bims-auttor 2025-12-07 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2025–12–07
thirty-six papers selected by
Viktor Korolchuk, Newcastle University

Development of a p62 biodegrader for autophagy targeted degradation.
A novel player in selective autophagy.
Reprogramming of cholesterol sensing in epithelial cells supports pancreatic inflammation.
Receptor-mediated mitophagy: a new target of neurodegenerative diseases.
TMEM251 loss-induced autophagy dysfunction in the anterior cingulate cortex contributes to chronic postoperative pain.
The transcription factor SKN-1 drives lysosomal enlargement during aging to maintain function.
Non-cell autonomous autophagy in amyotrophic lateral sclerosis: A new promising target?
Differential regulation of p62-ubiquitin conjugates in neurons versus astrocytes during cellular stress.
Molecular mechanisms of the lysosomal damage response and its roles in aging and disease.
Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants.
Autophagy cargo profiles in skeletal muscle during starvation and exercise.
Editorial: The role of autophagy in cardiovascular disease.
Involvement of ACSL3 in the formation of autophagosomes and lipid droplets during starvation conditions.
ERK-mTOR crosstalk suppresses Autophagy and upregulates proteasomal degradation pathway to confer Chronic Myeloid Leukemia cells resistant to Imatinib.
A Reversible Mitochondrial ROS Probe for Monitoring Mitophagy Dynamics: Development and Application of MitoFlare.
Navigating the Autophagy Maze: ATG and Their Impact on Neurodegenerative Diseases.
Neuronal alpha-synuclein-mediated autophagy drives lipid droplets accumulation in astrocytes and microglia and aggravates ischemic stroke.
Genetic factors and comorbid pathologies interact to drive regional mitophagy alterations in Lewy body dementia.
FAM134B Controls Collagen I Dynamics in Hepatic Stellate Cell-Driven Fibrosis.
Decoding protein kinases in autophagy with small-molecule modulators for cancer therapy.
Chaperone-mediated autophagy sustains muscle stem cell regenerative functions but declines with age.
Autophagy regulates MK-2206-induced LDL receptor expression and cholesterol efflux pathways.
Age-related decline of chaperone-mediated autophagy in skeletal muscle leads to progressive myopathy.
Lipid droplets promote the aberrant liquid-liquid phase separation of alpha-synuclein leading to impaired energy homeostasis.
Mitochondrial components secretion in extracellular vesicles promotes alveolar epithelial mitochondrial quality control.
A therapeutic-grade purified exosome system alleviates osteoarthritis by regulating autophagy through the BCL2-Beclin1 axis.
LRRK2 integrates Rab and GABARAP interactions to sense and respond to distinct lysosomal stresses.
Targeted tau protein degradation: a promising therapeutic approach for tauopathies.
E3 ligase AREL1 controls perinuclear localization of lysosomes and supports Purkinje cell survival.
MCL1 modulates mTORC1 signaling to promote bioenergetics and tumorigenesis.
Mitophagy and oxidative stress in chronic kidney disease (Review).
UBC9 mediates mitophagy to attenuate oxidative stress by regulating SUMOylation of PINK1 in the Parkinson's disease progression.
USP30 Knockdown Drives Mitophagy and Suppresses Pyroptosis in Heart Failure by Activating the PINK1/Parkin Pathway.
Membralin Assembles a MAN1B1-VCP Complex to Target Foreign Glycoproteins from the Endoplasmic Reticulum to Lysosomes for Degradation.
TRPA1 activation prompts lysosome-mediated Nrf2 degradation enhancing the killing of colorectal cancer cells.
Huntingtin protein in Health and Huntington's Disease: Molecular Mechanisms, Pathology and Therapeutic Strategies.

Nat Commun. 2025 Dec 03. 16(1): 10858

Development of a p62 biodegrader for autophagy targeted degradation.

Zacharias Thiel, David Marcellin, Carole Manneville, Benedikt Goretzki, Luca Egger, Rob Maher, Noémie Siccardi, Laura Torres, Alexandra Probst, Catrin S Müller, Nathalie George, Markus Vogel, Sabine Sinterhauf, Alexandra Lavoisier, Ji-Young Choi, Laurianne Forcellino, Alexandro Landshammer, Patrick Hauck, Celine Be, Frédéric Villard, Sascha Gutmann, Marc Meyer, Felix Freuler, Alexandra Hinniger, César Fernández, Suzanne Chau, Maude Patoor, Gilles Sansig, Gabriel Mitchell, Beat Nyfeler.

Autophagy-based targeted degradation offers a powerful complement to proteasomal degradation leveraging the capacity and versatility of lysosomes to degrade complex cargo. However, it remains unclear which components of the autophagy-lysosomal pathway are most effective for targeted degradation. Here, we describe two orthogonal induced-proximity strategies to identify autophagy effectors capable of degrading organelles and soluble targets. Recruitment of autophagy cargo receptors, ATG8-like proteins, or the kinases ULK1 and TBK1 is sufficient to trigger mitophagy, while only autophagy cargo receptors capable of self-oligomerization degrade soluble cytosolic proteins. We further report a single-domain antibody against p62 and its use as a heterobifunctional degrader to clear mitochondria. Fusing the p62 single-domain antibody to PINK1 enables selective targeting of damaged mitochondria. Our study highlights the importance of avidity for targeted autophagy and suggests that autophagy cargo receptors are attractive entry points for the development of heterobifunctional degraders for organelles or protein aggregates.

DOI: https://doi.org/10.1038/s41467-025-65868-9
Nat Plants. 2025 Dec 02.

A novel player in selective autophagy.

Raphael Trösch.

DOI: https://doi.org/10.1038/s41477-025-02191-7
Mol Metab. 2025 Dec 02. pii: S2212-8778(25)00199-1. [Epub ahead of print] 102292

Reprogramming of cholesterol sensing in epithelial cells supports pancreatic inflammation.

Giulia Milan, Olga A Mareninova, Marco Fantuz, Martina Spacci, Carlotta Paoli, Jerik A Pineda, Roberta Noè, Beatrice Calciolari, Roberto Zoncu, Anna S Gukovskaya, Alessandro Carrer.

  Pancreatitis is a common cause of hospitalization that necessitates attentive clinical management. Affected individuals are at risk for pancreatic cancer due to aberrant signaling and empowered cell plasticity. Yet, molecular and cellular dynamics that govern epithelial cell behavior in response to inflammation remain largely elusive. Here we found that inflammation induces Endoplasmic Reticulum-Associated Degradation protein (ERAD)-mediated downregulation of Niemann-Pick type C protein 1 (NPC1), which leads to the sequestration of free cholesterol within acinar cells' lysosomes. Reducing intra-pancreatic cholesterol levels through genetic ablation of Acly ameliorates cerulein-induced pancreatitis, while pharmacological targeting of NPC1 exacerbates tissue damage. Mechanistically, the accumulation of lysosomal cholesterol is sensed by the mechanistic Target of Rapamycin Complex 1 (mTORC1) that promotes metaplasia of pancreatic acinar cells, an event commonly associated to pancreatitis and tissue regeneration. Indeed, cholesterol supplementation or NPC1 inhibition facilitate acinar-to-ductal metaplasia (ADM) both ex vivo and in vivo, in an mTORC1-dependent manner. These results identify a metabolic/signaling axis driving the reprogramming of pancreatic epithelial cells in response to inflammation. This hinges on a nutrient sensing paradigm, previously documented exclusively in pathological conditions.

Keywords:  acinar-to-ductal metaplasia (ADM); cholesterol; lysosome; mTORC1; pancreatitis

DOI:  https://doi.org/10.1016/j.molmet.2025.102292
Front Neurol. 2025 ;16 1665315

Receptor-mediated mitophagy: a new target of neurodegenerative diseases.

Junlan Yang, Fuquan Yang, Guiyan Chen, Ming Liu, Shiqing Yuan, Tian-E Zhang.

  Neurodegenerative diseases are a category of neurological conditions with high prevalence that pose major treatment challenges. Common pathologies involve protein accumulation and mitochondrial damage. Mitophagy maintains cellular homeostasis by removing defective mitochondria, which are associated with the pathogenesis of neurodegenerative diseases. Although the ubiquitin-dependent mitophagy mediated by the PINK1-Parkin pathway has been extensively studied, growing evidence indicates that receptor-mediated mitophagy plays a crucial compensatory role in neurons, particularly when the PINK1-Parkin pathway is impaired. This review focuses on the emerging field of receptor-mediated mitophagy, systematically elaborating its role as a key homeostatic mechanism operating independently of the canonical PINK1/Parkin pathway. It provides a focused analysis of the specific functions and activation mechanisms of key receptors-including BNIP3, NIX, FUNDC1, and AMBRA1-in models of Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Furthermore, this review explores the clinical potential of targeting these specific receptors for precise intervention, aiming to provide a new theoretical foundation and direction for developing therapeutic strategies against neurodegenerative diseases.

