Biol. 2025 Feb 03. pii: S0022-2836(25)00047-6. [Epub ahead of print] 168981
    Multifaceted roles of the ATG8 protein family in plant autophagy: from autophagosome biogenesis to cargo recognition.
    Yixin Wu, Rui Xu, Xiaohong Zhuang.
      In plant cells, autophagy is an essential quality control process by forming a double-membrane structure named the autophagosome, which envelopes and transports the cargoes to the vacuole for degradation/recycling. Autophagy-related (ATG) 8, a key regulator in autophagy, exerts multifunctional roles during autophagy. ATG8 anchors on the phagophore membrane through the ATG8 conjugation system and participates in different steps during autophagosome formation. Accumulating evidence has demonstrated that ATG8 cooperates with other ATG or non-ATG proteins in autophagosome biogenesis. Meanwhile, ATG8 plays an important role in cargo recognition, which is mainly attributed by the specific interactions between ATG8 and the selective autophagy receptors (SARs) or cargos for selective autophagy. Emerging roles of ATG8 in non-canonical autophagy have been recently reported in plants for different stress adaptation. Here, we review the diverse functions of ATG8 in plants, focusing on autophagosome biogenesis and cargo recognition in canonical and non-canonical autophagy.
    Keywords:  ATG8 protein family; ATG8ylation; autophagosome formation; non-canonical autophagy; plants; selective autophagy
    DOI:  https://doi.org/10.1016/j.jmb.2025.168981
  2. Int J Biol Sci. 2025 ;21(3): 1014-1031
    Regulatory Mechanisms and Therapeutic Implications of Lysosomal Dysfunction in Alzheimer's Disease.
    Yeji Kim, Tae-Young Ha, Myung-Shik Lee, Keun-A Chang.
      Alzheimer's disease (AD) is characterized by the accumulation of amyloid-beta (Aβ) plaques, neurofibrillary tangles (NFTs) formed from hyperphosphorylated Tau, and widespread neuronal loss. The autophagy-lysosomal pathway plays a crucial role in maintaining cellular homeostasis by degrading and recycling of damaged organelles and aggregate amyloid proteins implicated in AD. Lysosomes are key effectors of autophagic process, responsible for the breakdown of a variety of damaged organelles and aggregate or dysfunctional proteins. This review examines the role of lysosomal dysfunction in AD pathophysiology, focusing on genetic factors, acidification abnormalities, and other contributing factors. We also explore the involvement of lysosomal dysfunction of microglia in AD pathology, and cover the role of lysosomal stress response (LSR) in cellular response to neuronal injury associated with AD. Furthermore, we discuss potential therapeutic strategies targeting lysosomal proteolysis pathway and addressing lysosomal dysfunction for AD treatment, including the pharmacologically activating lysosomal activity, regulating TFEB, and considering other emerging approaches.
    Keywords:  Alzheimer's disease; Autophagy-lysosomal pathway; Lysosomal dysfunction; Lysosomal stress response
    DOI:  https://doi.org/10.7150/ijbs.103028
  3. Biol Open. 2025 Feb 15. pii: bio061644. [Epub ahead of print]14(2):
    Impairment of proteasome-associated deubiquitinating enzyme Uchl5/UBH-4 affects autophagy.
    Sweta Jha, Johanna Pispa, Carina I Holmberg.
      The autophagy-lysosomal pathway (ALP) and the ubiquitin-proteasome system (UPS) are the two major intracellular proteolytic systems that mediate protein turnover in eukaryotes. Although a crosstalk exists between these two systems, it is still unclear how UPS and ALP interact in vivo. Here, we investigated how impaired function of the proteasome-associated deubiquitinating enzyme (DUB) Uchl5/UBH-4 affects autophagy in human cells and in a multicellular organism. We show that downregulation of Uchl5 by siRNA reduces autophagy by partially blocking the fusion of autophagosomes with the lysosomes in HeLa cells, which is similar to a previously reported role of the proteasome-associated DUB Usp14 on autophagy. However, exposure of Caenorhabditis elegans to ubh-4 or usp-14 RNAi, or to their pharmacological inhibitors, results in diverse effects on numbers of autophagosomes and autolysosomes, without blocking the lysosomal fusion, in the intestine, hypodermal seam cells and the pharynx. Our results reveal that impairment of Uchl5/UBH-4 and Usp14 affects autophagy in a tissue context manner. A deeper insight into the interplay between UPS and ALP in various tissues in vivo has the potential to promote development of therapeutic approaches for disorders associated with proteostasis dysfunction.
    Keywords:  Autolysosome; Autophagosome; Autophagy; Deubiquitinating enzyme (DUB); Proteasome-associated DUBs; Tissue specificity; Ubiquitin-proteasome system
    DOI:  https://doi.org/10.1242/bio.061644
  4. Life Sci Alliance. 2025 Apr;pii: e202402772. [Epub ahead of print]8(4):
    Sustained induction of autophagy enhances survival during prolonged starvation in newt cells.
    Md Mahmudul Hasan, Shinji Goto, Reiko Sekiya, Toshinori Hayashi, Tao-Sheng Li, Tsuyoshi Kawabata.
      Salamanders demonstrate exceptional resistance to starvation, allowing them to endure extended periods without food in their natural habitats. Although autophagy, a process involving evolutionarily conserved proteins, promotes survival during food scarcity, the specific mechanism by which it contributes to the extreme starvation resistance in newt cells remains unexplored. Our study, using the newt species Pleurodeles waltl, reveals that newt primary fibroblasts maintain constant autophagy activation during prolonged cellular starvation. Unlike normal mammalian fibroblasts, where autophagosome formation increases during acute starvation but returns to baseline levels after extended periods, newt cells maintain elevated autophagosome numbers even 4 d after autophagy initiation, surpassing levels observed in nutrient-rich conditions. Unique P. waltl mTOR orthologs show reduced lysosomal localization compared with mammalian cells in both nutrient-rich and starved states. However, newt cells exhibit dephosphorylation of mTOR substrates under starvation conditions, similar to mammalian cells. These observations suggest that newts may have evolved a distinctive system to balance seemingly conflicting factors: high regenerative capacity and autophagy-mediated survival during starvation.
    DOI:  https://doi.org/10.26508/lsa.202402772
  5. Autophagy. 2025 Feb 06. 1-16
    Development and validation of a sensitive sandwich ELISA against human PINK1.
    Zahra Baninameh, Jens O Watzlawik, Bernardo A Bustillos, Gabriella Fiorino, Tingxiang Yan, Szymon L Lewicki, Haonan Zhang, Dennis W Dickson, Joanna Siuda, Zbigniew K Wszolek, Wolfdieter Springer, Fabienne C Fiesel.
      The ubiquitin kinase and ligase PINK1 and PRKN together label damaged mitochondria for their elimination in lysosomes by selective autophagy (mitophagy). This cytoprotective quality control pathway is genetically linked to familial Parkinson disease but is also altered during aging and in other neurodegenerative disorders. However, the molecular mechanisms of these mitophagy changes remain uncertain. In healthy mitochondria, PINK1 protein is continuously imported, cleaved, and degraded, but swiftly accumulates on damaged mitochondria, where it triggers the activation of the mitophagy pathway by phosphorylating its substrates ubiquitin and PRKN. Levels of PINK1 protein can therefore be used as a proxy for mitochondrial damage and mitophagy initiation. However, validated methodologies to sensitively detect and quantify PINK1 protein are currently not available. Here, we describe the development and thorough validation of a novel immunoassay to measure human PINK1 on the Meso Scale Discovery platform. The final assay showed excellent linearity, parallelism, and sensitivity. Even in the absence of mitochondrial stress (i.e. at basal conditions), when PINK1 protein is usually not detectable by immunoblotting, significant differences were obtained when comparing samples from patient fibroblasts or differentiated neurons with and without PINK1 expression. Of note, PINK1 protein levels were found increased in human postmortem brain with normal aging, but not in brains with Alzheimer disease, suggesting that indeed different molecular mechanisms are at play. In summary, we have developed a novel sensitive PINK1 immunoassay that will complement other efforts to decipher the roles and biomarker potential of the PINK1-PRKN mitophagy pathway in the physiological and pathological context. Abbreviations: AD: Alzheimer disease; CCCP: carbonyl cyanide 3-chlorophenylhydrazone; ECL: electrochemiluminescence; ELISA: enzyme-linked immunosorbent assay; iPSC: induced pluripotent stem cell; KO: knockout; LLOQ: lower limit of quantification; MSD: Meso Scale Discovery; PD: Parkinson disease; p-S65-Ub: serine-65 phosphorylated ubiquitin; Ub: ubiquitin; ULOQ: upper limit of quantification; WT: wild-type.
    Keywords:  Autophagy; P-S65-Ub; PINK1; Parkin; mitophagy; ubiquitin
    DOI:  https://doi.org/10.1080/15548627.2025.2457915
  6. Vet Res. 2025 Jan 31. 56(1): 23
    The cholesterol metabolite 25-hydroxycholesterol suppresses porcine deltacoronavirus via lipophagy inhibition and mTORC1 modulation.
    Jia-Lu Zhang, Xue-Fei Wang, Jia-Lin Li, Cong Duan, Jiu-Feng Wang.
      25-Hydroxycholesterol (25HC) is a hydroxylated cholesterol with multiple antiviral activities, however, little is known about the mechanisms by which 25HC correlates antiviral ability with lipid droplet (LD) dynamic balance to ensure cholesterol homeostasis. In the present study, 25HC was applied to porcine deltacoronavirus (PDCoV)-infected LLC-PK1 (Lilly Laboratories Culture-Porcine Kidney 1) cells and piglets to explore its antiviral capacity and underlying mechanism. The results revealed that 25HC decreased free cholesterol (FC) levels but increased triglyceride (TG) levels in PDCoV-infected cells and piglets. The accumulation of LDs induced by oleic acid (OA) impedes PDCoV replication. In addition, 25HC administration increases LD accumulation and declines protein expression associated with lipophagy and lysosomes to facilitate LD accumulation. Moreover, 25HC inhibited TFEB (transcription factor-EB) expression, blocked its translocation into the nucleus and reversed Mechanistic Target of Rapamycin Complex 1 (mTORC1) activity, which in turn hindered lipophagy and PDCoV replication. Additionally, 25HC treatment ameliorated the clinical symptoms and intestinal injury of PDCoV-infected piglets. These findings reveal the beneficial effect of lipophagy on PDCoV infection and uncover the antiviral mechanism of 25HC, by which lipophagy and mTOR activity are tightly controlled by 25HC.
    Keywords:  25-Hydroxycholesterol; Porcine coronavirus; lipophagy; piglets; transcription factor EB
    DOI:  https://doi.org/10.1186/s13567-025-01452-9
  7. Int J Biol Macromol. 2025 Feb 03. pii: S0141-8130(25)01180-8. [Epub ahead of print] 140631
    TOLLIP inhibits the replication of PEDV by autophagic degradation of Nsp9.
    Yahui Li, Yutao Zhang, Jiexi Cheng, Jinyang Chen, Zhiwei Lin, Boli Hu, Bin Li, Xianghong Yang.
      Selective autophagy plays a crucial role in innate antiviral immunity by targeting essential viral components and host factors necessary for virus propagation. Among these factors, the nonstructural protein 9 (Nsp9) of Porcine Epidemic Diarrhea Virus (PEDV) is required for viral replication. However, the host factors regulating Nsp9 have remained elusive. In our study, we discovered that Nsp9 undergoes degradation through selective autophagy. Using coimmunoprecipitation combined with mass spectrometry analysis, we identified Toll-interacting protein (TOLLIP) as an autophagy cargo receptor binding to Nsp9 and facilitating its autophagic degradation. Additionally, we found that TOLLIP interacts with LC3A, LC3C, and GABARAPL1. Further investigations revealed that Nsp9 specifically enhances the binding of TOLLIP to LC3A, rather than LC3C or GABARAPL1. Importantly, TOLLIP promotes the engulfment of Nsp9 by LC3A-coated autophagosomes and mediates Nsp9 trafficking to lysosomes, ultimately leading to LC3A-dependent degradation of Nsp9. Consequently, TOLLIP suppresses PEDV replication. Overall, our findings highlight the role of TOLLIP in connecting viral proteins to LC3A-dependent autophagosome formation, emphasizing its significance in combating viruses through selective autophagy.
    Keywords:  Autophagy cargo receptors; LC3A; PEDV; Selective autophagy; TOLLIP
    DOI:  https://doi.org/10.1016/j.ijbiomac.2025.140631
  8. Free Radic Biol Med. 2025 Jan 31. pii: S0891-5849(25)00074-7. [Epub ahead of print]230 17-32
    Chikusetsu saponin IVa attenuates aging by improving autophagy and mitophagy.
    Jing-Zhi Wan, Cheng-Quan Li, Ying-Na Li, Ao-Zhong Li, Qi-Long Yang, Meng Kang, Jia-Hao Cao, Hui-Jie Ran, Qi-Ling Liu, Yi Wan, Song Zhai, Miao-Miao Xi, Hai-Feng Tang, Xu-Jun Qin, Ka Bian.
      Chikusetsu saponin IVa (CHS) is an essential active triterpenoid saponin found in various medicinal herbs, such as Aralia taibaiensis, Panax japonicus, and Aralia elata. While multiple health benefits have been documented, the effect of CHS on aging remains unclear. By employing the D-galactose-induced aging mice and the replicative senescence of primary mouse embryonic fibroblasts (MEFs) as the aging models, we found that CHS significantly attenuated aging both in vitro and in vivo. RNA sequencing analysis revealed that CHS greatly improved autophagy and mitophagy. Corresponding to the improved mitophagy, CHS remarkably reduced mitochondrial ROS and enhanced mitochondrial respiratory function. Mitophagy inhibition and Atg 7 genetic knockout (KO) almost abolished the anti-aging effect of CHS. AMPK pathway was activated during the attenuation of aging by CHS treatment, and a specific AMPK inhibitor reversed the induction of mitophagy and autophagy, as well as the attenuation of aging by CHS. Molecular docking data indicated AMPK as the direct binding target of CHS. In conclusion, our study initially demonstrates that CHS exhibits a potent anti-aging effect both in vitro and in vivo. CHS may directly bind to AMPK and activate the AMPK-dependent pathway to enhance autophagy and mitophagy, thereby reducing mitochondrial ROS and improving mitochondrial respiratory function, contributing to the anti-aging effect. These findings offer a new clue for the promising application of CHS in the improvement of aging and aging-related diseases in the future.
