bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2025–09–28
24 papers selected by
Viktor Korolchuk, Newcastle University
  1. Selective mitophagy activation and protein aggregate accumulation in MTMR5/SBF1-deficient fibroblasts.
  2. The Role of the Beclin1 Complex in Rab9-Dependent Alternative Autophagy.
  3. Role of autophagy in cell survival and death: Mechanisms and therapeutic implications.
  4. V-ATPase-dependent induction of selective autophagy.
  5. Characterization of the autophagic N-degron pathway and monitoring its chemical modulation for therapeutic development.
  6. The ubiquitin-binding protein ANKRD13A mediates VCP-dependent mitochondrial outer membrane rupture during PINK1/Parkin-mediated mitophagy.
  7. Isolation of functional lysosomes from skeletal muscle.
  8. Characterization of the E3 ligase KCMF1 as a ZZ/N-recognin of the autophagic Arg/N-degron pathway.
  9. Bridging structure and selectivity in chaperone-mediated autophagy: towards targeted therapeutics.
  10. cGAS-STING and autophagy: crosstalk, molecular mechanisms, and targeted therapy.
  11. Autophagy in Proteostasis AND AGING in C. ELEGANS.
  12. JIP4 and RILPL1 utilize opposing motor force to dynamically regulate lysosomal tubulation.
  13. Herbal terpenoids activate autophagy and mitophagy through modulation of bioenergetics and protect from metabolic stress, sarcopenia and epigenetic aging.
  14. Lysosomes signal through the epigenome to regulate longevity across generations.
  15. Loss of ATG5 impairs CD4+ T cell activation and promotes anti-tumor responses.
  16. Lysosomal LRRC8 complex impacts lysosomal pH, morphology, and systemic glucose metabolism.
  17. Membrane receptors cluster phosphatidylserine to activate LC3-associated phagocytosis.
  18. Atg4B-Activated Near-Infrared Nanoprobe for Precise Imaging of Autophagy In Vivo.
  19. Ubiquitination-activated TAB-TAK1-IKK-NF-κB axis modulates gene expression for cell survival in the lysosomal damage response.
  20. Polyphenols and exercise in autophagy regulation: potential benefits for cancer management and healthspan.
  21. The interplay of the cGAS-STING pathway with the lysosome.
  22. Loss of DJ-1 alleviates microglia-mediated neuroinflammation in Parkinson's disease via autophagy-lysosomal degradation of NLRP3.
  23. Impaired macroautophagy in oligodendrocyte precursor cells suppresses neuronal plasticity via a senescence-associated signaling.
  24. Vacuolar pH regulates clathrin-mediated endocytosis through TORC1 signaling during replicative aging.
  1. Life Sci. 2025 Sep 23. pii: S0024-3205(25)00631-9. [Epub ahead of print] 123995
    Selective mitophagy activation and protein aggregate accumulation in MTMR5/SBF1-deficient fibroblasts.
    Paola Zanfardino, Alessandro Amati, Stefano Doccini, Francesco Girolamo, Apollonia Tullo, Giovanna Longo, Filippo M Santorelli, Vittoria Petruzzella.
       AIMS: Charcot-Marie-Tooth disease type 4B3 (CMT4B3) is a rare autosomal recessive neuropathy caused by biallelic MTMR5/SBF1 variants, which encode a catalytically inactive myotubularin involved in phosphoinositide metabolism and autophagy regulation. This study investigates the impact of MTMR5/SBF1 dysfunction on autophagy and mitophagy in patient-derived fibroblasts and examines the relationship between protein aggregates and autophagic machinery.
    MATERIALS AND METHODS: Fibroblasts from a CMT4B3 patient with compound heterozygous MTMR5/SBF1 mutations were compared with a healthy control. Autophagic flux was analyzed via LC3B and SQSTM1; mitophagy was assessed through PINK1 and PRKN recruitment and by quantifying mitophagosomes and autolysosomes under mitochondrial stress. Protein aggregates were visualized using Proteostat and tested for colocalisation with autophagic structures.
    KEY FINDINGS: CMT4B3 fibroblasts showed normal basal macroautophagy but failed to increase autophagy in response to mitochondrial stress or protein aggregates. Conversely, mitophagy was strongly activated via the PINK1-PRKN pathway.
    SIGNIFICANCE: These results reveal an uncoupling between mitophagy and macroautophagy, indicating that MTMR5/SBF1 mutations modify autophagic selectivity. Our findings provide new mechanistic insights into the pathogenesis of CMT4B3 and highlight the value of patient-derived fibroblasts for studying selective autophagy defects.
    Keywords:  CMT4B3; Charcot-Marie-Tooth disease; Macroautophagy; PINK1–PRKN pathway; Phosphoinositide metabolism; Proteasome
    DOI:  https://doi.org/10.1016/j.lfs.2025.123995
  2. Int J Mol Sci. 2025 Sep 19. pii: 9151. [Epub ahead of print]26(18):
    The Role of the Beclin1 Complex in Rab9-Dependent Alternative Autophagy.
    Sohyeon Baek, Yunha Jo, Jihoon Nah.