Keywords:  PINK1/Parkin-independent mitophagy; autophagy receptors; mitochondria; mitochondrial dysfunction; mitophagy; neurodegenerative diseases

DOI:  https://doi.org/10.3389/fneur.2025.1665315
EMBO Rep. 2025 Dec 03.

TMEM251 loss-induced autophagy dysfunction in the anterior cingulate cortex contributes to chronic postoperative pain.

Yaowei Xu, Fei Xing, Xin Wei, Xiaoling Wang, Xiaoshan Shi, Zhongyu Wang, Na Xing, Jingjing Yuan, Zhisong Li, Wei Zhang.

  Macroautophagy/autophagy plays a crucial role in maintaining nervous system homeostasis but its role in chronic postoperative pain (CPOP) remains poorly understood. Here, we identify impaired autophagy and the accumulation of synaptic proteins in the anterior cingulate cortex (ACC) during the maintenance of CPOP after skin/muscle incision and retraction (SMIR). Lysosomal hydrolase levels are reduced upon SMIR, accompanied by a deficiency of the lysosomal trafficking protein transmembrane protein 251 (TMEM251, also named LYSET). TMEM251 overexpression alleviates impaired autophagy, accumulation of synaptic proteins within autophagy substrates, and maintenance of CPOP in SMIR mice. Conversely, TMEM251 knockdown induces autophagy impairment, accumulation of synaptic proteins, and chronic pain phenotypes in naive mice. Autophagy dysfunction is most pronounced in CaMKIIα-positive neurons in the ACC post-surgery, resulting in their activation, which is mitigated by TMEM251 overexpression. Chemogenetic activation of CaMKIIα neurons exacerbates autophagy impairment and CPOP, while their inhibition rescues SMIR-induced autophagy and pain phenotypes. Taken together, our study highlights the close relationship between impaired autophagy and neuronal activation in the promotion of chronic postoperative pain.

Keywords:  Anterior Cingulate Cortex; Autophagy; Chronic Postoperative Pain; Synaptic Plasticity; Transmembrane Protein 251

DOI:  https://doi.org/10.1038/s44319-025-00646-8
PLoS Biol. 2025 Dec 05. 23(12): e3003540

The transcription factor SKN-1 drives lysosomal enlargement during aging to maintain function.

Xinyu Wang, Huimin Liu, Xiaoman Wang, Ben Zhou, Haiqing Tang, Shanshan Pang.

Lysosomes are critical hubs for both cellular degradation and signal transduction, yet their function declines with age. Aging is also associated with significant changes in lysosomal morphology, but the physiological significance of these alterations remains poorly understood. Here, we find that a subset of aged lysosomes undergo enlargement resulting from lysosomal dysfunction in C. elegans. Importantly, this enlargement is not merely a passive consequence of functional decline but represents an active adaptive response to preserve lysosomal degradation capacity. Blocking lysosomal enlargement exacerbates the impaired degradation of dysfunctional lysosomes. Mechanistically, lysosomal enlargement is a transcriptionally regulated process governed by the longevity transcription factor SKN-1, which responds to lysosomal dysfunction by restricting fission and thereby induces lysosomal enlargement. Furthermore, in long-lived germline-deficient animals, SKN-1 activation induces lysosomal enlargement, thereby promoting lysosomal degradation and contributing to longevity. These findings unveil a morphological adaptation that safeguards lysosomal homeostasis, with potential relevance for lysosomal aging and life span.

DOI: https://doi.org/10.1371/journal.pbio.3003540
Neurobiol Dis. 2025 Nov 30. pii: S0969-9961(25)00420-6. [Epub ahead of print]218 107203

Non-cell autonomous autophagy in amyotrophic lateral sclerosis: A new promising target?

Francesca Rosso, Rocio Magdalena, Carola Torazza, Francesca Bacchetti, Marco Milanese, Angelo Poletti, Giambattista Bonanno, Riccardo Cristofani, Tiziana Bonifacino.

  Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative non-cell-autonomous disease with no cure, thus research is intensely focused on identifying pharmacological targets. Several studies aimed to clarify the pathogenic mechanisms and involvement in various cell types. A crucial factor in ALS is autophagy, which plays a key role in degrading intracellular protein aggregates. The connection between ALS and autophagy is reinforced by the fact that several genes mutated in ALS are linked to fundamental aspects of autophagy. The blockage of the autophagic flux was observed in ALS motor neurons, where it occurs earlier than in glia. However, the inconsistent effects of autophagy modulators in preclinical and clinical studies indicate the need for a deeper understanding of the role of autophagy in other cell types, such as astrocytes, microglia, and oligodendrocytes. Astrocytes and microglia are significantly impacted by autophagy dysregulation, contributing to neurodegeneration in both mouse and human-derived models. Autophagy is overactivated early in the disease, even before symptoms appear. This overactivation is influenced by the timing and specific tissue involved. It can alter cells' immunophenotype, favouring proinflammatory responses and affecting the cellular environment and autophagy in the surrounding cells. In contrast, oligodendrocytes show mild autophagic alterations. Additionally, sex hormones may affect proper autophagy function and ALS progression. The lack of information on how sex influences autophagy in glia highlights the need for more nuanced investigation into this mechanism. Future research should focus on these aspects, paving the way for personalised pharmacological approaches that consider the roles of cell types, time of intervention, and sex.

Keywords:  Amyotrophic lateral sclerosis; Astrocytes; Autophagy; Microglia; Oligodendrocyte; Sex

DOI:  https://doi.org/10.1016/j.nbd.2025.107203
bioRxiv. 2025 Nov 18. pii: 2025.11.17.688722. [Epub ahead of print]

Differential regulation of p62-ubiquitin conjugates in neurons versus astrocytes during cellular stress.

David K Sidibe, Erin M Smith, Maeve L Spivey, Maria C Vogel, Sandra Maday.

Sequestosome 1/p62 (hereafter referred to as p62) is a multifunctional protein that orchestrates various cellular stress response pathways including autophagy, proteasome-mediated degradation, antioxidant defense, nutrient sensing, and inflammatory signaling. Mutations in distinct functional domains of p62 are linked with the neurodegenerative disease amyotrophic lateral sclerosis (ALS), underscoring its importance in neural cells. Neurons and astrocytes perform distinct roles in brain physiology and thus encounter a unique landscape of cellular stress. However, how p62 is regulated in these cell types in response to various stress modalities remains largely unexplored. Several functions for p62 depend on engagement with ubiquitinated substrates. Thus, we investigated how the regulation of p62-ubiquitin conjugates differs between neurons and astrocytes exposed to two stress modalities: lysosomal membrane damage and metabolic stress. Lysosomal damage triggered ubiquitin-dependent assembly of p62 puncta in both neurons and astrocytes. In contrast, nutrient deprivation elicited different responses between neurons and astrocytes. Neurons formed p62-ubiquitin structures more prominently and displayed a greater dependence on ubiquitin for p62 clustering. Together, these findings reveal cell-type-specific and stress-specific regulation of p62-ubiquitin conjugates, indicating that neurons and astrocytes can deploy distinct quality control strategies.

DOI: https://doi.org/10.1101/2025.11.17.688722
J Cell Sci. 2025 Dec 01. pii: jcs264255. [Epub ahead of print]138(23):

Molecular mechanisms of the lysosomal damage response and its roles in aging and disease.

Shuhei Nakamura, Takayuki Shima, Tamotsu Yoshimori.

  Lysosomes are the main digestive organelles and serve as a signaling hub linking environmental cues to cellular metabolism. Through these functions, lysosomes play a crucial role in maintaining cellular and organismal homeostasis. However, how lysosomal homeostasis itself is maintained is not well understood. Lysosomes are frequently damaged by a variety of substances, including crystals, silica, lipids, bacteria, toxins, amyloid proteins and reactive oxygen species. When lysosomes are damaged, their acidic contents leak out, leading to oxidative stress, inflammation and cell death. Damaged lysosomes are thus harmful to cells, and to restore lysosomal function after damage, cells have developed several defense mechanisms, collectively called the lysosomal damage response (or endo-lysosomal damage response). Recent studies have shown that this response is composed of three main pathways depending on the degree and duration of damage - repair, removal of the damaged lysosomes, and lysosomal biogenesis and regeneration. Growing evidence suggest that the failure and/or dysregulation of this response is implicated in aging and several diseases, including neurodegenerative diseases and kidney disease. In light of the rapid growth of this field, this Review summarizes our current knowledge of the lysosomal damage response, its significance in aging and diseases, and future perspectives.

Keywords:  Aging; Autophagy; Disease; Lysosomal damage; Lysosome

DOI:  https://doi.org/10.1242/jcs.264255
Dev Cell. 2025 Dec 01. pii: S1534-5807(25)00693-8. [Epub ahead of print]

Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants.

