bims-auttor 2025-09-14 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2025–09–14
twenty-one papers selected by
Viktor Korolchuk, Newcastle University

PLEKHM1 Overexpression Impairs Autophagy and Exacerbates Neurodegeneration in rAAV-α-Synuclein Mice.
Urolithin a modulates inter-organellar communication via calcium-dependent mitophagy to promote healthy ageing.
Sex does not Influence Neuronal Autophagosome Biogenesis throughout Aging in Mice.
Exploring the role of mTOR pathway in aging and age-related disorders.
Evolutionary diversification of the autophagy initiation complex: reduced Atg101 dependency and changes in Atg9 binding to Atg13.
p62/SQSTM1 signaling nexus and orchestration of ERK and mTOR pathways are crucial for Bacoside A- induced autophagy-mediated apoptosis in chronic myelogenous leukemia.
BLTP3A is associated with membranes of the late endocytic pathway and is an effector of CASM.
Coordination of autophagosome closure and release by the Alzheimer's disease-associated protein BIN1.
ATG16L1 controls mammalian vacuolar proton ATPase.
The E3 ubiquitin ligase SIAH1 targets a bacterial pore-forming toxin to facilitate xenophagy.
NLRP3 autophagic degradation disruption in melanocytes contributes to vitiligo development.
Explainable AI to unveil cellular autophagy dynamics.
Microautophagy: definition, classification, and the complexity of the underlying mechanisms.
Counteracting lysosome defects alleviates the cellular senescence of Hutchinson-Gilford progeria syndrome.
Defective mitochondrial quality control in the aging of skeletal muscle.
Neurons sequester the cholesterol-inhibiting TFEB in oligodendrocyte cytoplasm to safeguard myelination and neural function.
Biomolecular condensates of ATG18 reshape ER for autophagy in plants.
Stress-induced organismal death is genetically regulated by the mTOR-Zeste-Phae1 axis.
An mTOR-Tfeb-Fabp7a Axis Ameliorates bag3 Cardiomyopathy via Decelerating Cardiac Aging.
Emerging strategies, applications and challenges of targeting NAD+ in the clinic.
α-Synuclein aggregates inhibit ESCRT-III through sequestration and collateral degradation.

Cells. 2025 Aug 29. pii: 1340. [Epub ahead of print]14(17):

PLEKHM1 Overexpression Impairs Autophagy and Exacerbates Neurodegeneration in rAAV-α-Synuclein Mice.

Lennart Höfs, David Geißler-Lösch, Björn H Falkenburger.

  The aggregation of α-synuclein (αSyn) is a central feature of Parkinson's disease (PD) and other synucleinopathies. The efficient clearance of αSyn depends largely on the autophagy-lysosomal pathway. Emerging genetic evidence highlights the role of pleckstrin homology and RUN domain-containing M1 protein (PLEKHM1), a critical regulator of autophagosome-lysosome fusion, in the pathogenesis of multiple neurodegenerative diseases. This study investigates the possible effects of increased PLEKHM1 expression on αSyn pathology and neurodegeneration in mice. We utilized a mouse model of PD that is based on A53T-αSyn overexpression, achieved by the stereotactic injection of recombinant adeno-associated viral vectors (rAAV) into the substantia nigra. Additionally, this study explores the effect of PLEKHM1 overexpression on the autophagy-lysosomal pathway under physiological conditions, using transgenic autophagy reporter mice. PLEKHM1 overexpression facilitated the αSyn-induced degeneration of dopaminergic somata in the substantia nigra and degeneration of dopaminergic axon terminals in the striatum. In concert with αSyn expression, PLEKHM1 also potentiated microglial activation. The extent of αSyn pathology, as reported by staining for phosphorylated αSyn, was not affected by PLEKHM1. Using RFP-EGFP-LC3 autophagy reporter mice, rAAV-mediated PLEKHM1 overexpression reduced lysosomal and autolysosomal area, increased LAMP1-LC3 colocalization, and decreased the autolysosome-to-autophagosome ratio. Concurrently, PLEKHM1 overexpression in both genotypes caused p62 accumulation, accompanied by reduced overlap with lysosomal and autophagosomal markers but increased colocalization with autolysosomal markers, indicating impaired cargo degradation during late-stage autophagy. Taken together, elevated PLEKHM1 levels exacerbate neurodegeneration in αSyn-overexpressing mice, possibly by impairing autophagic flux. Now, with in vivo evidence complementing genetic data, alterations in PLEKHM1 expression appear to compromise autophagy, potentially enhancing neuronal vulnerability to secondary insults like αSyn pathology.

Keywords:  RFP-EGFP-LC3 mice; alpha-synuclein; autophagic flux; autophagy; lysosomes; mouse model

DOI:  https://doi.org/10.3390/cells14171340
Autophagy. 2025 Sep 13.

Urolithin a modulates inter-organellar communication via calcium-dependent mitophagy to promote healthy ageing.

Antonis Roussos, Katerina Kitopoulou, Fivos Borbolis, Christina Ploumi, Despoina D Gianniou, Zhiquan Li, Haijun He, Eleni Tsakiri, Helena Borland, Ioannis K Kostakis, Martina Samiotaki, Ioannis P Trougakos, Vilhelm A Bohr, Konstantinos Palikaras.

