bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2025–03–02
sixty-one papers selected by
Viktor Korolchuk, Newcastle University
  1. Visualization of Subcellular mTOR Complex 1 Activity with a FRET-Based Sensor (TORCAR).
  2. A Distinctive Form of Autophagy Induced by Oncogenic RAS.
  3. Autophagy regulates cellular senescence by mediating the degradation of CDKN1A/p21 and CDKN2A/p16 through SQSTM1/p62-mediated selective autophagy in myxomatous mitral valve degeneration.
  4. Determination of Nutrient Ligand-Sensor Binding Affinity.
  5. Phase separation of p62: roles and regulations in autophagy.
  6. Autophagy-lysosome pathway in insulin & glucagon homeostasis.
  7. Establishment of a yeast essential protein conditional-degradation library and screening for autophagy-regulating genes.
  8. Lysosome-Mitochondrial Crosstalk in Cellular Stress and Disease.
  9. TAX1BP1-dependent autophagic degradation of STING1 impairs anti-tumor immunity.
  10. Cancer-associated mutations in autophagy-related proteins analyzed in yeast and human cells.
  11. Acinetobacter baumannii OmpA hinders host autophagy via the CaMKK2-reliant AMPK-pathway.
  12. Phosphorylation of BCL2L13 by PRKAA2/AMPKα2 activates mitophagy in pressure-overloaded heart.
  13. Autophagy repression by antigen and cytokines shapes mitochondrial, migration and effector machinery in CD8 T cells.
  14. Trehalose activates autophagy to alleviate cisplatin-induced chronic kidney injury by targeting the mTOR-dependent TFEB signaling pathway.
  15. Autophagy in High-Fat Diet and Streptozotocin-Induced Metabolic Cardiomyopathy: Mechanisms and Therapeutic Implications.
  16. The mTOR Signaling Pathway: Key Regulator and Therapeutic Target for Heart Disease.
  17. The therapeutic potential of (R)-carvedilol in Huntington's disease through enhancement of autophagy-lysosomal pathway via GSK-3β inhibition.
  18. RONIN/HCF1-TFEB Axis Protects Against D-Galactose-Induced Cochlear Hair Cell Senescence Through Autophagy Activation.
  19. Autophagy in Tissue Repair and Regeneration.
  20. Lysosomal degradation of ER client proteins by ER-phagy and related pathways.
  21. Alterations of PINK1-PRKN signaling in mice during normal aging.
  22. Citrus tristeza virus p20 suppresses antiviral RNA silencing by co-opting autophagy-related protein 8 to mediate the autophagic degradation of SGS3.
  23. Puerarin Reversing Autophagy-Lysosomal Dysfunction via Acid Sphingomyelinase Inhibition in Cardiomyocytes.
  24. Autophagy and Cancer: Insights into Molecular Mechanisms and Therapeutic Approaches for Chronic Myeloid Leukemia.
  25. TREM2 Alleviates Neuroinflammation by Maintaining Cellular Metabolic Homeostasis and Mitophagy Activity During Early Inflammation.
  26. Liver ALKBH5 regulates glucose and lipid homeostasis independently through GCGR and mTORC1 signaling.
  27. TFEB SUMOylation in Airway Epithelial Cells Impairs Lysosomal Biogenesis to Promote Asthma Development.
  28. Evolutionary Insights into Irisin/FNDC5: Roles in Aging and Disease from Drosophila to Mammals.
  29. Methods to Determine Lysosomal AMPK Activation.
  30. Hippocampal mitophagy alterations in MAPT-associated frontotemporal dementia with parkinsonism.
  31. Class I PI3Ks activate stretch-induced autophagy in trabecular meshwork cells.
  32. X-linked myopathy with excessive autophagy: characterization and therapy testing in a zebrafish model.
  33. Emerging Role of Hypoxia-Inducible Factors (HIFs) in Modulating Autophagy: Perspectives on Cancer Therapy.
  34. Targeting NLRC5 in cardiomyocytes protects postinfarction cardiac injury by enhancing autophagy flux through the CAVIN1/CAV1 axis.
  35. Genetic and pharmacological correction of impaired mitophagy in retinal ganglion cells rescues glaucomatous neurodegeneration.
  36. Cleaving PINK1 or PGAM5? Involvement of PARL in Methamphetamine-Induced Excessive Mitophagy and Neuronal Necroptosis.
  37. EPHB2 Promotes the Progression of Oral Squamous Cell Carcinoma Cells Through the Activation of VPS4A-Mediated Autophagy.
  38. Nuclear stiffness through lamin A/C overexpression differentially modulates chromosomal instability biomarkers.
  39. Neuronal autophagy in the control of synapse function.
  40. The spectrum of lysosomal stress and damage responses: from mechanosensing to inflammation.
  41. Spatiotemporal proteomics reveals the biosynthetic lysosomal membrane protein interactome in neurons.
  42. Lipophagy acts as a nutritional adaptation mechanism for the filamentous entomopathogenic fungus Beauveria bassiana to colonize within the hosts.
  43. RORA Regulates Autophagy in Hair Follicle Stem Cells by Upregulating the Expression Level of the Sqstm1 Gene.
  44. A Novel RHEB Germline Variant Associated With Intellectual Disability and Epilepsy: Expanding the Spectrum of mTORopathies.
  45. RNF167 mediates atypical ubiquitylation and degradation of RLRs via two distinct proteolytic pathways.
  46. Exposure to Manganese Induces Autophagy-Lysosomal Pathway Dysfunction-Mediated Tauopathy by Activating the cGAS-STING Pathway in the Brain.
  47. Autophagy is required for the therapeutic effects of the NAD+ precursor nicotinamide in obesity-related heart failure with preserved ejection fraction.
  48. Whole-cell Lysosome SMLM Imaging as Indicators for Functional Diagnostics with a Low-Phototoxic Spontaneously Blinking Probe.
  49. Chlorogenic Acid Enhances Beta-Lapachone-Induced Cell Death by Suppressing Autophagy in NQO1-Positive Cancer Cells.
  50. Extracellular Ubiquitin Enhances Autophagy and Inhibits Mitochondrial Apoptosis Pathway to Protect Neurons Against Spinal Cord Ischemic Injury via CXCR4.
  51. A bacterial RING ubiquitin ligase triggering stepwise degradation of BRISC via TOLLIP-mediated selective autophagy manipulates host inflammatory response.
  52. Sex Disparity in Cancer: Role of Autophagy and Estrogen Receptors.
  53. Evolutionary conserved regulation of TFEB stability by the E3 ubiquitin ligase WWP2 modulates response to stress in vivo.
  54. A double-edged sword in antiviral defence: ATG7 binding dicer to promote virus replication.
  55. Dexmedetomidine activates mitophagy and protects against pyroptosis in oxygen-glucose deprivation/reperfusion-induced brain damage via PINK1/Parkin pathway activation.
  56. The Role of Mitochondrial Quality Control in Liver Diseases: Dawn of a Therapeutic Era.
  57. Retinoic Acid Promotes Neuronal Differentiation While Increasing Proteins and Organelles Related to Autophagy.
  58. Inhibition of autophagy in platelets as a therapeutic strategy preventing hypoxia induced thrombosis.
  59. The Anti-Aging Mechanism of Metformin: From Molecular Insights to Clinical Applications.
  60. PDE4D inhibition ameliorates cardiac hypertrophy and heart failure by activating mitophagy.
  61. Semaglutide enhances PINK1/Parkin‑dependent mitophagy in hypoxia/reoxygenation‑induced cardiomyocyte injury.
  1. Methods Mol Biol. 2025 ;2882 139-162
    Visualization of Subcellular mTOR Complex 1 Activity with a FRET-Based Sensor (TORCAR).
    Ayse Z Sahan, Sohum Metha, Jin Zhang.
      The mechanistic target of rapamycin complex 1 (mTORC1) is a nutrient-sensing complex that integrates inputs from several pathways to promote cell growth and proliferation. mTORC1 localizes to many cellular compartments, including the nucleus, lysosomes, and plasma membrane. However, little is known about the spatial regulation of mTORC1 and the specific functions of mTORC1 at these locations. To address these questions, we previously developed a Förster resonance energy transfer (FRET)-based mTORC1 activity reporter (TORCAR) to visualize the dynamic changes in mTORC1 activity within live cells. Here, we describe a detailed protocol for using subcellularly targeted TORCAR constructs to investigate subcellular mTORC1 activities via live-cell fluorescence microscopy.
    Keywords:  Biosensor; Compartmentalized signaling; Fluorescence; Location-specific
    DOI:  https://doi.org/10.1007/978-1-0716-4284-9_7
  2. Autophagy. 2025 Feb 23.
    A Distinctive Form of Autophagy Induced by Oncogenic RAS.
    Xiaojuan Wang, Shulin Li, Min Zhang, Liang Ge.
      RAS mutations enhance macroautophagy/autophagy in tumor cells, crucial for their growth and survival, making autophagy a promising therapeutic target for RAS-mutant cancers. However, the distinction between RAS-induced autophagy and physiological autophagy is not well understood. We recently identified a unique form of autophagy, RAS-induced non-canonical autophagy via ATG8ylation (RINCAA), which differs from starvation-induced autophagy. RINCAA is regulated by different sets of autophagic factors and forms structures distinct from the double-membrane autophagosome known as RAS-induced multivesicular/multilaminar bodies of ATG8ylation (RIMMBA). A key feature of RINCAA is the phosphorylation of PI4KB by ULK1, and inhibiting this phosphorylation shows superior effects compared to general autophagy inhibitors. This work suggests a potential for specifically targeting autophagy in RAS-driven cancers as a therapeutic strategy.
    Keywords:  ATG8ylation; PtdIns4KB; RAS; autophagy; cancer
    DOI:  https://doi.org/10.1080/15548627.2025.2468917
  3. Autophagy. 2025 Feb 23.
    Autophagy regulates cellular senescence by mediating the degradation of CDKN1A/p21 and CDKN2A/p16 through SQSTM1/p62-mediated selective autophagy in myxomatous mitral valve degeneration.
    Qiyu Tang, Keyi Tang, Greg R Markby, Maciej Parys, Kanchan Phadwal, Vicky E MacRae, Brendan M Corcoran.
      Myxomatous mitral valve degeneration (MMVD) is one of the most important age-dependent degenerative heart valve disorders in both humans and dogs. It is characterized by the aberrant remodeling of extracellular matrix (ECM), regulated by senescent myofibroblasts (aVICs) transitioning from quiescent valve interstitial cells (qVICs), primarily under TGFB1/TGF-β1 control. In the present study, we found senescent aVICs exhibited impaired macroautophagy/autophagy as evidenced by compromised autophagy flux and immature autophagosomes. MTOR-dependent autophagy induced by rapamycin and torin-1 attenuated cell senescence and decreased the expression of cyclin-dependent kinase inhibitors (CDKIs) CDKN2A/p16INK4A and CDKN1A/p21CIP1. Furthermore, induction of autophagy in aVICs by ATG (autophagy related) gene overexpression restored autophagy flux, with a concomitant reduction in CDKN1A and CDKN2A expression and senescence-associated secretory phenotype (SASP). Conversely, autophagy deficiency induced CDKN1A and CDKN2A accumulation and SASP, whereas ATG re-expression alleviated senescent phenotypic transformation. Notably, CDKN1A and CDKN2A localized to autophagosomes and lysosomes following MTOR antagonism or MG132 treatment. SQSTM1/p62 was identified as the autophagy receptor to selectively sequester CDKN1A and CDKN2A cargoes for autophagic degradation. Our findings are the first demonstration that CDKN1A and CDKN2A are degraded through SQSTM1-mediated selective autophagy, independent of the ubiquitin-proteasome pathway. These data will inform development of therapeutic strategies for the treatment of canine and human MMVD, and for the treatment of Alzheimer disease, Parkinson disease and other age-related degenerative disorders.
    Keywords:  Autophagic degradation; CDKI; MMVD; SASP; TGFB; ubiquitin-proteasome pathway
    DOI:  https://doi.org/10.1080/15548627.2025.2469315
  4. Methods Mol Biol. 2025 ;2882 163-178
    Determination of Nutrient Ligand-Sensor Binding Affinity.
    Xin Gu.
      Cells contain dedicated mechanisms to sense nutrient levels in the environment to regulate their growth by balancing anabolism and catabolism [1, 2]. The mechanistic Target of Rapamycin Complex 1 (mTORC1), a multi-protein kinase complex, serves as an essential growth regulator that integrates various upstream inputs including growth factors and nutrients like amino acids [1, 2] Nutrient sensors upstream of mTORC1 directly bind cognate nutrient ligands to convey their availability and thereby regulate mTORC1 signaling [1, 2]. A reliable method is needed to quantitatively determine the binding affinity (Kd) of the nutrient sensor to its ligand. In parallel, quantitative metabolomic analysis can reveal metabolite levels in fed and starved cells; which represent the physiological range of the nutrient of interest. Whether or not the binding affinity is within the physiological range serves as an indicator to determine the physiological relevance of the sensing mechanism. This chapter describes a generalizable protocol that allows reproducible determination of nutrient ligand-nutrient sensor binding affinity. Here, the S-adenosylmethionine (nutrient ligand)-SAMTOR (nutrient sensor) pair is used as an example [3]. Nutrient sensor purification, radioactive nutrient ligand incubation, and eventual scintillation counting are included, along with a description of the mathematical equation that is used to calculate the binding affinity.
    Keywords:  Affinity beads; Competitive binding assays; Nutrient sensors; Nutrients; Protein purification; Radioactive ligands; Scintillation; mTORC1
    DOI:  https://doi.org/10.1007/978-1-0716-4284-9_8
  5. Trends Cell Biol. 2025 Feb 25. pii: S0962-8924(25)00033-9. [Epub ahead of print]
    Phase separation of p62: roles and regulations in autophagy.
    Xue Huang, Jinpei Zhang, Jia Yao, Na Mi, Aimin Yang.
      The phase separation of the cargo receptor sequestome-1/p62 (SQSTM1/p62) is a critical mechanism for assembling signaling complexes in autophagy. During this process, p62 undergoes phase separation upon binding to polyubiquitin chains, concentrating ubiquitinated substrates within p62 droplets. These droplets further gather membrane sources and core autophagy machineries to facilitate autophagosome formation. The dynamics of p62 droplets are finely tuned in response to autophagy signals triggered by cellular stresses. Recent studies have revealed new regulatory mechanisms that highlight the significance of p62 phase separation in regulating autophagy. This review summarizes and discusses the molecular mechanisms of p62 phase separation and its roles in autophagy, with particular emphasis on the regulation of p62 droplets and their interaction modes with autophagic membranes.