    Keywords:  Anti-aging; Chikusetsu saponin IVa (CHS); Mitophagy; Reactive oxygen species (ROS)
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2025.01.055
  9. Mol Cell. 2025 Feb 06. pii: S1097-2765(25)00045-0. [Epub ahead of print]85(3): 464-465
    CaMKIIβ Ca2+ptures ER signals to initiate autophagosome biogenesis.
    Leonardo Luís Artico, Ana Paula Arruda.
      Cytosolic Ca2+ transients are critical signals for autophagy regulation; however, how they translate into functional autophagic events remains unclear. In this issue of Molecular Cell, Zheng et al.1 identify CaMKIIβ as a key player decoding Ca2+ transients at the ER surface to initiate autophagosome formation through the FIP200 complex.
    DOI:  https://doi.org/10.1016/j.molcel.2025.01.011
  10. Nat Commun. 2025 Feb 04. 16(1): 1343
    The autophagy component LC3 regulates lymphocyte adhesion via LFA1 transport in response to outside-in signaling.
    Naoyuki Kondo, Yuko Mimori-Kiyosue, Keizo Tokuhiro, Giuseppe Pezzotti, Tatsuo Kinashi.
      The leukocyte integrin LFA1 is indispensable for immune responses, orchestrating lymphocyte trafficking and adhesion. While LFA1 activation induces LFA1 clustering at the cell contact surface via outside-in signaling, the regulatory mechanisms remain unclear. Here, we uncovered a previously hidden function of the autophagosome component LC3 beyond its role in autophagy by bridging two seemingly unrelated pathways: LFA1 transport and autophagosome transport. LFA1 clusters co-trafficked with LC3, facilitating LFA1 accumulation at the contact surface. LC3b knockout decreased lymphocyte adhesiveness. LFA1 activation did not induce autophagy, whereas it increased mTOR and AMPK activity. LFA1-dependent AMPK activation enhances LFA1 and LC3 clustering and adhesion. Inhibiting Mst1 kinase-mediated LC3 phosphorylation promoted LC3-mediated LFA1 recruitment to the contact surface through direct interaction with RAPL, uncovering an unprecedented integrin recruitment route. These findings uncover a function of LC3 and expand our understanding of lymphocyte regulation via LFA1.
    DOI:  https://doi.org/10.1038/s41467-025-56631-1
  11. Autophagy. 2025 Feb 07. 1-2
    Chaperone-mediated autophagy contributes to chromosomal stability by controlling TTC28 degradation.
    Ge Zhang, Wei Tian, Dajun Deng.
      While macroautophagy (autophagy) contributes to maintaining chromosomal stability via multiple pathways, including regulating chromatin ubiquitination and cytoplasmic DNA fragment degradation, the impacts of microautophagy and chaperone-mediated autophagy (CMA) on maintaining chromosomal stability are not known. The TTC28 (tetratricopeptide repeat domain 28) gene is frequently mutated and downregulated in human cancers. The molecular mass of the TTC28 protein is 271 kDa, which makes its functional study very difficult. Recently, we reported that TTC28 plays a key role in maintaining chromosomal stability, probably through regulating mitosis and cytokinesis, and that TTC28 downregulation may contribute to the high chromosomal instability (CIN) of cancer cells, according to the results of serial experiments and bioinformatics analyses. Notably, our findings demonstrate that TTC28 is a substrate of CMA and that the CMA pathway also plays a role in maintaining chromosomal stability in a TTC28-dependent manner. These findings demonstrate that CMA-mediated degradation is a master regulator of the ability of TTC28 to maintain genome stability.
    Keywords:  Cancer; HSPA8; TTC28; chaperone-mediated autophagy; genome stability
    DOI:  https://doi.org/10.1080/15548627.2025.2456685
  12. Exp Hematol Oncol. 2025 Feb 01. 14(1): 12
    Targeting secretory autophagy in solid cancers: mechanisms, immune regulation and clinical insights.
    Xinyu Li, Haiying Zhao.
      Secretory autophagy is a classical form of unconventional secretion that integrates autophagy with the secretory process, relying on highly conserved autophagy-related molecules and playing a critical role in tumor progression and treatment resistance. Traditional autophagy is responsible for degrading intracellular substances by fusing autophagosomes with lysosomes. However, secretory autophagy uses autophagy signaling to mediate the secretion of specific substances and regulate the tumor microenvironment (TME). Cytoplasmic substances are preferentially secreted rather than directed toward lysosomal degradation, involving various selective mechanisms. Moreover, substances released by secretory autophagy convey biological signals to the TME, inducing immune dysregulation and contributing to drug resistance. Therefore, elucidating the mechanisms underlying secretory autophagy is essential for improving clinical treatments. This review systematically summarizes current knowledge of secretory autophagy, from initiation to secretion, considering inter-tumor heterogeneity, explores its role across different tumor types. Furthermore, it proposes future research directions and highlights unresolved clinical challenges.
    DOI:  https://doi.org/10.1186/s40164-025-00603-0
  13. Neurotox Res. 2025 Feb 04. 43(1): 8
    Cannabidiol-Induced Autophagy Ameliorates Tau Protein Clearance.
    Talita A M Vrechi, Gabriel C Guarache, Rafaela Brito Oliveira, Erika da Cruz Guedes, Adolfo G Erustes, Anderson H F F Leão, Vanessa C Abílio, Antonio W Zuardi, Jaime Eduardo C Hallak, José Alexandre Crippa, Claudia Bincoletto, Rodrigo P Ureshino, Soraya S Smaili, Gustavo J S Pereira.
      Tau is a neuronal protein that confers stability to microtubules; however, its hyperphosphorylation and accumulation can lead to an impairment of protein degradation pathways, such as autophagy. Autophagy is a lysosomal catabolic process responsible for degrading cytosolic components, being essential for cellular homeostasis and survival. In this context, autophagy modulation has been postulated as a possible therapeutic target for the treatment of neurodegenerative diseases. Studies point to the modulatory and neuroprotective role of the cannabinoid system in neurodegenerative models and here it was investigated the effects of cannabidiol (CBD) on autophagy in a human neuroblastoma strain (SH-SY5Y) that overexpresses the EGFP-Tau WT (Wild Type) protein in an inducible Tet-On system way. The results demonstrated that CBD (100 nM and 10 µM) decreased the expression of AT8 and total tau proteins, activating autophagy, evidenced by increased expression of light chain 3-II (LC3-II) protein and formation of autophagosomes. Furthermore, the cannabinoid compounds CBD, ACEA (CB1 agonist) and GW-405,833 (CB2 agonist) decreased the fluorescence intensity of EGFP-Tau WT; and when chloroquine, an autophagic blocker, was used, there was a reversal in the fluorescence intensity of EGFP-Tau WT with CBD (1 and 10 µM) and GW-405,833 (2 µM), demonstrating the possible participation of autophagy in these groups. Thus, it was possible to conclude that CBD induced autophagy in EGFP-Tau WT cells which increased tau degradation, showing its possible neuroprotective role. Hence, this study may contribute to a better understanding of how cannabinoids can modulate autophagy and present a potential therapeutic target in a neurodegeneration model.
    Keywords:  Autophagy; CBD; Neuroprotection; Tau protein
    DOI:  https://doi.org/10.1007/s12640-025-00729-3
  14. Proc Natl Acad Sci U S A. 2025 Feb 11. 122(6): e2422582122
    Mec1-mediated Atg9 phosphorylation regulates the PAS recruitment of Atg9 vesicles upon energy stress.
    Siyu Fan, Shuling Dong, Weijing Yao, Yi Zhang, Mingzhu Fan, Shan Feng, Choufei Wu, Liqin Zhang, Cong Yi.
      Mec1 plays an essential role in both the DNA damage response and glucose starvation-induced autophagy. We recently reported that Mec1 regulates glucose starvation-induced autophagy through its direct binding to Atg13. However, the role of Mec1's kinase activity in autophagy remains unclear. In this study, we demonstrate that the kinase activity of Mec1 is required for glucose starvation-induced autophagy by regulating the phagophore assembly site (PAS) recruitment of Atg9 vesicles. Mechanistic and functional analyses identified Atg9 as a direct phosphorylation substrate of Mec1, with phosphorylation occurring at the S35, T203, and T243 sites. Mutations at these sites reduce the association of Atg9 with Atg17, Atg23, and Atg27, thereby impairing the PAS recruitment of Atg9 vesicles. Notably, we found that the Mec1-Atg13 binding is a prerequisite for the phosphorylation of Atg9 by Mec1. Furthermore, Mec1-mediated phosphorylation of Atg9 is also crucial for the PAS recruitment of Atg9 vesicles in response to DNA damage. We thus propose that Mec1's kinase activity regulates the PAS recruitment of Atg9 vesicles by phosphorylating Atg9 in response to energy stress and DNA damage.
    Keywords:  Atg9; DNA damage–induced autophagy; Mec1; Saccharomyces cerevisiae; glucose starvation–induced autophagy
    DOI:  https://doi.org/10.1073/pnas.2422582122
  15. Autophagy. 2025 Feb 07. 1-2
    Flavivirus NS2A orchestrates reticulophagy to enhance viral pathogenicity.
    Linliang Zhang, Yali Qin, Mingzhou Chen.
      Selective endoplasmic reticulum (ER) autophagy (reticulophagy) is essential for maintaining ER homeostasis. The E3 ligase AMFR facilitates the ubiquitination of the reticulophagy receptor RETREG1/FAM134B, thereby promoting the dynamic flux of the reticulophagy process. Flaviviruses exploit the ER during their replication cycles, highlighting the importance of ER quantity and accessibility in flavivirus infections. However, the role of reticulophagy in viral replication and the complex mechanisms by which viruses modulate reticulophagy to enhance pathogenicity remain poorly understood. In a recent study, we demonstrate that the Zika virus (ZIKV) hijacks the ER-located E3 ligase AMFR to ubiquitinate NS2A, leading to the degradation of the key reticulophagy receptor RETREG1. This inhibition of the reticulophagy process promotes virus-induced microcephaly in human brain organoids and enhances viral pathogenicity in mouse models. Notably, the AMFR-mediated ubiquitination of ZIKV-NS2A and its functional interaction with RETREG1 are conserved across the NS2A of other flaviviruses, including those from Dengue virus, West Nile virus, and Japanese encephalitis virus.
    Keywords:  FAM134B; NS2A; flavivirus; reticulophagy; ubiquitination
    DOI:  https://doi.org/10.1080/15548627.2025.2457112
  16. J Lipid Atheroscler. 2025 Jan;14(1): 40-53
    Cardioprotective Effects of Adiponectin-Stimulated Autophagy.
    Eddie Tam, Mireille Ouimet, Gary Sweeney.
      Cardiovascular diseases (CVDs), including heart failure, pose a significant economic and health burden worldwide. Current treatment strategies for heart failure are greatly limited, in that they mainly mitigate symptoms or delay further progression. In contrast, therapies aimed at proactively preventing the onset of heart failure could greatly improve outcomes. Adiponectin is an adipocyte-derived hormone that confers an array of cardioprotective effects. It exerts anti-inflammatory effects, improves metabolic function, mitigates endothelial cell dysfunction, and reduce cardiomyocyte cell death. Furthermore, it has gained increasing attention for its ability to activate autophagy, a conserved cellular pathway that facilitates the degradation and recycling of cell components. The disruption of autophagy has been linked to CVDs including heart failure. Additionally, growing evidence also points to specific forms of autophagy, namely mitophagy and lipophagy, as crucial adaptive responses in protection against CVDs. The protective effects of adiponectin, autophagy, mitophagy, and lipophagy against CVDs along with potential therapeutic implications will be discussed.
    Keywords:  Adiponectin; Autophagy; Cardiovascular diseases; Lipophagy; Mitophagy
    DOI:  https://doi.org/10.12997/jla.2025.14.1.40
  17. Nat Cell Biol. 2025 Feb 07.
    A quantitative ultrastructural timeline of nuclear autophagy reveals a role for dynamin-like protein 1 at the nuclear envelope.
    Philip J Mannino, Andrew Perun, Ivan V Surovtsev, Nicholas R Ader, Lin Shao, Elisa C Rodriguez, Thomas J Melia, Megan C King, C Patrick Lusk.
      Autophagic mechanisms that maintain nuclear envelope homoeostasis are bulwarks to ageing and disease. Here we define a quantitative and ultrastructural timeline of nuclear macroautophagy (nucleophagy) in yeast by leveraging four-dimensional lattice light sheet microscopy and correlative light and electron tomography. Nucleophagy begins with a rapid accumulation of the selective autophagy receptor Atg39 at the nuclear envelope and finishes in ~300 s with Atg39-cargo delivery to the vacuole. Although there are several routes to the vacuole, at least one pathway incorporates two consecutive membrane fission steps: inner nuclear membrane (INM) fission to generate an INM-derived vesicle in the perinuclear space and outer nuclear membrane fission to liberate a double-membraned vesicle to the cytosol. Outer nuclear membrane fission occurs independently of phagophore engagement and instead relies surprisingly on dynamin-like protein 1 (Dnm1), which is recruited to sites of Atg39 accumulation by Atg11. Loss of Dnm1 compromises nucleophagic flux by stalling nucleophagy after INM fission. Our findings reveal how nuclear and INM cargo are removed from an intact nucleus without compromising its integrity, achieved in part by a non-canonical role for Dnm1 in nuclear envelope remodelling.
    DOI:  https://doi.org/10.1038/s41556-025-01612-1
  18. Mol Cell Biochem. 2025 Feb 01.
    Autophagy and the peroxisome proliferator-activated receptor signaling pathway: A molecular ballet in lipid metabolism and homeostasis.
    Pouria Kiani, Elaheh Sadat Khodadadi, Ali Nikdasti, Sahar Yarahmadi, Mobina Gheibi, Zeynab Yousefi, Sajad Ehtiati, Sheida Yahyazadeh, Sayed Mohammad Shafiee, Motahareh Taghizadeh, Somayeh Igder, Seyyed Hossein Khatami, Saeed Karima, Omid Vakili, Morteza Pourfarzam.
