bims-auttor 2025-05-04 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2025–05–04
35 papers selected by
Viktor Korolchuk, Newcastle University

Inborn errors of canonical autophagy in neurodegenerative diseases.
Effects of tianeptine on mTORC1-mediated neuronal autophagy in primary rat hippocampal neurons under nutrient deprivation.
TFEB Orchestrates Stress Recovery and Paves the Way for Senescence Induction in Human Dermal Fibroblasts.
TSC-mTORC1 Pathway in Postnatal V-SVZ Neurodevelopment.
Induction of autophagy in one-cell stage somatic cell nuclear transfer embryos improves preimplantation embryonic development in goat species.
Image-based temporal profiling of autophagy-related phenotypes.
CASTOR1 : A Novel Tumor Suppressor Linking mTORC1 and KRAS Pathways in Tumorigenesis and Resistance to KRAS-Targeted Therapies in Non-Small Cell Lung Cancer.
Correlation of autophagy and Alzheimer's disease with special emphasis on the role of phosphodiesterase-4.
Proteostatic Imbalance Drives the Pathogenesis and Age-Related Exacerbation of Heart Failure With Preserved Ejection Fraction.
Retroviral foamy virus gag induces parkin-dependent mitophagy.
Sex and region-specific disruption of autophagy and mitophagy in Alzheimer's disease: linking cellular dysfunction to cognitive decline.
Recruitment of Atg1 to the phagophore by Atg8 orchestrates autophagy machineries.
The Emerging Roles of Vacuolar-Type ATPase-Dependent Lysosomal Acidification in Cardiovascular Disease.
The Role of mTOR in Amyotrophic Lateral Sclerosis.
SLC7A11 is an unconventional H+ transporter in lysosomes.
The ribonuclease RNase T2 mediates selective autophagy of ribosomes induced by starvation in Saccharomyces cerevisiae.
Programmed mitophagy at the oocyte-to-zygote transition promotes 1 species immortality.
Genome-wide association analysis identifies APOE as a mitophagy modifier in Lewy body disease.
LAPTM5 confers cisplatin resistance in NSCLC by suppressing LAMP1 ubiquitination to stabilize lysosomal membranes and sustain autophagic flux.
An Insight into Neuronal Processing of Ghrelin: Effects of a Bioactive Ghrelin Derivative on Proteolytic Pathways and Mitophagy.
Extracellular matrix mechanical cues (dys)regulate metabolic redox homeostasis due to impaired autophagic flux.
Macrophage ATG16L1 promotes liver regeneration after partial hepatectomy.
Age-Associated Decline in Autophagy Pathways in the Retinal Pigment Epithelium and Protective Effects of Topical Trehalose in Light-Induced Outer Retinal Degeneration in Mice.
HLH-30/TFEB Rewires the Chaperone Network to Promote Proteostasis Upon Perturbations to the Coenzyme A and Iron-Sulfur Cluster Biosynthesis Pathways.
PPAR-mediated reduction of lipid accumulation in hepatocytes involves the autophagy-lysosome-mitochondrion axis.
mTOR controls ependymal cell differentiation by targeting the alternative cell cycle and centrosomal proteins.
Muscle mTOR controls iron homeostasis and ferritinophagy via NRF2, HIFs and AKT/PKB signaling pathways.
SQST-1/p62-regulated SKN-1/Nrf mediates a phagocytic stress response via transcriptional activation of lyst-1/LYST.
Cathepsin B Regulates Ovarian Reserve Quality and Quantity via Mitophagy by Modulating IGF1R Turnover.
Autophagy disruption and mitochondrial stress precede photoreceptor necroptosis in multiple mouse models of inherited retinal disorders.
Gut microbiota modulate intestinal inflammation by endoplasmic reticulum stress-autophagy-cell death signaling axis.
USP14 inhibits mitophagy and promotes tumorigenesis and chemosensitivity through deubiquitinating BAG4 in microsatellite instability-high colorectal cancer.
Truncation mutation of CHMP2B disrupts late endosome function but reduces TDP-43 aggregation through HSP70 upregulation.
Knockdown of Atg1 Impairs Brain Regeneration and Downregulates ECM-Related Genes in the Planarian Dugesia japonica.
Maternal Myo-Inositol Deficiency Involved Autophagy Impairment by PI3K/Akt/mTOR Signaling in Neural Tube Defects During Pregnancy.

Hum Mol Genet. 2025 Apr 30. pii: ddae179. [Epub ahead of print]

Inborn errors of canonical autophagy in neurodegenerative diseases.

Dennis Freisem, Helene Hoenigsperger, Alberto Catanese, Konstantin M J Sparrer.

  Neurodegenerative disorders (NDDs), characterized by a progressive loss of neurons and cognitive function, are a severe burden to human health and mental fitness worldwide. A hallmark of NDDs such as Alzheimer's disease, Huntington's disease, Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and prion diseases is disturbed cellular proteostasis, resulting in pathogenic deposition of aggregated protein species. Autophagy is a major cellular process maintaining proteostasis and integral to innate immune defenses that mediates lysosomal protein turnover. Defects in autophagy are thus frequently associated with NDDs. In this review, we discuss the interplay between NDDs associated proteins and autophagy and provide an overview over recent discoveries in inborn errors in canonical autophagy proteins that are associated with NDDs. While mutations in autophagy receptors seems to be associated mainly with the development of ALS, errors in mitophagy are mainly found to promote PD. Finally, we argue whether autophagy may impact progress and onset of the disease, as well as the potential of targeting autophagy as a therapeutic approach. Concludingly, understanding disorders due to inborn errors in autophagy-"autophagopathies"-will help to unravel underlying NDD pathomechanisms and provide unique insights into the neuroprotective role of autophagy, thus potentially paving the way for novel therapeutic interventions.

Keywords:  autophagy; innate immunity; monogenic diseases; neurodegenerative diseases

DOI:  https://doi.org/10.1093/hmg/ddae179
Sci Rep. 2025 Apr 25. 15(1): 14488

Effects of tianeptine on mTORC1-mediated neuronal autophagy in primary rat hippocampal neurons under nutrient deprivation.

Mi Kyoung Seo, Hyewon Kim, Ah Jeong Choi, Dae-Hyun Seog, Weon-Gyu Kho, Sung Woo Park, Jung Goo Lee.

  The aim of this study was to investigate the effects of the antidepressant tianeptine on the mechanistic target of rapamycin complex 1(mTORC1)-mediated autophagy pathway in primary hippocampal neurons exposed to B27-deprived conditions. When primary hippocampal neurons were treated with tianeptine at doses of 1, 10, 50, and 100 µM for 3 days under B27-deprived conditions, we observed that it activated autophagy and increased the formation of autophagosomes through the upregulation of autophagic proteins, including autophagy-activating kinase 1 (ULK1), Beclin 1, LC3B-II/I, and p62. And at a concentration of 100 µM tianeptine, the decrease in mTORC1 phosphorylation induced by B27 deprivation was significantly reversed. Changes in the expression of autophagic proteins induced by B27 deprivation were reversed by tianeptine treatment in a concentration-dependent manner, and tianeptine significantly reduced the increase in LC3B membrane number induced by B27 deprivation, an effect that was blocked by pretreatment with rapamycin. In conclusion, tianeptine attenuated the activity of mTORC1-mediated autophagy in primary rat hippocampal neurons under B27-deprived conditions. These results may suggest a novel mechanism by which tianeptine may affect autophagy in neurons.

Keywords:  Autophagy; B27 deprivation; Hippocampal neurons; Tianeptine; mTORC1

DOI:  https://doi.org/10.1038/s41598-025-92988-5
Aging Cell. 2025 May 01. e70083

TFEB Orchestrates Stress Recovery and Paves the Way for Senescence Induction in Human Dermal Fibroblasts.

Lena Guerrero-Navarro, Pablo Monfort-Lanzas, Vinzenz Krichbaumer, Mariana E G De Araújo, Jlenia Monfregola, Lukas A Huber, Andrea Ballabio, Pidder Jansen-Dürr, Maria Cavinato.

  Cells experience oxidative stress and widespread cellular damage during stress-induced premature senescence (SIPS). Senescent cells show an increase in lysosomal content, which may contribute to mitigating cellular damage by promoting autophagy. This study investigates the dynamics of lysosomal quality control in human dermal fibroblasts (HDF), specifically examining lysosomal signaling pathways during oxidative stress-induced SIPS. Our results reveal distinct signaling responses between the initial stress phase and the ensuing senescent phenotype. During the stress phase, treatment with tBHP, which undermines the antioxidant response, leads to elevated reactive oxygen species (ROS) and lysosomal damage. ROS accumulation activates AMP-activated protein kinase (AMPK) and inhibits Akt, which correlates with the suppression of mammalian target of rapamycin (mTOR). Inactivation of mTOR during this phase aligns with the activation of transcription factor EB (TFEB), a key regulator of autophagy and lysosomal biogenesis. TFEB knockdown under stress increased apoptosis, highlighting the protective role of TFEB in the stress response. As cells transition to senescence, TFEB activity, required for the autophagic damage repair, becomes less critical. The decrease in ROS levels leads to the normalization of AMPK and Akt signaling, accompanied by the reactivation of mTOR. This reactivation of mTOR, which is critical for establishing the senescent state, is observed alongside the inactivation of TFEB. Consequently, as damage decreases, TFEB activity decreases. Our results suggest a dynamic interplay between TFEB and mTOR, highlighting a critical role of TFEB in ensuring cellular survival during SIPS induction but becoming dispensable once senescence is established.