    Keywords:  cargo receptor; p62; p62 droplets; phase separation; selective autophagy
    DOI:  https://doi.org/10.1016/j.tcb.2025.01.010
  6. Front Endocrinol (Lausanne). 2025 ;16 1541794
    Autophagy-lysosome pathway in insulin & glucagon homeostasis.
    Yi Wu, Hui Wang, Huoyan Xu.
      Lysosome, a highly dynamic organelle, is an important nutrient sensing center. They utilize different ion channels and transporters to complete the mission in degradation, trafficking, nutrient sensing and integration of various metabolic pathways to maintain cellular homeostasis. Glucose homeostasis relies on tightly regulated insulin secretion by pancreatic β cells, and their dysfunction is a hallmark of type 2 diabetes. Glucagon also plays an important role in hyperglycemia in diabetic patients. Currently, lysosome has been recognized as a nutrient hub to regulate the homeostasis of insulin and other hormones. In this review, we will discuss recent advances in understanding lysosome-mediated autophagy and lysosomal proteins involved in maintaining insulin and glucagon homeostasis, as well as their contributions to the etiology of diabetes.
    Keywords:  autophagy; diabetes; glucagon homeostasis; insulin homeostasis; lysosome
    DOI:  https://doi.org/10.3389/fendo.2025.1541794
  7. Autophagy. 2025 Feb 23.
    Establishment of a yeast essential protein conditional-degradation library and screening for autophagy-regulating genes.
    Cong Yi, Yi Zhang, Yingcong Chen, Choufei Wu, Zhengyi Cai, Weijing Yao, Huan Yang, Juan Song, Xiankuan Xie, Liqin Zhang.
      Macroautophagy/autophagy is an evolutionarily conserved intracellular degradation pathway that relies on vacuoles or lysosomes. Over 40 ATG genes have been identified in yeast cells as participants in various types of autophagy, although these genes are non-essential. While some essential genes involved in autophagy have been identified using temperature-sensitive yeast strains, systematic research on essential genes in autophagy remains lacking. To address this, we established an essential protein conditional degradation library using the auxin-inducible degron (AID) system. By introducing the GFP-Atg8 plasmid, we identified 29 essential yeast genes involved in autophagy, 19 of which had not been previously recognized. In summary, the yeast essential protein conditional degradation library we constructed will serve as a valuable resource for systematically investigating the roles of essential genes in autophagy and other biological functions.
    Keywords:  Autophagy; conditional degradation library; essential genes; yeast
    DOI:  https://doi.org/10.1080/15548627.2025.2469189
  8. Antioxidants (Basel). 2025 Jan 22. pii: 125. [Epub ahead of print]14(2):
    Lysosome-Mitochondrial Crosstalk in Cellular Stress and Disease.
    Szilvia Kiraly, Jack Stanley, Emily R Eden.
      The perception of lysosomes and mitochondria as entirely separate and independent entities that degrade material and produce ATP, respectively, has been challenged in recent years as not only more complex roles for both organelles, but also an unanticipated level of interdependence are being uncovered. Coupled lysosome and mitochondrial function and dysfunction involve complex crosstalk between the two organelles which goes beyond mitochondrial quality control and lysosome-mediated clearance of damaged mitochondria through mitophagy. Our understanding of crosstalk between these two essential metabolic organelles has been transformed by major advances in the field of membrane contact sites biology. We now know that membrane contact sites between lysosomes and mitochondria play central roles in inter-organelle communication. This importance of mitochondria-lysosome contacts (MLCs) in cellular homeostasis, evinced by the growing number of diseases that have been associated with their dysregulation, is starting to be appreciated. How MLCs are regulated and how their coordination with other pathways of lysosome-mitochondria crosstalk is achieved are the subjects of ongoing scrutiny, but this review explores the current understanding of the complex crosstalk governing the function of the two organelles and its impact on cellular stress and disease.
    Keywords:  crosstalk; lysosomes; membrane contact sites; mitochondria
    DOI:  https://doi.org/10.3390/antiox14020125
  9. Autophagy. 2025 Feb 25.
    TAX1BP1-dependent autophagic degradation of STING1 impairs anti-tumor immunity.
    Ruoxi Zhang, Chunhua Yu, Herbert J Zeh, Guido Kroemer, Daniel J Klionsky, Daolin Tang, Rui Kang.
      The activation of STING1 can lead to the production and secretion of cytokines, initiating antitumor immunity. Here, we screened an ion channel ligand library and identified tetrandrine, a bis-benzylisoquinoline alkaloid, as an immunological adjuvant that enhances antitumor immunity by preventing the autophagic degradation of the STING1 protein. This tetrandrine effect is independent of its known function as a calcium or potassium channel blocker. Instead, tetrandrine inhibits lysosomal function, impairing cathepsin maturation, and autophagic degradation. Proteomic analysis of lysosomes identified TAX1BP1 as a novel autophagic receptor for the proteolysis of STING1. TAX1BP1 recognizes STING1 through the physical interaction of its coiled-coil domain with the cyclic dinucleotide binding domain of STING1. Systematic mutation of lysine (K) residues revealed that K63-ubiquitination of STING1 at the K224 site ignites TAX1BP1-dependent STING1 degradation. Combined treatment with tetrandrine and STING1 agonists promotes antitumor immunity by converting "cold" pancreatic cancers into "hot" tumors. This process is associated with enhanced cytokine release and increased infiltration of cytotoxic T-cells into the tumor microenvironment. The antitumor immunity mediated by tetrandrine and STING1 agonists is limited by neutralizing antibodies to the type I interferon receptor or CD8+ T cells. Thus, these findings establish a potential immunotherapeutic strategy against pancreatic cancer by preventing the autophagic degradation of STING1.
    Keywords:  Autophagy; degradation; lysosome; pancreatic cancer; tumor immunity
    DOI:  https://doi.org/10.1080/15548627.2025.2471736
  10. Autophagy. 2025 Feb 28.
    Cancer-associated mutations in autophagy-related proteins analyzed in yeast and human cells.
    Yuchen Lei, Louise Uoselis, Dimitra Dialynaki, Ying Yang, Michael Lazarou, Daniel J Klionsky.
      Macroautophagy/autophagy is a conserved process among eukaryotes and is essential to maintain cell homeostasis; the dysregulation of autophagy has been linked with multiple human diseases, including cancer. However, not many studies have focused on the cancer-related mutations in ATG (autophagy related) proteins, which are likely to affect the protein function, influence autophagy activity and further contribute to the progression of the disease. In this study, we focused on the four ATG4 isoforms, which have a higher mutation frequency compared with the other core ATG proteins (i.e. those involved in autophagosome formation). We first studied the mutations in conserved residues and characterized one cancer-associated mutation that significantly impairs protein function and autophagy activity. Extending the study, we determined a region around the mutant residue to be essential for protein function, which had yet to be examined in previous studies. In addition, we created a yeast system expressing the human ATG4B protein to study mutations in the residues that are not conserved from human to yeast. Using this yeast model, we identified six cancer-associated mutations affecting autophagy. The effects of these mutations were further tested in mammalian cells using a quadruple ATG4 gene knockout cell line. Our study proves the principle of using human disease-associated mutations to study Atg proteins in yeast and generates a yeast tool that is helpful for a rapid screen of mutations to determine the autophagy phenotype, providing a new perspective in studying autophagy and its relation with cancer.
    Keywords:  ATG4; autophagy; cancer; mutation
    DOI:  https://doi.org/10.1080/15548627.2025.2471142
  11. mBio. 2025 Feb 25. e0336924
    Acinetobacter baumannii OmpA hinders host autophagy via the CaMKK2-reliant AMPK-pathway.
    Kyungho Woo, Dong Ho Kim, Ho-Sung Park, Man Hwan Oh, Je Chul Lee, Chul Hee Choi.
      Outer membrane protein A (OmpA) plays a vital role in the interactions between Acinetobacter baumannii and host cells. Autophagy is a defense mechanism that hinders the intracellular replication of bacteria, thereby safeguarding cells against microbial infections. While it has been observed that A. baumannii triggers cellular autophagy, the precise role of its virulence protein OmpA in this process remains uncertain. In this study, we investigated the effects of A. baumannii OmpA (AbOmpA) on autophagy and explored the underlying molecular mechanisms. We found that AbOmpA exerted its autophagy-suppressive effect through inhibition of CaMKK2 phosphorylation. Compared to the wild-type strain, the ompA-deletion mutant strain displayed considerably enhanced autophagy induction, via the AMPK-ULK1 pathway. AbOmpA hindered starvation-induced autophagy, while A. baumannii-Omp33 (AbOmp33) and Escherichia coli-OmpA (EcOmpA) did not. Importantly, we confirmed that exogenous AbOmpA suppressed autophagy through the CaMKK2-AMPK-ULK1 pathway during A. baumannii infection. These findings reveal a novel mechanism for AbOmpA-mediated autophagy evasion, providing new insights into the pathogenesis of A. baumannii infection.IMPORTANCEAcinetobacter baumannii is a significant clinical pathogen notorious for causing infections in hospitals. Its outer membrane protein A acts as a virulence factor and helps the bacteria evade host defenses. Autophagy is a defense mechanism that hinders the intracellular replication of bacteria. While it has been observed that A. baumannii triggers cellular autophagy, the precise role of its AbOmpA in this process remains uncertain. Our studies demonstrate the AbOmpA of A. baumannii inhibits the cellular defense process, autophagy, through the CaMKK2-AMPK-ULK1 signaling cascade, thereby enhancing bacterial survival. This insight into how AbOmpA bypasses autophagy sheds light on A. baumannii infection's novel virulence strategy and suggests possible treatments.
    Keywords:  Acinetobacter baumannii; CaMKK2; autophagy; outer membrane protein A
    DOI:  https://doi.org/10.1128/mbio.03369-24
  12. Autophagy. 2025 Feb 24. 1-2
    Phosphorylation of BCL2L13 by PRKAA2/AMPKα2 activates mitophagy in pressure-overloaded heart.
    Tomokazu Murakawa, Kinya Otsu.
      In heart failure patients, the accumulation of damaged mitochondria is frequently observed in cardiomyocytes. Damaged mitochondria are degraded through mitophagy, a form of mitochondria-specific autophagy. Previously, we identified BCL2L13 as a mitophagy receptor and demonstrated its ability to induce mitophagy and mitochondrial fission in mammalian cells and the necessity of phosphorylation at Ser272 for its activation. However, the in vivo role of BCL2L13 remains unclear. In this study, we investigated the cardiac function of BCL2L13 using bcl2l13 knockout mice and knock-in mice expressing a non-phosphorylatable BCL2L13S272A mutant. In the hearts of these genetically modified mice, pressure overload leads to suppressed mitochondrial fission and mitophagy, resulting in reduced ATP production. Additionally, we analyzed bcl2l13 and prkn/parkin double-knockout mice but found no additive effects of prkn deletion. Furthermore, we identified PRKAA2/AMPKα2 as the kinase responsible for phosphorylating BCL2L13 at Ser272. These findings highlight the critical role of BCL2L13 and its phosphorylation in activating mitophagy as part of the cardiac stress response and suggest that targeting BCL2L13 phosphorylation could serve as a potential therapeutic strategy for heart failure.Abbreviation: BCL2L13, BCL2 like 13; ATG, autophagy related; MAP1LC3B/LC3B, microtubule-associated protein 1 light chain 3 beta; KO, knockout; TAC, transverse aortic constriction; LVFS, left ventricular fractional shortening; ROS, reactive oxygen species; DKO, double knockout; siRNA, small interfering RNA; PRKAA2/AMPKα2, protein kinase, AMP-activated alpha 2 catalytic subunit; CCCP, carbonyl cyanide 3-chlorophenylhydrazone.
    Keywords:  BCL2L13; heart failure; kinase; mitophagy; pressure overload
    DOI:  https://doi.org/10.1080/15548627.2025.2465408
  13. Nat Immunol. 2025 Feb 27.
    Autophagy repression by antigen and cytokines shapes mitochondrial, migration and effector machinery in CD8 T cells.
    Linda V Sinclair, Tom Youdale, Laura Spinelli, Milica Gakovic, Alistair J Langlands, Shalini Pathak, Andrew J M Howden, Ian G Ganley, Doreen A Cantrell.
      Autophagy shapes CD8 T cell fate; yet the timing, triggers and targets of this process are poorly defined. Herein, we show that naive CD8 T cells have high autophagic flux, and we identify an autophagy checkpoint whereby antigen receptor engagement and inflammatory cytokines acutely repress autophagy by regulating amino acid transporter expression and intracellular amino acid delivery. Activated T cells with high levels of amino acid transporters have low autophagic flux in amino-acid-replete conditions but rapidly reinduce autophagy when amino acids are restricted. A census of proteins degraded and fueled by autophagy shows how autophagy shapes CD8 T cell proteomes. In cytotoxic T cells, dominant autophagy substrates include cytolytic effector molecules, and amino acid and glucose transporters. In naive T cells, mitophagy dominates and selective mitochondrial pruning supports the expression of molecules that coordinate T cell migration and survival. Autophagy thus differentially prunes naive and effector T cell proteomes and is dynamically repressed by antigen receptors and inflammatory cytokines to shape T cell differentiation.
    DOI:  https://doi.org/10.1038/s41590-025-02090-1
  14. Theranostics. 2025 ;15(6): 2544-2563
    Trehalose activates autophagy to alleviate cisplatin-induced chronic kidney injury by targeting the mTOR-dependent TFEB signaling pathway.
    Jingchao Yang, Longhui Yuan, Lan Li, Fei Liu, Jingping Liu, Younan Chen, Ping Fu, Yanrong Lu, Yujia Yuan.