      Lipids, which are indispensable for cellular architecture and energy storage, predominantly consist of triglycerides (TGs), phospholipids, cholesterol, and their derivatives. These hydrophobic entities are housed within dynamic lipid droplets (LDs), which expand and contract in response to nutrient availability. Historically perceived as a cellular waste disposal mechanism, autophagy has now been recognized as a crucial regulator of metabolism. Within this framework, lipophagy, the selective degradation of LDs, plays a fundamental role in maintaining lipid homeostasis. Dysregulated lipid metabolism and autophagy are frequently associated with metabolic disorders such as obesity and atherosclerosis. In this context, peroxisome proliferator-activated receptors (PPARs), particularly PPAR-γ, serve as intracellular lipid sensors and master regulators of gene expression. Their regulatory influence extends to both autophagy and lipid metabolism, indicating a complex interplay between these processes. This review explores the hypothesis that PPARs may directly modulate autophagy within the realm of lipid metabolism, thereby contributing to the pathogenesis of metabolic diseases. By elucidating the underlying molecular mechanisms, we aim to provide a comprehensive understanding of the intricate regulatory network that connects PPARs, autophagy, and lipid homeostasis. The crosstalk between PPARs and other signaling pathways underscores the complexity of their regulatory functions and the potential for therapeutic interventions targeting these pathways. The intricate relationships among PPARs, autophagy, and lipid metabolism represent a pivotal area of research with significant implications for understanding and treating metabolic disorders.
    Keywords:  Autophagy; Lipid metabolism; Lipophagy; Peroxisome proliferator-activated receptors; Signal transduction
    DOI:  https://doi.org/10.1007/s11010-025-05207-0
  19. J Pharmacol Exp Ther. 2025 Jan;pii: S0022-3565(24)00026-0. [Epub ahead of print]392(1): 100007
    Evidence for cytoprotective autophagy in response to HER2-targeted monoclonal antibodies.
    Ahmed M Elshazly, Aya A Elzahed, David A Gewirtz.
      The advent of HER2-targeted monoclonal antibodies such as trastuzumab has significantly improved the clinical outcomes for patients with breast cancer overexpressing HER2 and, more recently, also for gastric cancers. However, the development of resistance, as is frequently the case for other antineoplastic modalities, constrains their clinical efficacy. Multiple molecular mechanisms and signaling pathways have been investigated for their potential involvement in the development of resistance to HER2-targeted therapies, among which is autophagy. Autophagy is an inherent cellular mechanism whereby cytoplasmic components are selectively degraded to maintain cellular homeostasis via the generation of energy and metabolic intermediates. Although the cytoprotective form of autophagy is thought to predominate, other forms of autophagy have also been identified in response to chemotherapeutic agents in various tumor models; these include cytotoxic, cytostatic, and nonprotective functional forms of autophagy. In this review, we provide an overview of the autophagic machinery induced in response to HER2-targeted monoclonal antibodies, with a focus on trastuzumab and trastuzumab-emtansine, in an effort to determine whether autophagy targeting or modulation could be translated clinically to increase their effectiveness and/or overcome the development of resistance. SIGNIFICANCE STATEMENT: This manuscript is one in a series of papers that interrogate the role(s) of the autophagy induced in response to antineoplastic agents in various cancer models. This series of papers was developed in an effort to establish whether autophagy targeting or modulation is likely to be an effective adjuvant strategy to increase the efficacy of cancer chemotherapeutic agents. This review explores the relationship between the autophagic machinery and HER2-targeted therapies.
    Keywords:  Autophagy; Cytoprotective; HER2; Trastuzumab; Trastuzumab-emtansine
    DOI:  https://doi.org/10.1124/jpet.123.002048
  20. Neurobiol Dis. 2025 Feb 03. pii: S0969-9961(25)00041-5. [Epub ahead of print] 106825
    Unravelling a mechanistic link between mitophagy defect, mitochondrial malfunction, and apoptotic neurodegeneration in Mucopolysaccharidosis VII.
    Nishan Mandal, Apurba Das, Rupak Datta.
      Cognitive disability and neurodegeneration are prominent symptoms of Mucopolysaccharidosis VII (MPS VII), a lysosomal storage disorder caused by β-glucuronidase enzyme deficiency. Yet, the mechanism of neurodegeneration in MPS VII remains unclear thereby limiting the scope of targeted therapy. We aimed to bridge this knowledge gap by employing the β-glucuronidase-deficient (CG2135-/-) Drosophila model of MPS VII. Taking cues from our initial observation that the adult CG2135-/- flies displayed enhanced susceptibility to starvation, we investigated potential impairments in the autophagy-lysosomal clearance machinery in their brain to dissect the underlying cause of neurodegeneration. We found that both autophagosome biogenesis and lysosome-mediated autophagosomal turnover were impaired in the CG2135-/- fly brain. This was evidenced by lower Atg8a-II levels, reduced Atg1 and Ref(2)P expression along with accumulation of lipofuscin-like inclusions and multilamellar bodies. Mitophagy was also found to be defective in their brain, resulting in buildup of enlarged mitochondria with distorted cristae and reduced membrane potential. This, in turn, compromised mitochondrial function, as reflected by drastically reduced brain ATP levels. Energy depletion triggered apoptosis in neuronal as well as non-neuronal cells of the CG2135-/- fly brain, where apoptotic dopaminergic neurons were also detected. Interestingly, resveratrol treatment corrected the mitophagy defect and prevented ATP depletion in the CG2135-/- fly brain, providing an explanation for its neuroprotective effects. Collectively, our study reveals a pharmacologically targetable mechanistic link between mitophagy defect, mitochondrial malfunction, and apoptotic neurodegeneration in MPS VII.
    Keywords:  Apoptosis; Autophagy; MPS VII; Mitophagy; Neurodegeneration; Resveratrol
    DOI:  https://doi.org/10.1016/j.nbd.2025.106825
  21. NPJ Metab Health Dis. 2025 ;3(1): 4
    Calcium-mediated regulation of mitophagy: implications in neurodegenerative diseases.
    Fivos Borbolis, Christina Ploumi, Konstantinos Palikaras.
      Calcium signaling plays a pivotal role in diverse cellular processes through precise spatiotemporal regulation and interaction with effector proteins across distinct subcellular compartments. Mitochondria, in particular, act as central hubs for calcium buffering, orchestrating energy production, redox balance and apoptotic signaling, among others. While controlled mitochondrial calcium uptake supports ATP synthesis and metabolic regulation, excessive accumulation can trigger oxidative stress, mitochondrial membrane permeabilization, and cell death. Emerging findings underscore the intricate interplay between calcium homeostasis and mitophagy, a selective type of autophagy for mitochondria elimination. Although the literature is still emerging, this review delves into the bidirectional relationship between calcium signaling and mitophagy pathways, providing compelling mechanistic insights. Furthermore, we discuss how disruptions in calcium homeostasis impair mitophagy, contributing to mitochondrial dysfunction and the pathogenesis of common neurodegenerative diseases.
    Keywords:  Metabolic disorders; Mitochondria
    DOI:  https://doi.org/10.1038/s44324-025-00049-2
  22. J Am Heart Assoc. 2025 Feb 04. 14(3): e037640
    Vascular Contractility Relies on Integrity of Progranulin Pathway: Insights Into Mitochondrial Function.
    Shubhnita Singh, Ariane Bruder, Rafael M Costa, Juliano V Alves, Sivakama Bharathi, Eric S Goetzman, Thiago Bruder-Nascimento.
       BACKGROUND: The complex interplay between vascular contractility and mitochondrial function is central to cardiovascular disease. The progranulin gene (GRN) encodes glycoprotein PGRN (progranulin), a ubiquitous molecule with known anti-inflammatory property. However, the role of PGRN in cardiovascular disease remains undefined. In this study, we sought to dissect the significance of PGRN in the regulation vascular contractility and investigate the interface between PGRN and mitochondrial quality.
    METHODS AND RESULTS: We used aortae from male and female C57BL6/J wild-type (PGRN+/+) and B6(Cg)-Grntm1.1Aidi/J (PGRN-/-) mice. Our results showed suppression of contractile activity in PGRN-/-, followed by reduced α-smooth muscle actin expression. Mechanistically, PGRN deficiency suppressed mitochondrial respiration, induced mitochondrial fission, and disturbed autophagy process and redox signaling, while restoration of PGRN levels in aortae from PGRN-/- mice via lentivirus delivery ameliorated contractility and boosted mitochondria activity. In addition, in vivo treatment with mitochondrial fission inhibitor restored mitochondrial quality and vascular contractility, while vascular smooth muscle cells overexpressing PGRN displayed higher lysosome biogenesis, accelerated mitophagy flux, and mitochondrial respiration accompanied by vascular hypercontractility. Finally, angiotensin II failed to induce vascular contractility in PGRN-/-, suggesting a key role of PGRN to maintain the vascular tone.
    CONCLUSIONS: Our findings suggest that PGRN preserves the vascular contractility via regulating mitophagy flux, mitochondrial activity and dynamics, and redox signaling. Therefore, loss of PGRN function appears as a pivotal risk factor in cardiovascular disease.
    Keywords:  progranulin; vascular contractility; vasculature
    DOI:  https://doi.org/10.1161/JAHA.124.037640
  23. Expert Rev Neurother. 2025 Feb 06. 1-17
    An overview of the value of mTOR inhibitors to the treatment of epilepsy: the evidence to date.
    Patrick B Moloney, Norman Delanty.
       INTRODUCTION: Dysregulated mechanistic target of rapamycin (mTOR) activity is implicated in seizure development in epilepsies caused by variants in mTOR pathway genes. Sirolimus and everolimus, allosteric mTOR inhibitors, are widely used in transplant medicine and oncology. Everolimus is approved for treating seizures in tuberous sclerosis complex (TSC), the prototype mTORopathy. Emerging evidence suggests that mTOR inhibitors could also be effective in other mTORopathies, such as DEPDC5-related epilepsy and focal cortical dysplasia type 2 (FCD2).
    AREAS COVERED: This narrative review summarizes key regulatory proteins in the mTOR cascade and outlines epilepsy syndromes linked to variants in genes encoding these proteins, particularly TSC, GATOR1-related epilepsies, and FCD2. It discusses the clinical pharmacology of mTOR inhibitors and the evidence supporting their efficacy as antiseizure medications (ASM) in mTORopathies. Lastly, potential benefits of next-generation mTOR inhibitors for CNS indications are evaluated.
    EXPERT OPINION: The therapeutic benefits of mTOR inhibitors in TSC are well-established, but their value in other mTORopathies remains uncertain. Despite targeting the underlying disease biology, their efficacy in TSC is not significantly different from other ASM, likely due in part to pharmacokinetic constraints. Next-generation mTOR inhibitors that address these limitations may offer improved response rates, but they are in the preclinical development phase.
    Keywords:  DEPDC5; epilepsy; everolimus; focal cortical dysplasia; mTOR inhibitor; mechanistic target of rapamycin; precision medicine; tuberous sclerosis complex
    DOI:  https://doi.org/10.1080/14737175.2025.2462280
  24. PLoS Biol. 2025 Feb;23(2): e3002961
    VANGL2 alleviates inflammatory bowel disease by recruiting the ubiquitin ligase MARCH8 to limit NLRP3 inflammasome activation through OPTN-mediated selective autophagy.
    Huaji Jiang, Yingchao Xie, Zhiqiang Hu, Jiansen Lu, Jiahuan Zhang, Hongyu Li, Ke Zeng, Wenqiang Peng, Cheng Yang, Junsheng Huang, Zelong Han, Xiaochun Bai, Xiao Yu.
      Inflammatory bowel disease (IBD) is a chronic and potentially life-threatening inflammatory disease of gastroenteric tissue characterized by episodes of intestinal inflammation, but the underlying mechanisms remain elusive. Here, we explore the role and precise mechanism of Van-Gogh-like 2 (VANGL2) during the pathogenesis of IBD. VANGL2 decreases in IBD patients and dextran sulfate sodium (DSS)-induced colitis in mice. Myeloid VANGL2 deficiency exacerbates the progression of DSS-induced colitis in mice and specifically enhances the activation of NLRP3 inflammasome in macrophages. NLRP3-specific inhibitor MCC950 effectively alleviates DSS-induced colitis in VANGL2 deficient mice. Mechanistically, VANGL2 interacts with NLRP3 and promotes the autophagic degradation of NLRP3 through enhancing the K27-linked polyubiquitination at lysine 823 of NLRP3 by recruiting E3 ligase MARCH8, leading to optineurin (OPTN)-mediated selective autophagy. Notably, decreased VANGL2 in the peripheral blood mononuclear cells from IBD patients results in overt NLRP3 inflammasome activation and sustained inflammation. Taken together, this study demonstrates that VANGL2 acts as a repressor of IBD progression by inhibiting NLRP3 inflammasome activation and provides insights into the crosstalk between inflammation and autophagy in preventing IBD.
    DOI:  https://doi.org/10.1371/journal.pbio.3002961
  25. Biochem Biophys Res Commun. 2025 Feb 01. pii: S0006-291X(25)00146-9. [Epub ahead of print]750 151432
    Pharmacological activation of TRPML1 enhances autophagy regulating hypertonicity and TGF-β-induced EMT in proximal tubular epithelial cells.
    Takashi Miyano, Toshihiro Sera, Naoya Sakamoto.
      Proximal tubular epithelial cells (PTECs) are central to maintaining kidney homeostasis. Under pathological conditions, such as ischemia or inflammation, PTECs promote profibrotic signals, including transforming growth factor (TGF)-β, and undergo epithelial-mesenchymal transition (EMT). EMT is characterized by decreased epithelial markers (e.g., E-cadherin) and increased mesenchymal markers (e.g., α-smooth muscle actin [α-SMA]), which promote myofibroblast activation and fibrosis progression. We previously demonstrated that hyperosmotic stress, characterized by elevated extracellular solute concentrations, induces EMT in PTECs. However, we observed that hyperosmotic stress simultaneously activates autophagy, a cellular process that has antagonistic effects on EMT, primarily mediated by transient receptor potential mucolipin 1 (TRPML1). However, the interplay between hyperosmotic stress-induced EMT and autophagy remains unclear. This study examined whether enhancing autophagy via TRPML1 activation could modulate EMT under hyperosmotic stress. Using the TRPML1 agonist ML-SA1, we observed a significantly increased autophagic flux, indicated by elevated LC3-II levels, without cytotoxic effects. Under hyperosmotic conditions, ML-SA1 further amplified autophagic flux in PTECs compared to hyperosmotic stress alone. Notably, this enhanced autophagy suppressed EMT by maintaining E-cadherin expression and reducing α-SMA levels. Furthermore, the ML-SA1-mediated autophagy enhancement attenuated EMT and profibrotic factor production in TGF-β-treated cells, suggesting a broader protective role beyond hyperosmotic stress. These findings reveal a novel interaction between hyperosmotic stress-induced autophagy and EMT, emphasizing TRPML1 activation's therapeutic potential to mitigate PTEC injury and fibrosis progression.