      Autophagy is a conserved catabolic pathway that degrades intracellular cargo through the lysosomal system. Canonically, this process is orchestrated by the autophagy-related (Atg)5-Atg7 conjugation system, which facilitates the formation of microtubule-associated protein 1 light chain 3 (LC3)-decorated double-membrane vesicles known as autophagosomes. However, accumulating evidence has revealed the existence of an Atg5-Atg7-independent, alternative autophagy pathway that still relies on upstream regulators such as the unc-51 like autophagy activating kinase 1 (Ulk1) kinase and the Beclin1 complex. In this review, we provide a comprehensive overview of the role of the Beclin1 complex in canonical autophagy and highlight its emerging importance in alternative autophagy. Notably, the recent identification of transmembrane protein 9 (TMEM9) as a lysosomal protein that interacts with Beclin1 to promote member RAS oncogene family 9 (Rab9)-dependent autophagosome formation has significantly advanced our understanding of alternative autophagy regulation. Furthermore, this Ulk1-Rab9-Beclin1-dependent mitophagy has been shown to mediate to mitochondrial quality control in the heart, thereby contributing to cardioprotection under ischemic and metabolic stress conditions. We further examine how the Beclin1 complex functions as a central scaffold in both canonical and alternative autophagy, with a focus on its modulation by novel factors such as TMEM9 and the potential therapeutic implications of these regulatory mechanisms.
    Keywords:  Beclin1 complex; Rab9; TMEM9; WD-repeat protein, phosphoinositide interacting (Wipis); alternative autophagy; heart diseases
    DOI:  https://doi.org/10.3390/ijms26189151
  3. Prog Mol Biol Transl Sci. 2025 ;pii: S1877-1173(25)00096-1. [Epub ahead of print]217 109-134
    Role of autophagy in cell survival and death: Mechanisms and therapeutic implications.
    Sparsha Pallen, Shweta Tiwari, Rajan Kumar Pandey.
      Autophagy is a catabolic process that preserves cellular homeostasis by degrading and recycling damaged organelles and proteins, particularly during metabolic stress, nutrient deprivation, oxidative stress, and inflammation. It is tightly regulated by key molecular pathways, including AMP-activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR). Core autophagy-related proteins such as Unc-51-like kinase 1 (ULK1), autophagy-related genes (ATG4, ATG5, ATG7), and microtubule-associated protein 1 light chain 3 (LC3), orchestrate autophagosome formation and cargo degradation. Autophagy influences cellular fate, promoting survival or programmed cell death, and plays a critical role in stem cell differentiation. Impaired autophagy contributes to neurodegenerative diseases by enabling toxic protein accumulation, while its dysregulation affects lipid metabolism and insulin sensitivity in metabolic syndromes and cancers. This chapter explores the molecular mechanisms of autophagy, its regulatory networks, and its implications in disease, emphasizing potential therapeutic interventions. Understanding these pathways provides insights into novel strategies for targeting autophagy in various pathological conditions.
    Keywords:  Autophagy; Cancer; Cell death; P53
    DOI:  https://doi.org/10.1016/bs.pmbts.2025.06.015
  4. Nat Commun. 2025 Sep 26. 16(1): 8508
    V-ATPase-dependent induction of selective autophagy.
    Yuxiang Huang, Dimitra Dialynaki, Yuchen Lei, Zhihai Zhang, Charles R Evans, Daniel J Klionsky.
      The general consensus is that the vacuolar-type H+-translocating ATPase (V-ATPase) is critical for macroautophagy/autophagy. However, there is a fundamental conundrum because follicular lymphoma-associated mutations in the V-ATPase result in lysosomal/vacuolar deacidification but elevated autophagy activity under nutrient-replete conditions and the underlying mechanisms remain unclear. Here, working in yeast, we show that V-ATPase dysfunction activates a selective autophagy flux termed "V-ATPase-dependent autophagy ". By combining transcriptomic and proteomic profiling, along with genome-wide suppressor screening approaches, we found that V-ATPase-dependent autophagy is regulated through a unique mechanism distinct from classical nitrogen starvation-induced autophagy. Tryptophan metabolism negatively regulates V-ATPase-dependent autophagy via two parallel effectors. On the one hand, it activates ribosome biogenesis, thus repressing the translation of the transcription factor Gcn4/ATF4. On the other hand, tryptophan fuels NAD+ de novo biosynthesis to inhibit autophagy. These results provide an explanation for the mutational activation of autophagy seen in follicular lymphoma patients.
    DOI:  https://doi.org/10.1038/s41467-025-63472-5
  5. Methods Enzymol. 2025 ;pii: S0076-6879(25)00217-4. [Epub ahead of print]719 173-210
    Characterization of the autophagic N-degron pathway and monitoring its chemical modulation for therapeutic development.
    Jihoon Lee, Gee Eun Lee, Chan Hoon Jung, Yoon Jee Lee, Yong Tae Kwon.
      Cellular homeostasis relies on the regulated degradation of unnecessary or harmful biomaterials including proteins. The N-degron pathway plays a central role in quality control at the crossroad of the ubiquitin (Ub)-proteasome system (UPS) and the autophagy-lysosome system (ALS). In this pathway, single N-terminal (Nt) residues of substrate proteins act as degradation determinants, called N-degrons. In the UPS, N-degrons are recognized and bound by their cognate N-recognins such as a family of E3 Ub ligases carrying the UBR box to induce substrate ubiquitination for proteasomal degradation. Our earlier studies identified an autophagic version of the N-degron pathway that works cooperatively with the UPS. In this process, N-degrons bind the N-recognin p62/SQSTM1 and modulate its activity as an autophagy receptor, leading to lysosomal destruction of UPS-resistant cargoes. We also developed chemical mimetics of N-degrons that exert efficacy to accelerate the degradation of excessive or harmful biomaterials such as cellular wastes and subcellular organelles. Here, we describe biochemical assays to characterize p62 as an autophagic N-recognin. We also delve into methodologies to assess therapeutic efficacy of chemical N-degrons in the degradation of lipid droplets (LDs) through lipophagy and the clearance of invading bacteria through xenophagy. These protocols can be used to identify new ZZ-type N-recognins in mammals and other species as well as under various pathophysiological conditions in both the UPS and ALS.