      Rationale: Cisplatin is a potent chemotherapeutic agent limited by significant nephrotoxicity. Multiple cycles of cisplatin administration are necessary to confer chronic disease. Autophagy is a lysosomal degradation pathway that enables the clearance and reuse of cytoplasmic components and is essential for maintaining the integrity and normal physiological function of tissues and organs. However, the precise role of autophagy in renal fibrosis has been controversial. Trehalose, a well-known autophagy inducer, plays a cytoprotective role under various stress conditions, such as oxidative damage, dehydration, and temperature changes. In this study, we established a model of cisplatin-induced chronic kidney disease (CKD) and human renal tubular epithelial cells (HK2) injury to investigate the nephroprotective effects of trehalose on cisplatin-induced CKD and the underlying mechanisms involved. Methods: Firstly, we measured the role of autophagy in cisplatin-induced injury models both in vivo and in vitro by western blot and immunofluorescence staining, combined with transcriptomics. Then, biomedical, cellular, and molecular approaches were utilized to evaluate the potential protective effect of trehalose intervention in regulating autophagy. Mechanistically, we performed this study using proximal tubular epithelial cells-specific transcription factor EB (TFEB) knockout mice and TFEB small-interfering RNA technology to determine whether TFEB deficiency affects the pharmacological effected of trehalose in cisplatin-induced injury models. Results: Due to the activation of autophagy, trehalose inhibited mitochondrial dysfunction (mitochondrial fragmentation, depolarization, reactive oxygen species) and cellular senescence induced by cisplatin both in vitro and in vivo. Moreover, renal dysfunction, pathological changes and fibrosis were alleviated in CKD mice after trehalose treatment. Mechanistic investigations revealed that trehalose accumulated in lysosomes and inhibited mTORC1 activity, which triggered TFEB and TFEB-mediated autophagy. In addition, siRNA-mediated knockdown of TFEB in HK2 cells or renal proximal tubular epithelial cells-specific (TECs-specific) TFEB deficiency in mice markedly abolished the beneficial effects of trehalose. Conclusion: Our findings suggested that trehalose induced autophagy to alleviate cisplatin-induced chronic kidney injury by targeting the mTOR-dependent TFEB signaling pathway.
    Keywords:  TFEB; autophagy; chronic kidney disease; mTOR; mitochondrial dysfunction
    DOI:  https://doi.org/10.7150/thno.102559
  15. Int J Mol Sci. 2025 Feb 15. pii: 1668. [Epub ahead of print]26(4):
    Autophagy in High-Fat Diet and Streptozotocin-Induced Metabolic Cardiomyopathy: Mechanisms and Therapeutic Implications.
    Rong Zhou, Zutong Zhang, Xinjie Li, Qinchun Duan, Yuanlin Miao, Tingting Zhang, Mofei Wang, Jiali Li, Wei Zhang, Liyang Wang, Odell D Jones, Mengmeng Xu, Yingli Liu, Xuehong Xu.
      Metabolic cardiomyopathy, encompassing diabetic and obese cardiomyopathy, is an escalating global health concern, driven by the rising prevalence of metabolic disorders such as insulin resistance, type 1 and type 2 diabetes, and obesity. These conditions induce structural and functional alterations in the heart, including left ventricular dysfunction, fibrosis, and ultimately heart failure, particularly in the presence of coronary artery disease or hypertension. Autophagy, a critical cellular process for maintaining cardiac homeostasis, is frequently disrupted in metabolic cardiomyopathy. This review explores the role of autophagy in the pathogenesis of high-fat diet (HFD) and streptozotocin (STZ)-induced metabolic cardiomyopathy, focusing on non-selective and selective autophagy pathways, including mitophagy, ER-phagy, and ferritinophagy. Key proteins and genes such as PINK1, Parkin, ULK1, AMPK, mTOR, ATG7, ATG5, Beclin-1, and miR-34a are central to the regulation of autophagy in metabolic cardiomyopathy. Dysregulated autophagic flux impairs mitochondrial function, promotes oxidative stress, and drives fibrosis in the heart. Additionally, selective autophagy processes such as lipophagy, regulated by PNPLA8, and ferritinophagy, modulated by NCOA4, play pivotal roles in lipid metabolism and iron homeostasis. Emerging therapeutic strategies targeting autophagy, including plant extracts (e.g., curcumin, dihydromyricetin), endogenous compounds (e.g., sirtuin 3, LC3), and lipid/glucose-lowering drugs, offer promising avenues for mitigating the effects of metabolic cardiomyopathy. Despite recent advances, the precise mechanisms underlying autophagy in this context remain poorly understood. A deeper understanding of autophagy's regulatory networks, particularly involving these critical genes and proteins, may lead to novel therapeutic approaches for treating metabolic cardiomyopathy.
    Keywords:  ER-phagy; autophagy; ferritinophagy; high-fat diet (HFD); metabolic cardiomyopathy; streptozotocin (STZ)
    DOI:  https://doi.org/10.3390/ijms26041668
  16. Biomedicines. 2025 Feb 07. pii: 397. [Epub ahead of print]13(2):
    The mTOR Signaling Pathway: Key Regulator and Therapeutic Target for Heart Disease.
    Jieyu Wang, Yuxuan Huang, Zhaoxia Wang, Jing Liu, Zhijian Liu, Jinfeng Yang, Zuping He.
      Heart disease, including myocardial infarction, heart failure, cardiac hypertrophy, and cardiomyopathy, remains a leading cause of mortality worldwide. The mammalian target of rapamycin (mTOR) is a centrally regulated kinase that governs key cellular processes, including growth, proliferation, metabolism, and survival. Notably, mTOR plays a pivotal role in cardiovascular health and disease, particularly in the onset and progression of cardiac conditions. In this review, we discuss mTOR's structure and function as well as the regulatory mechanisms of its associated signaling pathways. We focus on the molecular mechanisms by which mTOR signaling regulates cardiac diseases and the potential of mTOR inhibitors and related regulatory drugs in preventing these conditions. We conclude that the mTOR signaling pathway is a promising therapeutic target for heart disease.
    Keywords:  heart disease; mTOR; signaling pathway; target
    DOI:  https://doi.org/10.3390/biomedicines13020397
  17. Neurotherapeutics. 2025 Feb 25. pii: S1878-7479(25)00035-2. [Epub ahead of print] e00557
    The therapeutic potential of (R)-carvedilol in Huntington's disease through enhancement of autophagy-lysosomal pathway via GSK-3β inhibition.
    Chih-Yuan Cheng, Kai-Po Chen, Tien-Sheng Tseng, Kuo-Feng Hua, Tz-Chuen Ju.
      Huntington's disease (HD) is a neurodegenerative disorder caused by the abnormal expansion of CAG repeats in the huntingtin (Htt) gene, leading to the aggregation of mutant huntingtin protein (mHTT) in cells, particularly in cortical and striatal neurons. This results in involuntary movements, cognitive impairment, and emotional instability. One of the critical pathogenic mechanisms in HD is impaired autophagy, which plays a vital role in cellular homeostasis by degrading damaged organelles and misfolded proteins through the formation of autophagosomes that fuse with lysosomes. However, the aggregation of mHTT disrupts autophagic function, leading to the accumulation of mHTT and exacerbating the disease's pathogenesis. Carvedilol is an established clinical medication used to treat hypertension and congestive heart failure. It exerts protective effects by blocking both β1-and β2-adrenergic receptors, reducing sympathetic nervous activity, and promoting vasodilation through α1-adrenergic blockade. Carvedilol has been shown to possess antioxidant and anti-inflammatory properties. In this study, we demonstrate that (R)-carvedilol promotes the nuclear translocation of the transcription factor binding to IGHM enhancer 3 (TFE3) by reducing glycogen synthase-3β (GSK-3β) activation, which increases the expression of autophagy-related proteins and facilitates the autophagy-lysosomal pathway (ALP), thereby enhancing mHTT degradation. Additionally, systemic administration of (R)-carvedilol improves mHTT degradation, provides neuroprotection, and inhibits gliosis, effectively ameliorating behavioral impairments and improving disease progression. Overall, these findings indicate that (R)-carvedilol has therapeutic potential for managing HD by promoting autophagy, facilitating the clearance of mHTT aggregates, and demonstrating advantageous properties in an HD transgenic mouse model, highlighting its promise as a treatment option for neurodegenerative diseases.
    Keywords:  Autophagy-lysosomal pathway (ALP); Cathepsin B (CTSB); Glycogen synthase 3β (GSK-3β); Mutant huntingtin (mHTT); Transcription factor binding to IGHM enhancer 3 (TFE3)
    DOI:  https://doi.org/10.1016/j.neurot.2025.e00557
  18. Adv Sci (Weinh). 2025 Feb 22. e2407880
    RONIN/HCF1-TFEB Axis Protects Against D-Galactose-Induced Cochlear Hair Cell Senescence Through Autophagy Activation.
    Yongjie Wei, Yuhua Zhang, Wei Cao, Nan Cheng, Yun Xiao, Yongjun Zhu, Yan Xu, Lei Zhang, Lingna Guo, Jun Song, Su-Hua Sha, Buwei Shao, Fang Ma, Jingwen Yang, Zheng Ying, Zuhong He, Renjie Chai, Qiaojun Fang, Jianming Yang.
      Age-related hearing loss is characterized by senescent inner ear hair cells (HCs) and reduced autophagy. Despite the improved understanding of these processes, detailed molecular mechanisms underlying cochlear HC senescence remain unclear. Transcription Factor EB (TFEB), a key regulator of genes associated with autophagy and lysosomes, crucially affects aging-related illnesses. However, intricate regulatory networks that influence TFEB activity remain to be thoroughly elucidated. The findings revealed that RONIN (THAP11), through its interaction with host cell factor C1 (HCF1/HCFC1), modulated the transcriptional activity of Tfeb, thus contributing to the mitigation (D-galatactose [D-gal]) senescent HC loss. Specifically, RONIN overexpression improved autophagy levels and lysosomal activity and attenuated changes associated with the senescence of HCs triggered by D-gal. These findings highlight the possibility of using RONIN as a viable therapeutic target to ameliorate presbycusis by enhancing the TFEB function.
    Keywords:  RONIN/THAP11; Tfeb; aging‐related hearing loss; autophagy; hair cell
    DOI:  https://doi.org/10.1002/advs.202407880
  19. Cells. 2025 Feb 14. pii: 282. [Epub ahead of print]14(4):
    Autophagy in Tissue Repair and Regeneration.
    Daniel Moreno-Blas, Teresa Adell, Cristina González-Estévez.
      Autophagy is a cellular recycling system that, through the sequestration and degradation of intracellular components regulates multiple cellular functions to maintain cellular homeostasis and survival. Dysregulation of autophagy is closely associated with the development of physiological alterations and human diseases, including the loss of regenerative capacity. Tissue regeneration is a highly complex process that relies on the coordinated interplay of several cellular processes, such as injury sensing, defense responses, cell proliferation, differentiation, migration, and cellular senescence. These processes act synergistically to repair or replace damaged tissues and restore their morphology and function. In this review, we examine the evidence supporting the involvement of the autophagy pathway in the different cellular mechanisms comprising the processes of regeneration and repair across different regenerative contexts. Additionally, we explore how modulating autophagy can enhance or accelerate regeneration and repair, highlighting autophagy as a promising therapeutic target in regenerative medicine for the development of autophagy-based treatments for human diseases.
    Keywords:  autophagy; injury; planarian; regeneration; senescence; stem cell; tissue repair
    DOI:  https://doi.org/10.3390/cells14040282
  20. J Mol Biol. 2025 Feb 22. pii: S0022-2836(25)00101-9. [Epub ahead of print] 169035
    Lysosomal degradation of ER client proteins by ER-phagy and related pathways.
    Carla Salomo-Coll, Natalia Jimenez-Moreno, Simon Wilkinson.
      The endoplasmic reticulum (ER) is a major site of cellular protein synthesis. Degradation of overabundant, misfolded, aggregating or unwanted proteins is required to maintain proteostasis and avoid the deleterious consequences of aberrant protein accumulation, at a cellular and organismal level. While extensive research has shown an important role for proteasomally-mediated, ER-associated degradation (ERAD) in maintaining proteostasis, it is becoming clear that there is a substantial role for lysosomal degradation of "client" proteins from the ER lumen or membrane (ER-to-lysosome degradation, ERLAD). Here we provide a brief overview of the broad categories of ERLAD - predominantly ER-phagy (ER autophagy) pathways and related processes. We collate the client proteins known to date, either individual species or categories of proteins. Where known, we summarise the molecular mechanisms by which they are selected for degradation, and the setting in which lysosomal degradation of the client(s) is important for correct cell or tissue function. Finally, we highlight the questions that remain open in this area.
    DOI:  https://doi.org/10.1016/j.jmb.2025.169035
  21. Autophagy Rep. 2024 ;pii: 2434379. [Epub ahead of print]3(1):
    Alterations of PINK1-PRKN signaling in mice during normal aging.
    Zahra Baninameh, Jens O Watzlawik, Xu Hou, Tyrique Richardson, Nicholas W Kurchaba, Tingxiang Yan, Damian N Di Florio, DeLisa Fairweather, Lu Kang, Justin H Nguyen, Takahisa Kanekiyo, Dennis W Dickson, Sachiko Noda, Shigeto Sato, Nobutaka Hattori, Matthew S Goldberg, Ian G Ganley, Kelly L Stauch, Fabienne C Fiesel, Wolfdieter Springer.
      The ubiquitin kinase-ligase pair PINK1-PRKN identifies and selectively marks damaged mitochondria for elimination via the autophagy-lysosome system (mitophagy). While this cytoprotective pathway has been extensively studied in vitro upon acute and complete depolarization of mitochondria, the significance of PINK1-PRKN mitophagy in vivo is less well established. Here we used a novel approach to study PINK1-PRKN signaling in different energetically demanding tissues of mice during normal aging. We demonstrate a generally increased expression of both genes and enhanced enzymatic activity with aging across tissue types. Collectively our data suggest a distinct regulation of PINK1-PRKN signaling under basal conditions with the most pronounced activation and flux of the pathway in mouse heart compared to brain or skeletal muscle. Our biochemical analyses complement existing mitophagy reporter readouts and provide an important baseline assessment in vivo, setting the stage for further investigations of the PINK1-PRKN pathway during stress and in relevant disease conditions.
    Keywords:  PINK1; PRKN; aging; brain; heart; mice; mitochondria; mitophagy; phosphorylated ubiquitin; skeletal muscle
    DOI:  https://doi.org/10.1080/27694127.2024.2434379
  22. PLoS Pathog. 2025 Feb 24. 21(2): e1012960
    Citrus tristeza virus p20 suppresses antiviral RNA silencing by co-opting autophagy-related protein 8 to mediate the autophagic degradation of SGS3.
    Yongle Zhang, Zuokun Yang, Zhe Zhang, Guoping Wang, Xiang-Dong Li, Ni Hong.
