bims-auttor 2025-08-10 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2025–08–10
28 papers selected by
Viktor Korolchuk, Newcastle University

Lysosomal membrane homeostasis and its importance in physiology and disease.
OPTN deficiency through CRISPR/Cas9 downregulates autophagy and mitophagy in a SOD1-G93A-expressing transgenic cell line.
Comprehensive genetic analyses of Arabidopsis autophagy-related 8 family reveal redundant regulatory roles during autophagy.
Building bridges for autophagy.
SOD1 is delivered to lysosomes via autophagy to maintain lysosomal function and integrity.
The cell autonomous and non-autonomous functions of Rab27 in longevity and neuroprotection in Drosophila.
Contrasting roles of autophagy in cellular prion infection.
Autophagy activator AA-20 improves proteostasis and extends Caenorhabditis elegans lifespan.
The intrinsically disordered regions of organellophagy receptors are interchangeable and control organelle fragmentation, ER-phagy and mitophagy flux.
PDZD8 links organelle crosstalk to synaptic remodeling via autophagy.
Basal autophagy during meiotic prophase I is required for accurate chromosome segregation in Drosophila oocytes and declines during oocyte aging.
Degradative Signaling in ATG7-Deficient Skeletal Muscle Following Cardiotoxin Injury.
Autophagy suppression via SRC induction represents a therapeutic vulnerability for BAP1-mutant cancers.
Condition-dependent effects of knockdown of autophagy on C. elegans longevity.
The interplay involving oxidative stress and autophagy: Mechanisms, implications, and therapeutic opportunities.
Mitophagy in the mechanisms of treatment resistance in solid tumors.
Functional and Structural Insights Into Complex Formation Between OPTN Leucine Zipper Domain and RAB8A.
Treatment of age-related decreases in GTP levels restores endocytosis and autophagy.
Inhibition of Sirtuin 2 enhances autophagy and restores neuronal function in aged hippocampal neurons.
Targeting the ATG12-ATG3 protein-protein interaction: From structural insights to therapeutic opportunities in autophagy modulation.
Peroxiredoxin Ⅲ mitigates mitochondrial H2O2-mediated damage and supports quality control in cardiomyocytes under hypoxia-reoxygenation stress.
Rag GTPases Suppress Renal Cystic Disease by Inhibiting TFEB Independently of mTORC1.
Impaired mitochondria-initiated crosstalk with lysosomes reciprocally aggravates mitochondrial defect through LManVI.
Loss of REP-1 in Retinal Pigmented Epithelium (RPE) cells leads to impaired phagosome processing and altered lysosomal pathway function.
Zinc induces neuronal autophagy via HMGB1 nuclear translocation in acute cerebral ischemia.
Sugar accelerates chronological aging in yeast via ceramides.
Establishment of the phagophore-ERES membrane contact site initiates phagophore elongation.
What is the clinical evidence to support off-label rapamycin therapy in healthy adults?

Nat Rev Mol Cell Biol. 2025 Aug 04.

Lysosomal membrane homeostasis and its importance in physiology and disease.

Maja Radulovic, Chonglin Yang, Harald Stenmark.

Lysosomes are membranous organelles that are crucial for cell function and organ physiology. Serving as the terminal stations of the endocytic pathway, lysosomes have fundamental roles in the degradation of endogenous and exogenous macromolecules and particles as well as damaged or superfluous organelles. Moreover, the lysosomal membrane is a docking and activation platform for several signalling components, including mTOR complex 1 (mTORC1), which orchestrates metabolic signalling in the cell. The integrity of their membrane is crucial for lysosomes to function as hubs for the regulation of cell metabolism. Various agents, including pathogens, nanoparticles and drugs, can compromise lysosomal membrane integrity. Membrane permeabilization causes leakage of proteases and cations into the cytosol, which can induce cell death pathways and innate immunity signalling. Multiple pathways repair damaged lysosomes, and severely damaged lysosomes are degraded by an autophagic process, lysophagy. Moreover, lysosome damage activates transcriptional programmes that orchestrate lysosome biogenesis to replenish the cellular lysosome pool. In this Review, we discuss recent insights into the mechanisms that ensure the maintenance of lysosomal membrane homeostasis, including novel mechanisms of lysosomal membrane repair and the interplay between lysosome damage, repair, lysophagy and lysosome biogenesis. We highlight the importance of lysosomal membrane homeostasis in cell function, physiology, disease and ageing, and discuss the potential for therapeutic exploitation of lysosomal membrane permeabilization.

DOI: https://doi.org/10.1038/s41580-025-00873-w
IBRO Neurosci Rep. 2025 Dec;19 307-316

OPTN deficiency through CRISPR/Cas9 downregulates autophagy and mitophagy in a SOD1-G93A-expressing transgenic cell line.

Di Wen, Qiusheng Li, Yuanyuan Li, Wenyu Yan, Yanyan Wang, Yakun Liu.

  Amyotrophic lateral sclerosis (ALS) is characterized by the loss of upper and lower motor neurons (MNs) and is the most common adult paralysis neurodegenerative disease. Dysregulated autophagy, which has been reported in the pathogenesis of familial ALS, has been found in superoxide dismutase 1 (SOD1) transgenic mice and cell lines. Optineurin (OPTN) is a signal regulator that coordinates many crucial cellular processes, including autophagy, mitophagy and aggrephagy. Recent studies have shown that OPTN gene mutations are correlated with ALS, glaucoma and Paget's disease of the bone. Indeed, defects in autophagosome-lysosome fusion have been reported in patients with ALS-associated OPTN mutations. However, the exact function of OPTN in the pathology of ALS remains unknown. To determine the function of OPTN, we generated OPTN-knockdown cell lines from SOD1-G93A-expressing NSC34 cells with the clustered regularly interspaced short palindromic repeats/associated system 9 (CRISPR/Cas9) approach. In our research, we observed that the loss of OPTN resulted in the impairment of autophagy and mitophagy pathways. Moreover, the mitochondrial transmembrane potential was depolarized by LV-sgRNA-OPTN. On the basis of observations of live cells, the production of reactive oxygen species (ROS) was increased, the autophagic flux decreased, and the autophagic flux merged with that of mitochondria according to confocal live-cell imaging. A decreased LC3-II and an increased p62 levels indicated that autophagy pathway activation was decreased. The protein levels of VDAC1 and TBK1 decreased after OPTN knockdown, suggesting that mitophagy was blocked. Our results suggest that OPTN plays a pivotal role in regulating autophagy and mitophagy.