Keywords:  SIPS; TFEB; mTOR; senescence; tBHP

DOI:  https://doi.org/10.1111/acel.70083
Biomolecules. 2025 Apr 12. pii: 573. [Epub ahead of print]15(4):

TSC-mTORC1 Pathway in Postnatal V-SVZ Neurodevelopment.

David M Feliciano, Angelique Bordey.

  In restricted regions of the rodent brain, neurogenesis persists throughout life, hinting that perhaps similar phenomena may exist in humans. Neural stem cells (NSCs) that reside within the ventricular-subventricular zone (V-SVZ) continually produce functional cells, including neurons that integrate into the olfactory bulb circuitry. The ability to achieve this feat is based on genetically encoded transcriptional programs that are controlled by environmentally regulated post-transcriptional signaling pathways. One such pathway that molds V-SVZ neurogenesis is the mTOR pathway. This pathway integrates nutrient sufficiency with growth factor signaling to control distinct steps of neurogenesis. Alterations in mTOR pathway signaling occur in numerous neurodevelopmental disorders. Here, we provide a narrative review for the role of the mTOR pathway in this process and discuss the use of this region to study the mTOR pathway in both health and disease.

Keywords:  TSC; TSC1; TSC2; mTOR; mTORC1; neurogenesis

DOI:  https://doi.org/10.3390/biom15040573
PLoS One. 2025 ;20(4): e0314176

Induction of autophagy in one-cell stage somatic cell nuclear transfer embryos improves preimplantation embryonic development in goat species.

Nasrin Mahvash, Reza Moradi-Hajidavaloo, Farnoosh Jafarpour, Mehdi Hajian, Mohsen Rahimi, Nafiseh Sanei Ata-Abadi, Marjan Sadeghi, Mohammad Hossein Nasr-Esfahani.

Autophagy is a lysosome-mediated catabolic pathway that is dependent on the mammalian target of rapamycin (mTOR). It plays a crucial role in the degradation of aged organelles and macromolecules. Several studies have explored the role of autophagy in embryonic genome activation and its significance during the early preimplantation development of mammals. In our study, we showed that autophagy is inhibited in one-cell stage SCNT embryos when compared to fertilized counterparts in goats. Notably, we found that 6-DMAP, a kinase inhibitor, reduces the phosphorylation of ERK1/2.This reduction correlates with a decrease in autophagy levels, as indicated by the presence of LC3 puncta in 6-DMAP treated embryos. To address the inhibition of autophagy in goat SCNT embryos, we induced autophagy using Rapamycin at concentrations of 10 and 100 nM for 6 hours, immediately following chemical activation. This induction led to a significant improvement in the development of goat SCNT embryos, as evidenced by an increased blastocyst rate compared to the control group. Our findings suggest that the induction of autophagy during early hours of one-cell stage embryos is critical for pre-implantation development in goat SCNT embryos warrant further investigation. This research opens new avenues for understanding the role of autophagy in embryonic development and its applications in reproductive biotechnology.

DOI: https://doi.org/10.1371/journal.pone.0314176
Autophagy Rep. 2025 ;pii: 2484835. [Epub ahead of print]4(1):

Image-based temporal profiling of autophagy-related phenotypes.

Nitin Sai Beesabathuni, Neil Alvin B Adia, Eshan Thilakaratne, Ritika Gangaraju, Priya S Shah.

  Autophagy is a dynamic process critical in maintaining cellular homoeostasis. Dysregulation of autophagy is linked to many diseases and is emerging as a promising therapeutic target. High-throughput methods to characterise autophagy are essential for accelerating drug discovery and characterising mechanisms of action. In this study, we developed a scalable image-based temporal profiling approach to characterise ~900 morphological features at a single cell level with high temporal resolution. We differentiated drug treatments based on morphological profiles using a random forest classifier with ~90% accuracy and identified the key features that govern classification. Additionally, temporal morphological profiles accurately predicted biologically relevant changes in autophagy after perturbation, such as total cargo degraded. Therefore, this study acts as proof-of-principle for using image-based temporal profiling to differentiate autophagy perturbations in a high-throughput manner and has the potential identify biologically relevant autophagy phenotypes. Ultimately, approaches like image-based temporal profiling can accelerate drug discovery.

Keywords:  Autophagy; autophagy flux; cargo degradation; fluorescence microscopy; live cell imaging; morphological features; rapamycin; temporal profiling; wortmannin

DOI:  https://doi.org/10.1080/27694127.2025.2484835
bioRxiv. 2025 Apr 26. pii: 2025.04.23.650349. [Epub ahead of print]

CASTOR1 : A Novel Tumor Suppressor Linking mTORC1 and KRAS Pathways in Tumorigenesis and Resistance to KRAS-Targeted Therapies in Non-Small Cell Lung Cancer.

Xian Wang, Ling Ding, Shenyu Sun, Suet Kee Loo, Luping Chen, Tingting Li, Man-Tzu Wang, Arjun Pennathur, Yufei Huang, Shou-Jiang Gao.

Cytosolic arginine sensor for mTORC1 Subunit 1 (CASTOR1) functions as a key regulator of mechanistic target of rapamycin complex 1 (mTORC1) signaling. Despite its frequent dysregulation in cancers via mechanisms such as KSHV microRNA-mediated inhibition or AKT-driven phosphorylation and degradation, the impact of CASTOR1 loss on tumor initiation and progression remains poorly understood. Here, we identify CASTOR1 as a critical tumor suppressor in non-small cell lung cancer (NSCLC) by demonstrating that its genetic ablation amplifies tumorigenesis in a KRAS -driven genetically engineered mouse model (GEMM;LSL- KRAS G12D ). CASTOR1 deficiency markedly enhances lung tumor incidence, accelerates tumor progression, and increases proliferative indices in KRAS G12D -driven tumors ( KRAS G12D ; C1 KO ) compared to CASTOR1 wild type (WT) tumors ( KRAS G12D ; C1 WT ). Advanced-stage tumors exhibit elevated phosphorylated CASTOR1 (pCASTOR1) and reduced total CASTOR1 levels, suggesting active degradation during tumorigenesis. Mechanistically, CASTOR1 loss amplifies mTORC1 signaling, as evidenced by heightened phosphorylation of downstream effectors 4EBP1 and S6, while also augmenting AKT and ERK activation, uncovering a crosstalk between the PI3K/AKT/mTORC1 and KRAS/ERK pathways. Furthermore, CASTOR1 ablation induces genome instability, which may contribute to enhanced tumor incidence and progression. Importantly, CASTOR1 deficiency confers resistance to KRAS G12D -specific inhibitors, while over half of KRAS G12D ; C1 WT tumors also display resistance. Organoids derived from KRAS G12D ; C1 KO and KRAS G12D ; C1 WT tumors reveal a correlation between KRAS inhibitor resistance and hyperactivation of mTORC1, with mTORC1 and PI3K inhibitors sensitizing resistant tumors to KRAS G12D -targeted therapies. These findings position CASTOR1 as a novel tumor suppressor that modulates mTORC1 and KRAS signaling to constrain NSCLC progression. Our study further highlights the therapeutic potential of combining mTORC1 or ERK inhibitors with KRAS-targeted therapies for NSCLC characterized by hyperactive KRAS signaling and impaired CASTOR1 activity.
Highlights: CASTOR1 functions as a tumor suppressor in NSCLC by limiting KRAS -driven tumor initiation and progression. CASTOR1 is frequently lost or inactivated in wild-type tumors during tumor progression, contributing to advanced-stage malignancies.CASTOR1 deficiency amplifies mTORC1 signaling and enhances PI3K/AKT and KRAS/ERK crosstalk, driving tumorigenesis and resistance to KRAS-specific inhibitors. Combining mTORC1 or PI3K inhibitors with KRAS-targeted therapies effectively overcomes resistance in KRAS -driven NSCLC.

DOI: https://doi.org/10.1101/2025.04.23.650349
3 Biotech. 2025 May;15(5): 139

Correlation of autophagy and Alzheimer's disease with special emphasis on the role of phosphodiesterase-4.

Aniruddha Banerjee, Dithu Thekkekkara, S N Manjula, Salini P Nair, Mankala Sree Lalitha.