  Mitochondrial dysfunction and impaired mitophagy are hallmarks of aging and age-related pathologies. Disrupted inter-organellar communication among mitochondria, endoplasmic reticulum (ER), and lysosomes, further contributes to cellular dysfunction. While mitophagy has emerged as a promising target for neuroprotection and geroprotection, its potential to restore age-associated defects in organellar crosstalk remains unclear. Here, we show that mitophagy deficiency deregulates the morphology and homeostasis of mitochondria, ER and lysosomes, mirroring age-related alterations. In contrast, urolithin A (UA), a gut-derived metabolite and potent mitophagy inducer, restores inter-organellar communication via calcium signaling, thereby, promoting mitophagy, healthspan and longevity. Our multi-omic analyses reveal that UA reorganizes ER, mitochondrial and lysosomal networks, linking inter-organellar dynamics to mitochondrial quality control. In C. elegans, UA induces calcium release from the ER, enhances lysosomal activity, and drives DRP-1/DNM1L/DRP1-mediated mitochondrial fission, culminating in efficient mitophagy. Calcium chelation abolishes UA-induced mitophagy, blocking its beneficial impact on muscle function and lifespan, underscoring the critical role of calcium signaling in UA's geroprotective effects. Furthermore, UA-induced calcium elevation activates mitochondrial biogenesis via UNC-43/CAMK2D and SKN-1/NFE2L2/Nrf2 pathways, which are both essential for healthspan and lifespan extension. Similarly, in mammalian cells, UA increases intracellular calcium, enhances mitophagy and mitochondrial metabolism, and mitigates stress-induced senescence in a calcium-dependent manner. Our findings uncover a conserved mechanism by which UA-induced mitophagy restores inter-organellar communication, supporting cellular homeostasis and organismal health.

Keywords:  Calcium; ER; cellular senescence; geroprotection; lysosome; mitochondria

DOI:  https://doi.org/10.1080/15548627.2025.2561073
Mol Biol Cell. 2025 Sep 10. mbcE25070312

Sex does not Influence Neuronal Autophagosome Biogenesis throughout Aging in Mice.

Mya Rodriguez, Andrea Kh Stavoe.

Autophagy is critical for the homeostasis and function of neurons, as misregulation of autophagy has been implicated in age-related neurodegenerative diseases and neuron-specific knockdown of early autophagy genes results in early neurodegeneration in mice. We previously found that autophagosome formation decreases with age in murine neurons. Sex differences have been intensely studied in neurodegenerative diseases, but whether sex differences influence autophagy at the neuronal level have not been investigated. We compared protein expression of 22 autophagy components between neural tissues of female and male mice across development and aging. We found minimal sex-related differences in autophagy protein expression throughout the murine lifespan. Additionally, we assayed the recruitment of autophagy complexes and autophagosome biogenesis; we found no sex-dependent differences in multiple stages of autophagosome formation in neurons, independent of age. Our data suggest that biological sex does not influence autophagosome formation in neurons across development and aging.

DOI: https://doi.org/10.1091/mbc.E25-07-0312
EXCLI J. 2025 ;24 992-1015

Exploring the role of mTOR pathway in aging and age-related disorders.

Komal Raghuvanshi, Disha Raghuvanshi, Dinesh Kumar, Eugenie Nepovimova, Marian Valko, Kamil Kuca, Rachna Verma.

  Aging is a highly intricate biochemical process. There is strong evidence suggesting that organismal aging, age-dependent diseases, and cellular senescence are related to the mammalian target of rapamycin (mTOR) signaling pathway. The signaling pathway of mTOR has become a prominent regulatory hub, managing crucial cellular activities that significantly affect lifespan and longevity. The mTOR is involved in controlling cell growth and metabolism in response to both internal and external energy signals as well as growth factors. The interaction between mTOR and cellular homeostasis is crucial in the aging process. This extensive review summarizes the most recent findings on mTOR inhibitors in the context of aging, highlighting their complex interactions with cellular systems, effect on longevity, and potential as therapeutic approaches for age-related diseases. Rapamycin and rapalogs (analogs of rapamycin), which have been proven to be effective mTOR inhibitors, have the ability to reduce the aging process in several model species while also enhancing metabolic health and stress responses. Despite cellular factors, mTOR inhibitors have revealed a potential path for therapeutics in age-related illnesses. These results suggest mTOR inhibitors as potential therapies to address the complex aspects of age-related diseases. However, obstacles stand in the way of clinical translation. Further research is required to improve dosing protocols, reduce potential side effects, and target mTOR inhibitors precisely at specific tissues. In summary, the mTOR signaling pathway is an important node in the intricate web of aging and its associated disorders.

Keywords:  aging; anti-aging interventions; mTOR; mTOR inhibitors; rapamycin

DOI:  https://doi.org/10.17179/excli2025-8384
Autophagy. 2025 Sep 11.

Evolutionary diversification of the autophagy initiation complex: reduced Atg101 dependency and changes in Atg9 binding to Atg13.

Zefeng Lai, Yutaro Hama, Masahide Oku, Sidi Zhang, Yasuyoshi Sakai, Hayashi Yamamoto, Noboru Mizushima.