    Keywords:  Autophagy; Epithelial-mesenchymal transition; Hyperosmotic stress; TGF-β; Transient receptor potential mucolipin 1; Tubular epithelial cell
    DOI:  https://doi.org/10.1016/j.bbrc.2025.151432
  26. Int J Biol Sci. 2025 ;21(3): 1158-1173
    Tetramethylpyrazine attenuates sodium arsenite-induced acute kidney injury by improving the autophagic flux blockade via a YAP1-Nrf2-p62-dependent mechanism.
    Zhiyong Song, Tom K Hei, Xuezhong Gong.
      With increased application, sodium arsenite (AS III)-induced acute kidney injury (AI-AKI) is becoming a new clinical challenge, but its potential pathogenesis remains poorly studied. Our previous data demonstrated that inducing autophagy and mitochondrial dysfunction in renal tubular cells are important links of AI-AKI and could be inhibited by tetramethylpyrazine (TMP). Recently, co-transcription factor YAP1 is reported to control autophagy and is mandatory to stimulate autophagic flux. This study constructed in vitro and in vivo models using clinically related dosages of AS III. Mitophagy, upregulated YAP1 expression, and Nrf2 activation were observed, with upregulation of p62 representing the occurrence of autophagic flux blockade. In HK-2 cells, oxidative stress induced by AS III promoted sustained Nrf2 activation, which enhanced p62 transcription at an early phase. Subsequently, p62 accumulation induced Nrf2 nuclear translocation, which in turn promoted p62 expression, forming a feedback loop to induce autophagic flux blockade, which was aggravated by the autophagic flux blocker chloroquine (CQ). TMP reversed such processes and protected tubular cells, while silencing YAP1 and Nrf2 attenuated TMP renoprotections. YAP1 agonist PY-60 increased Nrf2 expression, while YAP1 knockdown counteracted it and diminished TMP effect on autophagic flux. Furthermore, blocking Nrf2 caused YAP1 accumulation. CO-IP and immunofluorescence co-localization results confirmed co-nuclear translocations of YAP1 bound to dissociated Nrf2 that induced autophagic flux blockade. In conclusion, the present study identified novel mechanisms that TMP alleviated AI-AKI by improving the autophagic flux blockade via a YAP1-Nrf2-p62-dependent mechanism.
    Keywords:  YAP1; acute kidney injury; autophagic flux blockade; sodium arsenite; tetramethylpyrazine
    DOI:  https://doi.org/10.7150/ijbs.104107
  27. Int J Immunopathol Pharmacol. 2025 Jan-Dec;39:39 3946320251317284
    Rapamycin ameliorates inflammatory pain via recovery of autophagy flux mediated by mammalian target of rapamycin (mTOR) signaling pathway in the rat spinal cord.
    Jiawei Zhang, Shi Chen, Rongyi Zhang, Xiaoting Zheng, Chang Liu, Jiqian Zhang, Lei Zhang, Zhilai Yang, Likui Wang.
       OBJECTIVE: This study aimed to investigate the effect of rapamycin on inflammatory pain in rats.
    INTRODUCTION: Inflammatory pain is a kind of pathological pain caused by inflammatory mediators or factors such as TNF-α (Tumor Necrosis Factor-α), IL-1β (Interleukin-1β), and IL-6 (Interleukin-6). NSAIDs and opioid analgesics are commonly used for relieving inflammatory pain, but the side effects limit their clinical application. New drugs based on new mechanisms for inflammatory pain are urgently needed. Autophagy is an evolutionarily conserved homeostatic process for lysosomal degradation of intracellular components. Recent reports indicate the involvement of autophagy in the development and maintenance of neuropathic pain, but the role of autophagy in inflammatory pain still needs to be explored.
    METHODS: The pain-related behaviors of rats were studied by paw withdrawal threshold and paw withdrawal latency. The autophagy level of the rat spinal cord was detected by western blots. The concentrations of TNF-α, IL-1β, and IL-6 were detected by ELISA.
    RESULTS: We found that the paw withdrawal threshold and paw withdrawal latency were both significantly decreased after CFA (Complete Freund's Adjuvant) injection, accompanied by the activation of mTOR signaling pathway and the inhibited autophagy flux in the spinal cord. And inflammatory cytokines were increased in the spinal cord after CFA injection. Then, we studied the effect of rapamycin on CFA-induced inflammatory pain in rats, and found that rapamycin restored the autophagy flux and significantly reduced mechanical allodynia and thermal hyperalgesia. In addition, rapamycin significantly decreased the levels of TNF-α, IL-1β, and IL-6 after CFA injection in the spinal cord.
    CONCLUSION: Our results suggested that rapamycin might be a promising candidate for the treatment of inflammatory pain by restoring the autophagy flux in the spinal cord.
    Keywords:  autophagy; complete Freund’s adjuvant; inflammation factors; inflammatory pain; rapamycin
    DOI:  https://doi.org/10.1177/03946320251317284
  28. Structure. 2025 Feb 06. pii: S0969-2126(25)00009-7. [Epub ahead of print]33(2): 218-220
    Illuminating cholesterol-mTORC1 signaling: LYCHOS in focus.
    Hijai R Shin, Roberto Zoncu.
      In a recent issue of Nature, Bayly-Jones et al.1 report the first cryoelectron microscopy (cryo-EM) structure of the lysosomal transmembrane protein LYCHOS, which mediates cholesterol sensing by mTORC1. LYCHOS forms a homodimer, with cholesterol engagement at the transporter-GPCR domain interface, coupled to auxin binding at the transporter-like domain, suggesting multi-domain coordination as critical for cholesterol sensing.
    DOI:  https://doi.org/10.1016/j.str.2025.01.009
  29. Neurotherapeutics. 2025 Feb 03. pii: S1878-7479(25)00016-9. [Epub ahead of print] e00538
    Fibrinogen degradation products exacerbate alpha-synuclein aggregation by inhibiting autophagy via downregulation of Beclin1 in multiple system atrophy.
    Huanzhu Liu, Ruoyang Yu, Muwei Zhang, Xiaoyan Zheng, Lizi Zhong, Wanlin Yang, Yuqi Luo, Zifeng Huang, Jialing Zheng, Hui Zhong, Xiaobo Wei, Wenhua Zheng, Yinghua Yu, Qing Wang.
      Multiple system atrophy (MSA) is a rapidly progressive neurodegenerative disease arising from accumulation of the α-synuclein and aberrant protein clearance in oligodendrocytes. The mechanisms of autophagy involved in the progression of MSA remain poorly understood. It is reported that MSA patients have blood-brain barrier impairments, which may increase the entry of fibrinogen into the brain. However, the roles of fibrinogen and its degradation products (FDPs) on autophagy and α-synuclein accumulation in MSA remain unknown. Here, we established the MSA animal model by intraperitoneal injection of 1-methyl-4-phenyl-1,2,3,6- tetrahydropyridine (MPTP) and 3-nitropropionic acid (3-NP), and cellular models by adding fibrillar α-syn into oligodendrocytes to investigate the mechanisms of FDPs on autophagy and accumulation of α-synuclein in oligodendrocytes. We found that FDPs inhibit the entry of α-synuclein into lysosomes for degradation, increasing aggregation of α-synuclein in oligodendrocytes (OLN-93). Our findings indicated that in OLN-93, FDPs inhibited the expressions of Beclin1 and Bif-1, which could promote the fusion of autophagosomes with lysosomes. Furthermore, the expression of α-synuclein was elevated in FDPs-injected mice, accompanied by an increase in the protein level of p62. We detected elevated expression of FDPs in the striatum of MSA mice. Finally, FDPs inhibited the expression of Beclin1 and Bif-1, which led to aberrant autophagic degradation and increased aggregation of α-synuclein and phospho-α-synuclein in MSA mice. Our study illustrates that FDPs can cause aggregation of α-synuclein in MSA by inhibiting Beclin1-mediated autophagy, which may exacerbate disease progression. These results provide a new therapeutic approach for MSA, that targets the inhibitory effect of FDPs on oligodendrocyte autophagy.
    Keywords:  Autophagy; Beclin1; Fibrinogen; Fibrinogen degradation products; Multiple system atrophy; Oligodendrocyte
    DOI:  https://doi.org/10.1016/j.neurot.2025.e00538
  30. Clin Transl Med. 2025 Feb;15(2): e70221
    Sodium pump subunit NKAα1 protects against diabetic endothelial dysfunction by inhibiting ferroptosis through the autophagy-lysosome degradation of ACSL4.
    Xue-Xue Zhu, Jia-Bao Su, Fang-Ming Wang, Xiao-Ying Chai, Guo Chen, An-Jing Xu, Xin-Yu Meng, Hong-Bo Qiu, Qing-Yi Sun, Yao Wang, Zhuo-Lin Lv, Yuan Zhang, Yao Liu, Zhi-Jun Han, Na Li, Hai-Jian Sun, Qing-Bo Lu.
      The sodium pump Na+/K+-ATPase (NKA), an enzyme ubiquitously expressed in various tissues and cells, is a critical player in maintaining cellular ion homeostasis. Dysregulation of α1 subunit of NKA (NKAα1) has been associated with cardiovascular and metabolic disorders, yet the exact role of NKAα1 in diabetes-induced endothelial malfunction remains incompletely understood. The NKAα1 expression and NKA activity were examined in high-glucose (HG)-exposed endothelial cells (ECs) and mouse aortae, as well as in high-fat-diet (HFD)-fed mice. Acetylcholine (Ach) was utilised to assess endothelium-dependent relaxation (EDR) in isolated mouse aortae. We found that both NKAα1 protein and mRNA levels were significantly downregulated in the aortae of HFD-fed mice, and HG-incubated mouse aortae and ECs. Gain- and loss-of-function experiments revealed that NKAα1 preserves EDR by mitigating oxidative/nitrative stresses in ECs. Overexpression of NKAα1 facilitated EC viability, migration, and angiogenesis by inhibiting the overproduction of superoxide and peroxynitrite. Mechanistically, dysfunctional NKAα1 impaired autophagy process, and prevented the transfer of acyl-CoA synthetase long-chain family member 4 (ACSL4) to the lysosome for degradation, thereby resulting in lipid peroxidation and ferroptosis in ECs. Induction of ferroptosis and inhibition of the autophagy-lysosome pathway blocked the protective effects of NKAα1 on EDR. Eventually, we identified Hamaudol as a potent activator of NKAα1 by restraining the phosphorylation and endocytosis of NKAα1, restoring EDR in obese diabetic mice. Overall, NKAα1 facilitates the autophagic degradation of ACSL4 via the lysosomal pathway, preventing ferroptosis and oxidative/nitrative stress in ECs. NKAα1 may serve as an attractive candidate for the management of vascular disorders associated with diabetes. KEY POINTS: NKAα1 downregulation impairs endothelial function in diabetes by promoting oxidative/nitrative stress and ferroptosis. NKAα1 supports lysosomal degradation of ACSL4 via autophagy, preventing lipid peroxidation and ferroptosis. Hamaudol, an activator of NKAα1, restores endothelial relaxation in diabetic mice by inhibiting NKAα1 phosphorylation and endocytosis.
    Keywords:  diabetes; endothelial dysfunction; ferroptosis autophagy; lysosome; oxidative stress
    DOI:  https://doi.org/10.1002/ctm2.70221
  31. Nat Aging. 2025 Feb 05.
    Sex-specific and cell-type-specific changes in chaperone-mediated autophagy across tissues during aging.
    Rabia R Khawaja, Adrián Martín-Segura, Olaya Santiago-Fernández, Rebecca Sereda, Kristen Lindenau, Mericka McCabe, Adrián Macho-González, Maryam Jafari, Aurora Scrivo, Raquel Gomez-Sintes, Bhakti Chavda, Ana Rosa Saez-Ibanez, Inmaculada Tasset, Esperanza Arias, Xianhong Xie, Mimi Kim, Susmita Kaushik, Ana Maria Cuervo.
      Aging leads to progressive decline in organ and tissue integrity and function, partly due to loss of proteostasis and autophagy malfunctioning. A decrease with age in chaperone-mediated autophagy (CMA), a selective type of lysosomal degradation, has been reported in various organs and cells from rodents and humans. Disruption of CMA recapitulates features of aging, whereas activating CMA in mice protects against age-related diseases such as Alzheimer's, retinal degeneration and/or atherosclerosis. However, sex-specific and cell-type-specific differences in CMA with aging remain unexplored. Here, using CMA reporter mice and single-cell transcriptomic data, we report that most organs and cell types show CMA decline with age, with males exhibiting a greater decline with aging. Reduced CMA is often associated with fewer lysosomes competent for CMA. Transcriptional downregulation of CMA genes may further contribute to CMA decline, especially in males. These findings suggest that CMA differences may influence organ vulnerability to age-related degeneration.
    DOI:  https://doi.org/10.1038/s43587-024-00799-6
  32. Biol Open. 2025 Feb 06. pii: bio.061605. [Epub ahead of print]
    Glycogen synthase is required for heat shock-mediated autophagy induction in neuronal cells.
    Pratibha Bhadauriya, Akanksha Onkar, Kamali Nagarajan, Kavikumar Angamuthu Karuppusamy, Subramaniam Ganesh, Saloni Agarwal.
      Autophagy is an essential cellular process that facilitates the degradation of aggregated proteins and damaged organelles to maintain cellular homeostasis and promote cell survival. Recent studies have indicated a direct role for glycogen synthase (GS) in activating neuronal autophagy and in conferring protection against cytotoxic misfolded proteins. Since heat shock induces protein misfolding and autophagy is an essential component of the heat shock response that clears the misfolded proteins, we looked at the possible role of GS in heat shock response pathways in neuronal cells. We demonstrate an increase in the activity and level of GS and a concomitant increase in the glycogen level during the heat shock and post-heat shock recovery period. These changes had a direct correlation with autophagy induction. We further demonstrate that heat shock transcription factor 1 regulates the level and activation of GS during heat shock and that GS is essential for the induction of autophagy during heat stress in neuronal cells. Intriguingly, the partial knock-down of GS led to increased death due to heat shock in neuronal cells and Drosophila. Our study offers a novel insight into the role of GS and glycogen metabolic pathways in heat shock response in neuronal cells.