  Autophagy disruption is important in Alzheimer's disease (AD) as it prevents misfolded proteins from being removed, which leads to the accumulation of amyloid plaques and neurofibrillary tangles (NFTs). Restoring autophagy improves neuronal survival and cognitive function, according to experimental models. In AD models, mTOR inhibition and AMPK activation enhance synaptic plasticity and lessen learning deficits. Inhibitors of phosphodiesterase-4 (PDE4) improve cognition and reduce neuroinflammation via altering cyclic adenosine monophosphate (cAMP) transmission. Furthermore, autophagic-lysosomal clearance is encouraged by upregulating transcription factor EB (TFEB), which lessens the pathogenic damage linked to AD. These results point to autophagy modification as a promising therapeutic approach, with the mTOR, AMPK, cAMP, and TFEB pathways being possible targets for drugs. Though much evidence is based on animal studies, these findings provide valuable insights into autophagy's role in AD pathology, offering promising directions for future research and drug development.

Keywords:  Alzheimer's disease (AD); Autophagy; Cyclic adenosine monophosphate (cAMP); Phosphodiesterase-4 (PDE4); mTOR

DOI:  https://doi.org/10.1007/s13205-025-04306-5
JACC Basic Transl Sci. 2025 Apr;pii: S2452-302X(24)00434-0. [Epub ahead of print]10(4): 475-497

Proteostatic Imbalance Drives the Pathogenesis and Age-Related Exacerbation of Heart Failure With Preserved Ejection Fraction.

Kamil A Kobak, Weronika Zarzycka, Catherine J King, Agnieszka K Borowik, Frederick F Peelor, Leslie M Baehr, Mario Leutert, Ricard A Rodriguez-Mias, Judit Villén, Sue C Bodine, Michael T Kinter, Benjamin F Miller, Ying Ann Chiao.

  Heart failure with preserved ejection fraction (HFpEF) is a leading cause of hospitalization and mortality in older adults, yet the role of aging in its pathogenesis remains unclear. Old male mice subjected to chronic metabolic and hypertensive stress (2-hit) developed a more severe HFpEF phenotype compared with young counterparts. We identified that age-related disruptions in protein quality control (PQC) worsens proteostatic stress in HFpEF. Mammalian target of rapamycin complex 1 (mTORC1), a key regulator of PQC, is activated by both aging and 2-hit stress, and cardiac-specific mTORC1 inhibition protects against HFpEF. Our findings highlight the need to integrate aging into preclinical models of HFpEF and suggest targeting PQC as a therapeutic strategy.

Keywords:  HFpEF; autophagy; cardiac aging; mTORC1; protein degradation; protein quality control; protein synthesis; proteostasis

DOI:  https://doi.org/10.1016/j.jacbts.2024.11.006
Retrovirology. 2025 May 02. 22(1): 7

Retroviral foamy virus gag induces parkin-dependent mitophagy.

Shanshan Wang, Tongtong Du, Jun Yan, Yingcheng Zheng, Yinglian Tang, Juejie Wu, Qian Xu, Shanshan Xu, Luo Liu, Xiong Chen, Song Han, Jun Yin, Biwen Peng, Xiaohua He, Wanhong Liu.

   BACKGROUND: Prototype foamy virus (PFV) is a complex retrovirus that can maintain latent infection for life after viral infection of the host. However, the mechanism of latent infection with PFV remains unclear. Our previous studies have shown that PFV promotes autophagy flux, but whether PFV causes mitophagy remains unclear.
RESULTS: In this study, we demonstrated that PFV infection damages mitochondria, increases mitochondria reactive oxygen species (mtROS) production, and induces mitophagy in a time-dependent manner. Further investigation revealed that PFV Gag is a crucial protein responsible for triggering mitophagy. The overexpression of Gag leads to mitochondrial damage and stimulates mitophagy in a dose-dependent manner. Additionally, overexpression of Gag activates the PINK1-Parkin signaling pathway, while the knockdown of Parkin inhibits Gag-induced mitophagy. Furthermore, Rab5a was significantly upregulated in cells overexpressed Gag, and the inhibition of Rab5a reversed the effects of Gag-induced mitophagy.
CONCLUSIONS: Our data suggested that PFV can induce mitophagy and Gag induces Parkin-dependent mitophagy by upregulating Rab5a. These findings not only enhance a better understanding of the foamy virus infection mechanisms but also provide critical insights into novel virus-host cell interactions.

Keywords:  Gag; Mitophagy; Parkin; Prototype foamy virus; Rab5a

DOI:  https://doi.org/10.1186/s12977-025-00664-3
Cell Death Discov. 2025 Apr 26. 11(1): 204

Sex and region-specific disruption of autophagy and mitophagy in Alzheimer's disease: linking cellular dysfunction to cognitive decline.

Aida Adlimoghaddam, Fariba Fayazbakhsh, Mohsen Mohammadi, Zeinab Babaei, Amir Barzegar Behrooz, Farhad Tabasi, Teng Guan, Iman Beheshti, Mahmoud Aghaei, Daniel J Klionsky, Benedict C Albensi, Saeid Ghavami.

Macroautophagy and mitophagy are critical processes in Alzheimer's disease (AD), yet their links to behavioral outcomes, particularly sex-specific differences, are not fully understood. This study investigates autophagic (LC3B-II, SQSTM1) and mitophagic (BNIP3L, BNIP3, BCL2L13) markers in the cortex and hippocampus of male and female 3xTg-AD mice, using western blotting, transmission electron microscopy (TEM), and behavioral tests (novel object recognition and novel object placement). Significant sex-specific differences emerged: female 3xTg-AD mice exhibited autophagosome accumulation due to impaired degradation in the cortex, while males showed fewer autophagosomes, especially in the hippocampus, without significant degradation changes. TEM analyses demonstrated variations in mitochondrial and mitophagosome numbers correlated with memory outcomes. Females had enhanced mitophagy, with higher BNIP3L and BCL2L13 levels, whereas males showed elevated BNIP3 dimers. Cognitive deficits in females correlated with mitochondrial dysfunction in the cortex, while in males, higher LC3B-II levels associated positively with cognitive performance, suggesting protective autophagy effects. Using machine learning, we predicted mitophagosome and mitochondrial numbers based on behavioral data, pioneering a predictive approach to cellular outcomes in AD. These findings underscore the importance of sex-specific regulation of autophagy and mitophagy in AD and support personalized therapeutic approaches targeting these pathways. Integrating machine learning emphasizes its potential to advance neurodegenerative research. Sex-specific differences in autophagy and mitophagy regulation in Alzheimer's disease (AD) are highlighted. Female 3xTg-AD mice show autophagosome accumulation and cognitive deficits, while males exhibit variations in mitophagy markers and behavior.

DOI: https://doi.org/10.1038/s41420-025-02490-0
Nat Struct Mol Biol. 2025 Apr 28.

Recruitment of Atg1 to the phagophore by Atg8 orchestrates autophagy machineries.

Jing-Zhen Song, Hui Li, Haiyan Yang, Rui Liu, Wenting Zhang, Tianlong He, Meng-Xi Xie, Chen Chen, Li Cui, Shian Wu, Yueguang Rong, Li-Feng Pan, Jing Zhu, Qingqiu Gong, Juan Wang, Zhao Qin, Zhiping Xie.

Autophagy-related (Atg) proteins catalyze autophagosome formation at the phagophore assembly site (PAS). The assembly of Atg proteins at the PAS follows a semihierarchical order, in which Atg8 is thought to be quite downstream but still able to control the size of autophagosomes. Yet, how Atg8 coordinates multiple branches of autophagy machinery to regulate autophagosomal size is not clear. Here, we show that, in yeast, Atg8 positively regulates the autophagy-specific phosphatidylinositol 3-OH kinase complex and the retrograde trafficking of Atg9 vesicles through interaction with Atg1. Mechanistically, Atg8 does not enhance the kinase activity of Atg1; instead, it recruits Atg1 to the surface of the phagophore likely to orient Atg1's activity toward select substrates, leading to efficient phagophore expansion. Artificial tethering of Atg1 kinase domains to Atg8s enhanced autophagy in yeast, human and plant cells and improved muscle performance in worms. We propose that Atg8-mediated relocation of Atg1 from the PAS scaffold to the phagophore is a critical step in positive autophagy regulation.

DOI: https://doi.org/10.1038/s41594-025-01546-0
Biomolecules. 2025 Apr 03. pii: 525. [Epub ahead of print]15(4):

The Emerging Roles of Vacuolar-Type ATPase-Dependent Lysosomal Acidification in Cardiovascular Disease.

Yan-Yan Chen, Cai-Xia Liu, Hai-Xin Liu, Shi-Yuan Wen.

  The vacuolar-type ATPase (V-ATPase) is a multi-subunit enzyme complex that maintains lysosomal acidification, a critical process for cellular homeostasis. By controlling the pH within lysosomes, V-ATPase contributes to overall cellular homeostasis, helping to maintain a balance between the degradation and synthesis of cellular components. Dysfunction of V-ATPase impairs lysosomal acidification, leading to the accumulation of undigested materials and contributing to various diseases, including cardiovascular diseases (CVDs) like atherosclerosis and myocardial disease. Furthermore, V-ATPase's role in lysosomal function suggests potential therapeutic strategies targeting this enzyme complex to mitigate cardiovascular disease progression. Understanding the mechanisms by which V-ATPase influences cardiovascular pathology is essential for developing novel treatments aimed at improving outcomes in patients with heart and vascular diseases.