Víctor Sánchez de Medina Hernández, Marintia M Nava-García, Anita Bianchi, Marion Clavel, Ranjith K Papareddy, Lina Benchalel, Veselin I Andreev, Varsha Mathur, Azadeh Mohseni, Marta García-León, Peng Gao, Juan Carlos de la Concepción, Lorenzo Picchianti, Nenad Grujic, Roksolana Kobylinska, Alibek Abdrakhmanov, Héloïse Duvergé, Gaurav Anand, Nils Leibrock, Juncai Ma, Margot Raffeiner, Timothy Scott Crawford, Luca Argirò, Mateusz Matuszkiewicz, Cheuk-Ling Wun, Jakob Valdbjørn Kanne, Anton Meinhart, Elisabeth Roitinger, Isabel Bäurle, Byung Ho Kang, Morten Petersen, Suayib Üstün, Yogesh Kulathu, Tim Clausen, Silvia Ramundo, Yasin Dagdas.

  Selective autophagy is a fundamental protein quality control pathway that safeguards proteostasis by degrading damaged or surplus cellular components, particularly under stress. This process is orchestrated by selective autophagy receptors (SARs) that recruit specific cargo for degradation. Although significant strides have been made in understanding the molecular framework of selective autophagy, the diversity of SAR repertoires across species remains largely unexplored. Through a comparative interactome analysis across five model organisms, we identified a suite of conserved and lineage-specific SAR candidates. Among these, we validated coupling of ubiquitin to endoplasmic reticulum degradation- and protein rich in the amino acids E, L, K, and S-domain-containing SAR (CESAR) as a conserved SAR critical for proteostasis under heat stress. CESAR specifically facilitates the degradation of ubiquitinated protein aggregates and is indispensable for heat stress tolerance. Altogether, our study establishes a robust pipeline and a rich resource for SAR discovery. It also positions CESAR as a pivotal regulator of proteostasis, with broad implications for improving stress resilience in plants.

Keywords:  ATG8; aggrephagy; autophagic flux; heat stress; protein aggregate; proteostasis; proteotoxic stress; receptor evolution; selective autophagy; selective autophagy receptor

DOI:  https://doi.org/10.1016/j.devcel.2025.11.001
Autophagy Rep. 2025 ;4(1): 2593060

Autophagy cargo profiles in skeletal muscle during starvation and exercise.

Mohd Farhan, Shangze Lyu, Trezze P Nguyen, Dakai Zhang, Hong Liang, Yong Zhou, Yu A An, Jun Wang, Hongyuan Yang, Guangwei Du, Yang Liu.

  Autophagy is a cellular process to clear unwanted and dysfunctional cellular cargoes, which are sequestered in autophagosomes before their delivery to lysosomes for degradation. Autophagy cargo selection, mediated by cargo receptors, varies across cell types and conditions. Understanding the cargo features is essential for elucidating autophagy's function in specific physiological or pathological contexts. Here, we present a simple and rapid method for isolating LC3B-positive autophagosomes from the tissues of GFP-LC3 transgenic mice, a widely used autophagy reporter model, without relying on the complex ultracentrifugation steps required by traditional methods. When combined with quantitative proteomics, this approach enables efficient in vivo characterization of autophagy cargoes. We applied this method to establish autophagy cargo profiles in skeletal muscle during starvation and exercise, two physiological conditions that activate autophagy, and identified distinct cargo selection patterns, with significantly higher levels of ER-phagy and ribophagy observed during starvation. We further revealed the ER-phagy receptors TEX264 and RETREG1/FAM134B as potential mediators of the elevated ER-phagy under starvation. In summary, we report an efficient workflow for in vivo autophagy cargo characterization and provide detailed analysis and comparison of cargo profiles under starvation and exercise conditions.

Keywords:  Autophagy cargo; autophagosome isolation; exercise; selective autophagy; starvation

DOI:  https://doi.org/10.1080/27694127.2025.2593060
Front Cell Dev Biol. 2025 ;13 1697218

Editorial: The role of autophagy in cardiovascular disease.

Qinchun Duan, Xuehong Xu, Odell D Jones, Jianjie Ma, Joseph L Bryant, MengMeng Xu.



Keywords:  autophagy associated physiological homeostasis; cardioprotective function of autophagy; cellular conduction system of tunneling nanotube TNT; endocardial and myocardial precursors; selective and non-selective autophagy in heart

DOI:  https://doi.org/10.3389/fcell.2025.1697218
Autophagy Rep. 2025 ;4(1): 2593061

Involvement of ACSL3 in the formation of autophagosomes and lipid droplets during starvation conditions.

Shun Kato, Mitsuo Tagaya.

  Acyl-CoA synthetase long-chain (ACSL) catalyzes the conversion of fatty acids into acyl-CoA, which is used for neutral lipid and phospholipid synthesis. Previous studies revealed that yeast Faa1 and mammalian ACSL4 play a crucial role in phagophore expansion by locally synthesizing phospholipids. We found that another member of ACSL protein family, ACSL3, which is involved in lipid droplet biogenesis under energy-rich conditions and is regulated by SYNTAXIN17, also participates in autophagosome formation, but in a different manner. Knockdown of ACSL3 suppressed punctum formation of early autophagosomal marker proteins such as FIP200 and WIPI2 in starved cells, generating nonfunctional multi-membrane autophagosome-like structures. In contrast, ACSL4 suppression blocked autophagosome formation without affecting punctum formation of early autophagosomal marker proteins. Mechanistic analysis revealed that ACSL3 functions independently of its enzymatic activity, while catalytic activity of ACSL4 is required for autophagosome formation as well as LC3 (known as MAP1LC3 proteins) protein lipidation. Furthermore, ACSL3 has been shown to be essential for lipid droplet biogenesis during starvation. These findings establish ACSL3 as a key player in two events in early autophagy: formation of autophagosomes and lipid droplets.

Keywords:  ACSL3; ACSL4; autophagy; lipid droplet; syntaxin 17

DOI:  https://doi.org/10.1080/27694127.2025.2593061
Exp Hematol. 2025 Nov 28. pii: S0301-472X(25)00619-8. [Epub ahead of print] 105330

ERK-mTOR crosstalk suppresses Autophagy and upregulates proteasomal degradation pathway to confer Chronic Myeloid Leukemia cells resistant to Imatinib.

Rajdeep Roy, Tamalika Paul, Pritam Kumar Das, Samraj Sinha, Siddhartha Sankar Ray, Maitreyee Bhattacharyya, Nabendu Biswas.

  Drug resistance remains a critical barrier in effective cancer therapy. Previously, we demonstrated that expression of anti-apoptotic protein XIAP, contributes to the development of TRAIL resistance in chronic myeloid leukemia (CML) cells. However, upon acquiring drug resistance (K562R and KCL22R), XIAP degradation shifted from the lysosomal to the proteasomal pathway. Consistently, XIAP expression was markedly elevated in tumor samples compared to normal controls and was significantly higher in Imatinib-failure (IMA-FL) patients than in Imatinib-responsive (IMA-RP) counterparts within the patient cohort. Moreover, we have found that proteasomal activity increased in imatinib resistance cells and lysosomal pathway is inhibited. Mechanistically, we found that H₂O₂-induced activation of the ERK-mTOR axis suppressed autophagy in resistant cells, facilitating this shift in degradation pathway. Very interestingly, dual intervention by restoring autophagic flux via mTOR inhibition and inducing XIAP degradation using H2O2 reverted Imatinib resistance in K562R cells. Thus, our findings uncover a novel ERK-mTOR-axis for upregulation of proteasomal degradation of XIAP which could be targeted to overcome Imatinib-resistance by combinatorial inhibition of mTOR and XIAP in CML. This study holds the promise of a new therapeutic strategy for overcoming drug resistance in cancer.

Keywords:  Cell signaling; Leukemia; Lysosome; Proteasome; ROS

DOI:  https://doi.org/10.1016/j.exphem.2025.105330
bioRxiv. 2025 Nov 18. pii: 2025.11.18.689025. [Epub ahead of print]

A Reversible Mitochondrial ROS Probe for Monitoring Mitophagy Dynamics: Development and Application of MitoFlare.

Shanshan Hou, Xin Yan, Xiaoxu Li, Jingyue Ju, Zhiying Shan, Lanrong Bi.