    Keywords:  Metabolism; Misfolded proteins; Neuronal cells; Proteolysis; Stress response
    DOI:  https://doi.org/10.1242/bio.061605
  33. Bone Joint Res. 2025 Feb 06. 14(2): 97-110
    Melatonin alleviates senile osteoporosis by regulating autophagy and enhancing fracture healing in aged mice.
    Denghui Zhang, Tianer Zhu, Jingyao Bai, Chunchun Chen, Junru Wen, Yi Zhou, Xiaoxu Guan.
       Aims: In our previous research, we have found that melatonin (MEL) affects the osteoporotic process. By balancing bone remoulding, autophagy is involved in age-related bone loss. However, as a regulator of autophagy, whether MEL influences senile osteoporosis via regulating autophagy remains unclear.
    Methods: Cellular, radiological, and histopathological evaluations were performed on 36 16-month-old male C57BL6/L mice or aged bone marrow-derived mesenchymal stem cells. A MEL-gelatin methacrylamide system was constructed to aid osteoporotic fracture healing.
    Results: In this study, we found that bone loss, low level of MEL, and decreased autophagy coexisted in aged C57BL6/L mice. A physiological (low, 10 nM but not 100 nM) concentration of MEL restored bone loss, transformed the cytokine framework, and increased the autophagic level in aged mice, whereas inhibition of autophagy unfavourably reduced the positive effects of MEL on bone mass. The autophagy-conducted increased osteogenic lineage commitment and extracellular matrix mineralization, but not matrix synthesis of aged bone marrow-derived mesenchymal stem cells, was responsible for MEL anabolic effects on bone. PIK3C-AKT-MTOR signal was tested to be a main pathway that is involved in MEL-induced autophagy.
    Conclusion: Our data suggest that the application of MEL can restore degenerative osteogenesis of aged bone marrow-derived mesenchymal stem cells, and has the potential to regain bone mass in aged mice through activating autophagy via the PIK3C-AKT-MTOR pathway. MEL therefore may serve as a potential clinical therapy to treat senile osteoporosis.
    DOI:  https://doi.org/10.1302/2046-3758.142.BJR-2024-0112.R2
  34. Insect Mol Biol. 2025 Feb 05.
    Role of Atg3, Atg5 and Atg12 in the crosstalk between apoptosis and autophagy in the posterior silk gland of Bombyx mori.
    Ebru Goncu, Esen Poyraz Tinartas, Busra Gunay, Tugce Ordu, Gamze Turgay Izzetoglu.
      Autophagy is a cellular mechanism that enhances cell survival in response to various stressors, including nutrient deprivation; however, it also plays a pivotal role in the regulation of programmed cell death. This study examined the effects of autophagy-related genes Atg3, Atg5 and Atg12 on apoptosis and autophagy during the degeneration of the posterior silk gland in Bombyx mori, employing RNA interference techniques. Apoptosis-specific markers and autophagic processes were evaluated in both control and treatment groups. The knockdown of all three genes resulted in a significant reduction in autophagy, modifications in the apoptosis process, aberrant expression of p53 and impaired lysosomal function. It was determined that Atg3 is involved in the regulation of intracellular mitochondrial homeostasis. Following the silencing of Atg5, evidence was obtained indicating the gene's role in regulating lysosomal pH. Notably, the loss of Atg3 and Atg5 was associated with an increase in apoptotic markers, whereas the silencing of Atg12 inhibited apoptosis. Elevated levels of the p53 transcription factor following gene silencing suggested a potential interaction between these genes and p53. Our findings further underscore the importance of autophagy-mediated cell death, involving Atg3, Atg5 and Atg12, in the proper progression of degeneration in the posterior silk gland. A comprehensive understanding of the molecular mechanisms that mediate the interaction between apoptosis and autophagy is essential for elucidating their roles in both physiological and pathological contexts.
    Keywords:  Bombyx mori; apoptosis; autophagy; p53
    DOI:  https://doi.org/10.1111/imb.12985
  35. Trends Cell Biol. 2025 Feb 04. pii: S0962-8924(25)00002-9. [Epub ahead of print]
    Endoplasmic reticulum (ER) protein degradation by ER-associated degradation and ER-phagy.
    Shuangcheng Alivia Wu, Zexin Jason Li, Ling Qi.
      Protein misfolding and aggregation in the endoplasmic reticulum (ER) have been causally linked to a variety of human diseases. Two key pathways for eliminating misfolded proteins and aggregates in the ER are ER-associated degradation (ERAD) and ER-phagy, respectively. While both pathways have been well characterized biochemically, our understanding of their physiological relevance and significance remains limited. In recent years, significant advances have been made, including the generation and characterization of various knockout and knockin mouse models, the identification of human disease-associated or -causing variants, and insights into the coordination between ERAD and autophagy in physiological contexts. In this review, we summarize these advancements, highlighting the key roles of a highly conserved suppressor of lin-12-like-hydroxymethyl glutaryl-coenzyme A reductase degradation 1 (SEL1L-HRD1) protein complex of ERAD and ER-phagy in health and disease.
    Keywords:  ER-associated protein degradation (ERAD); ER-phagy; ER-phagy receptors; SEL1L-HRD1; disease variants; substrates
    DOI:  https://doi.org/10.1016/j.tcb.2025.01.002
  36. Anal Chem. 2025 Feb 03.
    Microenvironment-Specific Enrichment Strategy Enables Lysosomal Proteomic Dynamics Analysis.
    Yuwen Chen, Zhiying Li, Yongbao Mao, Hui Pan, Zhen Liang, Yukui Zhang, Qun Zhao, Lihua Zhang.
      Lysosomes are vital organelles for degradation, recycling, and cellular homeostasis, impacting signaling and metabolism. Analyzing the lysosomal proteome dynamics is key to understanding these roles, but the acidic environment and low abundance of lysosomes make proteomic analysis challenging. Herein, we developed a lysosome-localizable reactive diazirine molecule MDA and demonstrated its enhanced labeling capability in the lysosomal microenvironment. Furthermore, we introduced a novel microenvironment-specific enrichment (MiSE) strategy for profiling the lysosomal proteome, combining MDA-based labeling with affinity enrichment. We successfully applied MiSE to profile the lysosomal proteome in living SH-SY5Y cells, achieving coverage of 132 lysosome-annotated proteins. Moreover, by coupling MiSE with data-independent acquisition (DIA) analysis, we explored dynamic changes in the lysosomal proteome upon inhibition of the ubiquitin-proteasome system using four proteasome inhibitors. Our results reveal 117 UPS-inhibition-related lysosomal proteins, highlighting their involvement in stress response and cell cycle regulation. Notably, we observe distinct proteomic signatures for each inhibitor, suggesting unique mechanisms of lysosomal response to UPS inhibition. Therefore, MiSE offers a powerful tool for investigating the dynamic lysosomal proteome, providing insights into cellular homeostasis and disease pathogenesis. This approach holds significant potential for advancing the understanding of lysosomal function and developing novel therapeutic strategies.
    DOI:  https://doi.org/10.1021/acs.analchem.4c05797
  37. J Cell Sci. 2025 Feb 06. pii: jcs.263408. [Epub ahead of print]
    Mitophagy is induced in human engineered heart tissue after simulated ischemia and reperfusion.
    Mireia Nàger, Kenneth B Larsen, Zambarlal Bhujabal, Trine B Kalstad, Judith Rössinger, Truls Myrmel, Florian Weinberger, Asa B Birgisdottir.
      The paradoxical exacerbation of cellular injury and death during reperfusion remains a problem in treatment of myocardial infarction. Mitochondrial dysfunction plays a key role in the pathogenesis of myocardial ischemia and reperfusion injury. Dysfunctional mitochondria can be removed by mitophagy, culminating in their degradation within acidic lysosomes. Mitophagy is pivotal in maintaining cardiac homeostasis and emerges as a potential therapeutic target. Here we employ beating human engineered heart tissue (EHT) to assess mitochondrial dysfunction and mitophagy during ischemia and reperfusion simulation. Our data indicate adverse ultrastructural changes in mitochondrial morphology and impairment of mitochondrial respiration. Furthermore, our pH-sensitive mitophagy reporter EHTs, generated by CRISPR/Cas9 endogenous knock-in strategy, reveal induced mitophagy flux in EHTs after ischemia and reperfusion simulation. The induced flux requires the activity of the protein kinase ULK1, a member of the core-autophagy machinery. Our results demonstrate the applicability of the reporter EHTs for mitophagy assessment in a clinically relevant setting. Deciphering mitophagy in the human heart will facilitate development of novel therapeutic strategies.
    Keywords:  Engineered heart tissue; HiPSC; Ischemia-reperfusion; Mitochondria; Mitophagy
    DOI:  https://doi.org/10.1242/jcs.263408
  38. Genes Cells. 2025 Mar;30(2): e70004
    Vacuolar Sts1 Degradation-Induced Cytoplasmic Proteasome Translocation Restores Cell Proliferation.
    Noritaka Ohigashi, Shoshiro Hirayama, Hideki Yashiroda, Shigeo Murata.
      The proteasome is a large multicatalytic complex conserved across eukaryotes that regulates multiple cellular processes through the degradation of ubiquitinated proteins. The proteasome is predominantly localized to the nucleus in proliferating cells and translocates to the cytoplasm in the stationary phase. Sts1 reportedly plays a vital role in the nuclear import of the proteasome during proliferation in yeast Saccharomyces cerevisiae. However, the mechanisms underlying cytoplasmic translocation of the proteasome in the stationary phase remain unknown. Here, we showed that the ubiquitin ligase Hul5 promotes vacuolar sequestration of Sts1 in a catalytic activity-dependent manner and thus suppresses the nuclear import of the proteasome during the stationary phase. We further demonstrated that cytoplasmic translocation of the proteasome plays a vital role in the clearance of ubiquitinated protein aggregates, mitochondrial quality control, and resuming proliferation from cellular quiescence. Our results provide insights into the mechanisms and significance of the cytoplasmic localization of proteasomes in cellular quiescence.
    Keywords:  Hul5; Sts1; proteasome; quiescence; vacuole
    DOI:  https://doi.org/10.1111/gtc.70004
  39. Science. 2025 Feb 06.
    Structural pathway for PI3-kinase regulation by VPS15 in autophagy.
    Annan S I Cook, Minghao Chen, Thanh N Nguyen, Ainara Claveras Cabezudo, Grace Khuu, Shanlin Rao, Samantha N Garcia, Mingxuan Yang, Anthony T Iavarone, Xuefeng Ren, Michael Lazarou, Gerhard Hummer, James H Hurley.
      The class III phosphatidylinositol-3 kinase complexes I and II (PI3KC3-C1 and -C2) have vital roles in macroautophagy and endosomal maturation, respectively. We elucidated a structural pathway of enzyme activation through cryo-EM analysis of PI3KC3-C1. The inactive conformation of the VPS15 pseudokinase stabilizes the inactive conformation, sequestering its N-myristate in the N-lobe of the pseudokinase. Upon activation, the myristate is liberated such that the VPS34 lipid kinase catalyzes PI3P production on membranes. The VPS15 pseudokinase domain binds tightly to guanosine triphosphate (GTP), and stabilizes a web of interactions to autoinhibit the cytosolic complex and to promote the activation upon membrane binding. These findings show in atomistic detail how the VPS34 lipid kinase is activated in the context of a complete PI3K complex.
    DOI:  https://doi.org/10.1126/science.adl3787
  40. Neurosci Bull. 2025 Feb 05.
    Triple-Target Inhibition of Cholinesterase, Amyloid Aggregation, and GSK3β to Ameliorate Cognitive Deficits and Neuropathology in the Triple-Transgenic Mouse Model of Alzheimer's Disease.
    Junqiu He, Shan Sun, Hongfeng Wang, Zheng Ying, Kin Yip Tam.
      Alzheimer's disease (AD) poses one of the most urgent medical challenges in the 21st century as it affects millions of people. Unfortunately, the etiopathogenesis of AD is not yet fully understood and the current pharmacotherapy options are somewhat limited. Here, we report a novel inhibitor, Compound 44, for targeting cholinesterases, amyloid-β (Aβ) aggregation, and glycogen synthase kinase 3β (GSK-3β) simultaneously with the aim of achieving symptomatic relief and disease modification in AD therapy. We found that Compound 44 had good inhibitory effects on all intended targets with IC50s of submicromolar or better, significant neuroprotective effects in cell models, and beneficial improvement of cognitive deficits in the triple transgenic AD (3 × Tg AD) mouse model. Moreover, we showed that Compound 44 acts as an autophagy regulator by inducing nuclear translocation of transcription factor EB through GSK-3β inhibition, enhancing the biogenesis of lysosomes and elevating autophagic flux, thus ameliorating the amyloid burden and tauopathy, as well as mitigating the disease phenotype. Our results suggest that triple-target inhibition via Compound 44 could be a promising strategy that may lead to the development of effective therapeutic approaches for AD.
    Keywords:  Alzheimer’s disease; Amyloid-β aggregation; Autophagy; Cholinesterases; GSK-3β; Multi-targeted inhibitor
    DOI:  https://doi.org/10.1007/s12264-025-01354-y
  41. Cell Death Discov. 2025 Feb 01. 11(1): 37
    METTL3 regulates autophagy of hypoxia-induced cardiomyocytes by targeting ATG7.
    Linnan Li, Hao Cheng, Yufei Zhou, Di Zhao, Xiaoxue Zhang, Yajun Wang, Jianying Ma, Junbo Ge.