  Macroautophagy/autophagy is an evolutionarily conserved process through which cells degrade cytoplasmic substances via autophagosomes. During the initiation of autophagosome formation, the ULK/Atg1 complex serves as a scaffold that recruits and regulates downstream ATG/Atg proteins and ATG9/Atg9-containing vesicles. Despite the essential role of the ULK/Atg1 complex, its components have changed during evolution; the ULK complex in mammals consists of ULK1 (or ULK2), RB1CC1, ATG13, and ATG101, whereas the Atg1 complex in the yeast Saccharomyces cerevisiae lacks Atg101 but instead has Atg29 and Atg31 along with Atg17. In this study, we investigated how such changes have evolved. A BLAST analysis across the major eukaryotic clades revealed that ATG101, which is essential for autophagy in mammals, was lost in some Holomycota lineages after acquisition of ATG29 and ATG31 by their common ancestor. Additionally, the acquisition of a cap structure in Atg13 preceded the loss of ATG101. However, some Holomycota species have both ATG101 and ATG29-ATG31, including Aspergillus oryzae and Komagataella phaffii. Yeast two-hybrid assays showed that ATG101 is required for ATG13-ATG9 interaction in mammals but dispensable in A. oryzae, probably because of a shift in the AoAtg9-binding site in AoAtg13. We found an additive effect between atg101 and atg31 deletions in starvation-induced autophagy in K. phaffii. Furthermore, both KpAtg101 and KpAtg31 are involved in Atg1 complex assembly in K. phaffii. These findings suggest that the reduced importance of Atg101 in the Atg13-Atg9 interaction and Atg1 complex assembly enabled the eventual loss of ATG101 in some Holomycota species, including S. cerevisiae.

Keywords:  ATG101; Atg13-Atg9 interaction; Atg29-Atg31 subcomplex; HORMA; PAS formation; ULK/Atg1 complex; evolutionary diversification; komagataella phaffii; saccharomyces cerevisiae

DOI:  https://doi.org/10.1080/15548627.2025.2559683
Arch Pharm Res. 2025 Sep 09.

p62/SQSTM1 signaling nexus and orchestration of ERK and mTOR pathways are crucial for Bacoside A- induced autophagy-mediated apoptosis in chronic myelogenous leukemia.

Sweta Kundu, Suvodeep Saha, Suparna Ghosh, Sampriti Sarkar, Atanu Kotal, Avik Acharya Chowdhury.

  Bacoside A (BCA), a triterpenoid saponin isolated from Bacopa monnieri, exhibits diverse pharmacological properties, including neuroprotective, hepatoprotective, anti-stress, anti-inflammatory, and anti-ulcer effects. In the present study, BCA demonstrates pronounced anticancer activity against K562 chronic myelogenous leukemia (CML) cells by modulating autophagy-apoptosis dynamics. BCA induces dose- and time-dependent cytotoxicity in K562 cells while sparing normal human peripheral blood mononuclear cells (hPBMCs) and Vero cells, indicating therapeutic selectivity. Mechanistically, BCA elicits a biphasic cellular response characterized by autophagy induction at 24 h, followed by caspase-dependent apoptosis at 48 h. Autophagy activation was confirmed by the formation of Monodansylcadaverine-positive autophagic vacuoles, upregulation of Beclin-1 and LC3-II, and increased LC3 puncta in EGFP-LC3-transfected K562 cells. Notably, BCA treatment led to persistent accumulation of p62/SQSTM1 despite functional autophagic flux. Co-immunoprecipitation analysis revealed p62/SQSTM1-LC3-II interactions, while siRNA-mediated silencing of p62/SQSTM1 attenuated LC3-II accumulation, implicating p62/SQSTM1 as a positive modulator of autophagy. Moreover, p62/SQSTM1 facilitated apoptosis progression by interacting with and activating caspase-8, thereby bridging autophagy and apoptosis. Pharmacological inhibition of autophagy using 3-methyladenine abrogated both autophagic and apoptotic responses, establishing autophagy as a prerequisite for BCA-induced cell death. BCA promoted ERK1/2 activation and concomitant suppression of mTOR pathway via dephosphorylation of mTOR and 4E-BP1. Inhibition of ERK1/2 using PD98059 reversed mTOR dephosphorylation and autophagy induction, whereas mTOR overexpression restored ERK1/2 phosphorylation to basal levels. Collectively, these findings delineate BCA as a novel autophagy-inducing agent in CML, exerting cytotoxic effects via ERK1/2-mTOR signaling and p62/SQSTM1-mediated autophagy-apoptosis crosstalk.

Keywords:   Bacopa monnieri ; Apoptosis; Autophagy; Bacoside A; Chronic myelogenous leukemia; p62/SQSTM1

DOI:  https://doi.org/10.1007/s12272-025-01565-x
EMBO J. 2025 Sep 11.

BLTP3A is associated with membranes of the late endocytic pathway and is an effector of CASM.

Michael G Hanna, Hely O Rodriguez Cruz, Kenshiro Fujise, Yumei Wu, C Shan Xu, Song Pang, Zhuonging Li, Mara Monetti, Pietro De Camilli.