Mitochondrial dysfunction and defective mitophagy are defining features of numerous neurodegenerative and metabolic disorders, yet existing tools provide limited ability to quantify mitophagy dynamics in real time within living, post-mitotic cells. Here we present MitoFlare, a mitochondria-targeted, reversible mtROS-responsive fluorogenic probe that enables continuous, non-genetic visualization of mitochondrial oxidative activation and turnover. MitoFlare incorporates dual TEMPO nitroxide quenchers into a long-wavelength rhodamine scaffold, producing >95% basal quenching and rapid, fully reversible fluorescence activation in response to mitochondrial superoxide, hydroxyl radicals, lipid-derived peroxyl species, and peroxynitrite. When combined with LysoTracker Green, MitoFlare forms a dual-probe imaging platform that resolves the entire mitophagy cascade with high spatial and temporal fidelity in intact PC12 neuronal cells. Using this platform, we established a quantitative framework comprising three mechanistically distinct metrics: (i) a proximity index that reports early mitochondrial engagement with lysosomes, (ii) Manders' M1 coefficient that captures mid-stage mitochondria-lysosome fusion and mitophagosome formation, and (iii) a quenching/swelling index that resolves terminal lysosomal degradation. Nutrient deprivation induced a complete, temporally ordered mitophagy program, including mtROS priming, Parkin-OPTN-associated fusion, and efficient acidification-dependent cargo degradation. In contrast, inhibition of v-ATPase with bafilomycin A1 arrested mitophagy at the fusion stage, resulting in persistent redox-active mitochondrial cargo that failed to undergo lysosomal digestion. Importantly, MitoFlare's reversible redox chemistry uniquely revealed accumulation of undegraded, oxidatively active mitochondrial remnants within non-acidified vesicles-pathological intermediates that are undetectable using irreversible ROS dyes or genetically encoded reporters. These findings demonstrate that mitophagy proceeds through discrete, redox-regulated and lysosome-dependent phases that can be quantitatively mapped in real time. By enabling synchronized measurement of oxidative activation, organelle trafficking, fusion, and degradation, the MitoFlare-LysoTracker system establishes a new benchmark for dynamic mitophagy analysis in physiologically relevant models. This platform provides a powerful foundation for mechanistic interrogation of mitochondrial quality control and for accelerating the discovery of therapeutic strategies aimed at restoring mitophagic fidelity in neurodegenerative, cardiovascular, and metabolic diseases.

DOI: https://doi.org/10.1101/2025.11.18.689025
Mol Neurobiol. 2025 Dec 06. 63(1): 260

Navigating the Autophagy Maze: ATG and Their Impact on Neurodegenerative Diseases.

Roshanak Amirian, AmirHossein Merati, Mehregan Babamohamadi, Yasaman Mirahmadi, Mahsa Loran Esfahani, Shahla Rahmani, Zhila Izadi, Davood Rezazadeh.

  Autophagy, a tightly regulated process essential for maintaining cellular homeostasis, plays a critical role in the pathogenesis and progression of neurodegenerative diseases (NDs). These disorders-marked by diverse mechanisms and clinical heterogeneity-pose significant challenges in developing effective therapies. Central to the autophagic machinery are autophagy-related genes (ATGs), whose functions and variants are increasingly recognized as pivotal in modulating disease-specific pathways. This review explores the intricate roles of ATGs in NDs, emphasizing the need for a comprehensive understanding of molecular signaling networks, protein-protein interactions, and regulatory checkpoints that may serve as therapeutic targets. We highlight recent advancements in disease modeling, autophagy assays, and biomarker identification that facilitate the translation of ATG-related discoveries into clinical practice. Furthermore, we underscore the importance of interdisciplinary collaboration across academia, industry, clinical medicine, and regulatory bodies to harness the therapeutic potential of autophagy. This article aims to serve as a detailed roadmap for understanding the role of ATGs in NDs and to illuminate promising avenues for future research and therapeutic development.

Keywords:  Alzheimer’s disease (AD); Amyotrophic lateral sclerosis (ALS); Autophagy; Autophagy genes (ATG); Huntington’s disease (HD); Neurodegenerative diseases (NDs); Parkinson’s disease (PD)

DOI:  https://doi.org/10.1007/s12035-025-05332-3
Int J Biol Macromol. 2025 Nov 27. pii: S0141-8130(25)09744-2. [Epub ahead of print] 149187

Neuronal alpha-synuclein-mediated autophagy drives lipid droplets accumulation in astrocytes and microglia and aggravates ischemic stroke.

Wenqiang Xin, Wei Wei, Xiaoyue Luo, Zhongnan Hao, Lin Zhang, Yuanyang Zeng, Hao Wan, Shangsong Yang, Xiaobin Shang, Meihua Li, Zhipeng Xiao, Yongli Pan.

   BACKGROUND: Lipid droplets (LDs) agglomeration in glial cells after stroke contributes to cellular dysfunction and neuronal injury. Alpha-synuclein has been identified as a critical regulator in the uptake and metabolism of fatty acids across various neurological disorders. Moreover, alterations in autophagic function can impact the agglomeration of LDs following a stroke. It is also well-established that alpha-synuclein is directly involved in neuronal autophagy. Although substantial research has been conducted on the relationship between alpha-synuclein and lipid metabolism, the precise mechanisms by which alpha-synuclein modulates lipid metabolism in glial cells post-stroke are not yet fully understood.
METHODS: Primary neurons and glial cells from neonatal mice were used to establish in vitro oxygen-glucose deprivation/reoxygenation and neuron-glia co-culture models. In vivo studies employed alpha-synuclein knockdown mice subjected to middle cerebral artery occlusion. Analysis of readout parameters using various techniques, including qRT-PCR, immunofluorescence, western blot assays, phagocytosis and behavioral tests. Utilizing both in vitro and in vivo stroke models, we investigated how alpha-synuclein modulates the interactions between neurons and microglia/astrocytes.
RESULTS: We found that ischemic stroke induces LD agglomeration, triggers autophagy, and increases alpha-synuclein levels. Knockdown of alpha-synuclein reduced LD formation, restored autophagic balance, and improved neurological outcomes. In co-culture, silencing neuronal alpha-synuclein or enhancing neuronal autophagy decreased LD accumulation and modified LD-associated protein expression in microglia and astrocytes. Moreover, neuronal alpha-synuclein and autophagy regulation modulated glial phagocytic activity without directly altering glial autophagy. Additionally, changes in LD accumulation appear to play a pivotal role in mediating interactions between glial cells and neurons, thereby influencing cell viability and autophagy. Consistent with these findings, treatment with alpha-synuclein siRNA alleviates stroke-induced neurological deficits.
CONCLUSION: Alpha-synuclein regulates lipid metabolism and phagocytic activity in glial cells through autophagy mechanisms under ischemic conditions, providing new insight into therapeutic strategies for stroke.

Keywords:  Alpha-synuclein; Astrocyte; Ischemic stroke; Lipid droplets; Lipid metabolism; Microglia

DOI:  https://doi.org/10.1016/j.ijbiomac.2025.149187
Acta Neuropathol. 2025 Dec 01. 150(1): 59

Genetic factors and comorbid pathologies interact to drive regional mitophagy alterations in Lewy body dementia.

Xu Hou, Tyrique Richardson, Michael G Heckman, Fabienne C Fiesel, Launia J White, Shunsuke Koga, Owen A Ross, Dennis W Dickson, Wolfdieter Springer.

  The kinase-ligase pair PINK1-PRKN initiates mitophagy by recognizing and selectively tagging worn-out and dysfunctional mitochondria with phosphorylated ubiquitin (pS65-Ub) to facilitate their elimination via autophagy. In human autopsy brains, the number of pS65-Ub positive cells increases with age but is also associated with Lewy body (LB), neurofibrillary tangles (NFT), and senile plaque (SP) burden. Through a recent genome-wide association study, we identified two genetic modifiers of pS65-Ub levels, APOE4 and ZMIZ1 rs6480922. While LB, NFT, and SP pathologies often coexist in Lewy body dementia (LBD), it is unclear how genetic factors and comorbid neuropathologies interact to impact mitophagy in vulnerable brain regions. We therefore measured levels of the age and disease marker pS65-Ub in the hippocampus and amygdala of 371 LBD cases. Significant and independent associations with pS65-Ub levels were observed for each of the three pathologies LB, NFT, and SP in both regions, and the presence of APOE4 significantly strengthened the association between NFT and pS65-Ub in the hippocampus. While no interaction between LB and SP pathologies was observed regarding association with pS65-Ub, a significant interaction between LB and NFT pathologies on pS65-Ub accumulation was found in the amygdala, which was primarily observed in carriers of the minor allele of ZMIZ1 rs6480922. In summary, our study revealed complex interactions between LB pathology, NFT pathology, and genetic mitophagy modifiers in LBD brains, highlighting potential convergent molecular mechanisms underlying α-synuclein- and tau-associated mitophagy alterations.

Keywords:  APOE4; Mitochondria; Mitophagy; PARK2; PINK1; Parkin; Tau; Ubiquitin; ZMIZ1; α-Synuclein

DOI:  https://doi.org/10.1007/s00401-025-02964-6
Am J Physiol Gastrointest Liver Physiol. 2025 Dec 05.

FAM134B Controls Collagen I Dynamics in Hepatic Stellate Cell-Driven Fibrosis.

Jagannath Misra, Zachary Hanquier, Reese Baxter, NIpuni Barupala, Alexander Jackson, Jessica L Maiers.