      Viruses exploit autophagy to degrade host immune components for their successful infection. However, how viral factors sequester the autophagic substrates into autophagosomes remains largely unknown. In this study, we showed that p20 protein, a viral suppressor of RNA silencing (VSR) encoded by citrus tristeza virus (CTV), mediated autophagic degradation of SUPPRESSOR OF GENE SILENCING 3 (SGS3), a plant-specific RNA-binding protein that is pivotal in antiviral RNA silencing. CTV infection activated autophagy, and the overexpression of p20 was sufficient to induce autophagy. Silencing of autophagy-related genes NbATG5 and NbATG7 attenuated CTV infection in Nicotiana benthamiana plants. In contrast, knockdown of the autophagy negative-regulated genes NbGAPCs led to virus accumulation, indicating the proviral role of autophagy in CTV infection. Further investigation found that p20 interacted with autophagy-related protein ATG8 through two ATG8-interacting motifs (AIMs) and sequestered SGS3 into autophagosomes by forming the ATG8-p20-SGS3 ternary complex. The mutations of the two AIMs in p20 (p20mAIM1 and p20mAIM5) abolished the interaction of p20 with ATG8, resulting in the deficiency of autophagy induction, SGS3 degradation, and VSR activity. Consistently, N. benthamiana plants infected with mutated CTVmAIM1 and CTVmAIM5 showed milder symptoms and decreased viral accumulation. Taken together, this study uncovers the molecular mechanism underlying how a VSR mediates the interplay between RNA silencing and autophagy to enhance the infection of a closterovirus.
    DOI:  https://doi.org/10.1371/journal.ppat.1012960
  23. J Cell Mol Med. 2025 Feb;29(4): e70427
    Puerarin Reversing Autophagy-Lysosomal Dysfunction via Acid Sphingomyelinase Inhibition in Cardiomyocytes.
    Yin-Ping Li, Qian He, Xiao-Ying Yu, Sheng-Tao Xiong, Hong-Jing You, Yue Xuan, Wei-Yan Liao, Ze-Yu Chen, Hai-Yan Li, Wei Wang, Yang Chen, Xiao Wang.
      Heart failure (HF) is a major cardiovascular disorder characterised by high prevalence and mortality rate. Recent studies have emphasised the role of autophagy in development and progression of HF. Dysfunctions in lysosomes and autophagic processes are closely associated with the aetiology of HF. Puerarin (PUE), a traditional Chinese medicine known for its antioxidant, anti-inflammatory and antiapoptotic properties, is widely used for the treatment of HF. However, the effectiveness of PUE in HF management via the modulation of autophagy requires further investigation. We used a mouse model of transverse aortic constriction to investigate protective effects of PUE on the autophagy-lysosomal pathway (ALP). We assessed heart function using echocardiography and performed histological staining for fibrosis and hypertrophy. RT-qPCR for atrial natriuretic peptide (ANP)/brain natriuretic peptide (BNP) and Western blotting for p62/LC3/LAMP1/Beclin1 were performed. Immunofluorescence was used to identify the autophagosomes, autolysosomes and lysosomes. In addition, immunohistochemistry was performed to detect acid sphingomyelinase (ASM) and ceramides. ASM siRNA was transfected into cardiomyocytes to evaluate autophagy. PUE treatment significantly reduced myocardial fibrosis and hypertrophy in HF-induced mice. PUE also effectively ameliorated ALP impairment in HF-induced mice and H9c2 cells. Mechanistically, PUE restored lysosomal homeostasis by inhibiting ASM expression and lysosomal transport, thereby enhancing lysosomal activity. These results underscore the therapeutic potential of PUE in correcting the ASM-mediated disruption of the HF-linked autophagy-lysosomal pathway.
    Keywords:  ASM; autophagy; heart failure; lysosome; puerarin
    DOI:  https://doi.org/10.1111/jcmm.70427
  24. Biomolecules. 2025 Feb 02. pii: 215. [Epub ahead of print]15(2):
    Autophagy and Cancer: Insights into Molecular Mechanisms and Therapeutic Approaches for Chronic Myeloid Leukemia.
    Mohd Adnan Kausar, Sadaf Anwar, Yusuf Saleem Khan, Ayman A Saleh, Mai Ali Abdelfattah Ahmed, Simran Kaur, Naveed Iqbal, Waseem Ahmad Siddiqui, Mohammad Zeeshan Najm.
      Autophagy is a critical cellular process that maintains homeostasis by recycling damaged or aberrant components. This process is orchestrated by a network of proteins that form autophagosomes, which engulf and degrade intracellular material. In cancer, autophagy plays a dual role: it suppresses tumor initiation in the early stages but supports tumor growth and survival in advanced stages. Chronic myeloid leukemia (CML), a hematological malignancy, is characterized by the Philadelphia chromosome, a chromosomal abnormality resulting from a translocation between chromosomes 9 and 22. Autophagy has emerged as a key factor in CML pathogenesis, promoting cancer cell survival and contributing to resistance against tyrosine kinase inhibitors (TKIs), the primary treatment for CML. Targeting autophagic pathways is being actively explored as a therapeutic approach to overcome drug resistance and enhance cancer cell death. Recent research highlights the intricate interplay between autophagy and CML progression, underscoring its role in disease biology and treatment outcomes. This review aims to provide a comprehensive analysis of the molecular and cellular mechanisms underlying CML, with a focus on the therapeutic potential of targeting autophagy.
    Keywords:  BCR-ABL; autophagosome; autophagy; chronic myeloid leukemia; tyrosine kinase inhibitors
    DOI:  https://doi.org/10.3390/biom15020215
  25. Diseases. 2025 Feb 16. pii: 60. [Epub ahead of print]13(2):
    TREM2 Alleviates Neuroinflammation by Maintaining Cellular Metabolic Homeostasis and Mitophagy Activity During Early Inflammation.
    Lingfeng Hu, Jie Liu, Jie Peng, Xiao Li, Zhangqiong Huang, Caixing Zhang, Shengtao Fan.
       AIMS: Inflammation is a pivotal characteristic of neurodegenerative diseases. The triggering receptor expressed on the myeloid cells 2 (TREM2) gene has previously been shown to suppress inflammation by directly inhibiting inflammation-related pathways. Mitochondrial dysfunction has recently emerged as another critical pathological manifestation of neurodegenerative diseases. Although TREM2 is involved in the regulation of cellular energy metabolism and mitochondrial autophagy, its role in the relationship between inflammation and mitochondrial autophagy remains unclear.
    METHODS: In this study, we generated TREM2-overexpressing BV-2 cells and established a neuroinflammatory model with LPS. We compared these cells with wild-type cells in terms of inflammation, metabolism, autophagy, and mitochondria using methods such as RT-qPCR, Western blotting, immunocytochemistry, transmission electron microscopy, and flow cytometry.
    RESULTS: Microglia overexpressing TREM2 exhibited increased resistance to inflammation. Additionally, these cells inhibited the metabolic reprogramming that occurs early in LPS-induced inflammation, reduced ROS release, mitigated mitochondrial damage, maintained a certain level of autophagic activity, and cleared damaged mitochondria. Consequently, they alleviated the inflammation caused by the mitochondrial barrier.
    CONCLUSIONS: ur results suggest that TREM2 can alleviate inflammation by maintaining cellular metabolic homeostasis and mitochondrial autophagy activity.
    Keywords:  TREM2; microglia; mitochondrial; mitophagy; neuroinflammation
    DOI:  https://doi.org/10.3390/diseases13020060
  26. Science. 2025 Feb 28. 387(6737): eadp4120
    Liver ALKBH5 regulates glucose and lipid homeostasis independently through GCGR and mTORC1 signaling.
    Kaixin Ding, Zhipeng Zhang, Zhengbin Han, Lei Shi, Xinzhi Li, Yutong Liu, Zhenzhi Li, Chongchong Zhao, Yifeng Cui, Liying Zhou, Bolin Xu, Wenjing Zhou, Yikui Zhao, Zhiqiang Wang, He Huang, Liwei Xie, Xiao-Wei Chen, Zheng Chen.
      Maintaining glucose and lipid homeostasis is crucial for health, with dysregulation leading to metabolic diseases such as type 2 diabetes mellitus (T2DM) and metabolic dysfunction-associated fatty liver disease (MAFLD). This study identifies alkylation repair homolog protein 5 (ALKBH5), an RNA N6-methyladenosine (m6A) demethylase, as a major regulator in metabolic disease. ALKBH5 is up-regulated in the liver during obesity and also phosphorylated by protein kinase A, causing its translocation to the cytosol. Hepatocyte-specific deletion of Alkbh5 reduces glucose and lipids by inhibiting the glucagon receptor (GCGR) and mammalian target of rapamycin complex 1 (mTORC1) signaling pathways. Targeted knockdown of hepatic Alkbh5 reverses T2DM and MAFLD in diabetic mice, highlighting its therapeutic potential. This study unveils a regulatory mechanism wherein ALKBH5 orchestrates glucose and lipid homeostasis by integrating the GCGR and mTORC1 pathways, providing insight into the regulation of metabolic diseases.
    DOI:  https://doi.org/10.1126/science.adp4120
  27. Am J Respir Cell Mol Biol. 2025 Feb 25.
    TFEB SUMOylation in Airway Epithelial Cells Impairs Lysosomal Biogenesis to Promote Asthma Development.
    Qianying Yu, Yao Zhou, Jing Wang, Meng Zhang, Caixia Di, Yujiao Wu, Qun Wu, Wen Su, Jinke Cheng, Jiajia Lv, Min Wu, Zhenwei Xia.
      Lysosomal dysfunction is the primary cause of various immune disorders. Transcription factor EB (TFEB) SUMOylation is critically involved in the lysosomal biogenesis. Whether TFEB SUMOylation-associated lysosomal dysfunction contributes to asthma pathogenesis remain to be determined. Here, we observed that ovalbumin (OVA)-stimulation impaired lysosomal function through TFEB SUMOylation, which leads to increased NLRP3 and inflammatory factors. Mechanistically, mutation of TFEB SUMOylation site did not abolish the ability of its nuclear translocation, but increased TFEB stability and binding capability with target genes' promoters, thereby promoting lysosomal biogenesis and bioactivity through liquid-liquid phase separation (LLPS), and thus inhibiting the production of inflammatory factors and alleviating allergic airway inflammation. Our observations demonstrate that TFEB SUMOylation interferes with lysosomal biogenesis contributing to asthma pathogenesis, lending mechanistic insight into asthmatic disease and improving our understanding of the transcriptional regulation of host immune responses.
    Keywords:  NLRP3 inflammasome; SUMO1; TFEB; epithelial cells; lysosomes
    DOI:  https://doi.org/10.1165/rcmb.2024-0191OC
  28. Biomolecules. 2025 Feb 11. pii: 261. [Epub ahead of print]15(2):
    Evolutionary Insights into Irisin/FNDC5: Roles in Aging and Disease from Drosophila to Mammals.
    Kiwon Lee, Myungjin Kim.
      The Irisin/FNDC5 protein family has emerged as a pivotal link between exercise and the prevention of age-associated diseases. Irisin is highly expressed during exercise from skeletal and cardiac muscle cells, playing a critical role in mediating systemic health benefits through its actions on various tissues. However, Irisin levels decline with age, correlating with a heightened incidence of diseases such as muscle weakness, cardiovascular disorders, and neurodegeneration. Notably, the administration of Irisin has shown significant potential in both preventing and treating these conditions. Recently, an Irisin/FNDC5 homolog was identified in an invertebrate Drosophila model, providing valuable insights into its conserved role in exercise physiology. Importantly, Irisin/FNDC5 has been demonstrated to regulate autophagy-a process essential for clearing excessive nutrients, toxic aggregates, and dysfunctional organelles-in both flies and mammals. Dysregulated autophagy is often implicated in age-related diseases, highlighting its relevance to Irisin/FNDC5's functions. These findings deepen our understanding of Irisin/FNDC5's roles and its potential as a therapeutic target for mitigating aging-related health decline. Further studies are needed to elucidate the precise mechanisms by which Irisin regulates autophagy and its broader impact on physiological aging and related diseases.
    Keywords:  Drosophila; FNDC5; Iditarod; Irisin; aging; exercise
    DOI:  https://doi.org/10.3390/biom15020261
  29. Methods Mol Biol. 2025 ;2882 105-119
    Methods to Determine Lysosomal AMPK Activation.
    Chen-Song Zhang, Sheng-Cai Lin.
      Recent studies have revealed that AMP-activated protein kinase (AMPK) can be activated in a non-canonical, AMP- and ADP-independent manner on the lysosome surface in response to low glucose. This novel mode of activation requires the participation of the glycolytic enzyme aldolase, which acts as a sensor of falling levels of the glucose metabolite fructose-1,6-bisphosphate (FBP). The FBP-unoccupied aldolase blocks the V subfamily of transient receptor potential (TRPV) cation channel to generate a local low calcium environment, under which conditions the inhibited TRPVs contact the lysosome-localized vacuolar ATPase (v-ATPase). This in turn triggers the translocation of AXIN and the associated liver kinase B1 (LKB1) to the lysosomal surface to activate AMPK thereon. Interestingly, such a lysosomal AMPK activating pathway has now been demonstrated to be shared by both the anti-diabetic drug metformin and the anti-tumor/inflammation drug mannose. Here, we describe the experimental conditions and procedures for distinguishing if a certain activation of AMPK is mediated by the lysosomal pathway. We will update the previously described methods for determining AXIN lysosomal translocation and the AMP:ATP and ADP:ATP ratios that are used for differentiating the lysosomal pathway from the canonical, AMP-dependent pathway [1, 2]. We also describe how to determine the lysosomal pH and the inhibition of TRPV activity that are prerequisite for triggering the lysosomal pathway during sensing of low glucose.
    Keywords:  AMPK; AXIN; Aldolase; LKB1; Lysosome; Ragulator; TRPV; v-ATPase
    DOI:  https://doi.org/10.1007/978-1-0716-4284-9_5
  30. Acta Neuropathol Commun. 2025 Feb 24. 13(1): 41
    Hippocampal mitophagy alterations in MAPT-associated frontotemporal dementia with parkinsonism.
    Tyrique Richardson, Xu Hou, Fabienne C Fiesel, Zbigniew K Wszolek, Dennis W Dickson, Wolfdieter Springer.