  Recent studies have identified a family of rod-shaped proteins thought to mediate lipid transfer at intracellular membrane contacts by a bridge-like mechanism. We show that one such protein, bridge-like lipid transfer protein 3A (BLTP3A)/UHRF1BP1 binds VAMP7 vesicles via its C-terminal region, and anchors them to lysosomes via its chorein domain-containing N-terminal region binding to Rab7. Upon lysosome damage, BLTP3A-positive vesicles rapidly (within minutes) dissociate from lysosomes. Lysosome damage is known to activate the CASM (Conjugation of ATG8 to Single Membranes) pathway, leading to lipidation and lysosomal recruitment of mammalian ATG8 (mATG8) proteins. We find that this process drives the reassociation of BLTP3A with damaged lysosomes via an interaction of its LIR motif with mATG8 which coincides with a dissociation from the vesicles. Our findings reveal that BLTP3A is an effector of CASM, potentially as part of a mechanism to help repair or minimize lysosome damage.

Keywords:  BLTP3; LC3; Lysosome; Rab45; Urate Crystals

DOI:  https://doi.org/10.1038/s44318-025-00543-9
Cell Rep. 2025 Sep 09. pii: S2211-1247(25)01037-X. [Epub ahead of print]44(9): 116266

Coordination of autophagosome closure and release by the Alzheimer's disease-associated protein BIN1.

Jennifer E Palmer, Claudia Puri, Ryan S O'Rourke, Sung Min Son, Chun Sang, Yu-Wen Alvin Huang, David C Rubinsztein.

  Autophagosome closure by the endosomal sorting complex required for transport (ESCRT) complex is a prerequisite for their dynamin 2 (DNM2)-dependent release from the recycling endosome and subsequent lysosomal clearance. However, the mechanism that coordinates autophagosome closure and release is unknown. We identified that the Alzheimer's disease-associated protein bridging integrator 1 (BIN1) is a critical mediator of this coordination. Prior to autophagosome closure, BIN1 is held at autophagosomes by ESCRT-III and inhibits DNM2. Once the autophagosome has closed and ESCRT-III disassembles, BIN1 is released, removing the inhibition of DNM2. This mechanism provides insight into the functional consequences of increased BIN1 expression, as this occurs in microglia with Alzheimer's disease risk-associated polymorphisms. We find that the overexpression of BIN1 microglial isoforms inhibits DNM2-mediated autophagosome release and autophagic clearance. This provides a coherent explanation for the increased Alzheimer's disease risk associated with BIN1, as impaired microglial autophagy alters phagocytosis and is associated with microglial senescence and neuroinflammation.

Keywords:  Alzheimer’s disease; BIN1; CP: Cell biology; CP: Neuroscience; DNM2; ESCRT-III; autophagy; microglia

DOI:  https://doi.org/10.1016/j.celrep.2025.116266
J Cell Biol. 2025 Oct 06. pii: e202503166. [Epub ahead of print]224(10):

ATG16L1 controls mammalian vacuolar proton ATPase.

Thabata L A Duque, Masroor Paddar, Einar Trosdal, Ruheena Javed, Lee Allers, Michal H Mudd, Prithvi Akepati, Soumya R Mishra, Michelle Salemi, Brett Phinney, Shawn B Bratton, Thomas Wileman, Vojo Deretic.

The mechanisms governing mammalian proton pump V-ATPase function are of fundamental and medical interest. The assembly and disassembly of cytoplasmic V1 domain with the membrane-embedded V0 domain of V-ATPase is a key aspect of V-ATPase localization and function. Here, we show that the mammalian protein ATG16L1, primarily appreciated for its role in canonical autophagy and in noncanonical membrane atg8ylation processes, controls V-ATPase. ATG16L1 knockout elevated V-ATPase activity, increased V1 presence on endomembranes, and increased the number of acidified intracellular compartments. ATG16L1's ability to efficiently bind V-ATPase was required for its inhibitory role in endolysosomal acidification and for control of Mycobacterium tuberculosis infection in mice. These findings uncover a hitherto unappreciated role of ATG16L1 in regulating V-ATPase, a key pump governing acidification and functionality of the endolysosomal system along with its physiological roles.

DOI: https://doi.org/10.1083/jcb.202503166
Cell Rep. 2025 Sep 09. pii: S2211-1247(25)01028-9. [Epub ahead of print]44(9): 116257

The E3 ubiquitin ligase SIAH1 targets a bacterial pore-forming toxin to facilitate xenophagy.

Min Wu, Xin Hu, Junpei Iibushi, Kazunori Murase, Takashi Nozawa, Ichiro Nakagawa.

  Xenophagy, one form of selective autophagy, recognizes and eliminates the invading pathogen through the ubiquitination of bacterial surface components. Xenophagy is initiated by the damage of bacteria-surrounding endosomes by bacterial toxins; however, whether the host targets these xenophagy-inducible secretory factors to recognize bacteria remains unclear. Here, we report that E3 ligase SIAH1 recognizes and ubiquitinates streptolysin O (SLO), a pore-forming toxin secreted by group A Streptococcus (GAS). SIAH1 specifically recognizes the PSVP motif in SLO and mediates K48-linked polyubiquitination at Lys464. SIAH1 depletion significantly reduced GAS ubiquitination, impaired autophagosome formation, and enhanced bacterial survival. Studies with ATG16L1 and FIP200 knockout cell lines suggested that anti-GAS defense involves sequential deployment of the LC3-associated phagocytosis-like (LAP-like) process followed by canonical autophagy, and SIAH1 coordinates these pathways. Our findings reveal SIAH1's crucial role in bacterial toxin recognition and demonstrate a mechanism in which bacterial virulence factors themselves become targets of host xenophagy machinery.