    Keywords:  ATE1 R-transferase; Lipophagy; N-recognin; N-terminal arginylation; P62/SQSTSM-1; The N-degron pathway; The autophagy-lysosome system; Xenophagy
    DOI:  https://doi.org/10.1016/bs.mie.2025.06.009
  6. J Biol Chem. 2025 Sep 18. pii: S0021-9258(25)02591-8. [Epub ahead of print] 110739
    The ubiquitin-binding protein ANKRD13A mediates VCP-dependent mitochondrial outer membrane rupture during PINK1/Parkin-mediated mitophagy.
    Wei-Hua Chu, Yu-Shan Lin, Jing Guo, Wann-Neng Jane, Wong-Jing Wang, Yu-Yang Lin, Pei-Han Liu, Po-Yu Huang, Wei-Chung Chiang.
      PINK1/Parkin-mediated mitophagy is a major homeostatic mechanism by which cells selectively remove damaged, depolarized mitochondria. A signature event in this form of mitophagy is the rupture of the mitochondrial outer membrane (OMM), a process required for the proper disposal of the damaged, depolarized mitochondria. The OMM rupture results in the topological exposure of mitochondrial inner membrane (IMM) mitophagy receptors, which are recognized by autophagy machinery, thus promoting the turnover of the depolarized mitochondria. However, due to the lack of efficient tools to measure OMM rupture, our mechanistic understanding of this process has been limited. In this study, we identified ANKRD13A as a novel mitophagy factor that interacts with multiple mitochondrial proteins and re-localizes to the depolarized mitochondria. ANKRD13A promotes PINK1/Parkin-mediated mitophagy by recruiting Valosin-containing protein (VCP), an AAA-ATPase that functions to remodel protein complexes or membranes via the extraction of protein substrates. Through the development of a novel biosensor that fluorescently marks the sites of OMM rupture, we visualized the OMM rupture events in cellulo and revealed that VCP and its recruitment factors, including ANKRD13A, are required for the rupture of OMM. This finding demonstrated that VCP-dependent remodeling of OMM during PINK1/Parkin-mediated mitophagy is a key driving force behind the OMM rupture. Furthermore, our newly developed biosensor represents an effective, reliable method to detect OMM rupture during PINK1/Parkin-mediated mitophagy, and it is valuable for future mechanistic investigation of this process.
    DOI:  https://doi.org/10.1016/j.jbc.2025.110739
  7. Am J Physiol Cell Physiol. 2025 Sep 22.
    Isolation of functional lysosomes from skeletal muscle.
    Thulasi Mahendran, Anastasiya Kuznyetsova, Neushaw Moradi, David A Hood.
      Lysosomes are membrane-bound organelles responsible for the degradation of damaged or dysfunctional cellular components, including mitochondria. Their acidic internal environment and the presence of an array of hydrolytic enzymes facilitate the efficient breakdown of macromolecules such as proteins, lipids, and nucleic acids. Mitochondria play a critical role in maintaining skeletal muscle homeostasis to meet the energy demands under physiological and pathological conditions. Mitochondrial quality control within skeletal muscle during processes such as exercise, disuse, and injury is regulated by mitophagy, where dysfunctional mitochondria are targeted for lysosomal degradation. The limited understanding of quality control mechanisms in skeletal muscle necessitates the need for isolating intact lysosomes to assess organelle integrity and the degradative functions of hydrolytic enzymes. Although several methods exist for lysosome isolation, the complex structure of skeletal muscle makes it challenging to obtain relatively pure and functional lysosomes due to the high abundance of contractile proteins. Here we describe a method to isolate functional lysosomes from small amounts of mouse skeletal muscle tissue, preserving membrane integrity. We also describe functional assays that allow direct evaluation of lysosomal enzymatic activity and we provide data indicating reduced lysosomal degradative activity in lysosomes from aging muscle. We hope that this protocol provides a valuable tool to advance our understanding of lysosomal biology in skeletal muscle, supporting investigations into lysosome-related dysfunction in aging, disease, and exercise adaptations.
    Keywords:  differential centrifugation; lysosomal enzymes; mitochondria; mitophagy; proteolysis
    DOI:  https://doi.org/10.1152/ajpcell.00471.2025
  8. Methods Enzymol. 2025 ;pii: S0076-6879(25)00218-6. [Epub ahead of print]719 211-235
    Characterization of the E3 ligase KCMF1 as a ZZ/N-recognin of the autophagic Arg/N-degron pathway.
    Ji Su Lee, Min Ju Lee, Su Bin Kim, Yong Tae Kwon, Chang Hoon Ji.
      In the Arg/N-degron pathway, Arg/N-degrons share the N-terminal (Nt) arginine (Nt-Arg) residue and hydrophobic amino acid residues that can be generated through Nt-arginylation by ATE1-encoded R-transferases (EC 2.3.2). In the ubiquitin-proteasome system (UPS), N-degrons are recognized by the UBR box of N-recognins that facilitate ubiquitination and proteasomal degradation. Arg/N-degrons also modulate the lysosomal degradation of proteins and other biomaterials via the autophagy-lysosome system (ALS). In this autophagic process, N-degrons function through their recognition by the ZZ-type zinc finger domain of the N-recognin p62/SQSTM1-1/Sequestosome-1. Recently, we identified the E3 ligase KCMF1 (potassium channel modulatory factor 1) as an autophagic N-recognin at the crossroads of the UPS and ALS. KCMF1 binds Nt-Arg and structurally related Nt-motifs through its ZZ domain, a structural equivalent to the ZZ domain of p62 as well as the UBR box of N-recognins. Under oxidative stress such as prolonged hypoxia where protein aggregates accumulate, the cysteine (Cys) residue at position 2 is Nt-exposed through the Nt-methionine (Nt-Met) excision and undergoes chemical oxidation into Cys sulfonic acid (CysO3) followed by Nt-arginylation. The resulting Arg-CysO3 N-degron binds KCMF1 to induce the assembly of lysine 63 (Lys63)-linked Ub chains, to which p62-type autophagic receptors bind via their Ub-associated (UBA) domain for autophagic degradation. Through this collaboration between the UPS and ALS, Arg-CysO3 N-degrons contribute the degradation of harmful protein species generated under cellular stresses. Here, we describe biochemical assays to characterize KCMF1 as an emerging N-recognin, including its interaction with synthetic N-degrons and its activity to undergo self-polymerization stimulated by N-degrons.