      The enzyme pair PINK1 and PRKN together orchestrates a cytoprotective mitophagy pathway that selectively tags damaged mitochondria with phospho-serine 65 ubiquitin (pS65-Ub) and directs them for autophagic-lysosomal degradation (mitophagy). We previously demonstrated a significant accumulation of pS65-Ub signals in autopsy brains of sporadic Lewy body disease and Alzheimer's disease cases, which strongly correlated with early tau pathology. In this study, we extended our analysis to a series of pathologically confirmed cases of frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17) harboring different pathogenic mutations in MAPT, the gene encoding tau. We assessed the morphology, levels, and distribution of the mitophagy tag pS65-Ub in several affected brain regions and hippocampal subregions of these cases. While tau pathological burden was similarly increased across all FTDP-17 cases, pS65-Ub immunopositive signals were strongly accumulated in P301L cases and only weakly present in N279K cases. In the hippocampus of both mutation groups, the density of pS65-Ub positive cells was overall the greatest in the dentate gyrus followed by the subiculum, CA1, and CA2/3, with the CA4 showing only minimal presence. Notably, positive cells in the subiculum carried greater numbers and particularly vacuolar pS65-Ub structures, while cells in the dentate gyrus mostly contained fewer and rather granular pS65-Ub inclusions. Single cell analyses revealed differential co-localization of pS65-Ub with mitochondria, autophagosomes, and lysosomes in these two regions. Together, our study demonstrates distinct mitophagy alteration in different FTDP-17 MAPT cases and hint at selective organelle failure in the hippocampal subregions that was associated with the P301L mutation.
    Keywords:   MAPT P301L; Frontotemporal dementia with parkinsonism; Hippocampus; Mitochondria; Mitophagy; PINK1; PRKN; Parkin; Phosphorylated ubiquitin; Tau
    DOI:  https://doi.org/10.1186/s40478-025-01955-8
  31. Cell Mol Life Sci. 2025 Feb 22. 82(1): 82
    Class I PI3Ks activate stretch-induced autophagy in trabecular meshwork cells.
    Myoung Sup Shim, Ethan J Sim, Kevin Betsch, Vaibhav Desikan, Chien-Chia Su, Diego Pastor-Valverde, Yang Sun, Paloma B Liton.
      Elevated intraocular pressure (IOP) is the primary risk factor for glaucoma, a leading cause of irreversible blindness worldwide. IOP homeostasis is maintained through a balance between aqueous humor production and its drainage through the trabecular meshwork (TM)/Schlemm's Canal (SC) outflow pathway. Prior studies by our laboratory reported a key role of mechanical forces and primary cilia (PC)-dependent stretch-induced autophagy in IOP homeostasis. However, the precise mechanism regulating this process remains elusive. In this study, we investigated the upstream signaling pathway orchestrating autophagy activation during cyclic mechanical stretch (CMS) in primary cultured human TM cells, using biochemical and cell biological analyses. Our results indicate that TM cells express catalytic subunits of class IA PI3Ks (PIK3CA, B, and D), and that inhibition of class IA isoforms, but not class II and III, significantly prevent CMS-induced autophagy. Importantly, PIK3CA was found to localize in the PC. Furthermore, we identified a coordinated action of Class IA PI3Ks along INPP4A/B, a 4' inositol phosphatase, responsible for the formation of PI(3,4)P2 and PI(3)P and stretch-induced autophagy in TM cells. These findings contribute to a deeper understanding of the molecular mechanisms underlying IOP homeostasis.
    Keywords:  Autophagy; Glaucoma; Mechanical stress; PI3K; Primary cilia; Trabecular meshwork
    DOI:  https://doi.org/10.1007/s00018-025-05615-x
  32. EMBO Mol Med. 2025 Feb 24.
    X-linked myopathy with excessive autophagy: characterization and therapy testing in a zebrafish model.
    Lily Huang, Rebecca Simonian, Michael A Lopez, Muthukumar Karuppasamy, Veronica M Sanders, Katherine G English, Lacramioara Fabian, Matthew S Alexander, James J Dowling.
      X-linked myopathy with excessive autophagy (XMEA), a rare childhood-onset autophagic vacuolar myopathy caused by mutations in VMA21, is characterized by proximal muscle weakness and progressive vacuolation. VMA21 encodes a protein chaperone of the vacuolar hydrogen ion ATPase, the loss of which leads to lysosomal neutralization and impaired function. At present, there is an incomplete understanding of XMEA, its mechanisms, consequences on other systems, and therapeutic strategies. A significant barrier to advancing knowledge and treatments is the lack of XMEA animal models. Therefore, we used CRISPR-Cas9 editing to engineer a loss-of-function mutation in zebrafish vma21. The vma21 mutant zebrafish phenocopy the human disease with impaired motor function and survival, liver dysfunction, and dysregulated autophagy indicated by lysosomal de-acidification, the presence of characteristic autophagic vacuoles in muscle fibers, altered autophagic flux, and reduced lysosomal marker staining. As proof-of-concept, we found that two drugs, edaravone and LY294002, improve swim behavior and survival. In total, we generated and characterized a novel preclinical zebrafish XMEA model and demonstrated its suitability for studying disease pathomechanisms and identifying potential therapeutic targets.
    Keywords:  Autophagy; Myopathy; VMA21; XMEA; Zebrafish
    DOI:  https://doi.org/10.1038/s44321-025-00204-8
  33. Int J Mol Sci. 2025 Feb 19. pii: 1752. [Epub ahead of print]26(4):
    Emerging Role of Hypoxia-Inducible Factors (HIFs) in Modulating Autophagy: Perspectives on Cancer Therapy.
    Maroua Jalouli.
      Hypoxia-inducible factors (HIFs) are master regulators of cellular responses to low oxygen levels and modulate autophagy, a conserved process essential for maintaining homeostasis. Under hypoxic conditions, HIFs regulate the expression of autophagy-related genes and influence autophagic flux and cellular stress responses. Dysregulated hypoxia-induced autophagy promotes cancer cell survival, metabolism, and metastasis, thereby contributing to treatment resistance. Targeting HIF-mediated pathways or modulating autophagic processes offers the potential to improve traditional cancer therapies and overcome drug resistance. Pharmacological inhibitors of HIFs or autophagy, either alone or in combination with other treatments, may disrupt the pro-survival mechanisms within the hypoxic tumor microenvironment. Further research is needed to elucidate the intricate interplay between HIF signaling and the autophagy machinery in cancer cells. Understanding these processes could pave the way for novel therapeutic strategies to enhance treatment outcomes and combat drug resistance. This review highlights the complex relationship between HIFs and autophagy in cancer development and therapy, offering insights into how targeting these pathways may improve patient outcomes.
    Keywords:  autophagy; cancer therapy; drug resistance; hypoxia-inducible factors; tumor progression
    DOI:  https://doi.org/10.3390/ijms26041752
  34. Commun Biol. 2025 Feb 23. 8(1): 292
    Targeting NLRC5 in cardiomyocytes protects postinfarction cardiac injury by enhancing autophagy flux through the CAVIN1/CAV1 axis.
    Lingfeng Gu, Sibo Wang, Liuhua Zhou, Wenjing Wang, Yulin Bao, Ye He, Tongtong Yang, Jiateng Sun, Qiqi Jiang, Tiankai Shan, Chong Du, Zemu Wang, Hao Wang, Liping Xie, Aihua Gu, Yang Zhao, Yong Ji, Qiming Wang, Liansheng Wang.
      NOD-like receptor (NLR) family proteins are implicated in various cardiovascular diseases. However, the precise role of NLRC5, the largest member of this family, in myocardial infarction (MI) remains poorly understood. This study reveals that NLRC5 is upregulated in the hearts of both patients with MI and MI mice. Silencing NLRC5 in cardiomyocytes impairs cardiac repair and functional recovery, while its overexpression enhances these processes. Furthermore, NLRC5 promotes autophagy in cardiomyocytes, and its protective effects are diminished upon autophagy inhibition. Mechanistically, NLRC5 interacts with CAVIN1, facilitating its degradation and subsequent downregulation of CAV1, which in turn increases the expression of the ATG12-ATG5 complex to stimulate autophagy. Conversely, CAV1 overexpression partially suppresses autophagy and attenuates the improvements in cardiac function observed in NLRC5-overexpressing MI hearts. This study highlights the critical regulatory role of NLRC5 in modulating cardiomyocyte autophagy flux, suggesting that NLRC5 activation may represent a promising therapeutic strategy for MI.
    DOI:  https://doi.org/10.1038/s42003-025-07755-z
  35. bioRxiv. 2025 Feb 15. pii: 2025.02.13.638142. [Epub ahead of print]
    Genetic and pharmacological correction of impaired mitophagy in retinal ganglion cells rescues glaucomatous neurodegeneration.
    Prabhavathi Maddineni, Bindu Kodati, Balasankara Reddy Kaipa, Karthikeyan Kesavan, J Cameron Millar, Sam Yacoub, Ramesh B Kasetti, Abbot F Clark, Gulab S Zode.
      Progressive loss of retinal ganglion cells (RGCs) and degeneration of optic nerve axons are the pathological hallmarks of glaucoma. Ocular hypertension (OHT) and mitochondrial dysfunction are linked to neurodegeneration and vision loss in glaucoma. However, the exact mechanism of mitochondrial dysfunction leading to glaucomatous neurodegeneration is poorly understood. Using multiple mouse models of OHT and human eyes from normal and glaucoma donors, we show that OHT induces impaired mitophagy in RGCs, resulting in the accumulation of dysfunctional mitochondria and contributing to glaucomatous neurodegeneration. Using mitophagy reporter mice, we show that impaired mitophagy precedes glaucomatous neurodegeneration. Notably, the pharmacological rescue of impaired mitophagy via Torin-2 or genetic upregulation of RGC-specific Parkin expression restores the structural and functional integrity of RGCs and their axons in mouse models of glaucoma and ex-vivo human retinal-explant cultures. Our study indicates that impaired mitophagy contributes to mitochondrial dysfunction and oxidative stress, leading to glaucomatous neurodegeneration. Enhancing mitophagy in RGCs represents a promising therapeutic strategy to prevent glaucomatous neurodegeneration.
    DOI:  https://doi.org/10.1101/2025.02.13.638142
  36. CNS Neurosci Ther. 2025 Feb;31(2): e70293
    Cleaving PINK1 or PGAM5? Involvement of PARL in Methamphetamine-Induced Excessive Mitophagy and Neuronal Necroptosis.
    Di An, Chuling Zhang, Peng Zhou, Yifei Wang, Sining Meng, Yanlong Chen, Weixiao Xu, Jiankang Xuan, Jianping Xiong, Jie Cheng, Rong Gao, Jun Wang, Xufeng Chen.
       BACKGROUND: Methamphetamine (Meth) is a potent psychoactive stimulant that triggers complex neurotoxicity characterized by autophagy-associated neuronal death. However, the potential mechanisms remain poorly understood. This study aimed to decipher the Meth-induced neuronal necroptosis involving mitochondrial defect-initiated excessive mitophagy caused by aberrant presenilin-associated rhomboid-like (PARL) cleavage of PTEN-induced kinase 1 (PINK1) and phosphoglycerate mutase family member 5 (PGAM5).
    METHODS AND RESULTS: With the transcriptome analysis, Meth exposure significantly affected autophagy, mitophagy, and necroptosis pathways; meanwhile, the proteomic analysis revealed a marked decline in the level of PARL, which led to an imbalance in intramembrane proteolysis of PINK1 and PGAM5. In behavioral tests, Meth administration elicited pronounced cognitive decline in mice, accompanied by decreased neuronal numbers, massive autophagosomes, and mitochondrial fragmentation, and these processes can be dramatically reversed by knockin of PARL and knockdown of PGAM5 in the mouse hippocampus, molecularly manifesting as decreased necrosome formation and phosphorylated mixed lineage kinase domain-like (p-MLKL) mitochondrial membrane translocation, and improved autophagic flux.
    CONCLUSION: In summary, these findings collectively underscore the key roles of the PARL-PGAM5 axis in Meth-mediated neuronal necroptosis and that targeting this axis may provide promising therapeutic strategies for mitigating Meth-induced neurotoxicity.
    Keywords:  PARL; PGAM5; methamphetamine; mitophagy; necroptosis
    DOI:  https://doi.org/10.1111/cns.70293
  37. Cancer Sci. 2025 Feb 27.
    EPHB2 Promotes the Progression of Oral Squamous Cell Carcinoma Cells Through the Activation of VPS4A-Mediated Autophagy.
    Yongchun Peng, Jianbo Zhang, Haoxuan Guo, Zhijing He, Yi Jiang, Sheng Zhang, Tengfei Fan.
      Oral squamous cell carcinoma (OSCC) is a prevalent type of head and neck neoplasm distinguished by a high risk of metastasis and a poor prognosis. Nevertheless, the fundamental mechanisms of OSCC cell proliferation and metastasis remain poorly understood. Autophagy, as the principal intracellular degradation system, has been implicated in OSCC progression; however, its underlying mechanism remains unclear. In this study, transcriptomic sequencing analysis was performed using both The Cancer Genome Atlas (TCGA) database and samples from OSCC patients and revealed significant upregulation of EPHB2 expression, which is positively correlated with OSCC metastasis and a poor prognosis. In subsequent studies, we observed that the knockdown of EPHB2 resulted in the blockade of autophagic flux due to impaired lysosomal function, leading to inhibited proliferation, migration, and invasion in OSCC cells. Furthermore, the knockdown of EPHB2 significantly suppressed the expression of VPS4A, a key mediator that facilitates autolysosomal degradation. The overexpression of VPS4A restored lysosomal function and autophagic flux, thereby attenuating the inhibitory effects of EPHB2 knockdown on OSCC cell progression. The findings of this study demonstrate that the molecular mechanism underlying EPHB2 regulation of autophagic flux to promote OSCC progression is by regulating VPS4A activity and that EPHB2 may be a diagnostic biomarker and therapeutic target for OSCC prevention and treatment.
    Keywords:  EPHB2; OSCC; VPS4A; autophagy; metastasis
    DOI:  https://doi.org/10.1111/cas.70033
  38. Biol Cell. 2025 Feb;117(2): e12001
    Nuclear stiffness through lamin A/C overexpression differentially modulates chromosomal instability biomarkers.
    Mireia Bosch-Calvet, Alejandro Pérez-Venteo, Alex Cebria-Xart, Marta Garcia-Cajide, Caroline Mauvezin.
       BACKGROUND INFORMATION: Mitosis is crucial for the faithful transmission of genetic material, and disruptions can result in chromosomal instability (CIN), a hallmark of cancer. CIN is a known driver of tumor heterogeneity and anti-cancer drug resistance, thus highlighting the need to assess CIN levels in cancer cells to design effective targeted therapy. While micronuclei are widely recognized as CIN markers, we have recently identified the toroidal nucleus, a novel ring-shaped nuclear phenotype arising as well from chromosome mis-segregation.