Keywords:  cardiovascular disease; lysosomal acidification; vacuolar-type ATPase

DOI:  https://doi.org/10.3390/biom15040525
Biomedicines. 2025 Apr 13. pii: 952. [Epub ahead of print]13(4):

The Role of mTOR in Amyotrophic Lateral Sclerosis.

José Augusto Nogueira-Machado, Fabiana Rocha-Silva, Nathalia Augusta Gomes.

  Background: Amyotrophic lateral sclerosis (ALS) is a rare, progressive, and incurable disease characterized by muscle weakness and paralysis. Recent studies have explored a possible link between ALS pathophysiology and mTOR signaling. Recent reports have linked the accumulation of protein aggregates, dysfunctional mitochondria, and homeostasis to the development of ALS. mTOR plays a pivotal role in controlling autophagy and affecting energy metabolism, in addition to supporting neuronal growth, plasticity, and the balance between apoptosis and autophagy, all of which are important for homeostasis. Aim: This mini-review approaches the regulatory roles of mTOR signaling pathways, their interaction with other metabolic pathways, and their potential to modulate ALS progression. Significance: It discusses how these metabolic signaling pathways affect the neuromuscular junction, producing symptoms of muscle weakness and atrophy similar to those seen in patients with ALS. The discussion includes the concepts of neurocentric and peripheral and the possible connection between mTOR and neuromuscular dysfunction in ALS. Conclusions: It highlights the therapeutic potential of mTOR signaling and interconnections with other metabolic routes, making it a promising biomarker and therapeutic target for ALS.

Keywords:  ALS; amyotrophic lateral sclerosis; genetic biomarkers; mTOR; metabolic signaling; neurodegenerative diseases; neuromuscular degeneration

DOI:  https://doi.org/10.3390/biomedicines13040952
Cell. 2025 Apr 24. pii: S0092-8674(25)00406-4. [Epub ahead of print]

SLC7A11 is an unconventional H+ transporter in lysosomes.

Nan Zhou, Jingzhi Chen, Meiqin Hu, Na Wen, Weijie Cai, Ping Li, Liding Zhao, Yaping Meng, Dongdong Zhao, Xiaotong Yang, Siyu Liu, Fangqian Huang, Cheng Zhao, Xinghua Feng, Zikai Jiang, Enjun Xie, Hongxu Pan, Zhidong Cen, Xinhui Chen, Wei Luo, Beisha Tang, Junxia Min, Fudi Wang, Junsheng Yang, Haoxing Xu.

  Lysosomes maintain an acidic pH of 4.5-5.0, optimal for macromolecular degradation. Whereas proton influx is produced by a V-type H+ ATPase, proton efflux is mediated by a fast H+ leak through TMEM175 channels, as well as an unidentified slow pathway. A candidate screen on an orphan lysosome membrane protein (OLMP) library enabled us to discover that SLC7A11, the protein target of the ferroptosis-inducing compound erastin, mediates a slow lysosomal H+ leak through downward flux of cystine and glutamate, two H+ equivalents with uniquely large but opposite concentration gradients across lysosomal membranes. SLC7A11 deficiency or inhibition caused lysosomal over-acidification, reduced degradation, accumulation of storage materials, and ferroptosis, as well as facilitated α-synuclein aggregation in neurons. Correction of abnormal lysosomal acidity restored lysosome homeostasis and prevented ferroptosis. These studies have revealed an unconventional H+ transport conduit that is integral to lysosomal flux of protonatable metabolites to regulate lysosome function, ferroptosis, and Parkinson's disease (PD) pathology.

Keywords:  acidification; cystine; ferroptosis; lysosome; pH optimum

DOI:  https://doi.org/10.1016/j.cell.2025.04.004
J Biol Chem. 2025 Apr 26. pii: S0021-9258(25)00403-X. [Epub ahead of print] 108554

The ribonuclease RNase T2 mediates selective autophagy of ribosomes induced by starvation in Saccharomyces cerevisiae.

Atsushi Minami, Kohei Nishi, Rikusui Yamada, Gai Jinnai, Hikari Shima, Sakiko Oishi, Hirofumi Akagawa, Toshihiro Aono, Makoto Hidaka, Haruhiko Masaki, Tomohisa Kuzuyama, Yoichi Noda, Tetsuhiro Ogawa.

  RNase T2 is a conserved ribonuclease, playing essential and diverse roles despite its simple enzymatic activity. Saccharomyces cerevisiae RNase T2, known as Rny1p, is stress-responsive and localizes in the vacuole. Upon starvation, ribosomes are degraded by autophagy, in which Rny1p mediates rRNA degradation. However, whether the ribosomal degradation is selective or non-selective is still being determined in S. cerevisiae. Here, we elucidated novel aspects of ribosome degradation mechanisms and the function of Rny1p in stress response. We discovered that most ribosomes are selectively degraded, whose mechanism differs from the previously reported selective degradation process called "ribophagy." Rsa1p, a factor involved in assembling 60S ribosomal subunits, is revealed to interact with Atg8p and act as a receptor for selective ribosome degradation in the cytosol. The accumulation of rRNA in vacuoles, due to lack of Rny1p, leads to a decrease in non-selective autophagic activity. This is one of the reasons for the inability of Rny1p-deficient strains to adapt to starvation conditions. Rny1p is also reported to be secreted and associated with the cell wall. We revealed that a C-terminal extension of Rny1p, characteristic in some fungal RNase T2, is required to anchor the cell wall. Some non-fungal RNase T2 proteins also have C-terminal extensions. However, their sequences and structures differ from those of fungal RNase T2, suggesting that their biological functions may also be distinct. The diversity of C-terminal extensions across different organisms is thought to be one reason why RNase T2 plays various roles.

Keywords:  Ribonuclease; autophagy; molecular evolution; ribosome; structural model

DOI:  https://doi.org/10.1016/j.jbc.2025.108554
Res Sq. 2025 Apr 09. pii: rs.3.rs-6330979. [Epub ahead of print]

Programmed mitophagy at the oocyte-to-zygote transition promotes 1 species immortality.

David Sherwood, Siddharthan Balachandar Thendral, Sasha Bacot, Katherine Morton, Qiuyi Chi, Isabel Kenny-Ganzert, Joel Meyer.

The quality of mitochondria inherited from the oocyte determines embryonic viability, metabolic health throughout progeny lifetime, and future generation endurance. High levels of endogenous reactive oxygen species and exogenous toxicants are threats to mitochondrial DNA (mtDNA) in fully developed oocytes. Deleterious mtDNA is commonly detected in developed oocytes, but is absent in embryos, suggesting the existence of a cryptic purifying selection mechanism. Here we discover that in C. elegans, the onset of oocyte-to-zygote transition (OZT) developmentally triggers a rapid mitophagy event. We show that mitophagy at OZT (MOZT) requires mitochondrial fragmentation, the macroautophagy pathway, and the mitophagy receptor FUNDC1, but not the prevalent mitophagy factors PINK1 and BNIP3. Impaired MOZT leads to increased deleterious mtDNA inheritance and decreases embryonic survival. Inherited mtDNA damage accumulates across generations, leading to the extinction of descendent populations. Thus, MOZT represents a strategy that preserves mitochondrial health during the mother-to-offspring transmission and promotes species continuity.

DOI: https://doi.org/10.21203/rs.3.rs-6330979/v1
Alzheimers Dement. 2025 Apr;21(4): e70198

Genome-wide association analysis identifies APOE as a mitophagy modifier in Lewy body disease.

Xu Hou, Michael G Heckman, Fabienne C Fiesel, Shunsuke Koga, Alexandra I Soto-Beasley, Jens O Watzlawik, Jing Zhao, Rebecca R Valentino, Patrick W Johnson, Launia J White, Zachary S Quicksall, Joseph S Reddy, Jose Bras, Rita Guerreiro, Na Zhao, Guojun Bu, Dennis W Dickson, Owen A Ross, Wolfdieter Springer.

   INTRODUCTION: Phosphorylated ubiquitin (p-S65-Ub) is generated during PINK1-PRKN mitophagy as a specific marker of mitochondrial damage. Despite the widespread deposition of p-S65-Ub in aged and diseased human brain, the genetic contribution to its accumulation remains unclear.
METHODS: To identify novel mitophagy regulators, we performed a genome-wide association study using p-S65-Ub level as a quantitative trait in 1012 autopsy-confirmed Lewy body disease (LBD) samples.
RESULTS: We identified a significant genome-wide association with p-S65-Ub for rs429358 (apolipoprotein E ε4 [APOE4]) and a suggestive association for rs6480922 (ZMIZ1). APOE4 was associated with higher p-S65-Ub levels and greater neuropathological burden. Functional validation in mouse and human induced pluripotent stem cell (iPSC) models confirmed APOE4-mediated mitophagy alterations. Intriguingly, ZMIZ1 rs6480922 was associated with lower p-S65-Ub levels, reduced neuropathological load, and increased brain weight, indicating a potential protective role.
DISCUSSION: Our findings underscore the importance of mitochondrial quality control in LBD pathogenesis and nominate regulators that may contribute to disease risk or resilience.
HIGHLIGHTS: p-S65-Ub levels were used as a quantitative marker of mitochondrial damage. A GWAS identified two genetic variants that modify mitophagy in LBD autopsy brain. APOE4 was associated with increased p-S65-Ub accumulation and neuropathology. APOE4 altered mitophagy via pathology-dependent and pathology-independent mechanisms. ZMIZ1 was linked to reduced p-S65-Ub and neuropathology indicative of protection.