  Liver fibrosis is driven by the accumulation of scar tissue in response to injury. Activated hepatic stellate cells (HSCs) secrete fibrogenic proteins that deposit into the extracellular matrix, leading to fibrosis. Increased production of fibrogenic proteins by HSCs leads to ER stress, triggering the Unfolded Protein Response (UPR). The UPR is important in regulating HSC activation and fibrogenesis, but mechanisms driving this regulation are unclear. A key process regulated by the UPR is degradation of misfolded proteins through various pathways, including ER-to-Lysosome-Associated Degradation (ERLAD). ERLAD targets proteins for lysosomal degradation and can involve autophagosomes engulfing portions of the ER, termed ER-phagy. ER-phagy is implicated in degradation of misfolded fibrillar collagen, but its role in fibrogenesis is unknown. We show that collagen I levels are post-translationally regulated by autophagy, and this correlates with ER-phagy receptor expression. Furthermore, activation of HSCs induces ER-phagy flux and expression of ER-phagy receptors, including FAM134B, in a process dependent on UPR transducer ATF6α. Loss of FAM134B decreases intracellular collagen I without affecting COL1A1 mRNA. Moreover, FAM134B deletion blocks TGFβ-induced collagen I deposition despite increased secretion. Together, we show that ER-phagy receptor FAM134B is pivotal for collagen I deposition during fibrogenesis.

Keywords:  Cell-cycle Progression gene 1; ER-phagy; ER-to-Lysosomal Degradation; TGFbeta; Unfolded Protein Response

DOI:  https://doi.org/10.1152/ajpgi.00170.2025
Drug Discov Today. 2025 Nov 29. pii: S1359-6446(25)00278-8. [Epub ahead of print] 104565

Decoding protein kinases in autophagy with small-molecule modulators for cancer therapy.

Mengqiao Chen, Xiangyu Fu, Huiping Wang, Xinyi Qi, Leilei Fu.

  Autophagy is an intracellular degradation and recycling mechanism, crucial for maintaining cellular homeostasis. In recent years, the dual role of protein kinases in autophagy has gradually been elucidated. Designing small-molecule compounds to regulate these targets can actively or passively intervene in cell-protective autophagy or autophagy-related cell death. This approach could provide new clues for modern targeted cancer therapies. In this review, we focus on summarizing the regulatory roles of key protein kinases in autophagy, including positive regulation, negative regulation and bidirectional regulation of autophagy. Moreover, we explore the anticancer potential of small-molecule compounds targeting these kinases in cancer therapy, providing new clues for precise treatment by regulating autophagy pathways.

Keywords:  Protein kinase; autophagy; cancer therapy; drug discovery; small-molecule modulator

DOI:  https://doi.org/10.1016/j.drudis.2025.104565
Nat Metab. 2025 Dec 03.

Chaperone-mediated autophagy sustains muscle stem cell regenerative functions but declines with age.

Ignacio Ramírez-Pardo, Silvia Campanario, Bhakti Chavda, Olaya Santiago-Fernández, Marta Flández, Mercedes Grima-Terrén, Andrés Cisneros, Aina Calls-Cobos, Daniel N Itzhak, Bryan Ngo, Sudha Janaki-Raman, Edward D Kantz, Laura Ortet, Antonio Diaz, Kristen Lindenau, Julio Doménech-Fernández, Mari Carmen Gómez-Cabrera, Emilio Camafeita, Jesús Vázquez, Marta Martinez-Vicente, Antonio L Serrano, Eusebio Perdiguero, Joan Isern, Ana Maria Cuervo, Pura Muñoz-Cánoves.

Proteostasis supports stemness, and its loss correlates with the functional decline of diverse stem cell types. Chaperone-mediated autophagy (CMA) is a selective autophagy pathway implicated in proteostasis, but whether it plays a role in muscle stem cell (MuSC) function is unclear. Here we show that CMA is necessary for MuSC regenerative capacity throughout life. Genetic loss of CMA in young MuSCs, or failure of CMA in aged MuSCs, causes proliferative impairment resulting in defective skeletal muscle regeneration. Using comparative proteomics to identify CMA substrates, we find that actin cytoskeleton organization and glycolytic metabolism are key processes altered in aged murine and human MuSCs. CMA reactivation and glycolysis enhancement restore the proliferative capacity of aged mouse and human MuSCs, and improve their regenerative ability. Overall, our results show that CMA is a decisive stem cell-fate regulator, with implications in fostering muscle regeneration in old age.

DOI: https://doi.org/10.1038/s42255-025-01411-w
PLoS One. 2025 ;20(12): e0338076

Autophagy regulates MK-2206-induced LDL receptor expression and cholesterol efflux pathways.

Hilde Sundvold, Thea Bismo Strøm.

BACKGROUND: Hypercholesterolemia remains a key risk factor for atherosclerotic cardiovascular disease (CVD). The clearance of low-density lipoprotein (LDL) particles from plasma, primarily mediated by LDL receptor (LDLR) activity, is an established target of lipid-lowering therapies. Enhancing reverse cholesterol transport via high-density lipoprotein and modulating cholesterol efflux from macrophages further complements atherogenic risk reduction. Enhancing LDLR expression and supporting effective cholesterol efflux via ATP binding cassette subfamily A member 1 (ABCA1) are therefore essential therapeutic targets for CVD prevention. Recent studies implicate autophagy in lipid and cholesterol metabolism. This study examines the influence of autophagy on LDLR and ABCA1 expression in hepatocytes after treatment with the AKT inhibitors MK-2206 and triciribine.
METHODS: Autophagy was disrupted pharmacologically using SBI-0206965 and genetically via short-interfering RNA (siRNA) targeting autophagy-related genes ATG5 and ATG7 in HepG2. Stable knockout (KO) HAP1 cell lines for ATG5 and ATG7 were generated by CRISPR to ensure complete abrogation of autophagy. The possible effect of SREBP2 silencing on MK-2206-induced LDLR expression was assessed in HepG2 cells. Quantitative analyses included measurement of ABCA1, LDLR and MAP1LC3B (LC3B) expression at protein and mRNA levels, in addition to ULK1 and SQSTM1 (p62) mRNA levels.
RESULTS: MK-2206 administration increased hepatic LDLR and the autophagy marker LC3B. Triciribine did not show evidence of autophagy induction, and neither AKT inhibitors modified ABCA1 expression. Inhibition of autophagy, either by SBI-0206965 or by siRNA targeting ATG5 and ATG7, reduced the MK-2206-mediated LDLR upregulation by approximately 50% in HepG2. In KO-ATG5/ATG7 HAP1 cells, the MK-2206-induced LDLR expression decreased by 70% compared to wild-type cells, and ABCA1 expression was abolished.
CONCLUSION: Both pharmacological and genetic impairment of autophagy attenuate the LDLR-inducing effects of MK-2206, supporting a role for autophagy in the regulation of cholesterol metabolism. The substantial reduction of ABCA1 expression in autophagy-deficient cells further indicates that autophagy is involved in cholesterol efflux regulation.

DOI: https://doi.org/10.1371/journal.pone.0338076
Nat Metab. 2025 Dec 03.

Age-related decline of chaperone-mediated autophagy in skeletal muscle leads to progressive myopathy.

Olaya Santiago-Fernández, Luisa Coletto, Inmaculada Tasset, Susmita Kaushik, Axel R Concepcion, Rizwan Qaisar, Adrián Macho-González, Kristen Lindenau, Antonio Diaz, Rabia R Khawaja, Stefano Donega, Nirad Banskota, Ceereena Ubaida-Mohien, Gavin Pharaoh, Bumsoo Ahn, Lisa M Hartnell, Ignacio Ramírez-Pardo, Bhakti Chavda, Aiara Gazteluiturri, Michael Kinter, Luigi Ferrucci, Julie A Reisz, Angelo D'Alessandro, Holly Van Remmen, Pura Muñoz-Cánoves, Stefan Feske, Ana Maria Cuervo.

Chaperone-mediated autophagy (CMA) contributes to proteostasis maintenance by selectively degrading a subset of proteins in lysosomes. CMA declines with age in most tissues, including skeletal muscle. However, the role of CMA in skeletal muscle and the consequences of its decline remain poorly understood. Here we demonstrate that CMA regulates skeletal muscle function. We show that CMA is upregulated in skeletal muscle in response to starvation, exercise and tissue repair, but declines in ageing and obesity. Using a muscle-specific CMA-deficient mouse model, we show that CMA loss leads to progressive myopathy, including reduced muscle force and degenerative myofibre features. Comparative proteomic analyses reveal CMA-dependent changes in the mitochondrial proteome and identify the sarcoplasmic-endoplasmic reticulum Ca2+-ATPase (SERCA) as a CMA substrate. Impaired SERCA turnover in CMA-deficient skeletal muscle is associated with defective calcium (Ca2+) storage and dysregulated Ca2+ dynamics. We confirm that CMA is also downregulated with age in human skeletal muscle. Remarkably, genetic upregulation of CMA activity in old mice partially ameliorates skeletal muscle ageing phenotypes. Together, our work highlights the contribution of CMA to skeletal muscle homoeostasis and myofibre integrity.