Keywords:  CP: Microbiology; E3 ligase; LC3-associated phagocytosis; SIAH 1; group A Streptococcus; streptolysin O; ubiquitin; xenophagy

DOI:  https://doi.org/10.1016/j.celrep.2025.116257
Cell Death Differ. 2025 Sep 11.

NLRP3 autophagic degradation disruption in melanocytes contributes to vitiligo development.

Ke Zeng, Yuqi Zhu, Zhongxin Han, Siyi Xiong, Yan Zhao, Zilong Xiao, Yingchao Xie, Shiyu Jin, Tingru Dong, Lan Lan, Weiwei Liu, Yongzhong Du, Cuiping Guan, Xiao Yu, Xiuzu Song.

NLRP3 functions as a critical intracellular danger sensor for inflammasome activation, playing a crucial role in autoimmune diseases. Vitiligo progression has been linked to NLRP3, yet its specific involvement in melanocytes of vitiligo remains poorly understood. In this study, we demonstrate that NLRP3 expression is significantly upregulated in the melanocytes of vitiligo patients and melanoma-Treg-induced vitiligo mouse model. Genetic knockout of NLRP3 effectively alleviates vitiligo progression in these mice. Our mechanistic investigations reveal that the downregulation of the E3 ligase β-TrCP1 in vitiligo melanocytes decreases K27-linked ubiquitination levels of NLRP3, which in turn weakens its interaction with the autophagy receptor NDP52. This disruption impairs the selective autophagic degradation of NLRP3, leading to hyperactivation of inflammation and pyroptosis in melanocytes, thereby accelerating vitiligo pathogenesis. Notably, melanocyte-specific knockdown of NLRP3 using lysine-proline-valine (KPV)-modified deformable liposomes (KPV-Lipos) carrying Nlrp3 shRNA significantly alleviates vitiligo development. This study elucidates the mechanism by which autophagy dysfunction mediated excessive NLRP3 inflammasome activation in melanocytes contributes to vitiligo pathogenesis, highlighting potential therapeutic strategies targeting these pathways for the treatment of vitiligo and other pigment-related skin diseases. Overview of disrupted NLRP3 autophagic degradation in vitiligo melanocytes. In healthy melanocytes, NLRP3 expression is upregulated when subjected to oxidative stress, along with an increase in the E3 ligase β-TrCP1, which enhances the K27-linked ubiquitination of NLRP3 and further strengthens its binding to the autophagy receptor protein NDP52, thus effectively suppressing the excessive inflammatory response. Whereas in the melanocytes of vitiligo patients, decreased expression of β-TrCP1 leads to downregulation of K27-linked ubiquitination in NLRP3, thus inhibiting its autophagic degradation. The persistent activation of NLRP3 in vitiligo melanocytes promotes the cleavage of pro-IL-1β and GSDMD. GSDMD-N subsequently forms pores on the cell membrane, which causes the release of IL-1β and results in melanocyte pyroptosis. In our study, we utilize KPV-Lipos with Nlrp3 shRNA to precisely knockdown NLRP3 expression in melanocytes and effectively alleviate vitiligo development, which provide a potentially promising strategy for the treatment of vitiligo. MC, melanocytes.

DOI: https://doi.org/10.1038/s41418-025-01578-5
PLoS One. 2025 ;20(9): e0331045

Explainable AI to unveil cellular autophagy dynamics.

Oriana Presacan, María Hernández Mesa, Alexandru C Aldea, Siri Andresen, Amani Al Outa, Julie Aarmo Johannessen, Bogdan Ionescu, Helene Knævelsrud, Michael A Riegler.

Autophagy is a fundamental intracellular renovation process vital for maintaining cellular homeostasis through the degradation and recycling of damaged components. It is implicated in numerous pathological conditions, including cancer and neurodegenerative diseases. However, its dynamic nature and complexity pose challenges for manual analysis. In this study, we present a computational pipeline that leverages advanced deep learning models to automate the analysis of autophagic processes in 6,240 fluorescence microscopy images from the CELLULAR dataset. Our framework integrates object detection, cell segmentation, classification by autophagic state, cellular tracking, and explainability methods for interpretability. We achieved optimal results using YOLOv8 for object detection with a mAP50 of 0.80, U-Net++ for segmentation with an IoU of 0.82, and a vision transformer for classification with an accuracy of 0.86. To track cells, we developed a custom algorithm capable of handling complex scenarios such as cell division and morphological changes, all without requiring annotated tracking data. To enhance transparency, we employed explainability techniques based on class activation mappings to analyze model decision-making processes and validate classification outcomes, complemented by t-SNE visualizations for deeper insights into the data. Collaboration with biology experts validated our findings, highlighting the pipeline's potential to advance autophagy research. This study demonstrates the potential of deep learning and explainable AI to streamline biomedical research, reduce manual effort, and uncover key autophagy dynamics.

DOI: https://doi.org/10.1371/journal.pone.0331045
Autophagy. 2025 Sep 10.

Microautophagy: definition, classification, and the complexity of the underlying mechanisms.