Keywords:  Amyotrophic lateral sclerosis; Autophagy; CRISPR/Cas9; Mitophagy; OPTN; SOD1-G93A transgenic cell line

DOI:  https://doi.org/10.1016/j.ibneur.2025.07.011
New Phytol. 2025 Aug 02.

Comprehensive genetic analyses of Arabidopsis autophagy-related 8 family reveal redundant regulatory roles during autophagy.

Kuntian Dong, Guiling Deng, Yilin Liu, Kuo-En Chen, Huan Wei, Xiner Huang, Wanying Huang, Ping Zheng, Takashi Ueda, Richard D Vierstra, Xiao Huang, Faqiang Li.

  The ubiquitin-like protein ATG8 is a central component of the autophagy process and is required at multiple steps during both bulk and selective autophagy. Currently, our understanding of the roles of ATG8 in plants and the possible functional specialization of its family members is limited by genetic redundancy. Here, we employed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas)9 targeting technology to systematically inactivate all nine Arabidopsis thaliana ATG8 loci. Subsequent analyses of the resulting mutants revealed that, unlike mammalian ATG8 family members, which have distinct roles, Arabidopsis isoforms largely overlap in their functions controlling autophagic flux. Notably, combinatorial mutations have similarly impaired autophagy and misregulated proteomes much like other autophagy mutants. We further examined the functional redundancy of Arabidopsis ATG8s in late autophagy stages by investigating their interactions with Rab GTPase (RABG)3/RAB7 proteins. We found that all ATG8 representatives could interact with RABG3 proteins via ATG8-interacting motif-LC3-interacting region-docking site interfaces. Such interactions are crucial for RABG3 binding to the autophagosome membrane and probably for the fusion of autophagosomes with the vacuole. However, they are not necessary for endosomal trafficking. With this collection of multiple high-order atg8 mutants, we provide a venue to selectively study the roles of individual ATG8 isoforms during both canonical and noncanonical autophagy in Arabidopsis.

Keywords:  ATG8; Arabidopsis; Rab GTPase; autophagosome–vacuole fusion; autophagy; nutrient recycling; vacuole

DOI:  https://doi.org/10.1111/nph.70418
Nat Struct Mol Biol. 2025 Aug 07.

Building bridges for autophagy.

Anne Schreiber.

DOI: https://doi.org/10.1038/s41594-025-01628-z
J Cell Biol. 2025 Oct 06. pii: e202501007. [Epub ahead of print]224(10):

SOD1 is delivered to lysosomes via autophagy to maintain lysosomal function and integrity.

Yanzhe Zheng, Meng Li, Xuelin Chen, Ze Zheng, Zixuan Chen, Ruilin Tian, Yan G Zhao.

The gene encoding superoxide dismutase 1 (SOD1) is often mutated in familial amyotrophic lateral sclerosis (ALS), affecting motor neurons. Compared with ALS-associated mutant SOD1, the function of WT SOD1 is less explored. We demonstrate that during starvation, WT and mutant SOD1 are transported into lysosomes. Genome-wide CRISPR interference (CRISPRi) screening identified autophagy-related proteins and the autophagic receptor TP53INP1 as key mediators. TP53INP1 binds ATG8 family proteins, preferentially LC3C, and directly interacts with SOD1. Within lysosomes, SOD1 retains its enzymatic activity. Starvation induces elevated levels of lysosomal reactive oxygen species (ROS), which are further increased by knocking down SOD1 or TP53INP1. Lysosomal degradation activities and membrane integrity are also compromised in the absence of SOD1 or TP53INP1. We reveal a novel function of SOD1 in maintaining lysosomal activity and integrity, and a previously unrecognized role of autophagy in delivering cytosolic enzymes into lysosomes for catalytic purposes, rather than for degradation.

DOI: https://doi.org/10.1083/jcb.202501007
Autophagy. 2025 Aug 05. 1-17

The cell autonomous and non-autonomous functions of Rab27 in longevity and neuroprotection in Drosophila.

Chia-Heng Hsu, Yi-Jhan Li, Ting-Ni Guo, Fei-Yang Tzou, Cheng-Li Hong, Chin-Hsien Lin, Shu-Yi Huang, Chih-Chiang Chan.

  Autophagic decline accompanies age and causes a deterioration in proteostasis, rendering neuronal demise. Rab27 functions as a vesicle regulator for macroautophagic/autophagic degradation and exocytosis. Loss of Drosophila Rab27 in αβp brain neurons enhances longevity, underscoring its neuronal role and systemic effect. To understand the underlying mechanisms, we characterized the cell autonomous and non-autonomous functions of Rab27. Rab27 expression increased in midlife, providing a temporal manipulation window. Depleting Rab27 at that timepoint activated autophagy and sustained neuronal maintenance. At the organismic level, Egfr (Epidermal growth factor receptor) ligand was reduced and Akt kinase underphosphorylated in the Rab27 KO fly body, indicating a widespread signaling cascade. Finally, Rab27 KO ameliorates the neurotoxicity in a fly α-synucleinopathy model. Altogether, our results highlight a neuronal autophagy regulator exerting systemic effects that are crucial for neuronal maintenance and improving longevity.Abbreviation: Atg autophagy-related genes;EGF: epidermal growth factor; Egfr: Epidermal growth factor receptor;EGFR: epidermal growth factor receptor; foxo: forkhead box, sub-groupO; mTor: mechanistic target of rapamycin; MTOR: mechanistic target ofrapamycin; spi: spitz.

Keywords:  Autophagy; Egfr; Rab27; brain-fat body axis; lifespan; parkinson disease

DOI:  https://doi.org/10.1080/15548627.2025.2541384
Autophagy. 2025 Aug 08.

Contrasting roles of autophagy in cellular prion infection.

Basant Abdulrahman, Andreas Heiseke, Yasmine Aguib, Li Lu, Dalia Abdelaziz, Mariam Ansari, Simrika Thapa, Yuzuru Taguchi, Sabine Gilch, Hermann M Schätzl.