    Keywords:  K63-linked ubiquitination; KCMF1; N-recognin; Oligomerization; Pulldown; ZZ domain-containing E3 ligase
    DOI:  https://doi.org/10.1016/bs.mie.2025.06.010
  9. FEBS J. 2025 Sep 26.
    Bridging structure and selectivity in chaperone-mediated autophagy: towards targeted therapeutics.
    Devid Sahu, Ishwar Patel, Kharishni Lakshman, Koyeli Mapa, Nidhi Malhotra.
      Chaperone-mediated autophagy (CMA) is a pivotal cellular process essential for maintaining homeostasis by selectively degrading damaged or non-essential proteins, and its impairment is associated with numerous diseases. The allure of CMA lies in its selectivity, a trait that holds the potential of revolutionising healthcare, offering superior therapies and paving the way for a future in which drug resistance is conquered. Thus, understanding the factors that dictate selectivity in the pathway is indispensable. CMA degrades only a subset of proteins, and its selectivity is regulated by two key proteins, namely heat shock cognate 71 kDa protein (HSPA8; also known as Hsc70) and lysosome-associated membrane protein 2A (LAMP2A). However, structural insights into these proteins, which are responsible for CMA functionality, are still in their infancy. We collated literature in search of answering unresolved questions, such as: what unique structural cues mark a protein as a CMA target? How does the Hsc70 along with co-chaperones decipher these cues? Where does Hsc70 bind to its co-chaperone? What is the substrate binding site in Hsc70, and how does the Hsc70-substrate complex bind to LAMP2A? What are the structural secrets governing LAMP2A's assembly into multimers and its role in shuttling substrates to the lysosome? Although direct answers to some of these questions are currently elusive due to the absence of experimental structures of selectively bound complexes, we have collated existing information to assess their potential resolution. Additionally, we review current structural insights into the therapeutic strategies targeting these proteins and the pathway. Comprehension unveils potential avenues for therapeutic innovation.
    Keywords:  Hsc70; autophagy; binding site; chaperones; lysosome; motif; structure–function relationship; therapeutics
    DOI:  https://doi.org/10.1111/febs.70262
  10. Arch Toxicol. 2025 Sep 27.
    cGAS-STING and autophagy: crosstalk, molecular mechanisms, and targeted therapy.
    Yumin Wang, Shuang Wu, Xuan Zhang, Weihua Zheng, Zhiji Wang, Junjing Zhang, Jinxia Chen, Hongquan Wang.
      The cytosolic DNA-sensing cGAS-STING pathway and autophagy represent two evolutionarily conserved systems critical for innate immunity and cellular homeostasis. The cGAS-STING pathway detects mislocalized DNA, triggering inflammation via interferon and cytokine production. Conversely, autophagy maintains equilibrium by degrading damaged organelles and pathogens. Crucially, these systems engage in reciprocal regulation: autophagy constrains cGAS-STING hyperactivity through lysosomal degradation of immunostimulatory DNA and STING itself, while cGAS-STING signaling induces autophagy via TBK1-mediated phosphorylation of autophagy adaptors to mitigate self-damage. Dysregulation of this interplay drives pathology. For instance, defective autophagy in systemic lupus erythematosus permits mitochondrial DNA accumulation and cGAS-driven interferonopathy, whereas persistent STING activation in cancers suppresses autophagic tumor surveillance. This review aims to dissect the molecular mechanisms underpinning their crosstalk, delineate its disruption in autoimmune, neurodegenerative, and oncological diseases, and critically evaluate emerging therapies designed to pharmacologically rebalance this axis. These include combining cGAS-STING inhibitors with autophagy enhancers to suppress inflammation in interferonopathies, and pairing STING agonists with autophagy inducers to potentiate antitumor immunity.By synthesizing preclinical and clinical advances, we establish a framework for developing context-specific therapeutics that exploit the cGAS-STING-autophagy circuit-translating mechanistic insights into precision treatments for immune dysregulation disorders.
    Keywords:  Autophagy; Autophagy enhancers; Inhibitors; Interplay; cGAS-STING
    DOI:  https://doi.org/10.1007/s00204-025-04206-w
  11. Cell Stress Chaperones. 2025 Sep 18. pii: S1355-8145(25)00060-4. [Epub ahead of print] 100115
    Autophagy in Proteostasis AND AGING in C. ELEGANS.
    Caitlin M Lange, Ryo Higuchi-Sanabria, Caroline Kumsta.