    RESULTS: Here, we examined whether increasing nuclear envelope stiffness through lamin A/C overexpression could affect the formation of toroidal nuclei and micronuclei. Interestingly, lamin A/C overexpression led to an increase in toroidal nuclei while reducing micronuclei prevalence. We demonstrated that chromatin compaction and nuclear stiffness drive the formation of toroidal nuclei. Furthermore, inhibition of autophagy and lysosomal function elevated the frequency of toroidal nuclei without affecting the number of micronuclei in the whole cell population. We demonstrated that this divergence between the two CIN biomarkers is independent of defects in lamin A processing.
    CONCLUSIONS AND SIGNIFICANCE: These findings uncover a complex interplay between nuclear architecture and levels of CIN, advancing our understanding of the mechanisms supporting genomic stability and further contributing to cancer biology.
    Keywords:  autophagy (D001343); chromosomal Instability (D043171); lamins (D034882); lysosomes (D008247)
    DOI:  https://doi.org/10.1111/boc.12001
  39. Neuron. 2025 Feb 15. pii: S0896-6273(25)00045-5. [Epub ahead of print]
    Neuronal autophagy in the control of synapse function.
    Anna Karpova, P Robin Hiesinger, Marijn Kuijpers, Anne Albrecht, Janine Kirstein, Maria Andres-Alonso, Alexander Biermeier, Britta J Eickholt, Marina Mikhaylova, Marta Maglione, Carolina Montenegro-Venegas, Stephan J Sigrist, Eckart D Gundelfinger, Volker Haucke, Michael R Kreutz.
      Neurons are long-lived postmitotic cells that capitalize on autophagy to remove toxic or defective proteins and organelles to maintain neurotransmission and the integrity of their functional proteome. Mutations in autophagy genes cause congenital diseases, sharing prominent brain dysfunctions including epilepsy, intellectual disability, and neurodegeneration. Ablation of core autophagy genes in neurons or glia disrupts normal behavior, leading to motor deficits, memory impairment, altered sociability, and epilepsy, which are associated with defects in synapse maturation, plasticity, and neurotransmitter release. In spite of the importance of autophagy for brain physiology, the substrates of neuronal autophagy and the mechanisms by which defects in autophagy affect synaptic function in health and disease remain controversial. Here, we summarize the current state of knowledge on neuronal autophagy, address the existing controversies and inconsistencies in the field, and provide a roadmap for future research on the role of autophagy in the control of synaptic function.
    Keywords:  autophagy; memory; neurological diseases; neurotransmission; synapse; synaptic plasticity
    DOI:  https://doi.org/10.1016/j.neuron.2025.01.019
  40. EMBO Rep. 2025 Feb 27.
    The spectrum of lysosomal stress and damage responses: from mechanosensing to inflammation.
    Ori Scott, Ekambir Saran, Spencer A Freeman.
      Cells and tissues turn over their aged and damaged components in order to adapt to a changing environment and maintain homeostasis. These functions rely on lysosomes, dynamic and heterogeneous organelles that play essential roles in nutrient redistribution, metabolism, signaling, gene regulation, plasma membrane repair, and immunity. Because of metabolic fluctuations and pathogenic threats, lysosomes must adapt in the short and long term to maintain functionality. In response to such challenges, lysosomes deploy a variety of mechanisms that prevent the breaching of their membrane and escape of their contents, including pathogen-associated molecules and hydrolases. While transient permeabilization of the lysosomal membrane can have acute beneficial effects, supporting inflammation and antigen cross-presentation, sustained or repeated lysosomal perforations have adverse metabolic and transcriptional consequences and can lead to cell death. This review outlines factors contributing to lysosomal stress and damage perception, as well as remedial processes aimed at addressing lysosomal disruptions. We conclude that lysosomal stress plays widespread roles in human physiology and pathology, the understanding and manipulation of which can open the door to novel therapeutic strategies.
    Keywords:  Autophagy; Glycocalyx; Host–pathogen; Phagosolysosome; Pore-forming Toxins
    DOI:  https://doi.org/10.1038/s44319-025-00405-9
  41. Nat Commun. 2024 Dec 30. 15(1): 10829
    Spatiotemporal proteomics reveals the biosynthetic lysosomal membrane protein interactome in neurons.
    Chun Hei Li, Noortje Kersten, Nazmiye Özkan, Dan T M Nguyen, Max Koppers, Harm Post, Maarten Altelaar, Ginny G Farias.
      Lysosomes are membrane-bound organelles critical for maintaining cellular homeostasis. Delivery of biosynthetic lysosomal proteins to lysosomes is crucial to orchestrate proper lysosomal function. However, it remains unknown how the delivery of biosynthetic lysosomal proteins to lysosomes is ensured in neurons, which are highly polarized cells. Here, we developed Protein Origin, Trafficking And Targeting to Organelle Mapping (POTATOMap), by combining trafficking synchronization and proximity-labelling based proteomics, to unravel the trafficking routes and interactome of the biosynthetic lysosomal membrane protein LAMP1 at specified time points. This approach, combined with advanced microscopy, enables us to identify the neuronal domain-specific trafficking machineries of biosynthetic LAMP1. We reveal a role in replenishing axonal lysosomes, in delivery of newly synthesized axonal synaptic proteins, and interactions with RNA granules to facilitate hitchhiking in the axon. POTATOMap offers a robust approach to map out dynamic biosynthetic protein trafficking and interactome from their origin to destination.
    DOI:  https://doi.org/10.1038/s41467-024-55052-w
  42. J Adv Res. 2025 Feb 22. pii: S2090-1232(25)00123-7. [Epub ahead of print]
    Lipophagy acts as a nutritional adaptation mechanism for the filamentous entomopathogenic fungus Beauveria bassiana to colonize within the hosts.
    Jin-Li Ding, Ming-Guang Feng, Sheng-Hua Ying.
       INTRODUCTION: Metabolic adaptation to various nutrients is crucial for the pathogenic growth and virulence of filamentous fungal pathogens. Despite its importance, the mechanisms underlying fungal adaptation to nutrient shifts, especially at the subcellular level, remain incompletely understood.
    OBJECTIVES: Our study aims to investigate the mechanisms involved in metabolic adaptation in filamentous fungi.
    METHODS: The filamentous entomopathogenic fungus Beauveria bassiana was used as a representative of filamentous fungi. Gene functional analyses were conducted via gene disruption and complementation. Vacuolar targeting of lipid droplets were determined with transmission electron microscopy and fluorescence microscopy. Protein interaction was determined with yeast-two hybridization and co-immunoprecipitation methods.
    RESULTS: The filamentous entomopathogenic fungus Beauveria bassiana was found to initiate autophagy, and further lipophagy, when transitioning from utilizing fatty acids to carbohydrates, while also proliferating in the host hemocoel. The disruption of three critical autophagy-related genes (ATG), specifically BbATG1, BbATG8, and BbATG11, hindered the vacuolar targeting of lipid droplets (LD) and worsened the impaired growth and dimorphism in fatty acid medium subjected to cell-wall perturbance stress. Notably, BbSun4, a protein containing a SUN4 domain, was required for lipophagy, as it tagged the lipid droplets. BbMcp, which features a methyl-accepting chemotaxis-like domain, engaged directly with both BbAtg8 and BbSun4, thereby enhancing the interaction between these proteins. It is important to note that BbMcp solely facilitated lipophagy during nutrient shifts rather than during starvation stress. The loss of lipophagy was proved detrimental to fungal cytomembrane integrity, growth, and overall development, ultimately leading to a marked reduction in virulence.
    CONCLUSION: Lipophagy is a molecular pathway that consists of a selective autophagy receptor, a bridging factor, and Atg8, which is essential for fungal metabolic adaptation during colonizing within the host niches. This study deepens our understanding of the molecular mechanism underlying the fungus-host interaction and vacuolar targeting pathways in selective autophagy.
    Keywords:  Dimorphism; Fungal pathogenesis; Metabolic adaptation; Pathogenic fungi; Selective autophagy
    DOI:  https://doi.org/10.1016/j.jare.2025.02.025
  43. Biomolecules. 2025 Feb 18. pii: 299. [Epub ahead of print]15(2):
    RORA Regulates Autophagy in Hair Follicle Stem Cells by Upregulating the Expression Level of the Sqstm1 Gene.
    Xuefei Zhao, Yanchun Xu, Shuqi Li, Suying Bai, Wei Zhang, Yu Zhang.
      The hair coat is an adaptive evolutionary trait unique to mammals, aiding them in adapting to complex environmental challenges. Although some of the factors involved in regulating hair follicle development have been characterized, further in-depth research is still needed. Retinoic acid receptor-related orphan receptor alpha (RORA), as a member of the nuclear receptor family, is highly involved in the regulation of cellular states. Previous studies have shown that autophagy plays a significant role in hair follicle development. This study uses rat hair follicle stem cells (HFSCs) as a model to analyze the impact of RORA on the autophagy levels of HFSCs. Upon activation of RORA, autophagy indicators such as the LC3-II/LC3-I ratio and MDC staining significantly increased, suggesting an elevated level of autophagy in HFSCs. Following treatment with chloroquine, the LC3-II/LC3-I ratio, as well as the expression levels of BECN1 protein and SQSTM1 protein, were markedly elevated in the cells, indicating that the autophagic flux was unobstructed and ruling out the possibility that RORA activation impeded autophagy. Additionally, the level of the Sqstm1 gene increased markedly after RORA activation promoted autophagy in the cells. We found that RORA regulates the transcription level of Sqstm1 by binding to its promoter region. We believe that RORA activation significantly promotes the level of autophagy, particularly selective autophagy, in HFSCs, suggesting that RORA has the potential to become a new target for research on hair follicle development. This research provides a theoretical foundation for studies on hair follicle development and also offers new insights for the treatment of diseases such as alopecia.
    Keywords:  RORA; Sqstm1; autophagy; hair follicle; hair follicle stem cells
    DOI:  https://doi.org/10.3390/biom15020299
  44. Clin Genet. 2025 Feb 24.
    A Novel RHEB Germline Variant Associated With Intellectual Disability and Epilepsy: Expanding the Spectrum of mTORopathies.
    Juan Pablo Trujillo-Quintero, Anna Brunet-Vega, Nino Spataro, Joan Petanas, Oriol Gallego, Francesca Mateo, Miquel Angel Pujana, Anna Ruiz.
      The mTOR cascade is a critical player in the pathogenesis of focal epilepsies and cortical malformations, collectively referred to as mTORopathies. The Ras homolog enriched in brain (RHEB) gene is a member of the RAS-family GTPases and a potent activator of the mechanistic target of rapamycin complex (mTORC1). Brain somatic variants in the RHEB gene have been described in patients affected by focal cortical dysplasia and hemimegalencephaly abnormalities. Conversely, germline genetic variants in the RHEB gene have been poorly reported in patients with neurodevelopmental disorders. This study describes the phenotype of a patient with global developmental delay and epilepsy carrying a novel germline de novo heterozygous missense variant (c.71 T>C; p.Ile24Thr) in the RHEB gene. Previously reported patients are reviewed and compared to the case reported here, expanding the genotype and phenotype spectrum of mTORopathies.
    Keywords:  RHEB; epilepsy; mTOR; mTORopathies; neurodevelopmental disorder
    DOI:  https://doi.org/10.1111/cge.14734
  45. Nat Commun. 2025 Feb 24. 16(1): 1920
    RNF167 mediates atypical ubiquitylation and degradation of RLRs via two distinct proteolytic pathways.
    Miao He, Zixiao Yang, Luyang Xie, Junhai Chen, Shurui Liu, Liaoxun Lu, Zibo Li, Birong Zheng, Yu Ye, Yuxin Lin, Lang Bu, Jingshu Xiao, Yongheng Zhong, Penghui Jia, Qiang Li, Yinming Liang, Deyin Guo, Chun-Mei Li, Panpan Hou.
      The precise regulation of the RIG-I-like receptors (RLRs)-mediated type I interferon (IFN-I) activation is crucial in antiviral immunity and maintaining host immune homeostasis in the meantime. Here, we identify an E3 ubiquitin ligase, namely RNF167, as a negative regulator of RLR-triggered IFN signaling. Mechanistically, RNF167 facilitates both atypical K6- and K11-linked polyubiquitination of RIG-I/MDA5 within CARD and CTD domains, respectively, which leads to degradation of the viral RNA sensors through dual proteolytic pathways. RIG-I/MDA5 conjugated with K6-linked ubiquitin chains in CARD domains is recognized by the autophagy cargo adaptor p62, that delivers the substrates to autolysosomes for selective autophagic degradation. In contrast, K11-linked polyubiquitination in CTD domains leads to proteasome-dependent degradation of RLRs. Thus, our study clarifies a function of atypical K6- and K11-linked polyubiquitination in the regulation of RLR signaling. We also unveil an elaborate synergistic effect of dual proteolysis systems to control amplitude and duration of IFN-I activation, hereby providing insights into physiological roles of the cross-talk between these two protein quality control pathways.
    DOI:  https://doi.org/10.1038/s41467-025-57245-3
  46. Environ Health (Wash). 2025 Feb 21. 3(2): 199-212
    Exposure to Manganese Induces Autophagy-Lysosomal Pathway Dysfunction-Mediated Tauopathy by Activating the cGAS-STING Pathway in the Brain.
    Xin Zhang, Jingjing Liu, Shiyin Zhong, Zhimin Zhang, Qiongli Zhou, Jirui Yang, Xuhong Chang, Hui Wang.
      Manganese (Mn) exposure leads to pathological accumulation of Tau-associated neurodegenerative disease and has become a major public health concern. However, the precise mechanism underlying this effect remains unclear. Here, the mechanism by which Mn induces dysfunction of autophagy-lysosomal pathway-mediated tauopathy by activating the cGAS-STING pathway was explored both in vitro and in vivo. Mn exposure induced tauopathy in microglia and in mice while activating the cGAS-STING pathway, inducing type I interferon production, and impairing the degradation function of the autophagy-lysosomal pathway. Importantly, inactivation of the cGAS-STING pathway rescued the degradation activity of the autophagy-lysosomal pathway, while tauopathy was markedly attenuated, as shown in both cGAS-knockout and STING-knockout BV2 microglia and in mice. Moreover, the autophagy inhibitor 3-methyladenine (3-MA) restored the impaired degradation activity of the autophagy-lysosomal pathway by inactivating the cGAS-STING pathway, thereby clearing Tau aggregation. Taken together, these results indicate that Mn exposure induces tauopathy by impairing the function of the autophagy-lysosomal pathway through the activation of the cGAS-STING pathway. Thus, this study identifies a novel mechanism by which Mn exposure induces Tau aggregation, which in turn triggers potential neurotoxicity, providing a foundation for future drug target research.