Keywords:  GWAS; PINK1; PRKN; Parkin; Parkinson's disease; ZMIZ1; autophagy; mitochondria; phosphorylated ubiquitin; ubiquitin

DOI:  https://doi.org/10.1002/alz.70198
Cell Signal. 2025 Apr 23. pii: S0898-6568(25)00247-5. [Epub ahead of print]132 111834

LAPTM5 confers cisplatin resistance in NSCLC by suppressing LAMP1 ubiquitination to stabilize lysosomal membranes and sustain autophagic flux.

Fan Wu, Chunlan Li, Xianrang Song, Li Xie.

  Cisplatin is a widely used chemotherapeutic agent in the treatment of non-small cell lung cancer (NSCLC), but cisplatin resistance remains a significant clinical challenge. Lysosomal transmembrane protein 5 (LAPTM5) is a lysosomal membrane protein implicated in macroautophagy/autophagy, although its precise mechanism has yet to be fully elucidated.In this study, we demonstrated that LAPTM5 promotes cisplatin resistance in NSCLC by maintaining lysosomal membrane stability and preserving autophagic flux. Mechanistic investigations showed that LAPTM5 competes with LAMP1 for binding to WWP2, thereby inhibiting LAMP1 ubiquitination and degradation, which ultimately preserves lysosomal membrane stability. LAPTM5 knockdown increases lysosomal membrane permeability, leading to the release of cathepsin D (CTSD), which elevates intracellular reactive oxygen species (ROS) levels; further destabilizing the lysosomal membrane and accelerating cell death. Our findings elucidate the mechanism by which LAPTM5 contributes to cisplatin resistance through lysosomal membrane stabilization and identify LAPTM5 as a potential therapeutic target for overcoming cisplatin resistance in NSCLC.

Keywords:  Autophagy; Cisplatin; LAMP1; LAPTM5; Lysosomal membrane permeabilization; ROS

DOI:  https://doi.org/10.1016/j.cellsig.2025.111834
Mol Neurobiol. 2025 Apr 26.

An Insight into Neuronal Processing of Ghrelin: Effects of a Bioactive Ghrelin Derivative on Proteolytic Pathways and Mitophagy.

Daniela Lufrano, Chunmei Gong, Valentina Cecarini, Massimiliano Cuccioloni, Laura Bonfili, Chiara Sturaro, Barbara Bettegazzi, Chiara Ruzza, Mario Perelló, Mauro Angeletti, Anna Maria Eleuteri.

  Protein homeostasis (proteostasis) is preserved by an orchestrated network of molecular mechanisms that regulate protein synthesis, folding, and degradation, ensuring cellular integrity and function. Proteostasis declines with age and is related to pathologies such as neurodegenerative diseases and cardiac disorders, which are accompanied by the accumulation of toxic protein aggregates. In this context, therapeutic strategies enhancing the two primary degradative systems involved in the cellular clearance of those abnormal proteins, namely ubiquitin-proteasome system and autophagy-lysosomal pathway, represent a promising approach to counteract the collapse of proteostasis in such pathological conditions. In this work, we explored the processing of ghrelin, a pleiotropic peptide hormone linked to energy metabolism and higher brain functions, which is reported to modulate the protein degradative mechanisms. According to our data, ghrelin is processed by serine hydrolases secreted into the conditioned medium of SH-SY5Y neuroblastoma cell line, commonly used in neurotoxicology and neuroscience research. Ghrelin processing leads to the formation of a shorter peptide (ghrelin(1-11)) that stimulates both the cell proteasome system and autophagy-lysosomal pathway, encompassing the selective autophagy of mitochondria. Our findings suggest that ghrelin processing may contribute to the maintenance of neuronal proteostasis.

Keywords:  Autophagy; Ghrelin; Mitophagy; Neuronal Processing; Proteasome

DOI:  https://doi.org/10.1007/s12035-025-04976-5
Eur J Clin Invest. 2025 Apr 25. e70051

Extracellular matrix mechanical cues (dys)regulate metabolic redox homeostasis due to impaired autophagic flux.

Heloísa Gerardo, Tânia Lourenço, Júlio Torres, Manuela Ferreira, Célia Aveleira, Susana Simões, Lino Ferreira, Cláudia Cavadas, Paulo J Oliveira, José Teixeira, Mário Grãos.

   BACKGROUND: Extracellular matrix (ECM) stiffness is increasingly recognized as a critical regulator of cellular behaviour, governing processes such as proliferation, differentiation, and metabolism. Neurodegenerative diseases are characterized by mitochondrial dysfunction, oxidative stress, impaired autophagy, and progressive softening of the brain tissue, yet research into how mechanical cues influence cellular metabolism in this context remains scarce.
MATERIALS AND METHODS: In this study, we evaluated the long-term effects of brain-compliant, soft ECM on mitochondrial bioenergetics, redox balance, and autophagic capacity in human neuroblastoma (SH-SY5Y) and mouse hippocampal (HT22) cell lines, as well as primary mouse neurons.
RESULTS: We observed that prolonged exposure to soft ECM does not impact cell proliferative capacity of neuronal cells but results in mitochondrial bioenergetic dysfunction, redox imbalance, and disrupted autophagic flux. These findings were consistently validated across both human and mouse neuronal cells. Our data indicate a decreased maximal autophagic capacity in cells exposed to long-term soft ECM, potentially due to an imbalance in autophagosome formation and degradation, as demonstrated by decreased LC3 II levels following chloroquine-induced autophagic flux inhibition. This impairment in autophagy was coupled with increased cellular oxidative stress, further indicating metabolic alterations.
CONCLUSIONS: These findings emphasize the critical role of ECM stiffness in regulating neuronal cell metabolism and suggest that prolonged exposure to soft ECM may mimic key aspects of neurodegenerative disease pathology, thereby enhancing the physiological relevance of in vitro models. This study underscores the necessity for further research into ECM mechanics as a contributing factor in neurodegenerative disease progression and as a potential target for therapeutic strategies.

Keywords:  autophagy; extracellular matrix; mechanical cues; mitochondria bioenergetic; neuronal cells; redox homeostasis

DOI:  https://doi.org/10.1111/eci.70051
JHEP Rep. 2025 May;7(5): 101330

Macrophage ATG16L1 promotes liver regeneration after partial hepatectomy.

Xinyu Zhan, Yan Bai, Qing Zhu, Yiyun Gao, Fan Li, Qingfa Bu, Zeyu Zhu, Zhuqing Rao, Haoming Zhou.

   Background & Aims: Autophagy plays an important role in liver regeneration. However, most studies are limited to hepatocytes, and the function and mechanism of macrophage autophagy in liver regeneration remain unclear. This study investigated the role of the essential autophagy gene encoding autophagy-related 16-like 1 (ATG16L1), which regulates the macrophage phenotype in liver regeneration.
Methods: We generated FloxP-Atg16l1 (Atg16l1 FL/FL ), Lyz2-Cre Atg16l1 knockout (KO) (Atg16l1 M-KO ), and myeloid-specific Atg16l1-overexpression-knock-in (Atg16l1 OE ) mice. These mice were subjected to 70% partial hepatectomy to demonstrate the role of ATG16L1 in macrophages during liver regeneration.
Results: ATG16L1 expression was significantly upregulated in macrophages during the early stages of liver regeneration. ATG16L1 deletion in macrophages substantially delayed liver regeneration in mice and caused a marked imbalance in Ly6Chi and Ly6Clo macrophage proportions in the liver. RNA-sequencing analysis revealed that, compared with macrophages isolated from Atg16l1 FL/FL mice, those from Atg16l1 M-KO mice exhibited significant downregulation of genes associated with oxidative phosphorylation and upregulation of proinflammatory gene expression. Mechanistically, ATG16L1 loss impaired mitophagy in macrophages, leading to the accumulation of mitochondrial damage and a metabolic shift that promoted proinflammatory macrophage polarization. ATG16L1 deficiency not only promoted macrophage mitochondrial (mt)DNA release and cyclic GMP-AMP synthase-stimulator of interferon genes (STING) activation, but also suppressed STING degradation. Sustained STING hyperactivation and subsequent increased release of downstream interferons further contributed to the inhibition of liver regeneration. Notably, pharmacological activation or genetic overexpression of ATG16L1 significantly enhanced liver regeneration in mice.
Conclusions: ATG16L1 has a pivotal role in liver regeneration by affecting the phenotype and function of macrophages. Thus, targeting ATG16L1 in macrophages could present a novel strategy for promoting liver regeneration.
Impact and implications: The autophagy-related gene ATG16L1 mediates mitophagy, facilitating the clearance of damaged mitochondria in macrophages following partial hepatectomy and maintaining a reparative macrophage phenotype. ATG16L1 deficiency triggers excessive STING activation and inhibits its degradation, thereby suppressing liver regeneration. Thus, targeting ATG16L1 in macrophages could represent a novel strategy to promote liver regeneration.