  Autophagy is a cellular degradation program that can exert both beneficial and adverse effects in various neurodegenerative diseases. We tested the role of macroautophagy/autophagy in prion infection and how this machinery affects the life cycle of prions. In mouse embryonic fibroblasts, we found a pronounced dependence of prion replication on autophagy competence, suggesting that autophagy provides functions needed for prion propagation. However, in neuronal cells, autophagy had mostly the opposite role. Cells ablated for autophagy competence by gene editing harbored elevated amounts of misfolded prion protein, indicating that neuronal cells use autophagy for prion degradation. These data show that autophagy can have two functions in the replication of prions, and depending on the cellular context, this can be protective against or supportive of prion infection. These findings demonstrate that prions use cellular machineries to benefit propagation in certain cell types, whereas other cell types employ the same machinery as a defense mechanism.

Keywords:  Atg5 knockout; autophagy; disaggregase; neurodegeneration; prion; prion infection

DOI:  https://doi.org/10.1080/15548627.2025.2545604
Proc Natl Acad Sci U S A. 2025 Aug 12. 122(32): e2423455122

Autophagy activator AA-20 improves proteostasis and extends Caenorhabditis elegans lifespan.

Ee Phie Tan, Nora Lyang, Saam Doroodian, Pablo Sanz-Martinez, Jin Xu, Sviatlana Zaretski, José L Nieto-Torres, Hiroshi Ebata, Shaun H Y Lim, William C Hou, Khalyd J Clay, Leonard Yoon, Lynée A Massey, Derek Rhoades, Danny Garza, Kristen A Johnson, Alan To, Lydia Ambaye, Emily P Bentley, Michael Petrascheck, Alexandra Stolz, Jeffery W Kelly, Malene Hansen.

  The degradation of cellular components through autophagy is essential for longevity and healthy aging. However, autophagy function decreases with aging, contributing to age-related diseases. In this study, we characterized a small-molecule activator of autophagy called AA-20 that enhances autophagy and lipid droplet clearance in human cells and in the nematode Caenorhabditis elegans. AA-20 reduces polyglutamine aggregation in an autophagy-dependent manner in both human cells and C. elegans, where it also promotes fitness. Consistently, we found that AA-20 extends lifespan in WT C. elegans, but not in autophagy-deficient mutants. Interestingly, our findings suggest that AA-20 acts, at least in part, through a mechanism involving the transcription factor EB, but without inhibiting the protein kinase mammalian target of rapamycin complex 1. Collectively, our results identify an autophagy activator AA-20, which may have potential therapeutic implications for aging-related proteinopathies and lipid storage disorders.

Keywords:  C. elegans; autophagy activator; healthspan; lifespan; lipophagy

DOI:  https://doi.org/10.1073/pnas.2423455122
Nat Cell Biol. 2025 Aug 04.

The intrinsically disordered regions of organellophagy receptors are interchangeable and control organelle fragmentation, ER-phagy and mitophagy flux.

Mikhail Rudinskiy, Carmela Galli, Andrea Raimondi, Maurizio Molinari.

Organellophagy receptors control the generation and delivery of portions of their homing organelle to acidic degradative compartments to recycle nutrients, remove toxic or aged macromolecules and remodel the organelle upon physiologic or pathologic cues. How they operate is not understood. Here we show that organellophagy receptors are composed of a membrane-tethering module that controls organellar and suborganellar distribution and by a cytoplasmic intrinsically disordered region (IDR) with net cumulative negative charge that controls organelle fragmentation and displays an LC3-interacting region (LIR). The LIR is required for lysosomal delivery but is dispensable for organelle fragmentation. Endoplasmic reticulum (ER)-phagy receptors' IDRs trigger DRP1-assisted mitochondrial fragmentation and mitophagy when transplanted at the outer mitochondrial membrane. Mitophagy receptors' IDRs trigger ER fragmentation and ER-phagy when transplanted at the ER membrane. This offers an interesting example of function conservation on sequence divergency. Our results imply the possibility to control the integrity and activity of intracellular organelles by surface expression of organelle-targeted chimeras composed of an organelle-targeting module and an IDR module with net cumulative negative charge that, if it contains a LIR, eventually tags the organelle portions for lysosomal clearance.

DOI: https://doi.org/10.1038/s41556-025-01728-4
Autophagy. 2025 Aug 03. 1-2

PDZD8 links organelle crosstalk to synaptic remodeling via autophagy.

Rajan S Thakur, Kate M O'Connor-Giles.

  Synapse formation and plasticity require coordinating cellular processes from signaling to protein turnover over long distances, placing high demands on intracellular communication. Membrane contact sites (MCSs) between organelles are specialized compartments for coordinating cellular processes, yet their functions in the developing nervous system remain poorly understood. Through an in vivo CRISPR screen in Drosophila, we identified the conserved endoplasmic reticulum (ER) MCS tethering protein Pdzd8 as a regulator of activity-dependent synapse development. Our in vivo studies demonstrate that Pdzd8 functions at ER-late endosome/lysosome MCSs to promote lysosomal maturation and increase autophagic flux during periods of high demand such as prolonged neuronal activity.

Keywords:  Autophagy; PDZD8; lipid transfer; lysosomes; membrane contact sites; synapse

DOI:  https://doi.org/10.1080/15548627.2025.2537983
Mol Biol Cell. 2025 Aug 06. mbcE25050213

Basal autophagy during meiotic prophase I is required for accurate chromosome segregation in Drosophila oocytes and declines during oocyte aging.

Diana C Hilpert, Muhammad Abdul Haseeb, Sharon E Bickel.