    DOI:  https://doi.org/10.1021/envhealth.4c00176
  47. Eur Heart J. 2025 Feb 25. pii: ehaf062. [Epub ahead of print]
    Autophagy is required for the therapeutic effects of the NAD+ precursor nicotinamide in obesity-related heart failure with preserved ejection fraction.
    Mahmoud Abdellatif, Francisco Vasques-Nóvoa, Viktoria Trummer-Herbst, Sylvère Durand, Franziska Koser, Moydul Islam, Jihoon Nah, Eun-Ah Sung, Ruli Feng, Fanny Aprahamian, Andreas Prokesch, Pablo Zardoya-Laguardia, Junichi Sadoshima, Abhinav Diwan, Wolfgang A Linke, João Pedro Ferreira, Guido Kroemer, Simon Sedej.
      
    Keywords:  Autophagy; HFpEF; Metabolic cardiomyopathy; Mitophagy; NAD+ metabolism; Obesity
    DOI:  https://doi.org/10.1093/eurheartj/ehaf062
  48. Angew Chem Int Ed Engl. 2025 Feb 27. e202503177
    Whole-cell Lysosome SMLM Imaging as Indicators for Functional Diagnostics with a Low-Phototoxic Spontaneously Blinking Probe.
    Qinglong Qiao, Aoxuan Song, Guanyu Jiang, Yuxin Zhou, Yiyan Ruan, Wenhao Jia, Xiaogang Liu, Zhaochao Xu.
      Lysosomal morphology and pH dynamics are closely linked to lysosome functions, making long-term single-molecule localization microscopy (SMLM) imaging of whole-cell lysosomes a potential indicator for functional diagnostics. However, the phototoxicity of probes in SMLM imaging often compromises the reliability of the observed lysosomal dynamics. Here, we developed Aze-HMSiR, a spontaneously blinking silicon rhodamine probe with near-infrared excitation, enabling low phototoxicity, long-term SMLM imaging of lysosomal morphology, and pH dynamics for up to 50 minutes. This probe enables super-resolution imaging of key lysosomal characteristics-distribution, size, and lumen pH-critical for understanding lysosomal dynamics and their physiological and pathological roles. By analyzing these parameters, we investigated lysosomal function under acidosis and starvation and evaluated the effects of seven anticancer drugs (paclitaxel, rapamycin, periplocoside, metformin, erastin, polyphyllin and gefitinib). Our results revealed that periplocoside significantly reduced lysosomal size, while other drugs generally induced an increase. Notably, paclitaxel elevated lysosomal pH and led to a sparser lysosomal distribution. These findings underscore the potential of Aze-HMSiR as a powerful tool for diagnosing lysosomal function and monitoring dynamic changes in response to physiological conditions and pharmacological treatments, establishing it as a robust platform for functional diagnostics and drug screening, particularly in cancer therapy.
    Keywords:  Functional Diagnostics; Low-phototoxic; Lysosome; Near-Infrared Probe; SMLM Imaging
    DOI:  https://doi.org/10.1002/anie.202503177
  49. Cell Biol Int. 2025 Feb 27.
    Chlorogenic Acid Enhances Beta-Lapachone-Induced Cell Death by Suppressing Autophagy in NQO1-Positive Cancer Cells.
    Sahib Zada, Md Entaz Bahar, Wanil Kim, Deok Ryong Kim.
      Resistance to apoptosis-inducing drugs frequently occurs in cancer cells, limiting their usefulness in ongoing cancer treatment. Despite ongoing efforts to overcome drug resistance, a definitive solution remains elusive. However, autophagy inhibition has been shown to enhance the effectiveness of some anticancer drugs and is a possible strategy for overcoming drug resistance. In this study, we demonstrate that chlorogenic acid (CGA), a natural antioxidant, significantly enhances beta-lapachone (β-Lap)-induced cell death in cancer cells. The augmented apoptosis induced by CGA is associated with activation of protein kinase A (PKA) in β-Lap-treated cells, independent of the antioxidant properties of CGA. As a result, PKA activation in cancer cells co-treated with β-Lap and CGA effectively inhibits autophagy. Notably, PKA activation leads to phosphorylation of microtubule-associated protein 1 A/1B-light chain 3 (LC3) at the serine 12 residue, causing autophagy suppression irrespective of mTORC activity. Importantly, the cell death induced by β-Lap and CGA in NQO1-overexpressing breast or lung cancers is closely linked to autophagy inhibition. These findings suggest that combining β-Lap and CGA might be a novel strategy for cancer therapy, particularly for overcoming drug resistance caused by autophagy induction in cancer cells.
    Keywords:  PKA; apoptosis; autophagy; beta‐Lapachone; chlorogenic acid; combination therapy
    DOI:  https://doi.org/10.1002/cbin.70006
  50. Neurospine. 2025 Feb 27.
    Extracellular Ubiquitin Enhances Autophagy and Inhibits Mitochondrial Apoptosis Pathway to Protect Neurons Against Spinal Cord Ischemic Injury via CXCR4.
    Hao Feng, Dehui Chen, Huina Chen, Dingwei Wu, Dandan Wang, Zhengxi Yu, Linquan Zhou, Zhenyu Wang, Wenge Liu.
       Objective: : Neuronal apoptosis is considered to be a critical process in spinal cord injury (SCI). Despite growing evidence of the antiapoptotic, anti-inflammatory, and modulation of ischemic injury tolerance effects of extracellular ubiquitin (eUb), existing studies have paid less attention to the impact of eUb in neurological injury disorders, particularly in SCI. This study aimed to investigate whether eUb can play a protective role in neurons, both in vitro and in vivo, and explores the underlying mechanisms.
    Methods: : By utilizing an oxygen glucose deprivation cellular model and a SCI rat model, we firstly investigated the therapeutic effects of eUb on SCI and further explored its effects on neuronal autophagy and mitochondria-dependent apoptosis-related indicators, as well as the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt)/mechanical target of rapamycin (mTOR) signaling pathway.
    Results: : In the SCI models both in vivo and in vitro, early intervention with eUb enhanced neuronal autophagy and inhibited mitochondrial apoptotic pathways, significantly mitigating SCI. Further studies had shown that this protective effect of eUb was mediated through its receptor, CXC chemokine receptor type 4 (CXCR4). Additionally, eUb-enhanced autophagy and antiapoptotic effects were possibly associated with inhibiting the PI3K/Akt/mTOR pathway.
    Conclusion: : In summary, the study demonstrates that early eUb intervention can enhance autophagy and inhibit mitochondrial apoptotic pathways via CXCR4, protecting neurons and promoting SCI repair.
    Keywords:  Autophagy; CXCR4; Extracellular ubiquitin; Mitochondrial apoptosis pathway; Spinal cord injury
    DOI:  https://doi.org/10.14245/ns.2448878.439
  51. Autophagy. 2025 Feb 27. 1-20
    A bacterial RING ubiquitin ligase triggering stepwise degradation of BRISC via TOLLIP-mediated selective autophagy manipulates host inflammatory response.
    Xinming Pan, Yangyang Sun, Jianan Liu, Rong Chen, Zhen Zhang, Caiying Li, Huochun Yao, Jiale Ma.
      Numerous bacterial pathogens have evolved tactics to interfere with the host ubiquitination network to evade clearance by the innate immune system. Nevertheless, the subtle antagonism between a bacterial ubiquitinase and a host deubiquitinase, through which they modify their respective targets within a multifaceted network, has yet to be characterized. BRCC3 isopeptidase complex (BRISC) is a newly identified K63-specific deubiquitinase complex that plays a crucial role in cellular signaling pathways such as inflammation. NleG, a type III secretion system (T3SS) effector, contains a conserved RING E3 ubiquitin ligase domain that interacts with host ubiquitination machinery, along with a distinct substrate-recognition domain that targets host proteins. Here, one particular variant, NleG6, was identified as mediating K27- and K29-linked polyubiquitination at residues K89 and K114 of ABRAXAS2/FAM175B, a scaffolding protein within the BRISC complex, leading to its degradation through TOLLIP (toll interacting protein)-mediated selective autophagy. Further investigations elucidated that ABRAXAS2 degradation triggered the subsequent degradation of adjacent BRCC3, which in turn, hindered TNIP1/ABIN1 degradation, ultimately inhibiting NFKB/NF-κB (nuclear factor kappa B)-mediated inflammatory responses. This chain of events offers valuable insights into the NFKB activation by the K63-specific deubiquitinating role of BRISC, unveiling how bacteria manipulate ubiquitin regulation and selective autophagy within the BRISC network to inhibit the host's inflammatory response and thus dominate a pathogen-host tug-of-war.Abbreviations: 3-MA: 3-methyladenine; A/E: attaching and effacing; ATG7: autophagy related 7; BafA1: bafilomycin A1; BNIP3L/Nix: BCL2 interacting protein 3 like; BRISC: BRCC3 isopeptidase complex; Cas9: CRISPR-associated system 9; co-IP: co-immunoprecipitation; CQ: chloroquine; CRISPR: clustered regulatory interspaced short palindromic repeat; DAPI: 4',6-diamidino2-phenylindole; DMSO: dimethyl sulfoxide; DUB: deubiquitinating enzyme; E. coli: Escherichia coli; EHEC: enterohemorrhagic Escherichia coli; EPEC: enteropathogenic Escherichia coli; GFP: green fluorescent protein; LEE: locus of enterocyte effacement; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MG132: cbz-leu-leu-leucinal; MOI: multiplicity of infection; NBR1: NBR1 autophagy cargo receptor; NC: negative control; NFKB/NF-κB: nuclear factor kappa B; NH4Cl: ammonium chloride; OPTN: optineurin; SQSTM1/p62: sequestosome 1; sgRNAs: small guide RNAs; T3SS: type III secretion system; TNF: tumor necrosis factor; TOLLIP: toll interacting protein; TRAF: TNF receptor associated factor; TUBB: tubulin beta class I; WCL: whole cell lysate; WT: wide type.
    Keywords:  BRISC complex; E3 ubiquitin ligase; NFKB; NleG; selective autophagy; type III secretion system
    DOI:  https://doi.org/10.1080/15548627.2025.2468140
  52. Cells. 2025 Feb 13. pii: 273. [Epub ahead of print]14(4):
    Sex Disparity in Cancer: Role of Autophagy and Estrogen Receptors.
    Rosa Vona, Camilla Cittadini, Elena Ortona, Paola Matarrese.
      Autophagy, a cellular process essential for maintaining homeostasis, plays a fundamental role in recycling damaged components and in adapting to stress. The dysregulation of autophagy is implicated in numerous human diseases, including cancer, where it exhibits a dual role as both a suppressor and a promoter, depending on the context and the stage of tumor development. The significant sex differences observed in autophagic processes are determined by biological factors, such as genetic makeup and sex hormones. Estrogens, through their interaction with specific receptors, modulate autophagy and influence tumor progression, therapy resistance, and the immune response to tumors. In females, the escape from X inactivation and estrogen signaling may be responsible for the advantages, in terms of lower incidence and longer survival, observed in oncology. Women often show better responses to traditional chemotherapy, while men respond better to immunotherapy. The action of sex hormones on the immune system could contribute to these differences. However, women experience more severe adverse reactions to anticancer drugs. The estrogen/autophagy crosstalk-involved in multiple aspects of the tumor, i.e., development, progression and the response to therapy-deserves an in-depth study, as it could highlight sex-specific mechanisms useful for designing innovative and gender-tailored treatments from the perspective of precision medicine.
    Keywords:  autophagy; estrogen receptor; gender disparity
    DOI:  https://doi.org/10.3390/cells14040273
  53. iScience. 2025 Feb 21. 28(2): 111838
    Evolutionary conserved regulation of TFEB stability by the E3 ubiquitin ligase WWP2 modulates response to stress in vivo.
    Juan A Garcia-Sanchez, Estelle Bonnet, Céline Loubatier, Anne Doye, Guillaume Paillier, Fabien Segui, Frédéric Larbret, Paul Chaintreuil, Ludovic Batistic, Cédric Torre, Marcel Deckert, Jolanta Polanowska, Patrick Munro, Laurent Boyer, Orane Visvikis.
      Transcription factor EB (TFEB) is a key transcription factor that orchestrates the cellular response to stress. Dysregulation of TFEB is associated with a range of human diseases, and understanding the regulatory mechanisms of TFEB is crucial for identifying potential drug targets. In this study, we used Caenorhabditis elegans to screen for E3 ubiquitin ligases regulating the activity of TFEB's homolog, HLH-30, upon pathogenic infection. We identified WWP-1 as a regulator of HLH-30-dependent immune response controlling HLH-30 stability to mediate host defense in vivo. We found that HLH-30 interacts with WWP-1, supporting a model of WWP-1 directly regulating HLH-30. Furthermore, we found that WWP-1's human homolog WWP2 binds TFEB, directly induces TFEB ubiquitination and stabilizes TFEB. Finally, we found that WWP2 is required for TFEB-dependent host response in human monocytes-derived macrophages upon infection. Overall, our work has identified an evolutionarily conserved regulation of TFEB by WWP2 and highlighted its role in modulating stress response.
    Keywords:  Cell biology; Functional aspects of cell biology
    DOI:  https://doi.org/10.1016/j.isci.2025.111838
  54. Cell Mol Life Sci. 2025 Feb 22. 82(1): 89
    A double-edged sword in antiviral defence: ATG7 binding dicer to promote virus replication.
    Yaotang Wu, Yang Wu, Chenlu Wang, Ningna Xiong, Wenxin Ji, Mei Fu, Junpeng Zhu, Zhixin Li, Jian Lin, Qian Yang.
      RNA interference (RNAi) and autophagy are two pivotal biological processes that regulate virus replication. This study explored the complex relationship between autophagy and RNAi in controlling influenza virus replication. Initially, we reported that influenza virus (H9N2) infection increases the viral load and the expression of autophagy markers while inhibiting the RNAi pathway. Subsequent studies employing autophagy enhancer and inhibitor treatments confirmed that avian influenza virus (AIV, H9N2) promotes viral replication by enhancing autophagy pathways. Further analysis revealed that ATG7, an autophagy protein, can interact with dicer to affect its antiviral functions. Finally, we discovered that infection with other avian RNA viruses, including infectious bursal disease virus (IBDV) and infectious bronchitis virus (IBV), induced the upregulation of ATG7, which blocked the RNAi pathway to facilitate virus replication. Our findings suggested that virus infection might trigger the upregulation of autophagy and downregulation of the RNAi pathway, revealing a complex interaction between these two biological processes in the defence against viral replication.