Keywords:  IFN; Mitophagy; Oxidative phosphorylation; Proinflammatory; STING; mtDNA

DOI:  https://doi.org/10.1016/j.jhepr.2025.101330
Aging Cell. 2025 Apr 28. e70081

Age-Associated Decline in Autophagy Pathways in the Retinal Pigment Epithelium and Protective Effects of Topical Trehalose in Light-Induced Outer Retinal Degeneration in Mice.

Katherine Cox, Gongyu Shi, Neve Read, Mohamed T Patel, Kepeng Ou, Zijia Liu, Jiahui Wu, Suci Cendanawati, Jenna Le Brun Powell, Pola Goldberg Oppenheimer, Lisa J Hill, Lindsay B Nicholson, Andrew D Dick, Jian Liu.

  Age is a primary risk factor for chronic conditions, including age-related macular degeneration (AMD). Impairments in autophagy processes are implicated in AMD progression, but the extent of autophagy's contribution and its therapeutic potential remain ambiguous. This study investigated age-associated transcriptomic changes in autophagy pathways in the retinal pigment epithelium (RPE) and evaluated the protective effects of topical trehalose, an autophagy-enhancing small molecule, against light-induced outer retinal degeneration in mice. Transcriptomic analysis of human RPE/choroid and mouse RPE revealed consistent downregulation of autophagy pathways with age, alongside variable changes as AMD severity progressed. Given the age- and AMD-associated perturbation of autophagy pathways, we examined trehalose treatment in vitro, which enhanced autophagic flux and restored mitochondrial respiratory function in primary murine RPE cells exposed to oxidative stress. In vivo, topical trehalose improved autophagy-lysosome activity in mouse RPE, as demonstrated by elevated LC3B turnover and SQSTM1/p62 degradation. Furthermore, trehalose eyedrops protected mice from light-induced damage to the RPE and photoreceptors, preserving outer nuclear layer thickness, RPE morphology, and junctional F-actin organization. Taken together, the data support that age-related decline and severe dysregulation in autophagy contributed to AMD progression. By restoring autophagic flux, topical trehalose demonstrates therapeutic potential to address early autophagy-related pathological changes in AMD.

Keywords:  aging; autophagy; oxidative stress; retinal degeneration; retinal pigment epithelium; topical administration; trehalose

DOI:  https://doi.org/10.1111/acel.70081
Aging Cell. 2025 Apr 30. e70038

HLH-30/TFEB Rewires the Chaperone Network to Promote Proteostasis Upon Perturbations to the Coenzyme A and Iron-Sulfur Cluster Biosynthesis Pathways.

Rewayd Shalash, Dror Michael Solomon, Mor Levi-Ferber, Henrik von Chrzanowski, Mohammad Khaled Atrash, Barak Nakar, Matan Yosef Avivi, Hagit Hauschner, Aviya Swisa, Alicia Meléndez, Yaron Shav-Tal, Sivan Henis-Korenblit.

  The maintenance of a properly folded proteome is critical for cellular function and organismal health, and its age-dependent collapse is associated with a wide range of diseases. Here, we find that despite the central role of Coenzyme A as a molecular cofactor in hundreds of cellular reactions, inhibition of the first and rate-limiting step in CoA biosynthesis can be beneficial and promote proteostasis. Impairment of the cytosolic iron-sulfur cluster formation pathway, which depends on Coenzyme A, similarly promotes proteostasis and acts in the same pathway. Proteostasis improvement by interference with the Coenzyme A/iron-sulfur cluster biosynthesis pathways is dependent on the conserved HLH-30/TFEB transcription factor. Strikingly, under these conditions, HLH-30 promotes proteostasis by potentiating the expression of select chaperone genes, providing a chaperone-mediated proteostasis shield, rather than by its established role as an autophagy and lysosome biogenesis-promoting factor. This reflects the versatile nature of this conserved transcription factor, which can transcriptionally activate a wide range of protein quality control mechanisms, including chaperones and stress response genes alongside autophagy and lysosome biogenesis genes. These results highlight TFEB as a key proteostasis-promoting transcription factor and underscore it and its upstream regulators as potential therapeutic targets in proteostasis-related diseases.

Keywords:   C. elegans ; HLH‐30; TFEB; chaperones; coenzyme A; iron–sulfur clusters; pantothenate kinase; protein quality control; proteostasis

DOI:  https://doi.org/10.1111/acel.70038
Ann Med. 2025 Dec;57(1): 2497112

PPAR-mediated reduction of lipid accumulation in hepatocytes involves the autophagy-lysosome-mitochondrion axis.

Federica Cetti, Alice Ossoli, Carola Garavaglia, Lorenzo Da Dalt, Giuseppe Danilo Norata, Monica Gomaraschi.

   BACKGROUND AND AIM: Lipid accumulation in hepatocytes is reduced by the activation of the peroxisome proliferator-activated receptor (PPAR) α, which is associated with increased lysosomal acid lipase (LAL) activity, transcription factor EB (TFEB) expression, and mitochondrial β-oxidation.Aim of the study was to assess whether the three isoforms of PPAR, i.e. α, δ and γ, share the same ability to reduce lipid accumulation in hepatocytes and to clarify the involvement of autophagy activation, lysosomal hydrolysis, and mitochondrial β-oxidation in lipid clearance induced by PPARs.
METHODS: HepG2 cells were treated with oleate/palmitate (O/P) to induce lipid accumulation and exposed to the PPARα agonist fenofibric acid, the γ agonist pioglitazone, the δ agonist seladelpar, or the dual α/γ agonist saroglitazar.
RESULTS: The treatment of HepG2 cells with fenofibric acid, pioglitazone, seladelpar, or saroglitazar halved lipid accumulation induced by O/P. PPAR agonists increased TFEB, p62, and LC3 expression and rescued LAL impairment induced by O/P. Moreover, PPAR agonists significantly increased mitochondrial mass and the expression of genes involved in mitochondrial dynamics and fatty acid catabolism. Interestingly, PPAR agonists lost their ability to reduce lipid accumulation when autophagic flux, LAL activity, or fatty acid transport in the mitochondria were blocked by specific inhibitors.
CONCLUSION: All PPAR agonists were able to promote the clearance of lipids in cells loaded with long-chain fatty acids. The key role of acid hydrolysis to generate fatty acids, which can be then catabolized in the mitochondria, and the ability of the PPAR system to sustain each phase of this clearing process were elucidated.

Keywords:  Peroxisome proliferator-activated receptors; hepatocytes; lipid accumulation; lysosomal acid lipase

DOI:  https://doi.org/10.1080/07853890.2025.2497112
EMBO Rep. 2025 Apr 30.

mTOR controls ependymal cell differentiation by targeting the alternative cell cycle and centrosomal proteins.

Alexia Bankolé, Ayush Srivastava, Asm Shihavuddin, Khaled Tighanimine, Marion Faucourt, Vonda Koka, Solene Weill, Ivan Nemazanyy, Alissa J Nelson, Matthew P Stokes, Nathalie Delgehyr, Auguste Genovesio, Alice Meunier, Stefano Fumagalli, Mario Pende, Nathalie Spassky.

  Ependymal cells are multiciliated glial cells lining the ventricles of the mammalian brain. Their differentiation from progenitor cells involves cell enlargement and progresses through centriole amplification phases and ciliogenesis. These phases are accompanied by the sharp up-regulation of mTOR Complex 1 activity (mTORC1), a master regulator of macromolecule biosynthesis and cell growth, whose function in ependymal cell differentiation is unknown. We demonstrate that mTORC1 inhibition by rapamycin preserves the progenitor pool by reinforcing quiescence and preventing alternative cell cycle progression for centriole amplification. Overexpressing E2F4 and MCIDAS circumvents mTORC1-regulated processes, enabling centriole amplification despite rapamycin, and enhancing mTORC1 activity through positive feedback. Acute rapamycin treatment in multicentriolar cells during the late phases of differentiation causes centriole regrouping, indicating a direct role of mTORC1 in centriole dynamics. By phosphoproteomic and phosphomutant analysis, we reveal that the mTORC1-mediated phosphorylation of GAS2L1, a centrosomal protein that links actin and microtubule cytoskeletons, participates in centriole disengagement. This multilayered and sequential control of ependymal development by mTORC1, from the progenitor pool to centriolar function, has implications for pathophysiological conditions like aging and hydrocephalus-prone genetic diseases.

Keywords:  Cell Cycle; Ciliogenesis; Cytoskeleton; Differentiation; mTOR

DOI:  https://doi.org/10.1038/s44319-025-00460-2
Cell Mol Life Sci. 2025 Apr 28. 82(1): 178

Muscle mTOR controls iron homeostasis and ferritinophagy via NRF2, HIFs and AKT/PKB signaling pathways.