Meiotic segregation errors in human oocytes are the leading cause of miscarriages and trisomic pregnancies and their frequency increases exponentially for women in their thirties. One factor that contributes to increased segregation errors in aging oocytes is premature loss of sister chromatid cohesion. However, the mechanisms underlying age-dependent deterioration of cohesion are not well-defined. Autophagy, a cellular degradation process critical for cellular homeostasis, is known to decline with age in various organisms and cell types. Here we quantify basal autophagy in Drosophila oocytes and use GAL4/UAS inducible knockdown to ask whether disruption of autophagy in prophase oocytes impacts the fidelity of chromosome segregation. We find that individual knockdown of autophagy proteins in Drosophila oocytes during meiotic prophase causes a significant increase in segregation errors. In addition, Atg8a knockdown in prophase oocytes leads to premature loss of arm cohesion and missegregation of recombinant homologs during meiosis I. Using an oocyte aging paradigm that we have previously described, we show that basal autophagy decreases significantly when Drosophila oocytes undergo aging. Our data support the model that a decline in autophagy during oocyte aging contributes to premature loss of meiotic cohesion and segregation errors.

DOI: https://doi.org/10.1091/mbc.E25-05-0213
Muscles. 2023 Sep 15. 2(3): 299-316

Degradative Signaling in ATG7-Deficient Skeletal Muscle Following Cardiotoxin Injury.

Fasih Ahmad Rahman, Troy Campbell, Darin Bloemberg, Sarah Chapman, Joe Quadrilatero.

  Skeletal muscle is a complex tissue comprising multinucleated and post-mitotic cells (i.e., myofibers). Given this, skeletal muscle must maintain a fine balance between growth and degradative signals. A major system regulating the remodeling of skeletal muscle is autophagy, where cellular quality control is mediated by the degradation of damaged cellular components. The accumulation of damaged cellular material can result in elevated apoptotic signaling, which is particularly relevant in skeletal muscle given its post-mitotic nature. Luckily, skeletal muscle possesses the unique ability to regenerate in response to injury. It is unknown whether a relationship between autophagy and apoptotic signaling exists in injured skeletal muscle and how autophagy deficiency influences myofiber apoptosis and regeneration. In the present study, we demonstrate that an initial inducible muscle-specific autophagy deficiency does not alter apoptotic signaling following cardiotoxin injury. This finding is presumably due to the re-establishment of ATG7 levels following injury, which may be attributed to the contribution of a functional Atg7 gene from satellite cells. Furthermore, the re-expression of ATG7 resulted in virtually identical regenerative potential. Overall, our data demonstrate that catastrophic injury may "reset" muscle gene expression via the incorporation of nuclei from satellite cells.

Keywords:  apoptosis; autophagy; cardiotoxin; cell death; muscle injury; muscle regeneration; satellite cells

DOI:  https://doi.org/10.3390/muscles2030023
Autophagy. 2025 Aug 03. 1-20

Autophagy suppression via SRC induction represents a therapeutic vulnerability for BAP1-mutant cancers.

Silvia Vega-Rubin-de-Celis, Amanda Kristani, Matthias Kudla, Svenja Mergener, Andrés Corrochano-Ruiz, Safa Larafa, Jetsy Montero-Vergara, Laura-Marie Ahle, Rainer Will, Mael Lever, Viktor Grünwald, Boris Hadaschik, Verena Jendrossek, Nikolaos E Bechrakis, Samuel Peña-Llopis.

  BAP1 is a tumor suppressor and epigenetic modifier that is frequently mutated in cancer, leading to increased aggressiveness and metastasis, as well as poor patient survival. Unfortunately, there are currently no specific therapies for metastatic tumors harboring BAP1 mutations. In this study, we have identified a new targetable BAP1-associated autophagic vulnerability. We demonstrate that BAP1 transcriptionally regulates the proto-oncogene SRC, a non-receptor tyrosine kinase. SRC then binds to, phosphorylates, and inactivates BECN1 (Beclin 1), an essential autophagy protein. This inhibits autophagy in cells derived from various cancer types with BAP1 mutations. Treatment of these cells with SRC inhibitors (such as dasatinib, bosutinib and saracatinib) and autophagy-inducing drugs (such as Tat-BECN1, SW076956 and SW063058) demonstrated a synergistic interaction between these compounds both in vitro and in ovo using a chick Chorioallantoic Membrane (CAM) assay. Furthermore, ex vivo studies employing patient-derived tumor organoids (PDTOs) of uveal melanoma (UM) and clear-cell renal cell carcinoma (ccRCC) as preclinical models have substantiated the synergism of these drugs, preferentially in the context of BAP1 loss. Our findings elucidate a novel BAP1-SRC-BECN1-autophagy regulatory axis that can be exploited therapeutically in precision oncology through the combination of SRC inhibitors and autophagy inducers, contingent upon patient stratification for BAP1 loss.Significance: Deadly cancers with BAP1 mutations suppress autophagy by phosphorylating the autophagy regulator BECN1 via the proto-oncogene SRC. Treatment with SRC inhibitors and autophagy inducers exhibited synergism in vitro, in ovo and in patient-derived tumor organoids with BAP1 loss, paving the way for treating BAP1-deficient cancers with autophagy inducers and kinase inhibitors.

Keywords:  BRCA1-associated protein 1; PDOs; cholangiocarcinoma; patient-derived organoids; personalized medicine; tumoroids

DOI:  https://doi.org/10.1080/15548627.2025.2535265
bioRxiv. 2025 Jul 31. pii: 2025.07.28.667102. [Epub ahead of print]

Condition-dependent effects of knockdown of autophagy on C. elegans longevity.

Kuei Ching Hsiung, Hannah Chapman, Xiaoya Wei, Xiaoyu Sun, Isadora Rawlinson, David Gems.

Autophagy is thought to clear damaged cellular constituents that contribute to aging, and several life-extending interventions in model organisms show some degree of autophagy dependence. In C. elegans , inhibiting autophagy can shorten, lengthen or have no effect on lifespan. Differences between published findings likely reflect variability in experimental conditions. Here we investigate the condition dependence of effects on lifespan of RNA-mediated interference (RNAi) knockdown of autophagy pathway components. Effects on several interventions causing a strong Age (increased lifespan) phenotype were examined, including mutation of daf-2 (insulin/IGF-1 receptor). Factors varied included daf-2 mutant allele class, atg gene, temperature and presence of 5-fluoro-2'-deoxyuridine (FUDR). Effects on lifespan of atg RNAi proved to be highly condition dependent. Notably, for most atg genes tested lifespan was not usually reduced more in the long-lived mutant than in the wild-type control. This occurred at 20°C for certain atg genes with daf-2(e1368) but not daf-2(e1370) . At 25°C, little reduction in lifespan was seen. However, atg-18 knockdown behaved differently, suppressing daf-2 Age under all conditions, suggesting possible pleiotropic action. Presence of high concentration FUDR caused knockdown of several atg genes to increase lifespan. Thus, depending on experimental conditions, atg knockdown can increase, decrease or have no effect on daf-2 Age. The lack of suppression of Age by atg RNAi in most cases raises questions about the importance of autophagy in daf-2 Age. Moreover, condition dependence of effects creates a risk of possible condition selection bias.