Yasuyoshi Sakai, Christian Behrends, Ana Maria Cuervo, Jayanta Debnath, Masanori Izumi, Andreas Jenny, Maurizio Molinari, Shuhei Nakamura, Masahide Oku, Marisa S Otegui, Laura Santambrogio, Han-Ming Shen, Tomohiko Taguchi, Michael Thumm, Takashi Ushimaru, Zhiping Xie, Fulvio Reggiori.

  Recently, rapid progress in the field of microautophagy (MI-autophagy) revealed the existence of multiple subtypes that differ in both intracellular membrane dynamics and molecular mechanisms. As a result, a single umbrella term "microautophagy" has become too vague, even creating some confusion among researchers both within and outside the field. We herein describe different subtypes of MI-autophagic processes and propose a systematic approach for naming them more accurately.

Keywords:  Atg proteins; ESCRT proteins; lysosome; microautophagy; vacuole

DOI:  https://doi.org/10.1080/15548627.2025.2559687
Sci China Life Sci. 2025 Sep 05.

Counteracting lysosome defects alleviates the cellular senescence of Hutchinson-Gilford progeria syndrome.

Xiangyang Wang, Yihong Song, Mingkang Jia, Gan Zhao, Yumin Liu, Guangwei Xin, Bo Zhang, Qing Jiang, Chuanmao Zhang.

  Hutchinson-Gilford progeria syndrome (HGPS) is a rare progeroid disorder, and approximately 90% of cases are caused by LMNA mutation that yields the lamin A/C variant progerin. Progerin is toxic, and its clearance and disruption have positive benefits on HGPS cells and mice and even HGPS patients. However, accelerating progerin clearance is still an unaddressed issue. Here, we report that primary cells from HGPS patients displayed lysosome defects and that counteracting lysosome defects via the activation of lysosome biogenesis promoted progerin clearance and accordingly alleviated cellular senescence in HGPS. We revealed that nucleus-localized progerin was expelled into the cytoplasm via nuclear envelope (NE) budding and degraded through autophagy in HGPS cells. Lysosome defects occurred in HGPS cells and impaired progerin clearance. Activating lysosome biogenesis via the protein kinase C (PKC) activator phorbol 12-myristate 13-acetate (PMA) or the mTORC1 inhibitor Torin 1 promoted progerin clearance and accordingly mitigated DNA damage, cell cycle arrest, low proliferation ability and senescence-associated secretory phenotype (SASP) in HGPS cells. Overall, we propose that, in HGPS, lysosomes exhibit defects and that activating lysosome biogenesis can accelerate progerin clearance and alleviate cellular senescence. These findings highlight the anti-senescence roles of PKC activation and lysosome biogenesis and provide new insights for understanding and treating HGPS.

Keywords:  Hutchinson-Gilford progeria syndrome (HGPS); PKC; lysosome biogenesis; senescence

DOI:  https://doi.org/10.1007/s11427-025-2983-2
Mech Ageing Dev. 2025 Sep 08. pii: S0047-6374(25)00088-0. [Epub ahead of print]228 112112

Defective mitochondrial quality control in the aging of skeletal muscle.

Emanuele Marzetti, Riccardo Calvani, Helio José Coelho-Junior, Francesco Landi, Anna Picca.

  Age-related skeletal muscle decline is a major contributor to frailty, functional impairment, and loss of independence in advanced age. This process is characterized by selective atrophy of type II fibers, impaired excitation-contraction coupling, and reduced regenerative capacity. Emerging evidence implicates mitochondrial dysfunction as a central mechanism in the disruption of muscle homeostasis with age. Beyond ATP production, mitochondria orchestrate redox signaling, calcium handling, and apoptotic pathways, which are increasingly compromised in aged muscle due to chronic oxidative stress and defective quality control. High-resolution respirometry has revealed intrinsic, lifestyle-independent declines in mitochondrial respiratory capacity, while large-scale phenotyping and transcriptomic profiling have established robust associations between mitochondrial integrity, physical performance, and mobility. These findings have prompted a paradigm shift from static descriptions of mitochondrial decline toward dynamic analyses of mitochondrial signaling networks and stress adaptability. Several quality control mechanisms, including mitochondrial biogenesis, dynamics, mitophagy, and vesicle trafficking, emerge as critical regulators of myocyte integrity. Understanding how these systems deteriorate with age will be pivotal for developing therapeutic targets to preserve muscle function, mitigate sarcopenia, and extend health span.

Keywords:  Autophagy; Damage associated molecular patterns; Mitochondrial DNA; Mitochondrial dynamics; Mitophagy; Myocyte; Proteasome

DOI:  https://doi.org/10.1016/j.mad.2025.112112
Cell Rep. 2025 Sep 05. pii: S2211-1247(25)01023-X. [Epub ahead of print]44(9): 116252

Neurons sequester the cholesterol-inhibiting TFEB in oligodendrocyte cytoplasm to safeguard myelination and neural function.

Yihe Zhang, Zuolin Cheng, Shiyi Huang, Tripti Sharma, Daniela Barbosa, Guoqiang Yu, Lu O Sun.