DOI: https://doi.org/10.1038/s42255-025-01412-9
bioRxiv. 2025 Nov 21. pii: 2025.11.20.689615. [Epub ahead of print]

Lipid droplets promote the aberrant liquid-liquid phase separation of alpha-synuclein leading to impaired energy homeostasis.

Jose Cevallos, Elena Eubanks, Sunghoo Jung, Yiming Huang, Elyse Guadagno, Neeharika Rao Suvvari, Aryan Doshi, Nitya Ravinutala, Alejandro Mosera, Nagendran Ramalingam, Arati Tripathi, Tim Bartels, Ulf Dettmer, Eleanna Kara.

Alpha-synuclein (αSyn) inclusions, termed Lewy bodies, are the characteristic neuropathological feature of Parkinson's disease. Growing evidence points towards a role of aberrant liquid-liquid phase separation in the dysregulation of αSyn and sequence of events that lead to the formation of Lewy bodies. However, the triggers leading to aberrant phase separation are unknown, as is the relevance of this phenomenon to the neurodegeneration process. In this study, we showed that αSyn spontaneously phase separates into condensates in the presence of lipid droplets. These lipid droplet-rich condensates represent a toxic species of αSyn that prevents the turnover of the entrapped lipid droplets; they are also toxic to neighbouring mitochondria which are depolarized and undergo increased mitophagy. These findings underscore the increasing importance of lipid droplets in the pathogenesis of neurodegenerative diseases, and Parkinson's disease in particular. The lipid droplets are significantly enriched within the neuromelanin in midbrain dopaminergic neurons in the substantia nigra and could therefore uniquely facilitate the early αSyn-associated neurodegeneration of this region in PD. Our findings reveal a novel pathway implicated in the dysregulation of αSyn that connects aberrant liquid-liquid phase separation, lipid droplets and mitochondrial toxicity.

DOI: https://doi.org/10.1101/2025.11.20.689615
Nat Commun. 2025 Dec 05.

Mitochondrial components secretion in extracellular vesicles promotes alveolar epithelial mitochondrial quality control.

Bowen Liu, Yue Han, Yuan Jin, Meng Ye, Zeliang Yang, Jingyi Yang, Minglu Zhu, Xuyang Zhao, Yan Jin, Yuxin Yin.

The quality control network in type 2 alveolar epithelial cells (AEC2s) is essential to respond to intrinsic and extrinsic challenges. However, the mechanisms that regulate AEC2 mitochondrial homeostasis remain unclear understood. Here, we report a role of G protein-coupled receptor class C group 5 member A (GPRC5A) in mitochondrial quality control in AEC2s through promoting mitochondrial secretion in extracellular vesicles (EVs). Utilizing mice models, we demonstrate that the disruption of GPRC5A specifically in AEC2s aggravates lung injuries. We further observe that GPRC5A deficiency in AEC2s reduces secretion of mitochondrial components in small-EVs and disrupts mitochondrial functions both in vitro and in vivo. Mechanistically, we determine that the GPRC5A-MIRO2 pathway facilitates the transfer of mitochondrial fragments into late endosomes. Collectively, our findings provide evidence of the shedding of mitochondrial components dependent on GPRC5A as a pathway of mitochondrial quality control in AEC2s, which is crucial in the maintenance of epithelial physiological activities and lung tissue homeostasis.

DOI: https://doi.org/10.1038/s41467-025-66901-7
J Nanobiotechnology. 2025 Dec 05.

A therapeutic-grade purified exosome system alleviates osteoarthritis by regulating autophagy through the BCL2-Beclin1 axis.

Gongyin Zhao, Farbod Yousefi, Ichiro Tsukamoto, Steven Moran, Atta Behfar, Christopher Evans, Chunfeng Zhao.

   BACKGROUND: Osteoarthritis is a common and progressive degenerative joint disorder marked by cartilage degradation, subchondral bone remodeling, and chondrocyte apoptosis. Autophagy, a tightly regulated intracellular degradation process, is essential for maintaining chondrocyte homeostasis. Dysregulated autophagy can contribute to cartilage degeneration by disrupting the balance between cellular survival and death. The B-cell lymphoma 2 (BCL2) protein plays a dual role by inhibiting autophagy via its interaction with Beclin-1 while simultaneously suppressing apoptosis. This study aimed to investigate whether a therapeutic-grade purified exosome system derived from human plasma can modulate autophagy through regulation of BCL2 signaling, reduce chondrocyte apoptosis, and prevent osteoarthritis progression.
RESULTS: In vitro experiments demonstrated that exosome treatment increased autophagic activity and reduced apoptosis in both immortalized and osteoarthritic human chondrocytes. Mechanistic analysis revealed that exosomes downregulated BCL2 expression, disrupted the BCL2-Beclin-1 complex, and enhanced the expression of autophagy-related proteins LC3 and Beclin-1. Overexpression of BCL2 reversed these effects and led to impaired autophagic flux and elevated apoptosis, particularly in osteoarthritic chondrocytes. In a rat model of surgically induced osteoarthritis, intra-articular injection of the exosome product mixed with hyaluronic acid improved gait parameters, reduced mechanical pain sensitivity, and preserved cartilage architecture and subchondral bone structure. Histological and molecular analyses confirmed reduced chondrocyte apoptosis and elevated autophagic activity in exosome-treated joints, along with decreased BCL2 expression and complex formation with Beclin-1.
CONCLUSIONS: This study demonstrates that a therapeutic-grade exosome formulation can alleviate osteoarthritis by restoring the balance between autophagy and apoptosis through modulation of the BCL2-Beclin-1 signaling axis. These findings highlight the potential of exosome-based nanotherapeutics as a novel disease-modifying treatment strategy for degenerative joint disorders.

Keywords:  Apoptosis; Autophagy; BCL2; Beclin-1; Cartilage regeneration; Exosomes; Joint degeneration; Nanomedicine; Osteoarthritis; Therapeutic delivery system

DOI:  https://doi.org/10.1186/s12951-025-03807-y
bioRxiv. 2025 Nov 19. pii: 2025.11.19.689251. [Epub ahead of print]

LRRK2 integrates Rab and GABARAP interactions to sense and respond to distinct lysosomal stresses.

Devin Clegg, Amanda Bentley-DeSousa, Agnes Roczniak-Ferguson, Shawn M Ferguson.

Increased activity of leucine-rich repeat kinase 2 (LRRK2) is an important risk factor for Parkinson's disease. LRRK2 localizes to lysosomal membranes, and changes in lysosome physiology are emerging as key regulators of its activation, yet the mechanisms by which distinct perturbations engage this kinase remain unclear. Analysis of osmotic and membrane-integrity challenges revealed that LRRK2 integrates multiple upstream cues through parallel interactions with Rab GTPases and GABARAP. Manipulations that caused lysosome enlargement, including inhibition of PIKfyve, showed that osmotic swelling leads to the accumulation of multiple Rabs on lysosomes and Rab-dependent LRRK2 activation independently of GABARAP. In contrast, under conditions of lysosome deacidification, CASM-dependent lipidation of GABARAP creates a platform that cooperates with Rabs in LRRK2 activation. These findings demonstrate how LRRK2 interprets perturbations of lysosome function through a combination of Rab- and GABARAP-dependent mechanisms, providing a framework for understanding both normal physiological regulation and pathological dysregulation in Parkinson's disease.
Significance Statement: This study reveals how LRRK2 integrates lysosomal stress signals through coordinated interactions with Rab GTPases and GABARAP. Osmotic swelling drives strong Rab-dependent activation, whereas deacidification requires CASM-mediated GABARAP lipidation as a scaffold for LRRK2 activation at lysosomes. These results define how LRRK2 activation at lysosomes is tuned across physiological and pathogenic contexts.

DOI: https://doi.org/10.1101/2025.11.19.689251
Neuroscience. 2025 Dec 03. pii: S0306-4522(25)01139-X. [Epub ahead of print]

Targeted tau protein degradation: a promising therapeutic approach for tauopathies.

Narjes Baazaoui, Mohammad Y Alfaifi, Ali A Shati, Rania Ben Saad, Stefania Garzoli.