DOI: https://doi.org/10.1101/2025.07.28.667102
Exp Mol Pathol. 2025 Aug 01. pii: S0014-4800(25)00039-5. [Epub ahead of print]143 104989

The interplay involving oxidative stress and autophagy: Mechanisms, implications, and therapeutic opportunities.

Noha A Gouda, Assem Zhakupova, Ahmed M Abdelaal, Firdos Ahmad, Ahmed Elkamhawy.

  Reactive oxygen species (ROS) are extremely reactive molecules produced during cellular metabolism, which play important roles in signaling and immune responses. Excessive ROS accumulation results in oxidative stress and cellular damage. As a result, autophagy (a cellular recycling process) is induced to overcome oxidative stress conditions by eliminating impaired cellular components. By selectively targeting and degrading dysfunctional mitochondria and peroxisomes through mitophagy and pexophagy, respectively, cells can effectively reduce ROS accumulation. Conversely, oxidative stress can disrupt autophagy, impairing protein aggregate clearance and thereby exacerbating ROS accumulation. In this review, we discuss the complex correlation between oxidative stress and autophagy, highlighting the mechanisms of regulation and their pathological implications. Additionally, we discuss the latest advances and challenges in developing autophagy-modulating therapies.

Keywords:  Autophagy; Mitophagy; Oxidative stress; Pexophagy; Reactive oxygen species (ROS)

DOI:  https://doi.org/10.1016/j.yexmp.2025.104989
Oncol Rev. 2025 ;19 1607983

Mitophagy in the mechanisms of treatment resistance in solid tumors.

Xiaoyi Yan, Hui Ding, Mengxiao Ren, Lei Zang.

  This review aims to explore the mechanisms by which mitophagy contributes to treatment resistance in solid tumors. As advancements in cancer therapies continue to evolve, treatment resistance emerges as a significant barrier to successful tumor management. Mitophagy, a specific form of cellular autophagy, has been implicated in the survival, proliferation, and drug resistance of tumor cells. This article will summarize the latest research findings and analyze how mitophagy impacts the biological characteristics of solid tumors, thereby revealing its potential implications in cancer treatment strategies. By understanding the role of mitophagy in the context of treatment resistance, we may uncover new therapeutic targets and strategies to enhance the efficacy of existing cancer treatments.

Keywords:  cellular autophagy; mitophagy; solid tumors; treatment resistance; tumor biology

DOI:  https://doi.org/10.3389/or.2025.1607983
Genes Cells. 2025 Sep;30(5): e70043

Functional and Structural Insights Into Complex Formation Between OPTN Leucine Zipper Domain and RAB8A.

Kei Okatsu, Reika Kikuchi, Noriyuki Matsuda, Shuya Fukai, Koji Yamano.

Optineurin (OPTN) is a multifunctional adaptor protein involved in vesicular trafficking and selective autophagy. In this study, we investigated the molecular mechanism by which OPTN regulates these distinct processes through the leucine zipper (LZ) domain. OPTN interacts with the active form of RAB8A and closely related RAB proteins (RAB8B and RAB10). We determined the crystal structure of the OPTN-RAB8A complex at 1.83 Å resolution and elucidated the specific interaction mechanism between these proteins. Structure-guided mutational analysis at the molecular and cellular level suggested that OPTN interacts with RAB8A on two distinct surfaces. RAB8A-interacting surfaces of OPTN include residues that are located apart from the LZ-forming region. Furthermore, the interaction between OPTN and RAB8A was corroborated by cell biological approaches. Although RAB8A/8B/10 were not essential for mitophagy in experiments using their triple knockout cells, the RAB8A-binding residues of OPTN were critical for the recruitment of ATG9A vesicles. Therefore, our results provide molecular insights into the functional role of the LZ domain of OPTN in regulating vesicular trafficking and selective autophagy.

DOI: https://doi.org/10.1111/gtc.70043
Geroscience. 2025 Aug 02.

Treatment of age-related decreases in GTP levels restores endocytosis and autophagy.

R A Santana, J M McWhirt, G J Brewer.

  Age-related declines in neuronal bioenergetic levels may limit vesicular trafficking and autophagic clearance of damaged organelles and proteins. Age-related ATP depletion would impact cognition dependent on ionic homeostasis, but limits on proteostasis powered by GTP are less clear. We used neurons isolated from aged 3xTg-AD Alzheimer's model mice and a novel genetically encoded fluorescent GTP sensor (GEVAL) to evaluate live GTP levels in situ. We report an age-dependent reduction in ratiometric measurements of free/bound GTP levels in living hippocampal neurons. Free GTP colocalized in the mitochondria decreased with age accompanied by the accumulation of free GTP-labeled vesicular structures. The energy dependence of autophagy was demonstrated by depletion of GTP with rapamycin stimulation, while bafilomycin inhibition of autophagy raised GTP levels. Twenty-four-hour supplementation of aged neurons with the NAD precursor nicotinamide and the Nrf2 redox modulator EGCG restored GTP levels to youthful levels and mobilized endocytosis and lysosomal consumption for autophagy via the respective GTPases Rab7 and Arl8b. This vesicular mobilization promoted the clearance of intraneuronal Aβ aggregates, improved viability, and lowered protein oxidative nitration in AD model neurons. Our results reveal age- and AD-related neuronal GTP energy deficits that impair autophagy and endocytosis. GTP deficits were remediated by an external NAD precursor together with a Nrf2 redox modulator which suggests a translational path.

Keywords:  Aging; Alzheimer; EGCG; Energetics; Neuron; Nicotinamide; Redox

DOI:  https://doi.org/10.1007/s11357-025-01786-4
Brain Res Bull. 2025 Aug 07. pii: S0361-9230(25)00313-2. [Epub ahead of print]230 111501

Inhibition of Sirtuin 2 enhances autophagy and restores neuronal function in aged hippocampal neurons.