      N6-methyladenosine (m6A) mRNA modification is the most common mRNA internal modification in eukaryotes, which participates in a variety of biological processes. However, the role of m6A methylation in regulating autophagy induced by ischemia and hypoxia remains to be widely investigated. Here, we investigated the impact of METTL3, a key m6A methyltransferase, on the autophagy regulation in ischemic and hypoxic cardiomyocytes, as well as in mice following acute myocardial infarction (AMI). METTL3 negatively regulated autophagy in cardiomyocytes under ischemia and hypoxia conditions. Silencing METTL3 enhanced autophagy and mitigated cardiomyocyte injury, whereas overexpression of METTL3 exerted the opposite effect. Mechanistically, METTL3 methylated ATG7 mRNA, a crucial autophagy-related gene, leads to the recruitment of the m6A-binding protein YTHDF2. Subsequently, YTHDF2 facilitated the degradation of ATG7 mRNA, consequently inhibiting autophagy and exacerbating cellular damage. Our study shed light on the pivotal role of METTL3-mediated m6A modification in the regulation of autophagy during AMI, providing novel insights into the functional significance of m6A methylation and its regulatory mechanisms.
    DOI:  https://doi.org/10.1038/s41420-025-02320-3
  42. J Med Chem. 2025 Feb 05.
    Mitophagy in Neurodegenerative Diseases: Mechanisms of Action and the Advances of Drug Discovery.
    Panpan Yang, Wen Shuai, Xin Wang, Xiuying Hu, Min Zhao, Aoxue Wang, Yongya Wu, Liang Ouyang, Guan Wang.
      Neurodegenerative diseases (NDDs), such as Parkinson's disease (PD) and Alzheimer's disease (AD), are devastating brain diseases and are incurable at the moment. Increasing evidence indicates that NDDs are associated with mitochondrial dysfunction. Mitophagy removes defective or redundant mitochondria to maintain cell homeostasis, whereas deficient mitophagy accelerates the accumulation of damaged mitochondria to mediate the pathologies of NDDs. Therefore, targeting mitophagy has become a valuable therapeutic pathway for the treatment of NDDs. Several mitophagy modulators have been shown to ameliorate neurodegeneration in PD and AD. However, it remains to be further investigated for other NDDs. Here, we describe the mechanism and key signaling pathway of mitophagy and summarize the roles of defective mitophagy on the pathogenesis of NDDs. Further, we underline the development advances of mitophagy modulators for PD and AD therapy, discuss the therapeutic challenges and limitations of the existing modulators, and provide guidelines for mitophagy mechanism exploration and drug design.
    DOI:  https://doi.org/10.1021/acs.jmedchem.4c01779
  43. J Biol Chem. 2025 Feb 03. pii: S0021-9258(25)00104-8. [Epub ahead of print] 108257
    Aggregated proinsulin in pancreatic β-cells is degraded by the autophagy pathway.
    Yueh-Fu Madey, Samreen K Syed, Robert Daniel Van Horn, Annie R Pineros, Alexander M Efanov.
      Insulin, a critical metabolic hormone to maintain blood glucose homeostasis, is synthesized and folded in the endoplasmic reticulum (ER) of pancreatic β-cells as the insulin precursor proinsulin. Proinsulin misfolding and aggregation detected in diabetic β-cells induces ER stress and obstructs normal trafficking, processing, and secretion of insulin, which eventually can result in pancreatic β-cell dedifferentiation and death. We have developed quantitative methods to measure misfolded and aggregated proinsulin in β-cells by utilizing proinsulin oligomer specific ELISA and Proximity Ligation Assay (PLA) assays. Under conditions of induced ER stress, both assays detected significant accumulation of aggregated proinsulin in β-cells. Proinsulin aggregation was also observed in isolated pancreatic islets cultured at high glucose levels. Moreover, high glucose in β-cells downregulated expression of genes mediating clearance of misfolded proteins from the secretory pathway through ER autophagy and ER-associated degradation (ERAD). Inhibition of autophagy in β-cells induced strong induction of misfolded proinsulin accumulation, whereas ERAD inhibition was not effective in generating proinsulin aggregates. Finally, we observed subcellular colocalization of aggregated proinsulin with protein markers of autophagosomes. Our results indicate that autophagy controls degradation of aggregated misfolded proinsulin under conditions of hyperglycemia and diabetes.
    Keywords:  ER-associated degradation; autophagy; pancreatic islets; proinsulin; protein aggregation
    DOI:  https://doi.org/10.1016/j.jbc.2025.108257
  44. Med Oncol. 2025 Feb 03. 42(3): 62
    Autophagy induced by metabolic processes leads to solid tumor cell metastatic dormancy and recurrence.
    Saeid Ferdousmakan, Dorrin Mansourian, Fatemeh Sadat Seyedi Asl, Zeinab Fathi, Fahimeh Maleki-Sheikhabadi, Mohsen Nabi Afjadi, Hamidreza Zalpoor.
      A crucial cellular mechanism that has a complex impact on the biology of cancer, particularly in solid tumors, is autophagy. This review explores how metabolic processes trigger autophagy, which helps metastatic tumor cells go dormant and recur. During metastasis, tumor cells frequently encounter severe stressors, such as low oxygen levels and nutritional deprivation, which causes them to activate autophagy as a survival tactic. This process allows cancer stem cells (CSCs) to withstand severe conditions while also preserving their features. After years of dormancy, dormant disseminated tumor cells (DTCs) may reappear as aggressive metastatic cancers. The capacity of autophagy to promote resistance to treatments and avoid immune detection is intimately related to this phenomenon. According to recent research, autophagy promotes processes, such as the epithelial-to-mesenchymal transition (EMT) and helps build a pre-metastatic niche, which makes treatment strategies more challenging. Autophagy may be a promising therapeutic target because of its dual function as a tumor suppressor in early-stage cancer and a survival promoter in advanced stages. To effectively treat metastatic diseases, it is crucial to comprehend how metabolic processes interact with autophagy and affect tumor behavior. In order to find novel therapeutic approaches that can interfere with these processes and improve patient outcomes, this study highlights the critical need for additional investigation into the mechanisms by which autophagy controls tumor dormancy and recurrence.
    Keywords:  Autophagy; Cancer stem cell (CSC); Dormant disseminated tumor cells (DTCs); Metastatic dormancy; Recurrence
    DOI:  https://doi.org/10.1007/s12032-025-02607-6
  45. Stem Cell Res Ther. 2025 Feb 04. 16(1): 38
    Unraveling the function of TSC1-TSC2 complex: implications for stem cell fate.
    Shuang Wang, Ruishuang Ma, Chong Gao, Yu-Nong Tian, Rong-Gui Hu, Han Zhang, Lan Li, Yue Li.
       BACKGROUND: Tuberous sclerosis complex is a genetic disorder caused by mutations in the TSC1 or TSC2 genes, affecting multiple systems. These genes produce proteins that regulate mTORC1 activity, essential for cell function and metabolism. While mTOR inhibitors have advanced treatment, maintaining long-term therapeutic success is still challenging. For over 20 years, significant progress has linked TSC1 or TSC2 gene mutations in stem cells to tuberous sclerosis complex symptoms.
    METHODS: A comprehensive review was conducted using databases like Web of Science, Google Scholar, PubMed, and Science Direct, with search terms such as "tuberous sclerosis complex," "TSC1," "TSC2," "stem cell," "proliferation," and "differentiation." Relevant literature was thoroughly analyzed and summarized to present an updated analysis of the TSC1-TSC2 complex's role in stem cell fate determination and its implications for tuberous sclerosis complex.
    RESULTS: The TSC1-TSC2 complex plays a crucial role in various stem cells, such as neural, germline, nephron progenitor, intestinal, hematopoietic, and mesenchymal stem/stromal cells, primarily through the mTOR signaling pathway.
    CONCLUSIONS: This review aims shed light on the role of the TSC1-TSC2 complex in stem cell fate, its impact on health and disease, and potential new treatments for tuberous sclerosis complex.
    Keywords:  Mammalian target of rapamycin; Stem cell; Tuberous sclerosis complex
    DOI:  https://doi.org/10.1186/s13287-025-04170-3
  46. Open Biol. 2025 Feb;15(2): 240291
    Whole organism and tissue-specific analysis of pexophagy in Drosophila.
    Francesco G Barone, Marco Marcello, Sylvie Urbé, Natalia Sanchez-Soriano, Michael J Clague.
      Peroxisomes are essential organelles involved in critical metabolic processes in animals such as fatty acid oxidation, ether phospholipid production and reactive oxygen species detoxification. We have generated transgenic Drosophila melanogaster models expressing fluorescent reporters for the selective autophagy of peroxisomes, a process known as pexophagy. We show that these reporters are colocalized with a peroxisomal marker and that they can reflect pexophagy induction by iron chelation and inhibition by depletion of the core autophagy protein Atg5. Using light sheet microscopy, we have been able to obtain a global overview of pexophagy levels across the entire organism at different stages of development. Tissue-specific control of pexophagy is exemplified by areas of peroxisome abundance but minimal pexophagy, observed in clusters of oenocytes surrounded by epithelial cells where pexophagy is much more evident. Enhancement of pexophagy was achieved by feeding flies with the iron chelator deferiprone, in line with past results using mammalian cells. Specific drivers were used to visualize pexophagy in neurons, and to demonstrate that specific depletion in the larval central nervous system of Hsc70-5, the Drosophila homologue of the chaperone HSPA9/mortalin, led to a substantial elevation in pexophagy.
    Keywords:  Drosophila; Hsc70-5; mortalin; neurons; peroxisomes; pexophagy
    DOI:  https://doi.org/10.1098/rsob.240291
  47. Mol Cell Biol. 2025 Feb 02. 1-17
    Kinase Inhibitor-Induced Cell-Type Specific Vacuole Formation in the Absence of Canonical ATG5-Dependent Autophagy Initiation Pathway.
    Susan Jose, Himanshi Sharma, Janki Insan, Khushboo Sharma, Varun Arora, Sameera Puranapanda, Sonam Dhamija, Nabil Eid, Manoj B Menon.
      Pyridinyl-imidazole class p38 MAPKα/β (MAPK14/MAPK11) inhibitors including SB202190 have been shown to induce cell-type specific defective autophagy resulting in micron-scale vacuole formation, cell death, and tumor suppression. We had earlier shown that this is an off-target effect of SB202190. Here we provide evidence that this vacuole formation is independent of ATG5-mediated canonical autophagosome initiation. While SB202190 interferes with autophagic flux in many cell lines parallel to vacuolation, autophagy-deficient DU-145 cells and CRISPR/Cas9 gene-edited ATG5-knockout A549 cells also undergo vacuolation upon SB202190 treatment. Late-endosomal GTPase RAB7 colocalizes with these compartments and RAB7 GTP-binding is essential for SB202190-induced vacuolation. A screen for modulators of SB202190-induced vacuolation revealed molecules including multi-kinase inhibitor sorafenib as inhibitors of vacuolation and sorafenib co-treatment enhanced cytotoxicity of SB202190. Moreover, VE-821, an ATR inhibitor was found to phenocopy the cell-type specific vacuolation response of SB202190. To identify the factors determining the cell-type specificity of vacuolation induced by SB-compounds and VE-821, we compared the transcriptomics data from vacuole-forming and non-vacuole-forming cancer cell lines and identified a gene expression signature that may define sensitivity of cells to these small-molecules. Further analyses using small molecule tools and the gene signature discovered here, could reveal novel mechanisms regulating this interesting anti-cancer phenotype.
    Keywords:  Autophagy; RAB7; SB202190; VE-821; kinase inhibitor
    DOI:  https://doi.org/10.1080/10985549.2025.2454421
  48. Mol Neurodegener. 2025 Feb 04. 20(1): 15
    Cellular senescence induced by cholesterol accumulation is mediated by lysosomal ABCA1 in APOE4 and AD.
    Shaowei Wang, Boyang Li, Jie Li, Zhiheng Cai, Cristelle Hugo, Yi Sun, Lu Qian, Julia Tcw, Helena C Chui, Dante Dikeman, Isaac Asante, Stan G Louie, David A Bennett, Zoe Arvanitakis, Alan T Remaley, Bilal E Kerman, Hussein N Yassine.
       BACKGROUND: Cellular senescence, a hallmark of aging, has been implicated in Alzheimer's disease (AD) pathogenesis. Cholesterol accumulation is known to drive cellular senescence; however, its underlying mechanisms are not fully understood. ATP-binding cassette transporter A1 (ABCA1) plays an important role in cholesterol homeostasis, and its expression and trafficking are altered in APOE4 and AD models. However, the role of ABCA1 trafficking in cellular senescence associated with APOE4 and AD remains unclear.
    METHODS: We examined the association between cellular senescence and ABCA1 expression in human postmortem brain samples using transcriptomic, histological, and biochemical analyses. Unbiased proteomic screening was performed to identify the proteins that mediate cellular ABCA1 trafficking. We created ABCA1 knock out cell lines and mouse models to validate the role of ABCA1 in cholesterol-induced mTORC1 activation and senescence. Additionally, we used APOE4-TR mice and induced pluripotent stem cell (iPSC) models to explore cholesterol-ABCA1-senescence pathways.
    RESULTS: Transcriptomic profiling of the human dorsolateral prefrontal cortex from the Religious Order Study/Memory Aging Project (ROSMAP) cohort revealed the upregulation of cellular senescence transcriptome signatures in AD, which correlated with ABCA1 expression and oxysterol levels. Immunofluorescence and immunoblotting analyses confirmed increased lipofuscin-stained lipids and ABCA1 expression in AD brains and an association with mTOR phosphorylation. Discovery proteomics identified caveolin-1, a sensor of cellular cholesterol accumulation, as a key promoter of ABCA1 endolysosomal trafficking. Greater caveolin-1 expression was observed in APOE4-TR mouse models and AD human brains. Oxysterol induced mTORC1 activation and senescence were regulated by ABCA1 lysosomal trapping. Treatment of APOE4-TR mice with cyclodextrin reduced brain oxysterol levels, ABCA1 lysosome trapping, mTORC1 activation, and attenuated senescence and neuroinflammation markers. In human iPSC-derived astrocytes, the reduction of cholesterol by cyclodextrin attenuated inflammatory responses.
    CONCLUSIONS: Oxysterol accumulation in APOE4 and AD induced ABCA1 and caveolin-1 expression, contributing to lysosomal dysfunction and increased cellular senescence markers. This study provides novel insights into how cholesterol metabolism accelerates features of brain cellular senescence pathway and identifies therapeutic targets to mitigate these processes.