  Myelination is essential for normal brain function, yet the mechanisms governing neuron-oligodendrocyte interactions that ensure proper myelination levels remain poorly understood. Here, we identify transcription factor EB (TFEB) as a molecular link that connects extrinsic neuronal cues to intrinsic oligodendrocyte transcriptional programs, regulating central nervous system myelination. Using a TFEB epitope-tagged knock-in mouse model, we find that neurons sequester most of the TFEB protein in the cytoplasm of myelinating oligodendrocytes. Genetic induction of nuclear TFEB in myelinating oligodendrocytes leads to severe hypomyelination and altered neural function. Lastly, cleavage under targets & release using nuclease and functional analyses reveal that TFEB directly binds to the promoter regions of many cholesterol biosynthesis genes and represses their expression, thereby reducing cholesterol levels. Our findings uncover a mechanism by which neurons limit a repressive transcriptional network in oligodendrocytes to ensure proper myelination, highlighting the complex interplay between neuronal signals and glial gene regulation in health and disease.

Keywords:  CP: Molecular biology; CP: Neuroscience; CRISPR knock-in; Myelination; cholesterol biosynthesis; neural circuit function; neuron-oligodendrocyte interaction; transcription factor EB; transcriptional regulation

DOI:  https://doi.org/10.1016/j.celrep.2025.116252
Dev Cell. 2025 Sep 11. pii: S1534-5807(25)00533-7. [Epub ahead of print]

Biomolecular condensates of ATG18 reshape ER for autophagy in plants.

Yang Shao, Xunzheng Li, Benhui Shi, Songyang Wang, Zisheng Luo, Yanqun Xu, Baolei Li, Shuqing Feng, Li Liang, Huanquan Zheng, Jiaqi Sun.

  Autophagosomes originate from and maintain association with the endoplasmic reticulum (ER) during their formation, yet how these processes are molecularly coordinated in plants remains poorly understood. Here, we demonstrate that Arabidopsis autophagy-related protein 18a (ATG18a), a key organizer of early autophagosome formation, undergoes phase separation to form biomolecular condensates on the ER membrane, which progress from highly mobile droplets to stable ring-like structures, while the ER is reshaped. We discovered that ATG18a condensates work together with ROOT HAIR DEFECTIVE3 (RHD3), an ER membrane-shaping protein, with RABC1 serving as a molecular linker between them. Importantly, RABC1 facilitates both RHD3 assembly necessary for the formation of ring-like ER structures and its interaction with ATG18a condensates. These findings reveal a mechanism whereby biomolecular condensates work together with membrane-shaping proteins to reshape specialized membrane domains through wetting interactions, providing an insight into autophagosome formation in plant stress responses.

Keywords:  ATG18; RABC1; RHD3; autophagosomes; autophagy; biomolecular condensates; plant response to stresses; salt stress; the ER; wetting interaction

DOI:  https://doi.org/10.1016/j.devcel.2025.08.013
Proc Natl Acad Sci U S A. 2025 Sep 16. 122(37): e2427014122

Stress-induced organismal death is genetically regulated by the mTOR-Zeste-Phae1 axis.

Takashi Matsumura, Masasuke Ryuda, Hitoshi Matsumoto, Takumi Kamiyama, Kyoko Jinnai, Shu Kondo, Akira Nakamura, Yoichi Hayakawa, Ryusuke Niwa.

  All organisms are exposed to various stressors, which can sometimes lead to organismal death, depending on their intensity. While stress-induced organismal death has been observed in many species, the underlying mechanisms remain unclear. In this study, we investigated the molecular mechanisms of stress-induced organismal death in the fruit fly Drosophila melanogaster. We identified a chymotrypsin-like serine protease Phaedra1 (Phae1) as a death mediator in D. melanogaster larvae. Phae1 expression was up-regulated by lethal heat stress (40 °C) but not nonlethal heat stress (38 °C or lower). The most prominent induction of Phae1 occurred in the central nervous system (CNS). We found neuro-specific knockdown of Phae1 increased survival and reduced neuronal caspase activity following exposure to lethal heat stress, suggesting that the transcriptional upregulation of Phae1 in the CNS is essential for stress-induced organismal death. We next found via bioinformatic and biochemical analyses that the transcription factor Zeste (Z) bound the Phae1 enhancer region and that z loss-of-function impaired Phae1 induction in the CNS, increasing survival following lethal heat stress. In addition, we found via chemical screening that rapamycin, a chemical inhibitor of mechanistic target of rapamycin (mTOR), suppressed Phae1 expression. Neuro-specific knockdown of mTor reduced the protein levels of both Phae1 and Z, leading to an increase in survival following lethal heat stress. Together, these results indicate that heat stress-induced organismal death in D. melanogaster larvae is regulated by a genetically encoded transcriptional signaling pathway involving the mTOR-Z-Phae1 axis.

Keywords:  mTOR; organismal death; protease; stress; transcription factor

DOI:  https://doi.org/10.1073/pnas.2427014122
Aging Cell. 2025 Sep 08. e70216

An mTOR-Tfeb-Fabp7a Axis Ameliorates bag3 Cardiomyopathy via Decelerating Cardiac Aging.

Yonghe Ding, Xueling Ma, Feixiang Yan, Baul Yoon, Wei Wei, Yuji Zhang, Xueying Lin, Xiaolei Xu.