Zhenyuan Zhang, Lan Zhang, Yidan Zhang, Yuan Zhao, Ya Gao, Cong Zhang, Dongxiao Li, Xiangjian Zhang, Guofeng Yang, Jian Zhang.

  Age-related cognitive decline is linked to impaired autophagy and hippocampal dysfunction. This study investigates the role of Sirtuin 2 (SIRT2) in age-related cognitive decline, focusing on its impact on autophagy and hippocampal function. Quantitative proteomic analysis revealed 67 significantly dysregulated proteins in the hippocampus of naturally aged male mice, including upregulated SIRT2 and impaired autophagy. To explore the role of SIRT2 in brain aging and its association with autophagy, naturally aged male mice received AK7, a SIRT2-specific inhibitor, for four consecutive weeks, followed by behavioral assessment using the Morris water maze. Western blot and immunofluorescence analyses were applied to assess mTOR phosphorylation, LC3B-II turnover, and SQSTM1/p62 degradation, complemented by in vitro validation in a D-galactose-induced HT-22 cellular senescence model. The results indicated that AK7 administration improved cognitive performance in aged mice, while simultaneously reducing mTOR phosphorylation and enhancing autophagy markers. In vitro, SIRT2 genetic knockdown restored the mTOR phosphorylation, LC3B-II/LC3I ratio, and SQSTM1/p62 accumulation, while also reducing senescence markers (including TNF-α, P21,Trp53) in D-galactose-induced HT-22 cells. These effects were abolished by mTOR activation, confirming mTOR as a downstream mediator of SIRT2. Our findings highlight SIRT2 inhibition as a promising therapeutic strategy to counteract age-related cognitive decline through the modulation of mTOR-dependent autophagy in the hippocampus.

Keywords:  Autophagy; Brain aging; Proteomic; Sirtuin 2 (SIRT2)

DOI:  https://doi.org/10.1016/j.brainresbull.2025.111501
Pathol Res Pract. 2025 Aug 04. pii: S0344-0338(25)00349-8. [Epub ahead of print]273 156156

Targeting the ATG12-ATG3 protein-protein interaction: From structural insights to therapeutic opportunities in autophagy modulation.

Emadeldin M Kamel, Sally Mostafa Khadrawy, Ahmed A Allam, Noha A Ahmed, Faris F Aba Alkhayl, Al Mokhtar Lamsabhi.

  Autophagy sustains cellular metabolism, shapes immune signaling and, when dysregulated, contributes to cancer progression and cytokine-storm syndromes. A crucial catalytic step is conjugation of microtubule-associated protein 1 light chain 3 (LC3) to phosphatidylethanolamine, driven by direct binding of the E2-like enzyme autophagy-related protein 3 (ATG3) to the ubiquitin-like protein autophagy-related protein 12 (ATG12). Disrupting this ATG12-ATG3 protein-protein interaction (PPI) could silence both the degradative and secretory arms of autophagy with high pathway selectivity. Here we review the rapid evolution of ATG12-ATG3 inhibition from structural insight to drug-like chemical matter. High-resolution crystallography pinpointed a hydrophobic pocket around ATG12 Trp73 that accommodates ATG3 Met157, revealing an "anchor-and-latch"-a motif in which one residue ('anchor') buries deeply while flanking residues ('latch') secure the complex- topology ideal for small-molecule competition. A split Gaussia luciferase screen of more than 40 000 compounds, guided by in-silico pocket bias, yielded 17 micromolar disruptors; systematic structure-activity-relationship (SAR) exploration transformed an off-target casein kinase 2 (CK2) hit into naphthalene lead compound 189, which binds ATG12 directly (dissociation constant, KD ≈ 5 µM). This lead collapses autophagic flux at single-digit micromolar concentrations, arrests autophagy-addicted tumor cells and suppresses interleukin-1β (IL-1β) secretion from macrophages-all without kinase or lysosomal liabilities. Medicinal-chemistry principles distilled from more than 150 analogues define the hydrophobic "plug," polar "claw," and polarity-tuning handles that govern potency and selectivity. An integrated assay toolbox-spanning surface plasmon resonance (SPR), dual-color LC3 flux reporters and disease-relevant phenotypes-now drives nanomolar optimization and safety profiling. We conclude by mapping future directions: covalent-reversible chemotypes, proteolysis-targeting chimera (PROTAC) degraders, targeted-delivery platforms and combination regimens poised to translate ATG12-ATG3 disruption into first-in-class therapeutics for oncology, immunology and infectious disease.

Keywords:  ATG12-ATG3 interaction; Autophagy; Cancer Immunotherapy; Protein-protein interaction disruption; Small molecule inhibitors

DOI:  https://doi.org/10.1016/j.prp.2025.156156
Redox Biol. 2025 Aug 05. pii: S2213-2317(25)00312-X. [Epub ahead of print]86 103799

Peroxiredoxin Ⅲ mitigates mitochondrial H2O2-mediated damage and supports quality control in cardiomyocytes under hypoxia-reoxygenation stress.

Ji Won Park, Seong Keun Sonn, Byung-Hoon Lee, Goo Taeg Oh, Tong-Shin Chang.