  Tauopathies are a spectrum of diseases characterized by the pathological aggregation of tau proteins. Several therapeutic strategies have been developed to treat or stop the progression of these diseases, but all have failed in clinical trials. One potential reason for these failures is that disease-causing proteins are resilient to treatment with conventional drugs since they lack a predefined monomeric structure and an active binding site. Tau is an intrinsically disordered protein; paradoxically, its flexible conformation makes it an ideal candidate for targeted protein degradation (TPD) approaches, which bypass the need for structured binding pockets by inducing proximity-based recruitment to degradative machinery. TPD uses bifunctional molecules to recruit proteins to the ubiquitin-proteasome system (UPS) or autophagy-lysosomal pathways, overcoming limitations of traditional small-molecule inhibitors (SMIs). As these technologies have been effective in degrading several disease-related proteins, they hold significant promise for treating tauopathies caused by protein aggregation. Herein, we review the tau structure and functions, summarize the main post-translational modifications (PTMs) of tau including those causing pathological aggregation of tau, the major degradative cellular machinery and their defects in pathological state, and discuss the advantages and current progress of targeted protein degradation strategies compared to traditional approaches.

Keywords:  Autophagy lysosomal pathway; Post-translational modifications; Targeted protein degradation; Tau; Tau aggregation; Tau seeding; Tauopathies; Ubiquitin–proteasome pathway

DOI:  https://doi.org/10.1016/j.neuroscience.2025.11.041
EMBO J. 2025 Dec 02.

E3 ligase AREL1 controls perinuclear localization of lysosomes and supports Purkinje cell survival.

Luyi Jiang, Jiangfen Tang, Ya-Fen Zhang, Wen-Xuan Zou, Gang Deng, Na Tian, Xiaolu Zhao, Lei Han, Kai Liu, Bao-Liang Song, Jie Luo.

  Localization of lysosomes influences their properties, e.g., perinuclear lysosomes are more acidic but less mobile compared with the peripheral ones. Furthermore, the endoplasmic reticulum (ER) can actively regulate the dynamics and functions of lysosomes via membrane contact sites. In this study, we find that ER-resident apoptosis-resistant E3 ubiquitin protein ligase 1 (AREL1) establishes membrane contacts with lysosomes by directly interacting with the Voa subunit of V-ATPase. AREL1 also catalyzes K33-linked polyubiquitylation of V-ATPase V1B2 subunit, inducing its binding to UBAC2 localized in the perinuclear ER. Depletion of AREL1 or UBAC2 increases the number of peripheral lysosomes that possess partially assembled V-ATPase, elevated luminal pH, and attenuated degradative capacity. Knockdown of ZRANB1, the deubiquitylating enzyme that antagonizes AREL1-mediated V1B2 ubiquitylation, promotes perinuclear clustering of lysosomes and increases lysosomal acidity and degradation. Mice lacking Arel1 exhibit age-dependent Purkinje cell loss, an ataxic phenotype, and motor impairment. Lipofuscin accumulation in the residual Purkinje cells of Arel1-/- mice indicates lysosomal dysfunction. Orchestration of lysosomal positioning and function by the AREL1-UBAC2-V-ATPase axis underscores the physiological significance of ER-regulated perinuclear lysosomal positioning in neurons.

Keywords:  AREL1; Lysosomal Positioning; Purkinje Neurons; UBAC2; V-ATPase

DOI:  https://doi.org/10.1038/s44318-025-00654-3
Nat Commun. 2025 Dec 01. 16(1): 10841

MCL1 modulates mTORC1 signaling to promote bioenergetics and tumorigenesis.

Wentao Gui, Petr Paral, Bhavuk Dhamija, Eman Hagag, Martin Dusa, Jana Humajova, Pavla V Francova, Jan Kucka, Jan Pankrac, Caroline Schütz, Vasileios Armenis, Filippo Ferrucci, Mario Schubert, Kaomei Guan, Franziska Baenke, Daniel E Stange, Lorenz H Lehmann, Wolfram Weckwerth, Peter Mirtschink, Sofia Traikov, Belmonte Giuseppe, Clelia Miracco, Martin Bornhäuser, Saverio Minucci, Ludek Sefc, Libor Macurek, Mohamed Elgendy.

Myeloid cell leukemia-1 (MCL1) is among the most overexpressed proteins in tumors. MCL1 contributes to tumorigenesis by antagonizing apoptosis. However, apoptosis-unrelated functions are emerging. Screening an array of signaling switches identifies mTORC1 to be modulated by MCL1 but not by the anti-apoptotic Bcl-2 or Bcl-xL. mTORC1 is a central metabolic regulator. MCL1 impacts metabolism via modulating the expression of hexokinase 2 (HK2) in an mTORC1-dependent manner, which ultimately contributes to the tumor-promoting effects of MCL1. MCL1 inhibitors suppress mTORC1 in tumor cells but are associated with cardiotoxicity due to mTORC1 inhibition in the heart. Dietary leucine supplementation rescues mTORC1 signaling in the hearts of humanized Mcl-1 mice and greatly ameliorates the cardiotoxicity of MCL1 inhibitors. Taken together, here we describe tumor-promoting roles for MCL1 in regulating mTORC1 signaling and subsequently in bioenergetics, besides its role in antagonizing apoptosis, identifying MCL1 as a hinge of cell bioenergetics and survival.

DOI: https://doi.org/10.1038/s41467-025-66831-4
Mol Med Rep. 2026 Feb;pii: 61. [Epub ahead of print]33(2):

Mitophagy and oxidative stress in chronic kidney disease (Review).

Quwu Mushuo, Yihuai Tian, Jianchun Li, Yanqin Qiu, Hui Fan, Qiongdan Hu, Qiong Zhang.

  Chronic kidney disease (CKD) progression is driven by a harmful interplay between impaired mitophagy and sustained oxidative stress. Under normal conditions, mitophagy serves as a protective mechanism by removing damaged mitochondria and limiting the production of reactive oxygen species. However, in CKD, a self‑reinforcing cycle of mitochondrial dysfunction, defective mitophagy oxidative stress, and inflammation occurs, which promotes fibrosis. The present review examines the molecular mechanisms governing mitophagy, with a specific focus on the regulatory roles of core signaling pathways, namely the PTEN‑induced kinase l/Parkin, BCL2 interacting protein 3/Nip3‑like protein X and FUN14 domain‑containing protein l pathways, and how their disruption contributes to CKD. The mechanistic crosstalk between mitophagy and oxidative stress is highlighted as a central pathogenic axis in CKD progression. In addition, emerging therapeutic strategies that aim to restore mitophagy and enhance antioxidant capacity are discussed, suggesting new strategies for targeted CKD treatment.

Keywords:  mitophagy; oxidative stress; reactive oxygen species; signaling pathways; therapeutic strategies

DOI:  https://doi.org/10.3892/mmr.2025.13771
Cell Biol Toxicol. 2025 Dec 06.

UBC9 mediates mitophagy to attenuate oxidative stress by regulating SUMOylation of PINK1 in the Parkinson's disease progression.

Jian Liu, Ge Jia, Yu Zhou, Junmei Zhang, Yanjin Wang, Yuxiang Cai.

   BACKGROUND: Parkinson's disease (PD) is a neurodegenerative disease characterized by progressive loss of dopaminergic neurons. UBC9 is related to the formation of several cancers. Nevertheless, the function of UBC9 in PD and the potential mechanisms are vague.
METHODS: MPP⁺-induced SH-SY5Y cells and MPTP-treated C57BL/6 mice were applied to induce PD models. Cell viability, proliferation and apoptosis were measured using CCK-8, EdU and Annexin V/PI staining, respectively. JC-1 staining and fluorescent probes DCFH-DA were employed to measure mitochondrial membrane potential and ROS production. The SOD, GSH and MDA content were determined by the commercially kits. SUMOylation of PINK1 were predicted by SUMOplot and verified by co-IP/Western blot. Mitophagy-related proteins, SUMO enzymes, and TH were analyzed by qRT-PCR/Western blot. LC3 expression was detected via immunofluorescence staining. Transmission electron microscopy was performed to detect autophagy. MPTP-induced brain injury was evaluated using Nissl staining, IHC and TUNEL assay. Motor function was observed via open field test and pole test.
RESULTS: PINK1 and UBC9 were low-expressed in MPP+-induced SH-SY5Y cells. UBC9 mediated PINK1 SUMOylation. UBC9 overexpression promoted cell viability and reduced cells apoptosis in MPP+-stimulated SH-SY5Y cells, which was reversed after PINK1 silence or CsA treatment. Moreover, UBC9 overexpression counteracted MPP+-induced mitophagy, and oxidative stress. However, these findings were reversed by CsA or PINK1 silencing. PINK1 bound SUMO1 at the K522, K363 and K193 sites, further regulating cells viability and apoptosis. In MPTP-treated mice, UBC9 overexpression alleviated mitochondrial dysfunction and motor deficits via PINK1 SUMOylation.
CONCLUSION: UBC9 mediated mitophagy to attenuate MPP+/MPTP-induced neurotoxicity and oxidative stress by regulating PINK1 SUMOylation, suggesting that UBC9 may play a preventive role in PD progression.