Agnès Conjard-Duplany, Alexis Osseni, Aline Lamboux, Sandrine Mouradian, Flavien Picard, Vincent Moncollin, Céline Angleraux, Tiphaine Dorel-Dubois, Hélène Puccio, Pascal Leblanc, Bruno Galy, Vincent Balter, Laurent Schaeffer, Yann-Gaël Gangloff.

  Balanced mTOR activity and iron levels are crucial for muscle integrity, with evidence suggesting mTOR regulates cellular iron homeostasis. In this study, we investigated iron metabolism in muscle-specific mTOR knockout mice (mTORmKO) and its relation to their myopathy. The mTORmKO mice exhibited distinct iron content patterns across muscle types and ages. Slow-twitch soleus muscles initially showed reduced iron levels in young mice, which increased with the dystrophy progression but remained within control ranges. In contrast, the less affected fast-twitch muscles maintained near-normal iron levels from a young age. Interestingly, both mTORmKO muscle types exhibited iron metabolism markers indicative of iron excess, including decreased transferrin receptor 1 (TFR1) and increased levels of ferritin (FTL) and ferroportin (FPN) proteins. Paradoxically, these changes were accompanied by downregulated Ftl and Fpn mRNA levels, indicating post-transcriptional regulation. This discordant regulation resulted from disruption of key iron metabolism pathways, including NRF2/NFE2L2, HIFs, and AKT/PKB signaling. Mechanistically, mTOR deficiency impaired transcriptional regulation of iron-related genes mediated by NRF2 and HIFs. Furthermore, it triggered ferritin accumulation through two NRF2 mechanisms: (1) derepression of ferritin translation via suppression of the FBXL5-IRP axis, and (2) autophagosomal sequestration driven by NCOA4-dependent ferritin targeting to autophagosomes, coupled with age-related impairments of autophagy linked to chronic AKT/PKB activation. Three-week spermidine supplementation in older mTORmKO mice was associated with normalized AKT/PKB-FOXO signaling, increased endolysosomal FTL and reduced total FTL levels in the dystrophic soleus muscle. These findings underscore mTOR's crucial role in skeletal muscle iron metabolism and suggest spermidine as a potential strategy to address impaired ferritinophagy due to autophagy blockade in dystrophic muscle.

Keywords:  Autophagy; Dystrophy; Glycogen; Iron-sulfur cluster; Myoglobin; Oxidative stress

DOI:  https://doi.org/10.1007/s00018-025-05695-9
PLoS Genet. 2025 May 02. 21(5): e1011696

SQST-1/p62-regulated SKN-1/Nrf mediates a phagocytic stress response via transcriptional activation of lyst-1/LYST.

Aladin Elkhalil, Alec Whited, Piya Ghose.

Cells may be intrinsically fated to die to sculpt tissues during development or to maintain homeostasis. Cells can also die in response to various stressors, injury or pathological conditions. Additionally, cells of the metazoan body are often highly specialized with distinct domains that differ both structurally and with respect to their neighbors. Specialized cells can also die, as in normal brain development or pathological states and their different regions may be eliminated via different programs. Clearance of different types of cell debris must be performed quickly and efficiently to prevent autoimmunity and secondary necrosis of neighboring cells. Moreover, all cells, including those programmed to die, may be subject to various stressors. Some largely unexplored questions include whether predestined cell elimination during development could be altered by stress, if adaptive stress responses exist and if polarized cells may need compartment-specific stress-adaptive programs. We leveraged Compartmentalized Cell Elimination (CCE) in the nematode C. elegans to explore these questions. CCE is a developmental cell death program whereby three segments of two embryonic polarized cell types are eliminated differently. We have previously employed this in vivo genetic system to uncover a cell compartment-specific, cell non-autonomous clearance function of the fusogen EFF-1 in phagosome closure during corpse internalization. Here, we introduce an adaptive response that serves to aid developmental phagocytosis as a part of CCE during stress. We employ a combination of forward and reverse genetics, CRISPR/Cas9 gene editing, stress response assays and advanced fluorescence microscopy. Specifically, we report that, under heat stress, the selective autophagy receptor SQST-1/p62 promotes the nuclear translocation of the oxidative stress-related transcription factor SKN-1/Nrf via negative regulation of WDR-23. This in turn allows SKN-1/Nrf to transcribe lyst-1/LYST (lysosomal trafficking associated gene) which subsequently promotes the phagocytic resolution of the developmentally-killed internalized cell even under stress conditions.

DOI: https://doi.org/10.1371/journal.pgen.1011696
Aging Cell. 2025 Apr 28. e70066

Cathepsin B Regulates Ovarian Reserve Quality and Quantity via Mitophagy by Modulating IGF1R Turnover.

Aradhana Mohanty, Anjali Kumari, Lava Kumar S, Ajith Kumar, Pravin Birajdar, Rohit Beniwal, Mohd Athar, Kiran Kumar P, H B D Prasada Rao.

  The quality and quantity of the ovarian reserve are meticulously regulated through various cell death pathways to guarantee the availability of high-quality oocytes for fertilization. While apoptosis is recognized for contributing to maintaining ovarian reserve, the involvement of other cell death pathways remains unclear. Employing chemical genetics and proteomics, this study reveals the crucial involvement of Cathepsin B in maintaining the ovarian reserve. Results indicate that apoptosis and autophagy play pivotal roles, and inhibiting these pathways significantly increases follicle numbers. Proteomics reveals a dynamic shift from apoptosis to autophagy during follicular development, with Cathepsin B emerging as a key player in this transition. Inhibiting Cathepsin B not only mimics the augmented oocyte reserve observed with autophagy inhibition but also upregulated IGF1R and AKT-mTOR pathways without compromising fertility in pre- and postpubertal mice. Further, IGF1R inhibition partially compromised the protective effects of Cathepsin B inhibition on oocyte reserves, suggesting their interdependence. This association is further supported by the finding that Cathepsin B can degrade IGF1R in vitro. Moreover, the increased IGF1R levels enhance the oocyte mitochondrial membrane potential via transcriptional regulation of mitochondrial biogenesis and mitophagy genes. Remarkably, this Cathepsin B-dependent ovarian reserve maintenance mechanism is conserved in higher-order vertebrates. Cumulatively, our study sheds valuable light on the intricate interplay of autophagy, Cathepsin B, and growth factors in ovarian reserve maintenance, offering potential therapeutic strategies to delay ovarian aging and preserve fertility.

Keywords:  IGF1R; autophagy; cathepsin B; mitophagy; ovarian reserve

DOI:  https://doi.org/10.1111/acel.70066
Nat Commun. 2025 Apr 29. 16(1): 4024

Autophagy disruption and mitochondrial stress precede photoreceptor necroptosis in multiple mouse models of inherited retinal disorders.

Fay Newton, Mihail Halachev, Linda Nguyen, Lisa McKie, Pleasantine Mill, Roly Megaw.

Inherited retinal diseases (IRDs) are a leading cause of blindness worldwide. One of the greatest barriers to developing treatments for IRDs is the heterogeneity of these disorders, with causative mutations identified in over 280 genes. It is therefore a priority to find therapies applicable to a broad range of genetic causes. To do so requires a greater understanding of the common or overlapping molecular pathways that lead to photoreceptor death in IRDs and the molecular processes through which they converge. Here, we characterise the contribution of different cell death mechanisms to photoreceptor degeneration and loss throughout disease progression in humanised mouse models of IRDs. Using single-cell transcriptomics, we identify common transcriptional signatures in degenerating photoreceptors. Further, we show that in genetically and functionally distinct IRD models, common early defects in autophagy and mitochondrial damage exist, triggering photoreceptor cell death by necroptosis in later disease stages. These results suggest that, regardless of the underlying genetic cause, these pathways likely contribute to cell death in IRDs. These insights provide potential therapeutic targets for novel, gene-agnostic treatments for IRDs applicable to the majority of patients.

DOI: https://doi.org/10.1038/s41467-025-59165-8
J Anim Sci Biotechnol. 2025 May 02. 16(1): 63

Gut microbiota modulate intestinal inflammation by endoplasmic reticulum stress-autophagy-cell death signaling axis.

Feiyang He, Yi Zheng, Mabrouk Elsabagh, Kewei Fan, Xia Zha, Bei Zhang, Mengzhi Wang, Hao Zhang.

  The intestinal tract, a complex organ responsible for nutrient absorption and digestion, relies heavily on a balanced gut microbiome to maintain its integrity. Disruptions to this delicate microbial ecosystem can lead to intestinal inflammation, a hallmark of inflammatory bowel disease (IBD). While the role of the gut microbiome in IBD is increasingly recognized, the underlying mechanisms, particularly those involving endoplasmic reticulum (ER) stress, autophagy, and cell death, remain incompletely understood. ER stress, a cellular response to various stressors, can trigger inflammation and cell death. Autophagy, a cellular degradation process, can either alleviate or exacerbate ER stress-induced inflammation, depending on the specific context. The gut microbiome can influence both ER stress and autophagy pathways, further complicating the interplay between these processes. This review delves into the intricate relationship between ER stress, autophagy, and the gut microbiome in the context of intestinal inflammation. By exploring the molecular mechanisms underlying these interactions, we aim to provide a comprehensive theoretical framework for developing novel therapeutic strategies for IBD. A deeper understanding of the ER stress-autophagy axis, the gut microbial-ER stress axis, and the gut microbial-autophagy axis may pave the way for targeted interventions to restore intestinal health and mitigate the impact of IBD.