  Peroxiredoxin Ⅲ (PrxⅢ) is a mitochondria-localized peroxidase that plays a key role in detoxifying hydrogen peroxide (H2O2) and preserving organelle homeostasis. While its antioxidant function is well established under physiological conditions, the role of PrxⅢ in the context of cardiac hypoxia/reoxygenation (H/R) injury remains incompletely understood. In this study, we investigated the protective function of PrxⅢ in cardiomyocytes exposed to H/R stress, a widely used in vitro model to mimic ischemia/reperfusion injury. Using H9c2 cells and primary neonatal rat cardiomyocytes, we found that PrxⅢ knockdown significantly increased mitochondrial H2O2 accumulation, leading to excessive mitochondrial fragmentation, impaired mitophagy, and reduced cell survival following H/R. Western blot analysis revealed that mitophagy regulators Parkin and BNIP3 were upregulated under moderate oxidative stress but were markedly suppressed in PrxⅢ-deficient cells after H/R, indicating that mitophagy activation is sensitive to the degree of oxidative stress. These findings were confirmed in vivo using mt-Keima transgenic mice, which showed significantly reduced mitophagic flux in PrxⅢ knockout hearts subjected to ischemia/reperfusion. In addition, PrxⅢ loss impaired lysosomal acidification and proteolytic activity, further contributing to defective autophagic flux. Re-expression of PrxⅢ restored mitochondrial morphology, mitophagy activity, and lysosome function, highlighting its central role in maintaining mitochondrial quality control (MQC). Collectively, our results demonstrate that PrxⅢ mitigates mitochondrial oxidative damage and preserves MQC by coordinating mitochondrial dynamics, mitophagy, and lysosomal integrity. These findings suggest that PrxⅢ may serve as a promising therapeutic target for preventing cardiac injury induced by oxidative stress during ischemia/reperfusion.

Keywords:  Cardiomyocyte injury; Hypoxia/reoxygenation injury; Mitochondrial oxidative stress; Mitophagy dysfunction; Peroxiredoxin Ⅲ

DOI:  https://doi.org/10.1016/j.redox.2025.103799
bioRxiv. 2025 Jul 31. pii: 2025.07.24.664930. [Epub ahead of print]

Rag GTPases Suppress Renal Cystic Disease by Inhibiting TFEB Independently of mTORC1.

Flaviane de Fatima Silva, Alexander R Boucher, Huawei Li, Qingbo Chen, Maria Gaughan, Ekaterina D Korobkina, Marie Sophie Isidor, Abigail O Smith, Kuang Shen, Derek B Allison, Pamela V Tran, Gregory J Pazour, David A Guertin.

Aberrant mTORC1 activation in renal tubular epithelial cells (rTECs) is implicated as a critical driver of renal cystic diseases (RCDs), including autosomal dominant polycystic kidney disease (ADPKD) and tuberous sclerosis (TSC), yet its precise role remains unclear. Rag GTPases recruit mTORC1 to lysosomes, its intracellular activation site. Unexpectedly, we found that deleting RagA/B in rTECs, despite inhibiting mTORC1, triggers renal cystogenesis and kidney failure. We identify TFEB as the key driver of cystogenesis downstream of RagA/B loss and show that Rag GTPases, rather than mTORC1, are the primary suppressors of TFEB in vivo . We further highlight increased nuclear TFEB as a shared feature of several RCD models, whereas differences in mTORC1 activity may explain the variable efficacy of mTORC1 inhibitors. Finally, we provide evidence that nuclear TFEB, rather than mTORC1 activation, is a more consistent biomarker of cyst-lining epithelial cells in ADPKD. Overall, these findings challenge the prevailing view that mTORC1 hyperactivation is required for renal cystogenesis, which has important translational implications.
Teaser: A serendipitous finding uncovers the Rag GTPases as strong suppressors of renal cystogenesis with important disease implications.

DOI: https://doi.org/10.1101/2025.07.24.664930
Nat Commun. 2025 Aug 07. 16(1): 7304

Impaired mitochondria-initiated crosstalk with lysosomes reciprocally aggravates mitochondrial defect through LManVI.

Shengnan Li, Zhaoliang Shan, Guochun Zhao, Yuwei Li, Minghui Du, Xiuxiu Ti, Yuxue Gao, Wenting Li, Hui Zuo, Yan Wang, Qing Zhang.

Mitochondria coordinate with lysosomes to maintain cellular homeomstasis. However, in mitochondrial defect condition, how they communicate is less clear. Here, utilizing dMterf4 RNAi fly model, we find that expression of lysosomal alpha-mannosidase VI (LManVI) is significantly downregulated. Mechanistically, we show that dMterf4 RNAi-triggered mitochondrial defect mediates downregulation of lysosomal LManVI through Med8/Tfb4-E(z)/pho axis, causing impairment of lysosomal function. Reciprocally, downregulation of lysosomal LManVI further decreases many mitochondrial genes expression through downregulation of transcriptional coactivator PGC-1, leading to aggravating the dMterf4 RNAi-mediated mitochondrial defect, suggesting that mitochondrial defect can crosstalk with lysosomes to make mitochondrial status worse in a positive feedback way. Finally, we demarcate that this interaction between mitochondria and lysosomes may be conserved in mammalian cells. Therefore, our findings unveil a communication mechanism between mitochondria and lysosomes in mitochondrial defect case, which provides insights about the treatments of related mitochondrial and lysosomal diseases through modulation of the mitochondria-lysosomes axis.

DOI: https://doi.org/10.1038/s41467-025-62147-5
Mol Biol Cell. 2025 Aug 06. mbcE24110497

Loss of REP-1 in Retinal Pigmented Epithelium (RPE) cells leads to impaired phagosome processing and altered lysosomal pathway function.

Rita Coelho, Pedro Antas, Ana Fragoso Fonseca, Daniela Oliveira, Cláudia Carvalho, Margarida L Pedro, Michael J Hall, Ana Sofia Falcão, Miguel C Seabra, Mafalda Lopes-da-Silva.

Choroideremia (CHM) is a rare form of retinal degeneration caused by mutations in the ubiquitously expressed CHM gene, encoding for Rab escort-protein-1 (REP-1). REP-1 is required for the prenylation of Rab GTPase proteins, regulators of intracellular membrane traffic, yet what specific cellular pathways are affected in CHM and how this contributes to disease progression remains unclear. Using both ARPE-19 and iPSC-derived retinal pigmented epithelium (RPE) cells, where the CHM gene was knocked-out using CRISPR/Cas9, we show that CHM- cells have an increased number of lysosomes. Cathepsins and BSA-Gold were correctly delivered to the lysosomes, suggesting that lysosome organelle identity and targeting machinery are largely unaffected, yet, digestion of photoreceptor outer segments (POS)-derived-phagosomes is impaired, resulting in a doubling of undigested POS-derived autofluorescent material in CHM- cells. Delayed acquisition of LAMP1 by the phagosome was observed. These findings reveal that REP-1 loss leads to subtle lysosomal pathway dysfunction, resulting in defects in phagosome targeting and/or digestion. Our data is consistent with the idea that gradual lysosomal impairment is associated with a premature aging process, characterized by the accumulation of lipofuscin toxic material and eventual RPE and photoreceptor degeneration, which likely drives the progressive vision loss observed in CHM patients.