While BAG3 has been identified as a causative gene for dilated cardiomyopathy, the major pathological events in BAG3-related cardiomyopathy that could be targeted for therapeutic benefit remain to be discovered. Here, we aim to uncover novel pathological events through genetic studies in a zebrafish bag3 cardiomyopathy model. Given the known cardioprotective effects of mtor inhibition and the fact that transcription factor EB (tfeb) encodes a direct downstream phosphorylation target of mTOR signaling, we generated a cardiomyocyte-specific transgenic line overexpressing tfeb (Tg[cmlc2:tfeb]). This overexpression was sufficient to restore defective proteostasis and rescue cardiac dysfunction in the bag3 cardiomyopathy model. Importantly, we detected accelerated cardiac senescence in the bag3 cardiomyopathy model, which can be mitigated by Tg(cmlc2:tfeb). We compared cardiac transcriptomes between the Tg(cmlc2:tfeb) transgenic fish and the mtorxu015/+ mutant and found that inhibition of the fatty acid binding protein a (fabp7a) gene exerts therapeutic effects. Consistent with this genetic evidence, we detected elevated fabp7a expression in the bag3 cardiomyopathy model, whereas cardiomyocyte-specific overexpression of fabp7a induced dysregulated proteostasis, accelerated cardiac senescence, and cardiac dysfunction. To elucidate the functions of Fabp7a in normative cardiac aging, we turned to the African Turquoise Killifish. We noted elevated Fabp7a expression in the hearts of aged killifish, and pharmacological inhibition of Fabp7a mitigated the cardiac aging process. Together, this study uncovered accelerated cardiac senescence as a key pathological event in bag3 cardiomyopathy and reveals that manipulating the mTOR-Tfeb-Fabp7a axis can mitigate this pathology and confer cardioprotective effects.

DOI: https://doi.org/10.1111/acel.70216
Nat Aging. 2025 Sep 09.

Emerging strategies, applications and challenges of targeting NAD+ in the clinic.

Jianying Zhang, He-Ling Wang, Sofie Lautrup, Hilde Loge Nilsen, Jonas T Treebak, Leiv Otto Watne, Geir Selbæk, Lindsay E Wu, Torbjørn Omland, Eija Pirinen, Tin Cho Cheung, Jun Wang, Mathias Ziegler, Ole-Bjørn Tysnes, Rubén Zapata-Pérez, Santina Bruzzone, Carles Canto, Michela Deleidi, Georges E Janssens, Riekelt H Houtkooper, Morten Scheibye-Knudsen, Masaya Koshizaka, Koutaro Yokote, Eric Verdin, Vilhelm A Bohr, Charalampos Tzoulis, David A Sinclair, Evandro Fei Fang.

Beyond their classical functions as redox cofactors, recent fundamental and clinical research has expanded our understanding of the diverse roles of nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) in signaling pathways, epigenetic regulation and energy homeostasis. Moreover, NAD and NADP influence numerous diseases as well as the processes of aging, and are emerging as targets for clinical intervention. Here, we summarize safety, bioavailability and efficacy data from NAD+-related clinical trials, focusing on aging and neurodegenerative diseases. We discuss the established NAD+ precursors nicotinic acid and nicotinamide, newer compounds such as nicotinamide riboside and nicotinamide mononucleotide, and emerging precursors. We also discuss technological advances including in industrial-scale production and real-time detection, which are facilitating NAD+ research and clinical translation. Finally, we emphasize the need for further large-scale studies to determine optimal dose, administration routes and frequency, as well as long-term safety and interindividual variability in response.

DOI: https://doi.org/10.1038/s43587-025-00947-6
Mol Cell. 2025 Sep 10. pii: S1097-2765(25)00707-5. [Epub ahead of print]

α-Synuclein aggregates inhibit ESCRT-III through sequestration and collateral degradation.

Cole S Sitron, Victoria A Trinkaus, Ana Galesic, Maximilian Garhammer, Patricia Yuste-Checa, Ulrich Dransfeld, Dennis Feigenbutz, Jiuchun Zhang, Larysa Ivashko, Irina Dudanova, J Wade Harper, F Ulrich Hartl.

  α-Synuclein aggregation is a hallmark of Parkinson's disease and related synucleinopathies. Extracellular α-synuclein fibrils enter naive cells via endocytosis, followed by transit into the cytoplasm to seed endogenous α-synuclein aggregation. Intracellular aggregates sequester numerous proteins, including subunits of the endosomal sorting complexes required for transport (ESCRT)-III system for endolysosome membrane repair, but the toxic effects of these events remain poorly understood. Using cellular models and in vitro reconstitution, we found that α-synuclein fibrils interact with a conserved α-helix in ESCRT-III proteins. This interaction sequesters ESCRT-III subunits and triggers their proteasomal destruction in a process of "collateral degradation." These twin mechanisms deplete the available ESCRT-III pool, initiating a toxic feedback loop. The ensuing loss of ESCRT function compromises endolysosome membranes, thereby facilitating escape of aggregate seeds into the cytoplasm, facilitating a "second wave" of templated aggregation and ESCRT-III sequestration. We suggest that collateral degradation and the triggering of self-perpetuating systems are general mechanisms of sequestration-induced proteotoxicity.

Keywords:  CHMP2B; ESCRT; ESCRT-III; Parkinson’s disease; aggregation; lysosome; protein aggregate spreading; proteostasis; sequestration; α-synuclein

DOI:  https://doi.org/10.1016/j.molcel.2025.08.022