    Keywords:  ABCA1; Alzheimer’s disease; Caveolin-1; Cholesterol; Lysosome; Senescence
    DOI:  https://doi.org/10.1186/s13024-025-00802-7
  49. Spectrochim Acta A Mol Biomol Spectrosc. 2025 Jan 31. pii: S1386-1425(25)00137-4. [Epub ahead of print]332 125831
    Aggregation-induced emission-twisted intramolecular charge transfer-activated fluorescent probe for analyzing mitochondrial viscosity in cells and zebrafish.
    Shu-Long He, Guo-Bin Wang, Xue-Li Cheng, Lin-Lin Han, Wei Pan, Han-Yang Zou, Shi-Li Shen, Xian-Hong Pang, Yan Zhu.
      Mitochondria are crucial energy-supplying organelles that support cellular activities and play vital roles in cell metabolism, aging, autophagy, and apoptosis. Abnormal viscosity can alter the mitochondrial microenvironment, disrupt normal mitochondrial function, and lead to disease. To address this, we designed and developed two aggregation-induced emission-twisted intramolecular charge transfer fluorescent probes, namely, (E)-1,1,3-trimethyl-2-(4-(1,2,2-triphenylvinyl)styryl)-1H-benzo[e]indol-3-ium (HSL-1) and (E)-2-(4-(di-p-tolylamino)styryl)-1,3,3-trimethyl-1H-benzo[e]indol-3-ium (HSL-2). In vitro fluorescence detection revealed that both HSL-1 and HSL-2 were sensitive to viscosity and demonstrated a strong log-linear relationship, with linear coefficients of 0.982 and 0.980, respectively. Notably, the responses of HSL-1 and HSL-2 to viscosity changes were unaffected by pH, polarity, or interfering ions. HSL-1 exhibited stronger resistance to background interference than HSL-2 and significantly enhanced fluorescence intensity; thus, it was selected for cell experiments and animal fluorescence intensity assessments. Furthermore, HSL-1 showed excellent biocompatibility, enabling real-time detection of mitochondrial viscosity changes and identification of viscosity abnormalities triggered by mitophagy in HeLa cells. It could also monitor changes in mitochondrial viscosity in zebrafish. In conclusion, HSL-1 is a valuable tool for studying viscosity and understanding diseases associated with abnormal mitochondrial viscosity.
    Keywords:  Aggregation-induced emission; Mitochondria; Viscosity; Zebrafish
    DOI:  https://doi.org/10.1016/j.saa.2025.125831
  50. Heliyon. 2025 Feb 15. 11(3): e42031
    USP14 is crucial for proteostasis regulation and α-synuclein degradation in human SH-SY5Y dopaminergic cells.
    Vignesh Srinivasan, Rabah Soliymani, Larisa Ivanova, Ove Eriksson, Nina Peitsaro, Maciej Lalowski, Mati Karelson, Dan Lindholm.
      Ubiquitin specific protease-14 (USP14) is critical for controlling proteostasis disturbed in human disorders, including Parkinson's disease (PD). Here we investigated USP14 in the regulation of α-synuclein (α-syn) degradation via the proteasome and autophagy. α-Syn and pS129 α-syn were elevated in USP14 gene-deleted SH-SY5Y dopaminergic cells with decreased proteasome activity. However, autophagy and coordinated lysosomal expression and regulation pathways were elevated in USP14 lacking cells with higher levels of the transcription factor TFEB. There was an increase in reactive oxidative species (ROS) and elongated mitochondria in USP14 deficient cells and counteracting oxidative stress decreased α-syn levels. Phosphoproteomics revealed that USP14 is phosphorylated at residue S143 that reduces its binding to the proteasome. Re-expression of wild-type and phospho-mimetic S143D-USP14 mutant lowered ROS and α-syn levels in USP14 lacking cells. USP14 is a promising factor to consider in PD to target α-syn through its regulation of proteasomes and oxidative stress in dopaminergic neurons.
    Keywords:  Autophagy; Oxidative stress; Phosphorylation; Proteasome; USP14; pS129 α-Synuclein; α-Synuclein
    DOI:  https://doi.org/10.1016/j.heliyon.2025.e42031
  51. Biofactors. 2025 Jan-Feb;51(1):51(1): e70004
    The in vitro and in vivo skin-whitening activity of Ectoine through enhanced autophagy in melanocytes and keratinocytes and zebrafish model.
    Wei-Chen Jane, Siang-Jyun Chen, Jhih-Hsuan Hseu, Xuan-Zao Chen, Sudhir Pandey, Hsueh-Wei Chang, Hsin-Ling Yang, You-Cheng Hseu, Yung-Luen Yu.
      Ectoine, a natural bacterial osmolyte, suppressed UVA irradiated-α-melanocyte stimulating hormone (MSH) stimulated melanogenesis through antioxidant Nrf2 pathways in human keratinocytes; however, the underlying skin whitening mechanisms were not elucidated. The depigmenting efficiency of Ectoine (0-400 μM) through antimelanogenesis and melanin degradation by autophagy promotion was investigated in melanoma (B16F10) and melanin-feeding keratinocyte (HaCaT) cells and in vivo zebrafish model. MTT assay, Western blotting, GFP-LC3 puncta, AVO formation, melanin assay, immunofluorescence staining, TEM techniques, siLC3 transfection, and zebrafish model were utilized. Ectoine-induced autophagy in B16F10 and HaCaT cells was shown by enhanced LC3-II accumulation, autophagosome GFP-LC3 puncta, autolysosome AVOs formation, ATG4B downregulation, and Beclin-1/Bcl-2 dysregulation. The immunoprecipitation data revealed that Ectoine increased the association between LC3-II and p62 proteins in B16F10 and HaCaT cells. Importantly, antioxidant NAC pretreatment antagonized the Ectoine-induced ATG4B diminution in B16F10 and HaCaT cells. Ectoine inhibited melanogenesis by suppressing melanosome gp100, tyrosinase, TRP-1/-2, and/or melanin formation via autophagy in α-MSH-stimulated B16F10 and melanin-feeding HaCaT cells. TEM findings displayed that Ectoine increased melanosome-engulfing autophagosomes and autolysosomes in α-MSH-stimulated B16F10 and melanin-feeding HaCaT cells. Ectoine-inhibited melanogenesis in α-MSH-stimulated B16F10 cells and melanin-feeding HaCaT cells was reversed by pretreatment with the autophagy inhibitor 3-MA or LC3 silencing. In vivo study demonstrated that Ectoine (5 mM) suppressed endogenous body pigmentation by antimelanogenesis and melanin degradation through autophagy induction in a zebrafish model. The in vitro and in vivo study demonstrated that Ectoine inhibits melanogenesis and enhances melanin degradation by triggering autophagy. Ectoine could be utilized as a whitening ingredient in cosmetic formulations.
    Keywords:  Ectoine; antimelanogenesis; autophagy; melanin degradation; zebrafish
    DOI:  https://doi.org/10.1002/biof.70004
  52. J Cell Biol. 2025 Apr 03. pii: e202405002. [Epub ahead of print]224(4):
    VPS41 recruits biosynthetic LAMP-positive vesicles through interaction with Arl8b.
    Paolo Sanzà, Jan van der Beek, Derk Draper, Cecilia de Heus, Tineke Veenendaal, Corlinda Ten Brink, Ginny G Farías, Nalan Liv, Judith Klumperman.
      Vacuolar protein sorting 41 (VPS41), a component of the homotypic fusion and protein sorting (HOPS) complex for lysosomal fusion, is essential for the trafficking of lysosomal membrane proteins via lysosome-associated membrane protein (LAMP) carriers from the trans-Golgi network (TGN) to endo/lysosomes. However, the molecular mechanisms underlying this pathway and VPS41's role herein remain poorly understood. Here, we investigated the effects of ectopically localizing VPS41 to mitochondria on LAMP distribution. Using electron microscopy, we identified that mitochondrial-localized VPS41 recruited LAMP1- and LAMP2A-positive vesicles resembling LAMP carriers. The retention using selective hooks (RUSH) system further revealed that newly synthesized LAMPs were specifically recruited by mitochondrial VPS41, a function not shared by other HOPS subunits. Notably, we identified the small GTPase Arl8b as a critical factor for LAMP carrier trafficking. Arl8b was present on LAMP carriers and bound to the WD40 domain of VPS41, enabling their recruitment. These findings reveal a unique role of VPS41 in recruiting TGN-derived LAMP carriers and expand our understanding of VPS41-Arl8b interactions beyond endosome-lysosome fusion, providing new insights into lysosomal trafficking mechanisms.
    DOI:  https://doi.org/10.1083/jcb.202405002
  53. J Biol Chem. 2025 Feb 03. pii: S0021-9258(25)00100-0. [Epub ahead of print] 108253
    Transmembrane Parkinson's Disease mutation of PINK1 leads to altered mitochondrial anchoring.
    Raelynn Brassard, Elena Arutyunova, Emmanuella Takyi, L Michel Espinoza-Fonseca, Howard Young, Nicolas Touret, M Joanne Lemieux.
      Parkinson's disease (PD) is a devastating neurodegenerative disease resulting from the death of dopaminergic neurons in the substantia nigra pars compacta of the midbrain. Familial and sporadic forms of the disease have been linked to mitochondrial dysfunction. Pathology has been identified with mutations in the PARK6 gene encoding PTEN-induced kinase 1 (PINK1), a quality control protein in the mitochondria. Disease-associated mutations at the transmembrane region of PINK1 protein were predicted to disrupt the cleavage of the transmembrane region by the PARL protease at the inner mitochondrial membrane. Here, using microscopy, kinetic analysis and molecular dynamic simulations, we analyzed 3 PD associated TM mutations; PINK1-C92F, PINK1-R98W and PINK1-I111S, and found that mitochondrial localization and cleavage by the PARL protease were not significantly impaired. However, clearance of hydrolyzed PINK1-R98W appears to be compromised due to altered positioning of the protein in the outer mitochondrial membrane, preventing association with TOM complexes and slowing cleavage by PARL. This single amino acid change slows degradation of proteolyzed PINK1, increasing its accumulation at the outer mitochondrial membrane and resulting in increased mitophagy and decreased mitochondrial content among these cells.
    Keywords:  MD Simulation; PARL; Parkinson’s Disease; Proteostasis; Rhomboid Protease
    DOI:  https://doi.org/10.1016/j.jbc.2025.108253
  54. JCI Insight. 2025 Feb 06. pii: e183560. [Epub ahead of print]
    GADD45α is a direct target of TFEB and contributes to tacrolimus-induced chronic nephrotoxicity.
    Ping Gao, Xinwei Cheng, Maochang Liu, Hui Peng, Guodong Li, Tianze Shang, Jianqiao Wang, Qianyan Gao, Chenglong Zhu, Zhenpeng Qiu, Chengliang Zhang.
      Tacrolimus-induced chronic nephrotoxicity (TICN) hinders its long-term use, but its mechanism remains unclear. Tacrolimus exerts its pharmacological effect by inhibiting calcineurin and its substrate NFAT. Whether the inhibition of other calcineurin substrates is related to TICN remains to be explored. Transcription factor EB (TFEB), a substrate of calcineurin, plays a crucial role in various homeostasis. Herein, we found that tacrolimus inhibited TFEB nuclear translocation and activity in mouse kidneys and HK-2 cells. Then, TFEB gain- and loss-of-function rescued the effect of tacrolimus in HK-2 cells. Furthermore, TFEB activation both by phosphorylation sites mutation and agonist rescued TICN in mice. To elucidate the mechanism of TFEB, we analyzed ChIP-seq data. Growth arrest and DNA damage-inducible 45α (GADD45α) was identified as a transcriptional target of TFEB via chromatin immunoprecipitation and dual luciferase reporter assays. And then we revealed that GADD45α overexpression rescued DNA damage and kidney injury caused by tacrolimus or TFEB knockdown in vitro, and vise versa. The protective effect of GADD45α against TICN and DNA damage was further demonstrated by overexpressing it in mice. In conclusion, the persistent inhibition of TFEB-GADD45α pathway by tacrolimus contributes to TICN. This study identifies a specific target for intervention of TICN.
    Keywords:  Nephrology; Therapeutics; Toxicology
    DOI:  https://doi.org/10.1172/jci.insight.183560
  55. Exp Gerontol. 2025 Feb 03. pii: S0531-5565(25)00025-7. [Epub ahead of print]201 112697
    Autophagy inhibitor 3-methyladenine mitigates the severity of colitis in aged mice by inhibiting autophagy.
    Ailing Liu, Hongying Wang, Hong Lv, Hong Yang, Yue Li, Jiaming Qian.
       BACKGROUND: The elderly ulcerative colitis (UC) patients pose unique challenges due to their comorbidities, diminished functional capacity, and heightened risk of treatment-related complications. Thus, finding a safe and effective treatment for this age group is crucial.
    AIM: This study investigates the role of autophagy in the pathogenesis of UC in young and elderly patients, and explores the therapeutic potential and mechanisms of autophagy modulators in aged mice with dextran sulfate sodium (DSS)-induced colitis.
    METHODS: Colonic biopsies were collected from young and old UC patients as well as comparable healthy subjects. Young (6-8 weeks) and aged (56 weeks) C57BL/6 mice were treated with DSS to induce acute colitis model. The autophagy inhibitor 3-methyladenine was administered intraperitoneally to aged DSS-induced mice. The autophagy activity was detected by the protein expressions of LC3B-II, p62 and ATG5 by western blot and immunohistochemistry. The levels of TNF -α, IL-6, CCL4, CXCL12 and CD86 were measured by qRT-PCR. The transcriptional activity of NF-κB was measured by electrophoretic mobility shift assay (EMSA).
    RESULTS: Increased autophagy activity was observed in aged DSS-induced mice. Treatment with 3-methyladenine suppressed autophagy in intestinal epithelial cells (IECs) and alleviated colitis severity. Additionally, 3-methyladenine reduced macrophage recruitment, decreased IL-6 levels, and inhibited NF-κB signaling, thereby mitigating inflammation.
    CONCLUSION: Significant differences in autophagy activity were identified between young and aged DSS-induced mice. These findings underscore the potential therapeutic benefits of autophagy inhibition in elderly UC patients.
    Keywords:  Cell autophagy; Inflammation; Inflammatory bowel disease; Macrophagy; Senescence
    DOI:  https://doi.org/10.1016/j.exger.2025.112697
  56. Dev Cell. 2025 Feb 03. pii: S1534-5807(24)00779-2. [Epub ahead of print]60(3): 337-339
    Autophagy-dependent changes in alternative splicing bias translation toward inflammation in senescent cells.