      Proteostasis (protein homeostasis), the balance of protein synthesis, folding, and degradation, is critical for cellular function and organismal health. Its disruption leads to the accumulation of misfolded and aggregated proteins, hallmarks of aging and age-related diseases including neurodegeneration. Autophagy, a conserved lysosome-mediated degradation pathway, is central to proteostasis by clearing toxic proteins and damaged organelles. In Caenorhabditis elegans, studies across conserved longevity paradigms and models of neurodegenerative diseases have defined key mechanisms by which autophagy maintains proteostasis during aging and stress. Beyond its degradative functions, autophagy contributes to spatial quality control by promoting the formation of potentially protective protein inclusions and coordinating with the ubiquitin-proteasome system. Emerging evidence also points to noncanonical autophagy pathways, such as unconventional secretion and inter-tissue communication, that broaden its role in systemic proteostasis. Together, these advances underscore autophagy's multifaceted contribution to protein quality control, with wide-ranging implications for aging, stress resistance and neurodegenerative disease.
    Keywords:  Aggresome; Aging; Autophagy; C. elegans; Inclusion body; Inter-tissue signaling; Longevity; Neurodegeneration; Protein Aggregation; Proteostasis; Secretion; Stress Response
    DOI:  https://doi.org/10.1016/j.cstres.2025.100115
  12. J Cell Biol. 2025 Nov 03. pii: e202404018. [Epub ahead of print]224(11):
    JIP4 and RILPL1 utilize opposing motor force to dynamically regulate lysosomal tubulation.
    Luis Bonet-Ponce, Tsion Tegicho, Nuria Fernandez-Martinez, Irene A Rozenberg, Mia Ashriem, Alexandra Beilina, Jillian H Kluss, Yan Li, Mark R Cookson.
      Lysosomes are dynamic organelles that remodel their membrane in response to stimuli. We previously uncovered a process we term LYsosomal Tubulation/sorting driven by LRRK2 (LYTL), wherein damaged lysosomes generate tubules sorted into vesicles. LYTL is orchestrated by the Parkinson's disease kinase LRRK2 that recruits the motor adaptor protein and RHD family member JIP4 to lysosomes. JIP4 enhances LYTL tubule extension toward the plus-end of microtubules. To identify new players involved in LYTL, we mapped the lysosomal proteome after LRRK2 kinase inhibition. We found that RILPL1 is recruited to dysfunctional lysosomes in an LRRK2 kinase activity-dependent manner, facilitated by pRAB proteins. Unlike JIP4, RILPL1 induces retraction of LYTL tubules by binding to p150Glued, thereby moving lysosomal tubules toward the minus-end of microtubules. Our findings emphasize the dynamic regulation of LYTL tubules by two distinct RHD proteins and pRAB effectors, acting as opposing motor adaptor proteins. These opposing forces create a metastable lysosomal membrane deformation, enabling dynamic tubulation events.
    DOI:  https://doi.org/10.1083/jcb.202404018
  13. Nat Aging. 2025 Sep 24.
    Herbal terpenoids activate autophagy and mitophagy through modulation of bioenergetics and protect from metabolic stress, sarcopenia and epigenetic aging.
    Gabriele Civiletto, Dario Brunetti, Giulia Lizzo, Kamila Muller, Guillaume E Jacot, Ioanna Daskalaki, Federico Sizzano, Minji Huh, Ivano Di Meo, Maria Nicol Colombo, José L Sanchez-Garcia, Bertrand J Bétrisey, Alix Zollinger, Patricia Lino, Christopher Neal, Anne-Laure Egesipe, Joy Richard, Myriam Chimen, Aurélie Hermant, Benjamin Brinon, Lorane Texari, Sylviane Metairon, Mohammed Adnan Qureshi, Dhaval S Patel, Siva A Vanapalli, Marco Malavolta, Arwen W Gao, Amelia Lalou, Mauro Provinciali, Fiorenza Orlando, Valeria Tiranti, Robert T Brooke, Steve Horvath, Johan Auwerx, Jerome N Feige, Philipp Gut.
      Small molecular food components contribute to the health benefits of diets rich in fruits, vegetables, herbs and spices. The cellular mechanisms by which noncaloric bioactives promote healthspan are not well understood, limiting their use in disease prevention. Here, we deploy a whole-organism, high-content screen in zebrafish to profile food-derived compounds for activation of autophagy, a cellular quality control mechanism that promotes healthy aging. We identify thymol and carvacrol as activators of autophagy and mitophagy through a transient dampening of the mitochondrial membrane potential. Chemical stabilization of thymol-induced mitochondrial depolarization blocks mitophagy activation, suggesting a mechanism originating from the mitochondrial membrane. Supplementation with thymol prevents excess liver fat accumulation in a mouse model of diet-induced obesity, improves pink-1-dependent heat stress resilience in Caenorhabditis elegans, and slows the decline of skeletal muscle performance while delaying epigenetic aging in SAMP8 mice. Thus, terpenoids from common herbs promote autophagy during aging and metabolic overload, making them attractive molecules for nutrition-based healthspan promotion.
    DOI:  https://doi.org/10.1038/s43587-025-00957-4
  14. Science. 2025 Sep 25. 389(6767): 1353-1360
    Lysosomes signal through the epigenome to regulate longevity across generations.
    Qinghao Zhang, Weiwei Dang, Meng C Wang.
      The epigenome is sensitive to metabolic inputs and is crucial for aging. Lysosomes act as a signaling hub to sense metabolic cues and regulate longevity. We found that lysosomal metabolic pathways signal through the epigenome to regulate transgenerational longevity in Caenorhabditis elegans. Activation of lysosomal lipid signaling and lysosomal adenosine monophosphate-activated protein kinase (AMPK) or reduction of lysosomal mechanistic target of rapamycin (mTOR) signaling increased the expression of a histone H3.3 variant and increased its methylation on K79, leading to life-span extension across multiple generations. This transgenerational prolongevity effect required intestine-to-germline transportation of histone H3.3 and a germline-specific H3K79 methyltransferase and was recapitulated by overexpressing H3.3 or the H3K79 methyltransferase. Thus, signals from a lysosome affect the epigenome and link the soma and germ line to mediate transgenerational inheritance of longevity.