Keywords:  Autophagy; Cell death; Endoplasmic reticulum stress; Gut microbes; Intestinal inflammation

DOI:  https://doi.org/10.1186/s40104-025-01196-8
Mol Med. 2025 May 02. 31(1): 163

USP14 inhibits mitophagy and promotes tumorigenesis and chemosensitivity through deubiquitinating BAG4 in microsatellite instability-high colorectal cancer.

Zhiyong Wang, Cheng Yu, Gengchen Xie, Kaixiong Tao, Zhijie Yin, Qing Lv.

   BACKGROUND: Mitophagy, essential for cellular homeostasis, is involved in eliminating damaged mitochondria and is associated with cancer progression and chemoresistance. The specific impact of mitophagy on microsatellite instability-high (MSI-H) colorectal cancer (CRC) is still under investigation. Ubiquitination, a post-translational modification, is essential for controlling protein stability, localization, and function. This study identifies USP14, a deubiquitinating enzyme, as a key regulator of mitophagy in MSI-H CRC.
METHODS: A deubiquitinating enzyme (DUBs) siRNA library screening identified USP14 as a key regulator of mitophagy. Tissue samples from patients were analyzed using immunohistochemistry and Western blot. USP14 knockdown cell lines were generated using lentiviral transfection. Protein interactions between USP14 and BAG4 were confirmed by co-immunoprecipitation, while quantitative PCR was used to measure gene expression. Mitochondrial proteins were extracted to analyze mitophagy, and flow cytometry was used to assess apoptosis. Finally, a mouse xenograft model was employed to study USP14's role in tumor growth and oxaliplatin sensitivity.
RESULTS: Screening reveals that USP14 inhibits mitophagy and CRC (MSI-H) show high USP14 expression which correlates with poor prognosis. Functional analyses reveal that knocking down USP14 reduces tumor growth, and increases sensitivity to oxaliplatin. Mechanically, USP14 inhibits mitophagy by K48-deubiquitinating and stabilizing BAG4 at K403, which prevents the recruitment of Parkin to damaged mitochondria. The significant clinical relevance of USP14, BAG4, and PRKN are proved in tumor tissues.
CONCLUSIONS: The study highlights the USP14/BAG4/PRKN axis as a critical pathway in CRC (MSI-H), suggesting that targeting USP14 could inhibit tumor progression and improve chemotherapeutic outcomes. These findings underscore the importance of ubiquitination and mitophagy in cancer biology, indicating a potential therapeutic target for MSI-H CRC.

Keywords:  Colorectal cancer; Mitophagy; Oxaliplatin; Tumorigenesis; USP14

DOI:  https://doi.org/10.1186/s10020-025-01182-w
Neurochem Int. 2025 Apr 30. pii: S0197-0186(25)00055-5. [Epub ahead of print] 105982

Truncation mutation of CHMP2B disrupts late endosome function but reduces TDP-43 aggregation through HSP70 upregulation.

Yohei Iguchi, Yuhei Takahashi, Jiayi Li, Yoshinobu Amakusa, Yu Kawakami, Takashi Yoshimura, Ryo Chikuchi, Madoka Iida, Satoshi Yokoi, Masahisa Katsuno.

  TAR DNA-binding protein 43 (TDP-43)-positive cytoplasmic aggregation is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). This aggregation contributes substantially to the neurodegeneration of ALS and FTLD. The endosome, a key component of membrane trafficking in eukaryotic cells and is involved in the autophagy-lysosome pathway. Endosome-related genes such as CHMP2B, Alsin, and TMEM106B, are either causative or act as genetic modifiers in ALS and FTLD. However, the association between endosomal functions and TDP-43 aggregations remain poorly understood. The C-terminal truncation mutation CHMP2B, which causes frontotemporal dementia associated with chromosome 3 (FTD3), disrupts late endosome (LE)-lysosomes fusion. Nevertheless, FTD3 does not induce TDP-43 pathology. In this study, we showed that CHMP2B mutation-induced LE dysfunction promotes TDP-43 aggregate degradation through enhanced recruitment to juxtanuclear quality control compartments. Transcriptomic analysis revealed that CHMP2Bintron5 overexpression upregulates HSP70 expression. New insights into the connection between CMHP2B and HSP70 as well as the role of HSP70-mediated membrane trafficking in TDP-43 aggregation, offer a valuable understanding of the disease mechanism of ALS and FTLD.

Keywords:  ALS; CHMP2B; FTD; TDP-43; endosome; juxtanuclear quality control compartment

DOI:  https://doi.org/10.1016/j.neuint.2025.105982
Mol Neurobiol. 2025 Apr 25.

Knockdown of Atg1 Impairs Brain Regeneration and Downregulates ECM-Related Genes in the Planarian Dugesia japonica.

Kexue Ma, Fangying Guo, Rui Li, Gege Song, Hecai Zhang, Qiong Lu, Keshi Ma, Shaoqing Gong.

  Planarian regeneration is a complex process that involves the precise orchestration of cell proliferation, differentiation, migration, and autophagy. However, the role of autophagy in planarian regeneration remains poorly understood. In this study, we identified autophagy-related gene 1 from the planarian Dugesia japonica (designated as DjAtg1) and investigated its role in planarian brain regeneration. DjAtg1 transcripts are highly expressed in the cephalic ganglia of intact planarians. Following amputation, DjAtg1 is prominently expressed in the newly regenerated brain tissues. Knockdown of DjAtg1 via RNA interference (RNAi) induces head regression, with all RNAi-treated animals regenerating a small triangular-shaped head. Neoblast-marker labeling experiments demonstrate that DjAtg1 knockdown does not affect cell proliferation but impairs neoblast behavior. Notably, RNA-seq reveals that most of these down-regulated transcripts are linked to the extracellular matrix (ECM). Based on our findings and prior literature, we propose that the DjAtg1-mediated secretory pathway is essential for ECM remodeling. DjAtg1 knockdown disrupts the secretory pathway, which feedback-inhibits the expression of ECM-related genes. Our work provides new insights into the non-canonical role of autophagy in regulating of ECM remodeling during planarian regeneration.

Keywords:   DjAtg1 ; Brain regeneration; Cell migration; Extracellular matrix; Planarian; Secretory pathway

DOI:  https://doi.org/10.1007/s12035-025-04978-3
Mol Neurobiol. 2025 Apr 28.

Maternal Myo-Inositol Deficiency Involved Autophagy Impairment by PI3K/Akt/mTOR Signaling in Neural Tube Defects During Pregnancy.

Jin Guo, Zhongzhong Chen, Huixuan Yue, Shen Li, Guohui Sun, Feng Zhang, Rugang Zhong, Jianjun Lyu, Yanwei Yang, Xiuwei Wang, Yihua Bao, Jizhen Zou, Zhen Guan, Ting Zhang, Jianhua Wang.

  Previous studies have demonstrated that peri-conceptional inositol supplementation could effectively ameliorate the recurrence of neural tube defects (NTDs); though, the mechanism remains unclear. In the current investigation, we detected the myo-inositol (MI) levels in maternal plasma and embryonic tissues in a Chinese population with high prevalence of NTDs and found maternal MI deficiency increased NTD susceptibility in this area. Pregnant mice were randomly divided into 2 groups. The control group was treated with 0.9% saline, while the experimental group was treated with IMPase inhibitor by intraperitoneal injection on E7.5 to generate the maternal MI-deficient mouse model, followed by comprehensive phenotypic and molecular analysis at E13.5. Corresponding in vitro experiments treated neural stem cells (NSCs) for 16 h with IMPase inhibitor, MI supplementation, or specific PI3K and mTOR inhibitors to systematically investigate the downstream signaling pathways. We observed aberrant activation PI3K/Akt/mTOR signaling and reduced autophagy in a maternal MI deficiency mouse model after ruling out the genetic perturbations. Further in vitro kinase assay showed that MI negatively regulated PI3K activity, in a dose-dependent manner, which possibly due to the hydrogen bond interactions between amino acid residues in the ATP-binding site of PI3K and inositol. MI deficiency NSCs also presented PI3K/AKT/mTOR pathway activation concurrent with reduced autophagy level; MI supplementation or inhibition of the PI3K/Akt/mTOR pathway could rescue MI deficiency-induced autophagy impairment. Finally, we validated decreased autophagy levels as well as hyperactivation of the PI3K/Akt/mTOR pathway by MI deficient human NTD embryonic neural tissues. Our results suggested that maternal MI deficiency might increase susceptibility to NTDs. Low levels of MI might impair autophagy in the developing neural tube involving upregulation of PI3K/Akt/mTOR pathway.

Keywords:  Autophagy; Inositol; Neural tube defects; Phosphatidylinositide 3-kinase; Pregnancy

DOI:  https://doi.org/10.1007/s12035-025-04972-9