Keywords:  Mitophagy; Oxidative stress; PINK1; Parkinson’s disease; UBC9

DOI:  https://doi.org/10.1007/s10565-025-10126-3
Int Heart J. 2025 ;66(6): 1002-1014

USP30 Knockdown Drives Mitophagy and Suppresses Pyroptosis in Heart Failure by Activating the PINK1/Parkin Pathway.

Yanna Yang, Congfei Zhu, Xiaobin Zhou, Xinwei Zhang.

  This study probed into the mechanism of USP30 in mitophagy and pyroptosis during heart failure (HF).A cell model was constructed with oxygen-glucose deprivation (OGD), and an HF rat model was generated by permanently ligating the left anterior descending branch of the left coronary artery. Loss-of-function experiments were carried out with the use of si-USP30 and si-PINK1. Cell viability was assessed using MTT, and cell death was measured by LDH release. Mitophagy was analyzed using immunofluorescence double staining, mitochondrial membrane potential (MMP) changes were detected by JC-1, and ROS levels were measured using specific kits. WB was performed to detect autophagy markers LC3II/I and p62, pyroptosis-related proteins NLRP3, active-caspase-1, GSDMD-N, and PINK1/Parkin protein expression. The inflammatory cytokines IL-18 and IL-1β were measured by ELISA. Histological changes and fibrosis in heart tissue were observed by H&E and Masson staining.USP30 was expressed abundantly in OGD-induced H9C2 cells and HF rats. USP30 knockdown enhanced viability, mitophagy, MMP, and LC3II/I but reduced death, NLRP3, p62, active-caspase-1, and GSDMD-N protein expression, and ROS, IL-1β, and IL-18 levels in OGD-treated H9C2 cells. PINK1 knockdown or mitophagy inhibition abolished the effects of USP30 knockdown on mitophagy and pyroptosis in OGD-treated H9C2 cells. Additionally, USP30 knockdown improved cardiac function and mitophagy while repressing pyroptosis in HF rats.In summary, USP30 controls mitophagy and pyroptosis in HF by mediating the PINK1/Parkin pathway.

Keywords:  Autophagy; Inflammatory response; Myocardial damage; Oxygen-glucose deprivation

DOI:  https://doi.org/10.1536/ihj.24-738
Adv Sci (Weinh). 2025 Dec 01. e19256

Membralin Assembles a MAN1B1-VCP Complex to Target Foreign Glycoproteins from the Endoplasmic Reticulum to Lysosomes for Degradation.

Jing Zhang, Xiaoran Lu, Sunan Li, Tao Wang, Iqbal Ahmad, Yong-Hui Zheng.

  Protein quality control in the endoplasmic reticulum (ER) maintains proteostasis by eliminating aberrant or foreign proteins through ER-associated degradation (ERAD) or ER-to-lysosome-associated degradation (ERLAD). Here, Membralin (TMEM259) is identified as a previously unrecognized ER-phagy receptor that assembles a selective degradation machinery targeting viral class I fusion glycoproteins. Membralin recruits MAN1B1, an α-mannosidase that trims high-mannose N-glycans, through its luminal loop, and VCP/p97 through its cytoplasmic loop, while its cytoplasmic tail contains a functional LC3-interacting region (LIR) essential for autophagic delivery. This Membralin-MAN1B1-VCP axis directs viral glycoproteins such as SARS-CoV-2 spike, Ebola GP, influenza HA, and HIV-1 Env to lysosomes for degradation independently of polyubiquitination or canonical ER-phagy receptors. In contrast, misfolded host glycoproteins are degraded through conventional ERAD or FAM134B-dependent ERLAD pathways. Mechanistically, the Membralin complex selectively recognizes densely glycosylated substrates, likely by sensing clustered N-glycans characteristic of viral envelope proteins. Loss of Membralin or MAN1B1 markedly enhances pseudoviral infectivity, underscoring its antiviral role. These findings reveal a ubiquitin-independent ERLAD pathway that discriminates foreign from host glycoproteins and establish Membralin as a central scaffold coordinating ER quality control and innate antiviral defense.

Keywords:  ER‐phagy receptor; MAN1B1; TMEM259; membralin; reticulophagy; viral glycoprotein

DOI:  https://doi.org/10.1002/advs.202519256
Redox Biol. 2025 Nov 25. pii: S2213-2317(25)00455-0. [Epub ahead of print]88 103942

TRPA1 activation prompts lysosome-mediated Nrf2 degradation enhancing the killing of colorectal cancer cells.

Najmeh Eskandari, Davide Delisi, Maedeh Vakili Saatloo, Gizem Keceli, Nathalia Pinheiro, Scott Eblen, Nazareno Paolocci, Saverio Gentile.

Redox homeostasis is crucial for cancer cell survival and resistance to therapy. The transcription factor NRF2, a master regulator of antioxidant and metabolic genes, is often upregulated in tumors to mitigate oxidative stress. Although NRF2 stability is canonically governed by KEAP1-CUL3-proteasome degradation, emerging evidence implicates lysosomal and autophagic pathways in non-canonical NRF2 turnover. The mechanisms by which these alternative pathways are engaged during chronic oxidative signaling remain unclear. We investigated whether sustained activation of the redox-sensitive ion channel TRPA1 by cannabidiol (CBD) disrupts redox homeostasis and promotes NRF2 degradation in colorectal cancer models. Using five independent CRC cell lines (RKO, HCT116, HT29, SW480, and MC38), we assessed reactive oxygen species (ROS), mitochondrial function, autophagy, and NRF2 protein dynamics through biochemical assays, lysosomal fractionation, and imaging. Xenograft models were used for in vivo validation. Chronic TRPA1 activation induced a biphasic ROS response, characterized by an early increase linked to mitochondrial Ca2+ influx and a delayed ROS surge associated with mitochondrial dysfunction. This oxidative trajectory initially stabilized but subsequently led to its degradation after 24 h via a KEAP1-independent, autophagy-lysosome pathway. Proteasome inhibition failed to rescue NRF2, whereas bafilomycin A1 restored its levels and blocked co-localization with lysosomal markers (e.g., LAMP2A). Importantly, CBD-induced TRPA1 activation sensitized CRC cells to oxaliplatin, triggering apoptotic-not senescent-cell death. These effects were dose-dependent and consistent across all tested cell lines. Our findings reveal a non-canonical bioelectric-lysosomal axis that links TRPA1 activity to NRF2 destabilization in colorectal cancer. This work expands the understanding of NRF2 proteostasis under sustained oxidative stress and highlights TRPA1 as a tractable redox-modulating target for overcoming chemoresistance.

DOI: https://doi.org/10.1016/j.redox.2025.103942
Ageing Res Rev. 2025 Dec 03. pii: S1568-1637(25)00330-7. [Epub ahead of print] 102984

Huntingtin protein in Health and Huntington's Disease: Molecular Mechanisms, Pathology and Therapeutic Strategies.

Rinku Shaha, Angel Godad.

  Huntington's Disease (HD) is a neurodegenerative, genetic disorder that affects the brain and is caused by the expansion of cytosine-adenine-guanine (CAG) trinucleotide in the huntingtin (HTT) gene exceeding 35 units. Further, the mutation occurs, which leads to the generation of mutant huntingtin (mHTT) protein, which is a toxic protein that damages the neurons and their functions, leading to disease progression. Phosphorylation, SUMOylation, O-GlcNAcylation, and ubiquitination are some of the post-translational modifications (PTMs) that affect the toxicity, location, and aggregation of this altered protein. The survival of neurons depends on autophagy, vesicle trafficking, transcriptional control, and mitochondrial function, all of which are disrupted by HTT. This protein tends to form aggregates, which disrupt vital neuronal functions and ultimately result in neuronal death, especially in the cortex and striatum. The three clinical manifestations of HD include mental health problems, cognitive impairment, and motor symptoms (bradykinesia, chorea). In this review, the HTT protein is examined, along with its normal functions, post-translational modifications, and role in HD pathogenesis. The therapeutic intervention under investigation includes PTM-targeted medications, which are those drugs that enhance neuroprotection and proteostasis, and gene silencing strategies such as antisense oligonucleotides and RNA interference. Disease models are being improved with several novel approaches, which include induced pluripotent stem cells (iPSCs) and CRISPR-based editing and preclinical models. By integrating these technologies, the mechanisms of the underlying disease have also been enhanced. The recent treatment approaches have also been explored by using molecular targets and diagnostic tools, including FANCD2 and FANCI-associated nuclease 1 (FAN1), which are genetic regulators of somatic CAG expansion; EPS8 dysregulation, which causes protein aggregation; and mismatch negativity (MMN), which is a brain response detected by EEG, a non-invasive biomarker for early cognitive impairment. These measures aim to slow down disease progression and improve the health and outcomes of patients.

Keywords:  AMT-130; Autophagy; Huntington’s Disease; Oxidative phosphorylation; Polyglutamine expansion

DOI:  https://doi.org/10.1016/j.arr.2025.102984