    Keywords:  ATG7; Autophagy; Dicer; H9N2; RNAi
    DOI:  https://doi.org/10.1007/s00018-025-05603-1
  55. J Bioenerg Biomembr. 2025 Feb 22.
    Dexmedetomidine activates mitophagy and protects against pyroptosis in oxygen-glucose deprivation/reperfusion-induced brain damage via PINK1/Parkin pathway activation.
    Jieru Zhang, Ruxia Li, Luyong Wang, Shuqin Ni.
      Accumulating studies have unraveled that dexmedetomidine (DEX) is neuroprotective against brain damage. However, it remains largely unknown about the mechanism involved in the neuroprotective effect of DEX. Therefore, this study explored whether DEX could affect mitophagy and pyroptosis in hypoxic-ischemic brain damage. We established a hippocampal neuron model of oxygen glucose-deprivation (OGD) and a rat model of cerebral ischemia/reperfusion (I/R) injury, which were then intervened with DEX and the autophagy inhibitor (3-MA). It was found that DEX intervention significantly increased neuron viability and mitophagy. Additionally, DEX intervention reversed increased oxidative stress and pyroptosis caused by OGD. DEX intervention further maintained the activation of the PINK1/Parkin pathway, while 3-MA treatment partly counteracted the protective effect of DEX on OGD-induced hippocampal neurons, suggesting that the inhibition of the PINK1/Parkin pathway reversed the function of DEX to increase cell viability and mitophagy and inhibit oxidative stress, pyroptosis, and apoptosis. Animal experiments also revealed that DEX intervention induced PINK1/Parkin pathway activation, reduced cerebral infarction and mitochondrial damage, promoted mitophagy, and inhibited pyroptosis, which was nullified by 3-MA treatment. Conclusively, DEX protects against pyroptosis and activates mitophagy in OGD/R-induced brain damage by activating the PINK1/Parkin pathway.
    Keywords:  Dexmedetomidine; Mitophagy; Oxidative stress; Oxygen-glucose deprivation; PINK1/Parkin pathway; Pyroptosis; Reperfusion injury
    DOI:  https://doi.org/10.1007/s10863-025-10051-4
  56. Int J Biol Sci. 2025 ;21(4): 1767-1783
    The Role of Mitochondrial Quality Control in Liver Diseases: Dawn of a Therapeutic Era.
    Jia Li, Wenqin Liu, Jie Zhang, Chao Sun.
      The liver is a vital metabolic organ that detoxifies substances, produces bile, stores nutrients, and regulates versatile metabolic processes. Maintaining normal liver cell function requires the prompt and delicate modulation of mitochondrial quality control (MQC), which encompasses a spectrum of processes such as mitochondrial fission, fusion, biogenesis, and mitophagy. Recent studies have shown that disruptions to this homeostatic status are closely linked to the advent and progression of a variety of acute and chronic liver diseases, including but not limited to alcohol-associated liver disease and metabolic dysfunction-associated fatty liver disease. However, the explicit mechanisms by which mitochondrial dysfunction impacts inflammatory pathways and cell death in the context of liver diseases remain unclear. In this narrative review, we provide a detailed description of MQC, analyze the mechanisms underpinning mitochondrial dysfunction induced by different detrimental insults, and further elucidate how imbalanced/disrupted MQC promotes the progression and aggravation of liver diseases, ultimately shedding light on the mitochondrion-centric therapeutic strategies for these pathophysiological entities.
    Keywords:  liver diseases; macrophage heterogeneity; mitochondrial dynamics; mitochondrial quality control; mitophagy; mtDNA; reactive oxygen species
    DOI:  https://doi.org/10.7150/ijbs.107777
  57. Int J Mol Sci. 2025 Feb 16. pii: 1691. [Epub ahead of print]26(4):
    Retinoic Acid Promotes Neuronal Differentiation While Increasing Proteins and Organelles Related to Autophagy.
    Gloria Lazzeri, Paola Lenzi, Giulia Signorini, Sara Raffaelli, Elisa Giammattei, Gianfranco Natale, Riccardo Ruffoli, Francesco Fornai, Michela Ferrucci.
      Retinoic acid (RA) is commonly used to differentiate SH-SY5Y neuroblastoma cells. This effect is sustained by a specific modulation of gene transcription, leading to marked changes in cellular proteins. In this scenario, autophagy may be pivotal in balancing protein synthesis and degradation. The present study analyzes whether some autophagy-related proteins and organelles are modified during RA-induced differentiation of SH-SY5Y cells. RA-induced effects were compared to those induced by starvation. SH-SY5Y cells were treated with a single dose of 10 µM RA or grown in starvation, for 3 days or 7 days. After treatments, cells were analyzed at light microscopy and transmission electron microscopy to assess cell morphology and immunostaining for specific markers (nestin, βIII-tubulin, NeuN) and some autophagy-related proteins (Beclin 1, LC3). We found that both RA and starvation differentiate SH-SY5Y cells. Specifically, cell differentiation was concomitant with an increase in autophagy proteins and autophagy-related organelles. However, the effects of a single dose of 10 μM RA persist for at least 7 days, while prolonged starvation produces cell degeneration and cell loss. Remarkably, the effects of RA are modulated in the presence of autophagy inhibitors or stimulators. The present data indicate that RA-induced differentiation is concomitant with an increased autophagy.
    Keywords:  3-methiladenine; Beclin 1; LC3; NeuN; autophagy vacuoles; cell morphometry; immunoelectron microscopy; nestin; rapamycin; ultrastructural morphology
    DOI:  https://doi.org/10.3390/ijms26041691
  58. Sci Rep. 2025 Feb 26. 15(1): 6855
    Inhibition of autophagy in platelets as a therapeutic strategy preventing hypoxia induced thrombosis.
    Propanna Bandyopadhyay, Yash T Katakia, Sudeshna Mukherjee, Syamantak Majumder, Shibasish Chowdhury, Rajdeep Chowdhury.
      Hypoxia triggers activation of platelets, leading to thrombosis. If not addressed clinically, it can cause severe complications and fatal consequences. The current treatment regime for thrombosis is often palliative and include long-term administration of anticoagulants, causing over-bleeding risk and other secondary effects as well. This demands a molecular understanding of the process and exploration of an alternative therapeutic avenue. Interestingly, recent studies demonstrate that platelets exhibit functional autophagy. This cellular homeostatic process though well-studied in non-platelet cells, is under-explored in platelets. Herein, we report autophagy activation under physiologically relevant hypoxic condition (10% O2; associated with high altitude) in ex-vivo platelets and in vivo as well. We show that autophagy inhibition using chloroquine (CQ), a repurposed FDA-approved drug, can significantly reduce platelet activation, both in ex-vivo and in-vivo settings. Further, surgical ligation of inferior vena cava (IVC) was performed to induce thrombus formation. Interestingly, CQ pre-treated rats showed reduced clotting ability in surgical animals as well. Importantly, thrombosis inhibitory dose of CQ was considerably lower than the currently used drug-acetazolamide; CQ was also found to be non-toxic to the tissues. Hence, we propose that repurposing of CQ can attenuate hypoxia-induced thrombosis through inhibition of autophagy and can be explored as an effective therapeutic alternative.
    Keywords:  Autophagy; Chloroquine; Hypobaric hypoxia; IVC ligation; Platelet aggregation
    DOI:  https://doi.org/10.1038/s41598-025-91181-y
  59. Molecules. 2025 Feb 10. pii: 816. [Epub ahead of print]30(4):
    The Anti-Aging Mechanism of Metformin: From Molecular Insights to Clinical Applications.
    Ting Zhang, Lijun Zhou, Meagan J Makarczyk, Peng Feng, Jianying Zhang.
      Aging represents a complex biological phenomenon marked by the progressive deterioration of physiological functions over time, reduced resilience, and increased vulnerability to age-related diseases, ultimately culminating in mortality. Recent research has uncovered diverse molecular mechanisms through which metformin extends its benefits beyond glycemic control, presenting it as a promising intervention against aging. This review delves into the anti-aging properties of metformin, highlighting its role in mitochondrial energy modulation, activation of the AMPK-mTOR signaling pathway, stimulation of autophagy, and mitigation of inflammation linked to cellular aging. Furthermore, we discuss its influence on epigenetic modifications that underpin genomic stability and cellular homeostasis. Metformin's potential in addressing age-associated disorders including metabolic, cardiovascular, and neurodegenerative diseases is also explored. The Targeting Aging with Metformin (TAME) trial aims to provide key evidence on its efficacy in delaying aging in humans. Despite these promising insights, significant challenges persist in gaining a more comprehensive understanding into its underlying mechanisms, determining optimal dosing strategies, and evaluating long-term safety in non-diabetic populations. Addressing these challenges is crucial to fully realizing metformin's potential as an anti-aging therapeutic.
    Keywords:  anti-aging; autophagy; clinical trials; epigenetic regulation; inflammation; metformin; mitochondrial function; nutrient sensing
    DOI:  https://doi.org/10.3390/molecules30040816
  60. Redox Biol. 2025 Feb 22. pii: S2213-2317(25)00076-X. [Epub ahead of print]81 103563
    PDE4D inhibition ameliorates cardiac hypertrophy and heart failure by activating mitophagy.
    Jing Fu, Congping Su, Yin Ge, Zhou Ao, Li Xia, Yingxiang Chen, Yizheng Yang, Shiwei Chen, Rui Xu, Xiaoyan Yang, Kai Huang, Qin Fu.
      Cyclic adenosine monophosphate (cAMP) plays a major role in normal and pathologic signaling in the heart. Phosphodiesterase 4 (PDE4) is a major PDE degrading cAMP in the heart. There are inconsistencies concerning the roles of the PDE4 isoforms 4B and 4D in regulation of cardiac function. Cardiac PDE4B overexpression is beneficial in remodeling and heart failure (HF), however, the effect of PDE4D and PDE4 inhibitor in HF remains unclear. We generated global and conditional cardiac-specific heterozygous PDE4D knockout mice and adeno-associated virus serotype 9-PDE4D overexpression to determine the role of PDE4D in cardiac hypertrophy and HF. PDE4D upregulation was observed in failing hearts from human and isoproterenol injection and TAC mice. In vitro, isoproterenol stimulation increased PDE4D expression via PKA but had no effect on PDE4B expression in cardiomyocytes. PDE4D overexpression per se induced oxidative stress, mitochondrial damage and cardiomyocyte hypertrophy by decreasing PINK1/Parkin-mediated mitophagy through inhibiting cAMP-PKA-CREB-Sirtuin1 (SIRT1) signaling pathway, while PDE4B overexpression did not affect CREB-SIRT1 pathway and mitophagy but exhibited a protective effect on isoproterenol-induced oxidative stress and hypertrophy in cardiomyocytes. PDE4D silencing or inhibition with PDE4 inhibitor roflumilast ameliorated isoproterenol-induced mitochondrial injury and cardiomyocyte hypertrophy. In vivo, ISO injection or TAC inhibited cardiac mitophagy and caused cardiac hypertrophy and HF, which were ameliorated by roflumilast or cardiac-specific PDE4D haploinsufficiency. Conversely, cardiac PDE4D overexpression suppressed cardiac mitophagy and abolished the protective effects of global PDE4D haploinsufficiency on TAC-induced cardiac hypertrophy and HF. In conclusion, these studies elucidate a novel mechanism by which sustained adrenergic stimulation contributes to cardiac hypertrophy and HF by increasing PDE4D via cAMP-PKA signaling, which in turn reduces cAMP-PKA activity, resulting in cardiomyocyte hypertrophy and mitochondrial injury via inhibition of CREB-SIRT1 signaling-mediated mitophagy. PDE4D inhibition may represent a novel therapeutic strategy for HF.
    Keywords:  CREB; Heart failure; Hypertrophy; Mitophagy; PDE4D; PKA; Phosphodiesterase 4; SIRT1; cAMP
    DOI:  https://doi.org/10.1016/j.redox.2025.103563
  61. Mol Med Rep. 2025 May;pii: 111. [Epub ahead of print]31(5):
    Semaglutide enhances PINK1/Parkin‑dependent mitophagy in hypoxia/reoxygenation‑induced cardiomyocyte injury.
    Liqin Li, Lili Jin, Yaping Tian, Jun Wang.
      The present study aimed to explore how semaglutide can help protect the heart from injury caused by hypoxia/reoxygenation (H/R) and to reveal the underlying mechanism. Briefly, AC16 cardiomyocytes were subjected to 8 h of hypoxia followed by 12 h of reoxygenation to simulate H/R. The cells were divided into the following five groups: Normoxia, H/R, H/R + semaglutide, H/R + semaglutide + rapamycin (autophagy inducer), and H/R + semaglutide + 3‑methyladenine (3‑MA; autophagy inhibitor) groups. Cell viability was examined using a Cell Counting Kit‑8 assay, ATP levels were examined using a bioluminescent detection kit, reactive oxygen species (ROS) production was detected using a ROS Assay Kit, and monomeric red fluorescent protein (mRFP)‑green fluorescent protein (GFP)‑LC3 was assessed using tandem mRFP‑GFP fluorescence microscopy, while autophagosomes were observed using transmission electron microscopy. Furthermore, the protein expression levels of autophagy markers (LC3, p62 and Beclin1) and regulators of mitochondrial autophagy [PTEN‑induced putative kinase protein‑1 (PINK1) and Parkin] were examined using western blot analysis. In AC16 cells, exposure to hypoxia followed by reoxygenation led to an increase in oxidative stress. This condition also induced an increase in autophagy activity, as evidenced by an increase in the number of autophagosomes, elevated LC3‑II/LC3‑I ratio, and upregulation of p62, Beclin1, PINK1 and Parkin expression compared with those in cells cultured under normoxia. Notably, treatment with semaglutide or rapamycin effectively reversed the H/R‑induced oxidative stress, enhanced the changes in autophagy activity, autophagosome levels and elevated LC3BII/LC3BI ratio, and increased the expression levels of Beclin1, PINK1, Parkin and p62 expression. Notably, the use of 3‑MA exhibited distinct effects under the same conditions; it exacerbated oxidative stress, decreased autophagy activity and reduced the LC3BII/LC3BI ratio. In conclusion, semaglutide was found to reduce oxidative stress caused by H/R and to increase autophagy via the ROS/PINK1/Parkin/p62 pathway. The present study offers a novel understanding of how semaglutide may protect the heart, and suggests its potential use in the treatment of myocardial ischemia/reperfusion injury.
    Keywords:  PTEN‑induced putative kinase protein‑1/Parkin pathway; autophagy; cardioprotection; hypoxia/reoxygenation; semaglutide
    DOI:  https://doi.org/10.3892/mmr.2025.13476
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