DOI: https://doi.org/10.1091/mbc.E24-11-0497
Neuropharmacology. 2025 Jul 31. pii: S0028-3908(25)00325-9. [Epub ahead of print] 110617

Zinc induces neuronal autophagy via HMGB1 nuclear translocation in acute cerebral ischemia.

Mingqi Zhang, Jian Yang, Xuying Zhang, Tingting Ma, Peng Wang, Jia Liang.

  The process of autophagy following a stroke is a highly complex phenomenon. Damaged brain cells can produce multifactorial signals that may act as activators of autophagy. Zinc, which is abundantly present in the central nervous system, regulates numerous biological processes, including autophagy. Studies conducted on mammalian cells have consistently demonstrated that zinc promotes autophagy. However, the precise mediator of zinc-induced autophagy following acute ischemic stroke remains unclear. In this study, we investigated whether High Mobility Group Box 1 (HMGB1) is involved in the process of zinc-mediated neuronal autophagy after cerebral ischemia. We established a rat model of middle cerebral artery occlusion (MCAO), and our results indicated that chelating zinc significantly reduced infarct volume and improved neurological function after acute ischemic stroke. Additionally, chelating zinc diminished ischemia-induced neuronal autophagy and inhibited the translocation of HMGB1 from the nucleus to the cytoplasm during acute cerebral ischemia. In cellular experiments utilizing oxygen-glucose deprivation (OGD) treatment, we found that excessive intracellular zinc facilitates the translocation of HMGB1 from the nucleus to the cytoplasm, while HMGB1 regulates zinc-mediated autophagy. Furthermore, inhibiting HMGB1 in cultured neurons impeded the effects of zinc on autophagy. These findings provide evidence that zinc mediates neuronal autophagy by regulating the translocation of HMGB1 to the cytoplasm during acute ischemic stroke.

Keywords:  Autophagy; Cerebral ischemia; HMGB1; Neuron; Zinc

DOI:  https://doi.org/10.1016/j.neuropharm.2025.110617
Cell Stress. 2025 ;9 158-173

Sugar accelerates chronological aging in yeast via ceramides.

Vera Schmiedhofer, Julian Sommersguter-Wagner, Oskar Knittelfelder, Helmut Jungwirth, Gerald N Rechberger, Didac Carmona-Gutierrez, Patrick Rockenfeller, Christoph Ruckenstuhl, Frank Madeo.

  High carbohydrate intake, a characteristic of many Western diets, is a major contributor to age-associated pathologies. Here, we explored the molecular consequences of sugar overload during chronological aging in the yeast Saccharomyces cerevisiae. High levels of glucose and fructose resulted in a decrease of chronological lifespan as well as an increase of cell death, ROS and neutral lipids. Interestingly, these changes were accompanied by significantly altered ceramide profiles. Deletion of either the kinase Tor1, a master regulator of growth and autophagy in response to nutrients, or the vacuole-anchored receptor Vac8, an important player in various autophagy pathways, improved survival and normalized ceramide profiles. This suggests that ceramides might play a role in sugar stress-induced cell death. In line, pharmacological inhibition of sphingolipid synthesis normalized ceramide profiles and improved chronological lifespan, whereas pharmacologically induced ceramide accumulation decreased chronological lifespan. In sum, our findings causally link nutrient signaling and an altered ceramide profile to sugar cytotoxicity in aging yeast, providing a basis for further search of feasible interventions against sugar-induced cell death.

Keywords:  TOR1; VAC8; aging; cell stress; chronological lifespan; lipid homeostasis; lipotoxicity; metabolic syndrom; nutrient signaling

DOI:  https://doi.org/10.15698/cst2025.07.308
Nat Struct Mol Biol. 2025 Aug 07.

Establishment of the phagophore-ERES membrane contact site initiates phagophore elongation.

Rubén Gómez-Sánchez, Sabrina Chumpen Ramirez, Prado Vargas Duarte, Yan Hu, Muriel Mari, Katharina Olschewski, Ralph Hardenberg, J Christopher Fromme, Christian Ungermann, Fulvio Reggiori.

The de novo generation of membrane contact sites (MCSs) between the phagophore and the endoplasmic reticulum exit sites (ERES) is important for the acquisition of the lipids necessary for phagophore elongation and autophagosome formation during autophagy. However, it is currently unclear how these MCSs are established. Here, we show that the TRAPPIII complex, the guanine nucleotide exchange factor of the Rab GTPase Ypt1, localizes to and regulates the formation of the MCS between the phagophore and the ERES. In particular, TRAPPIII and the lipid transfer protein Atg2 appear equally essential for the association of the phagophore with the ERES, TRAPPIII activation and Ypt1 activation onto the phagophore. Ypt1 redistributes over the entire surface of the phagophore and promotes its elongation through both stimulation of the local biosynthesis of phosphatidylinositol-3-phosphate and recruitment of the downstream effectors Atg18 and Atg21. Our data suggest that de novo generation of the phagophore-ER MCSs and subsequent Ypt1 activation initiates phagophore elongation.

DOI: https://doi.org/10.1038/s41594-025-01621-6
Aging (Albany NY). 2025 Aug 07. 17

What is the clinical evidence to support off-label rapamycin therapy in healthy adults?

Jacob M Hands, Michael S Lustgarten, Leigh A Frame, Bradley Rosen.

  Low dose rapamycin therapy has been proposed as a longevity candidate in healthy aging adults. We present a review of the evidence for low dose rapamycin and rapalog therapies in healthy human adults and model the findings of one cohort study using the PhenoAge model. Despite the preclinical evidence supporting the use of sirolimus to enhance mean and maximal lifespan, the data in humans have yet to establish that rapamycin, or its analogues, is a proven seno-therapeutic that can delay aging in healthy older adults. Rapamycin and rapalogs warrant further study with larger cohorts to better establish their contribution to human aging.

Keywords:  aging; mTOR; rapamycin

DOI:  https://doi.org/10.18632/aging.206300