    DOI:  https://doi.org/10.1126/science.adn8754
  15. Front Immunol. 2025 ;16 1284391
    Loss of ATG5 impairs CD4+ T cell activation and promotes anti-tumor responses.
    Carlos Plaza-Sirvent, Clara Bessen, Alisha W Bronietzki, Katjana Klages, Marc Schuster, Jochen Huehn, Ingo Schmitz.
      Macroautophagy (hereafter called autophagy) is an ancient catabolic process that delivers bulky cargo to lysosomal degradation. The autophagic pathway is regulated by autophagy-related (ATG) proteins that govern the formation of double-membraned vesicles called autophagosomes. Autophagy has been shown to be important for T cell survival and proliferation. However, all studies performed so far used genetic models, in which deletion of an essential Atg gene occurs at early stages of thymic T cell development, raising the question whether developmental defects account for the phenotypes observed in mature T cells. Especially regarding CD4+ T helper cells, little is known about the function of autophagy in specific subsets. Therefore, we generated mice that lack Atg5, an essential component of the core autophagy machinery, in activated CD4+ T cells using OX40-Cre mice. As expected, thymic T cell development was unaffected in these mice. Despite impaired CD4+ T cell activation, Atg5ΔOX40 mice developed lymphadenopathy and exhibited increased T cell numbers, pointing to a defect in immune regulation. Accordingly, frequencies of Foxp3+ regulatory T (Treg) cells were decreased. While activation-induced cell death and in vitro suppressive activity of Treg cells were not affected, ATG5 deficiency in CD4+ T cells led to increased anti-tumor responses against melanoma. In conclusion, our data suggest that ATG5 is crucial for the functional properties of CD4+ T cells and the homeostasis of Treg cells.
    Keywords:  ATG5; CD4 T cell; T cell activation; autophagy; regulatory T cell
    DOI:  https://doi.org/10.3389/fimmu.2025.1284391
  16. Sci Adv. 2025 Sep 26. 11(39): eadt6366
    Lysosomal LRRC8 complex impacts lysosomal pH, morphology, and systemic glucose metabolism.
    Ashutosh Kumar, Yonghui Zhao, Litao Xie, Rahul Chadda, John D Tranter, Ryan T Mikami, Nihil Abraham, Juan Hong, Ethan Feng, David R Rawnsley, Haiyan Liu, Kayla M Henry, Gretchen Meyer, Meiqin Hu, Haoxing Xu, Antentor Hinton, Chad E Grueter, E Dale Abel, Andrew W Norris, Abhinav Diwan, Rajan Sah.
      The lysosome integrates anabolic signaling and nutrient sensing to regulate intracellular growth pathways. The leucine-rich repeat-containing 8 (LRRC8) channel complex forms a lysosomal anion channel and regulates PI3K-AKT-mTOR signaling, skeletal muscle differentiation, growth, and systemic glucose metabolism. Here, we define the endogenous LRRC8 subunits localized to a subset of lysosomes in differentiated myotubes. We show that LRRC8A affects leucine-stimulated mTOR; lysosome size; number; pH; expression of lysosomal proteins LAMP2, P62, and LC3B; and lysosomal function. Mutating an LRRC8A lysosomal targeting dileucine motif sequence (LRRC8A-L706A;L707A) in myotubes recapitulates the abnormal AKT signaling and altered lysosomal morphology and pH observed in LRRC8A knockout cells. In vivo, LRRC8A-L706A;L707A knock-in mice exhibit increased adiposity, impaired glucose tolerance and insulin resistance associated with reduced skeletal muscle PI3K-AKT-mTOR signaling, glucose uptake, and impaired incorporation of glucose into glycogen. These data reveal a lysosomal LRRC8-mediated metabolic signaling function regulating lysosomal function, systemic glucose homeostasis, and insulin sensitivity.
    DOI:  https://doi.org/10.1126/sciadv.adt6366
  17. Nat Cell Biol. 2025 Sep 22.
    Membrane receptors cluster phosphatidylserine to activate LC3-associated phagocytosis.
    Emilio Boada-Romero, Clifford S Guy, Gustavo Palacios, Luigi Mari, Suresh Poudel, Zhenrui Li, Piyush Sharma, Douglas R Green.
      LC3-associated phagocytosis (LAP) represents a non-canonical function of autophagy proteins in which ATG8-family proteins (LC3 and GABARAP proteins) are lipidated onto single-membrane phagosomes as particles are engulfed by phagocytic cells. LAP plays roles in innate immunity, inflammation and anticancer responses, and is initiated following phagocytosis of particles that stimulate Toll-like receptors (TLR) and Fc receptors as well as following engulfment of dying cells. However, how this molecular process is initiated remains elusive. Here we report that receptors that engage LAP enrich phosphatidylserine (PS) in the phagosome membrane via membrane-proximal domains that are necessary and sufficient for LAP to proceed. Subsequently, PS recruits the Rubicon-containing PI3-kinase complex to initiate the enzymatic cascade leading to LAP. Manipulation of plasma membrane PS content, PS binding by Rubicon or the PS-clustering domains of receptors prevents LAP and delays phagosome maturation. Therefore, the initiation of LAP represents a novel mechanism of PS-mediated signal transduction following ligation of surface receptors.
    DOI:  https://doi.org/10.1038/s41556-025-01749-z
  18. Anal Chem. 2025 Sep 23.
    Atg4B-Activated Near-Infrared Nanoprobe for Precise Imaging of Autophagy In Vivo.