    Anson Ming Yan Lee, Anne Schreiber.
      Despite limited translational capacity, senescent cells trigger inflammation by upregulating the translation and secretion of proinflammatory factors. In this issue of Developmental Cell, Kim et al. identify that altered autophagy and SFPQ-dependent EIF4H splicing during senescence redirects translation to promote inflammation, informing therapeutic strategies for cancer and other age-related diseases.
    DOI:  https://doi.org/10.1016/j.devcel.2024.12.040
  57. bioRxiv. 2025 Jan 22. pii: 2025.01.21.634088. [Epub ahead of print]
    Inhibition of SQSTM1/p62 oligomerization and Keap1 sequestration by the Cullin-3 adaptor SHKBP1.
    Lin Luan, Xiaofu Cao, Jeremy M Baskin.
      SQSTM1/p62 is a master regulator of the autophagic and ubiquitination pathways of protein degradation and the antioxidant response. p62 functions in these pathways via reversible assembly and sequestration of additional factors into cytoplasmic phase-separated structures termed p62 bodies. The physiological roles of p62 in these various pathways depends on numerous mechanisms for regulating p62 body formation and dynamics that are incompletely understood. Here, we identify a new mechanism for regulation of p62 oligomerization and incorporation into p62 bodies by SHKBP1, a Cullin-3 E3 ubiquitin ligase adaptor, that is independent of its potential functions in ubiquitination. We map a SHKBP1-p62 protein-protein interaction outside of p62 bodies that limits p62 assembly into p62 bodies and affects the antioxidant response by preventing sequestration and degradation of Keap1. These studies provide a non-ubiquitination-based mechanism for an E3 ligase adaptor in regulating p62 phase separation and cellular responses to oxidative stress.
    DOI:  https://doi.org/10.1101/2025.01.21.634088
  58. Front Cell Dev Biol. 2025 ;13 1508714
    The Batten disease gene Cln3 is required for the activation of intestinal stem cell during regeneration via JAK/STAT signaling in Drosophila.
    Zihua Yu, Jinhua Yan, Zhiming Liu, Haiyan Wang, Guanzheng Luo, Haiyang Chen.
      CLN3 mutation causes Juvenile neuronal ceroid lipofuscinosis (JNCL, also known as Batten disease), an early onset neurodegenerative disorder. Patients who suffer from Batten disease often die at an early age. However, the mechanisms underlying how CLN3 loss develops Batten disease remain largely unclear. Here, using Drosophila midgut system, we demonstrate that Drosophila Cln3 has no effect on midgut homeostasis maintaince, including cellular component, intestinal stem cells (ISCs) proliferation and differentiation, but is necessary for ISC activation upon tissue damage. Cell type-specific Gal4 screening reveals that the failure of ISC activation during regeneration caused by Cln3 loss is ISC-autonomous. Through genetic analyses, we elucidate that JAK/STAT signaling in ISCs is not activated with Cln3 depletion upon tissue damage, and functions downstream of Cln3. Our study provides a potential mechanism underlying the development of CLN3-mediated Batten disease at cellular level.
    Keywords:  Batten disease; CLN3; Drosophila; JAK/STAT signaling pathway; intestinal stem cell (ISC)
    DOI:  https://doi.org/10.3389/fcell.2025.1508714
  59. Aging Cell. 2025 Feb 05. e14450
    Novel TORC1 inhibitor Ecl1 is regulated by phosphorylation in fission yeast.
    Hokuto Ohtsuka, Sawa Kawai, Yurika Ito, Yuka Kato, Takafumi Shimasaki, Kazuki Imada, Yoko Otsubo, Akira Yamashita, Emi Mishiro-Sato, Keiko Kuwata, Hirofumi Aiba.
      Extender of chronological lifespan 1 (Ecl1) inhibits target of rapamycin complex 1 (TORC1) and is necessary for appropriate cellular responses to various stressors, such as starvation, in fission yeast. However, little is known about the effect of posttranslational modifications on Ecl1 regulation. Thus, we investigated the phosphorylation levels of Ecl1 extracted from yeast under conditions of sulfur or metal starvation. Mass spectrometry analysis revealed that Ecl1 was phosphorylated at Thr7, and the level was decreased by starvation. The phosphorylation-mimetic mutation of Thr7 significantly reduced the effects of Ecl1-induced cellular responses to starvation, suggesting that Ecl1 function was suppressed by Thr7 phosphorylation. By contrast, regardless of starvation exposure, TORC1 was significantly suppressed, even when Thr7 phosphorylation-mimetic Ecl1 was overexpressed. This indicated that Ecl1 suppressed TORC1 regardless of Thr7 phosphorylation. We newly identified that Ecl1 physically interacted with TORC1 subunit RAPTOR (Mip1). Based on these evidences, we propose that, Ecl1 has dual functional modes: quantity-dependent TORC1 inhibition and Thr7 phosphorylation-dependent control of cellular function.
    Keywords:  Ecl1; TORC1; fission yeas; phosphorylation; starvation
    DOI:  https://doi.org/10.1111/acel.14450
  60. J Transl Med. 2025 Feb 04. 23(1): 156
    Staphylococcus aureus induces mitophagy via the HDAC11/IL10 pathway to sustain intracellular survival.
    Yaji Yang, Haotian Zhou, Feilong Li, Yanhao Zhang, Jianye Yang, Yidong Shen, Ning Hu, Quanming Zou, Leilei Qin, Hao Zeng, Wei Huang.
       BACKGROUND: The immune evasion and prolonged survival of Staphylococcus aureus (S. aureus) within macrophages are key factors contributing to the difficulty in curing osteomyelitis. Although macrophages play a vital role as innate immune cells, the mechanisms by which S. aureus survives within them and suppresses host immune functions remain incompletely understood.
    METHODS: This study employed confocal microscopy, flow cytometry, ELISA, and siRNA technology to assess the survival capacity of S. aureus within macrophages and the impact of inflammatory cytokines on its persistence. Proteomics was used to investigate the potential mechanisms and differential proteins involved in S. aureus intracellular survival. Additionally, confocal microscopy, flow cytometry, Mdivi-1 intervention, and Western blot were utilized to validate the role of mitophagy in supporting S. aureus survival. The study further explored how the HDAC11/IL10 axis enhances mitophagy to promote intracellular S. aureus survival by using HDAC11 overexpression, siRNA, and rapamycin intervention combined with confocal microscopy and flow cytometry.
    RESULTS: The findings demonstrated that IL10 promotes mitophagy to clear mitochondrial reactive oxygen species (mtROS), thereby enhancing the intracellular survival of S. aureus within macrophages. Additionally, we discovered that the transcriptional repressor of IL10, HDAC11, was significantly downregulated during S. aureus infection. Overexpression of HDAC11 and the use of the autophagy activator rapamycin further validated that the HDAC11/IL10 axis regulates mitophagy via the mTOR pathway, which is essential for supporting S. aureus intracellular survival.
    CONCLUSION: This study reveals that S. aureus enhances IL10 production by inhibiting HDAC11, thereby promoting mitophagy and mtROS clearance, which supports its survival within macrophages. These findings offer new insights into the intracellular survival mechanisms of S. aureus and provide potential therapeutic approaches for the clinical management of osteomyelitis.
    Keywords:  Histone deacetylase 11; Interleukin 10; Intracellular survival; Macrophage; Mitochondrial reactive oxygen species; Mitophagy; Staphylococcus aureus
    DOI:  https://doi.org/10.1186/s12967-025-06161-7
  61. Int J Biol Sci. 2025 ;21(3): 1259-1274
    TRIM32 promotes neuronal ferroptosis by enhancing K63-linked ubiquitination and subsequent p62-selective autophagic degradation of GPX4.
    Xin Zhou, Yuqing Zhao, Shixue Huang, Haoming Shu, Yinuo Zhang, Haiyuan Yang, Yilong Ren, Xuhui Zhou, Wei Liu, Tengfei Song, Jianquan Zhao, Jun Ma.
      Ferroptosis, characterized by iron-dependent phospholipid peroxidation, is recognized as one of the cell death pathways activated following spinal cord injury (SCI). However, the precise regulatory mechanisms governing this process remain poorly understood. Here, this study identified TRIM32, an E3 ubiquitin ligase, as a key enhancer of neuronal ferroptosis. TRIM32 promoted neuronal ferroptosis by accelerating the degradation of GPX4, which is an essential inhibitor of ferroptosis. Conditional deletion of Trim32 in neurons markedly inhibited neuronal ferroptosis and promoted neuronal survival, eventually improving mouse locomotor functional recovery after SCI. However, overexpression of Trim32 showed aggravated neuronal loss and poor behavioral function, which could be attenuated by ferroptosis inhibitor Liproxstatin-1. Mechanistically, TRIM32 interacted with GPX4, promoted K63-linked ubiquitination modification of GPX4 at K107, thus enhanced p62-dependent autophagic degradation of GPX4. Moreover, ROS-ATM-Chk2 signaling pathway phosphorylates TRIM32 at S55, further contributing to GPX4 ubiquitination and degradation and subsequent neuronal ferroptosis after SCI, suggesting a positive feedback loop between ROS and TRIM32. Clinically, lipid peroxidation was significantly promoted in patients with SCI. These findings reveal that TRIM32 functions as a neuronal ferroptosis enhancer which is detrimental to neuronal survival and locomotor functional recovery in mice after SCI by promoting K63-linked ubiquitination and subsequent p62-dependent autophagic degradation of GPX4, suggesting a promising therapeutic target for SCI.
    Keywords:  GPX4; TRIM32; autophagic degradation; neuronal ferroptosis; ubiquitination
    DOI:  https://doi.org/10.7150/ijbs.106690
  62. Mol Neurobiol. 2025 Feb 07.
    OSBP Participates in Neural Damage Repair by Regulating Lysosome Transport Under Oxidative Stress.
    Maoxing Fei, Shiqiao Luo, Chaochao Gao, Xiwen Huang, Lan Wang, Tianle Jin, Mingda Liu, Mengliang Zhou, Handong Wang.
      Oxidative stress is a major pathological factor in acute brain injury, such as traumatic brain injury (TBI). As highly branched cells, the transport of lysosomes plays a crucial role in neuronal homeostasis. However, the effects and mechanisms of oxidative damage on axonal lysosome transport remain unknown. In this study, we demonstrated that the downregulation of the membrane lipid orchestrator oxysterol-binding protein (OSBP) induced by oxidative stress alters the subcellular distribution of lysosomes in neurons through regulating lysosomal phosphatidylinositol-4-monophosphate (PI(4)P)/phosphatidylinositol-3-monophosphate (PI(3)P) contents, thus disrupting lysosomal transport. The results of the cell experiments confirmed the occurrence of an autophagic pressure burst, disordered anterograde lysosome transport, and an imbalance in the PI(4)P/PI(3)P ratio in neurons after H2O2 treatment. Mechanistically, oxidative damage reduced neuronal OSBP protein levels, thus contributing to lysosomal PI(4)P storage. Furthermore, a protein‒liposome binding assay revealed that compared with liposomes containing PI(4)P, liposomes containing PI(3)P or cholesterol presented decreased coprecipitation of Arl8. The overexpression of OSBP restored the PI(4)P/PI(3)P content, improved the binding ability of Arl8 to bind to lysosomes, increased lysosome localization in neurites, and promoted axonal injury repair. Finally, overexpression of neuronal OSBP through adeno-associated virus intervention in vivo alleviated dendritic damage and improved the neurological function of mice with TBI. Taken together, these findings suggest that disturbance of OSBP induced by oxidative stress results in abnormal lysosomal distribution and contributes to neuronal malfunction in TBI, and OSBP could be a potential target to promote neuronal repair and regeneration by regulating lysosomal lipid composition and axonal localization.
    Keywords:  Anterograde transport; Lysosome; Oxidative stress; Oxysterol-binding protein; Traumatic brain injury
    DOI:  https://doi.org/10.1007/s12035-025-04698-8
  63. Glia. 2025 Feb 06.
    Ibudilast Protects Retinal Bipolar Cells From Excitotoxic Retinal Damage and Activates the mTOR Pathway.
    Sumaya Hamadmad, Tyler Heisler-Taylor, Sandeep Goswami, Evan Hawthorn, Sameer Chaurasia, Dena Martini, Diana Summitt, Ali Zatari, Rahaf Shalash, Misha Sohail, Elizabeth G Urbanski, Kayla Bernstein, Julie Racine, Abhay Satoskar, Heithem M El-Hodiri, Andy J Fischer, Colleen M Cebulla.
      Ibudilast, an inhibitor of macrophage migration inhibitory factor (MIF) and phosphodiesterase (PDE), has been recently shown to have neuroprotective effects in a variety of neurologic diseases. We utilize a chick excitotoxic retinal damage model to investigate ibudilast's potential to protect retinal neurons. Using single cell RNA-sequencing (scRNA-seq), we find that MIF, putative MIF receptors CD74 and CD44, and several PDEs are upregulated in different retinal cells during damage. Intravitreal ibudilast is well tolerated in the eye and causes no evidence of toxicity. Ibudilast effectively protects neurons in the inner nuclear layer from NMDA-induced cell death, restores retinal layer thickness on spectral domain optical coherence tomography (SD-OCT), and preserves retinal neuron function, particularly for the ON bipolar cells, as assessed by electroretinography. PDE inhibition seems essential for ibudilast's neuroprotection, as AV1013, the analogue that lacks PDE inhibitor activity, is ineffective. scRNA-seq analysis reveals upregulation of multiple signaling pathways, including mTOR, in damaged Müller glia (MG) with ibudilast treatment compared to AV1013. Components of mTORC1 and mTORC2 are upregulated in both bipolar cells and MG with ibudilast. The mTOR inhibitor rapamycin blocked accumulation of pS6 but did not reduce TUNEL positive dying cells. Additionally, through ligand-receptor interaction analysis, crosstalk between bipolar cells and MG may be important for neuroprotection. We have identified several paracrine signaling pathways that are known to contribute to cell survival and neuroprotection and might play essential roles in ibudilast function. These findings highlight ibudilast's potential to protect inner retinal neurons during damage and show promise for future clinical translation.
    Keywords:  Ibudilast; Müller glia; NMDA; mTOR; retina; retinal neuroprotection; scRNA‐seq
    DOI:  https://doi.org/10.1002/glia.24657
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