    Xiaotong Cheng, Tiantian Xia, Guowei Liang, Hai-Dong Xu, Xiaoyang Liu, Gaolin Liang.
      Autophagy plays a crucial role in maintaining cellular homeostasis, and its dysregulation is implicated in various diseases. High-precision imaging of autophagy activity in deep tissues is vital for elucidating the mechanisms of autophagy-related disorders, yet existing near-infrared (NIR) fluorescent probes often lack sufficient accuracy. To overcome this limitation, we developed an Atg4B-activated NIR nanoprobe for highly selective detection of autophagy. The "dual quenched" fluorescent probe, IR780-CBT NP, was synthesized via a CBT-Cys click condensation reaction using the fluorescent precursor Cys(StBu)-Thr-Phe-Gly-Lys(IR780)-CBT (IR780-CBT) under reducing conditions. Upon cellular uptake by autophagy-active cells, Atg4B-specific hydrolysis induces disassembly of IR780-CBT NPs, restoring NIR fluorescence. In autophagy-activated MDA-MB-231 cells and tumor-bearing mice, IR780-CBT NPs exhibited 4.5-fold and 3.1-fold enhanced fluorescence signals, respectively, compared to the "RAPA + Inh."-treated controls. These findings highlight the potential of IR780-CBT NPs for precise autophagy imaging in vivo, offering a promising tool for early diagnosis and mechanistic studies of autophagy-related diseases.
    DOI:  https://doi.org/10.1021/acs.analchem.5c03954
  19. Elife. 2025 Sep 24. pii: RP106901. [Epub ahead of print]14
    Ubiquitination-activated TAB-TAK1-IKK-NF-κB axis modulates gene expression for cell survival in the lysosomal damage response.
    Akinori Endo, Chikage Takahashi, Naoko Ishibashi, Yasumasa Nishito, Koji Yamano, Keiji Tanaka, Yukiko Yoshida.
      The lysosomal damage response is important for the maintenance of cellular homeostasis in human cells. Although the mechanisms underlying the repair and autophagic elimination of damaged lysosomes have been elucidated, the early signal transduction pathways and genes induced in response to lysosomal damage remain elusive. We performed transcriptome and proteome analyses and found that the TAB-TAK1-IKK-NF-κB axis is activated by K63-linked ubiquitin chains that accumulate on damaged lysosomes. This activates the expression of various transcription factors and cytokines that promote anti-apoptosis and intercellular signaling. The findings highlight the crucial role of ubiquitin-regulated signal transduction and gene expression in cell survival and cell-cell communication in response to lysosomal damage. The results suggest that the ubiquitin system is not only involved in the removal of damaged lysosomes by lysophagy, but also functions in the activation of cellular signaling for cell survival.
    Keywords:  NF-κB; TAB; TAK1; cell biology; human; lysosomal damage response; ubiquitin
    DOI:  https://doi.org/10.7554/eLife.106901
  20. Front Nutr. 2025 ;12 1618813
    Polyphenols and exercise in autophagy regulation: potential benefits for cancer management and healthspan.
    Wei Liu, MengDi Hu, Feng Cao, Shen Jin.
      Autophagy, a regulated cellular process, serves as both a tumor suppressor and a survival mechanism for tumor cells under stress in cancer. Recent studies demonstrate that polyphenols, bioactive compounds present in plant-derived foods, and exercise, a potent physiological stimulus, can efficiently modulate autophagy in both cancer patients and healthy individuals. This review explores the synergistic effects of polyphenols and exercise in regulating autophagy through key molecular pathways, including AMPK/mTOR, PI3K/Akt, and SIRT1/FOXO. Polyphenols such as quercetin, resveratrol, and curcumin possess autophagy-inducing properties, which may enhance exercise-induced cellular adaptations, contribute to cancer prevention, and improve metabolic health. Moreover, regular physical activity promotes autophagic flux, reducing oxidative stress, inflammation, and apoptosis resistance-factors critical in cancer progression and overall health maintenance. The review highlights the potential of polyphenol-exercise synergy in modulating autophagy, which may result in innovative therapeutic approaches for cancer treatment and metabolic health.
    Keywords:  autophagy; cancer; exercise; metabolic health; oxidative stress; polyphenols
    DOI:  https://doi.org/10.3389/fnut.2025.1618813
  21. Trends Biochem Sci. 2025 Sep 23. pii: S0968-0004(25)00218-X. [Epub ahead of print]
    The interplay of the cGAS-STING pathway with the lysosome.
    Yinfeng Xu, Wei Wan.
      The cyclic GMP-AMP (cGAMP) synthase (cGAS)-stimulator of interferon (IFN) genes (STING) pathway detects cytoplasmic DNA and elicits the innate immune response. Several recent studies show that cGAS-STING signaling not only terminates at the lysosome but also regulates lysosomal function. Here, we discuss the interplay of the cGAS-STING pathway with the lysosome.
    Keywords:  ESCRT; STING; TFEB; cGAS; innate immunity; lysosome
    DOI:  https://doi.org/10.1016/j.tibs.2025.08.010
  22. Front Immunol. 2025 ;16 1656729
    Loss of DJ-1 alleviates microglia-mediated neuroinflammation in Parkinson's disease via autophagy-lysosomal degradation of NLRP3.
    Qianqian Miao, Tiantian Wang, Haoran Wang, Yanxia Yu, Xing Jin.
       Objective: This study aimed to investigate the role and underlying mechanism of DJ-1 in regulating NLRP3 inflammasome-mediated neuroinflammation during Parkinson's disease.
    Methods: We used LPS to stimulate primary microglia in vitro and performed stereotactic injection of LPS into the substantia nigra of mice in vivo to investigate changes in DJ-1 expression following inflammatory stimulation. To evaluate the functional effects of DJ-1 on NLRP3 inflammasome activation, we used siRNA to knock down DJ-1 in primary microglia or BMDMs and analyzed downstream inflammatory responses as well as the specificity of this regulation. In vivo, we used microglia-specific AAV to selectively silence DJ-1 in the substantia nigra to further evaluate the anti-inflammatory effect of DJ-1 deficiency. To validate the direct interaction between DJ-1 and NLRP3, we performed co-immunoprecipitation and proximity ligation assay. We used the autophagy inhibitor 3-MA and activator rapamycin to investigate how NLRP3 is degraded upon DJ-1 deficiency in CRISPR-Cas9-engineered DJ-1 knockout HEK-293 cells.
    Results: DJ-1 were significantly upregulated following LPS or LPS plus ATP stimulation in primary microglia. Similarly, after stereotactic LPS injection into the substantia nigra, we observed a significant upregulation of DJ-1 expression. Knockdown of microglial DJ-1 markedly suppressed NLRP3 inflammasome activation, as evidenced by reduced mature caspase-1 and decreased IL-1β secretion. We confirmed this phenomenon in BMDM and found that DJ-1 knockdown specifically inhibited NLRP3 inflammasome activation, with no effect on NLRC4 or AIM2 inflammasomes. In vivo, microglia-specific DJ-1 knockdown significantly attenuated microglial NLRP3 inflammasome activation in the substantia nigra and exerted neuroprotective effects after LPS treatment. Furthermore, DJ-1 was found to directly bind NLRP3 and stabilize its conformation, thereby preventing autophagic degradation.
    Conclusion: This study demonstrates that DJ-1 deficiency in microglia inhibits NLRP3-driven inflammation by promoting NLRP3 degradation through the autophagy-lysosome pathway. Future studies should focus on identifying the specific binding sites and structure of DJ-1 with NLRP3, as well as investigating whether inhibiting DJ-1 in microglia could serve as a potential therapeutic target for suppressing neuroinflammation in Parkinson's disease.
    Keywords:  DJ-1 (PARK7); NLRP3 inflammasome; Parkinson’s disease; microglia; neuroinflammation
    DOI:  https://doi.org/10.3389/fimmu.2025.1656729
  23. Sci Adv. 2025 Sep 26. 11(39): eadq7665
    Impaired macroautophagy in oligodendrocyte precursor cells suppresses neuronal plasticity via a senescence-associated signaling.
    Hong Chen, Yan-Yun Sun, Qi-Fa Li, Yu-Tong Du, Na-Na Hu, Ao-Ran Sui, Xiao-Qing Luo, Xin Huang, Chao Zhu, Gang Yang, Lin-Lin Yao, Yong Tang, Hua Hu, Chun-Feng Liu, Jin Tao, Lei Feng, Frank Kirchhoff, Wenhui Huang, Shao Li, Quan-Hong Ma.
      Aging drives cognitive decline in the adult brain with unclear mechanisms. Previously, oligodendrocyte precursor cells (OPCs), the source cells of myelin-forming cells in the central nervous system, have been linked to brain aging by their compromised differentiation and regeneration capability. Whether a myelination-independent function of OPCs is involved in brain aging remains unknown. In this study, we herein report a myelination-independent role of OPCs in exaggerating cognitive decline in the aging brain via suppressing neuronal plasticity. Our results demonstrate that macroautophagic flux declines in aged OPCs. Inactivation of autophagy promotes the senescence of OPCs, which activates C-C motif chemokine ligand 3 (CCL3)/CCL5-C-C motif chemokine receptor 5 signaling. Through this, autophagy-defective OPCs impair glutamatergic transmission, neuronal excitability, and long-term potentiation, exaggerating the cognitive decline in the aging brain. Our study demonstrates a myelination-independent role of OPCs in brain aging and identifies that a declined autophagy in OPCs is a pivotal factor in driving aging-associated cognitive decline.
    DOI:  https://doi.org/10.1126/sciadv.adq7665
  24. J Cell Biol. 2025 Nov 03. pii: e202412064. [Epub ahead of print]224(11):
    Vacuolar pH regulates clathrin-mediated endocytosis through TORC1 signaling during replicative aging.
    Kenneth Gabriel Antenor, Jaime Lee-Dadswell, Natasha Salahshour, Nina Grishchenko, Shaimaa Swaleh, Gurjyot Makhija, Allie Spangaro, Mojca Mattiazzi Usaj.
      Clathrin-mediated endocytosis (CME) is a critical cellular process that regulates nutrient uptake, membrane composition, and signaling. Although replicative aging affects many cellular functions, its impact on CME remains largely unknown. We show that in budding yeast, older cells have slower assembly of early and coat CME modules, resulting in longer endocytic turnover and reduced Mup1 internalization. This change in CME dynamics is mother cell-specific, and not observed in daughters. Our data also show that perturbing vacuolar pH, a key driver of aging phenotypes, in young cells mimics aging-like CME dynamics, while maintaining an acidic vacuolar pH in aging cells preserves CME dynamics typical of young cells. We demonstrate that the vacuolar pH effect on CME is regulated through TORC1 via the effector kinase Npr1. Finally, we show that rescuing CME in aging cells improves mitochondrial health. These findings reveal that age-associated changes in cellular and vacuolar pH impair CME, and suggest CME as a potential driver of early cellular aging.
    DOI:  https://doi.org/10.1083/jcb.202412064
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