bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2026–05–10
forty-one papers selected by
Viktor Korolchuk, Newcastle University



  1. Autophagy. 2026 May 05.
      Ryanodine receptors (RYRs) are ER-resident Ca2 + -release channels enriched in excitable cells, including neurons. RYR hyperactivity is implicated in early pathogenesis of disorders such as Alzheimer's disease (AD), which is associated with impaired autophagy. We recently uncovered a mechanism linking RYR activity to lysosome availability for autophagy. RYRs localize to ER - lysosome contact sites via direct binding to ATP6V0A1, a V-ATPase subunit that also suppresses RYR-mediated Ca2 + release. In human iPSC-derived cortical neurons, spontaneous RYR activity promotes lysosomal secretion, depleting the intracellular lysosomal pool and inhibiting autophagic flux. RYR inhibition promotes ER - lysosome contacts, limits lysosomal secretion, and restores lysosome availability for autophagosome fusion and cargo degradation (including APP). Conversely, disrupting the RYR:ATP6V0A1 interaction using a RYR-derived protein fragment serving as a "decoy" for ATP6V0A1 evokes RYR hyperactivity and stimulates lysosomal secretion. In this Punctum, we discuss how this RYR2:ATP6V0A1 "contact-site hub" may be perturbed in disease and highlight open questions on how lysosomes decode RYR-derived Ca2 + signals.
    Keywords:  Calcium signaling; V-type ATPase; endoplasmic reticulum; lysosome; membrane contact site; ryanodine receptor
    DOI:  https://doi.org/10.1080/15548627.2026.2669981
  2. FEBS Lett. 2026 May 03.
      Cells rely on metabolic control; the mechanistic target of rapamycin complex 1 (mTORC1) senses nutrient availability, particularly amino acids. Lysosomes maintain amino acid homeostasis through recycling. SLC38A9, a lysosomal amino acid transporter, functions as a critical sensor in the mTORC1 pathway. Here, we investigate how pH regulates SLC38A9 activity. We show that arginine uptake is pH-dependent, with His544 residue serving as the pH sensor. Mutating His544 abolishes pH dependence without impairing overall transport, indicating His544 influences transport through protonation/deprotonation, instead of involving in the substrate binding. We propose a working model for pH-induced activation, through comparing two determined SLC38A9 structures at different pH. These findings reveal how local ionic shifts regulate lysosomal transporters and fine-tune SLC38A9 function to control mTORC1 signaling.
    Keywords:  SLC family; amino acid transport; mTOR complex; pH‐regulation; transceptor
    DOI:  https://doi.org/10.1002/1873-3468.70352
  3. J Biol Chem. 2026 May 06. pii: S0021-9258(26)02000-4. [Epub ahead of print] 113128
      Mitochondria play a major role in cellular health, yet their contribution to chronic diseases has been underestimated. Mitochondria are essential for all tissues, and a major source of ATP in high-energy-demand organs such as brain and heart being vulnerable to mitochondrial dysfunction. Failure to repair or remove damaged mitochondria contributes to aging and chronic diseases. Cells have evolved quality control mechanisms, including mitophagy to eliminate damaged mitochondria and mitobiogenesis to replenish them. The ubiquitin-proteasome system (UPS) is responsible for removing misfolded proteins, a process that is highly ATP dependent and therefore reliant on mitochondrial function. In turn, damaged mitochondria are eliminated through coordinated actions of the UPS and lysosomal degradation through mitophagy. Many neurodegenerative diseases are characterized by the presence of disease-specific protein aggregates, such as α-synuclein aggregates in Parkinson's disease and tau neurofibrillary tangles in Alzheimer's disease. These aggregates impair mitochondrial function, while dysfunctional mitochondria generate reactive oxygen species that further exacerbate proteotoxic stress, creating a pathogenic cycle. This highlights the functional interplay between mitochondria and the UPS. Recent studies have uncovered phosphorylation of ubiquitin at Serine 65 by the mitochondrial kinase PINK1 as a key signal of mitochondrial dysfunction. Phospho-Ser65-Ubiquitin (pUb) has emerged as an indicator of mitochondrial health and a potential biomarker for aging and neurodegenerative disease. However, due largely to a lack of tools, little is known about the role of pUb in cellular physiology. Here we review the current landscape of pUb biology, the phospho-ubiquitome, and its role as biomarker for mitochondrial health, and neurodegeneration.
    Keywords:  (10): mitochondria; PINK1; Parkin; aging; autophagy; biomarker; mitophagy; neurodegeneration; phospho-ubiquitin; proteasome
    DOI:  https://doi.org/10.1016/j.jbc.2026.113128
  4. Autophagy. 2026 May 06. 1-3
      Tauopathies are characterized by the accumulation of misfolded tau and lysosomal dysfunction, yet whether defects in the autophagy-lysosome pathway are causal or secondary remains unclear. Recent work using human iPSC-derived neurons harboring the MAPT p.R406W mutation demonstrates that pathogenic tau is sufficient to disrupt lysosomal function upstream of tau accumulation. Tau species are differentially processed within lysosomes, with phosphorylated tau retained at the lysosomal membrane, consistent with a barrier to efficient cargo processing. Importantly, pharmacologic activation of autophagy restores degradative capacity and reduces tau burden without rescuing lysosomal motility, suggesting that trafficking and degradation represent separable axes of lysosomal biology. These findings position tau as an active disruptor of proteostasis and define a degradative bottleneck that shares features with lysosomal storage disorders. Together, this work reframes autophagy dysfunction in tauopathy as a modular defect with distinct therapeutic entry points.
    Keywords:  Induced pluripotent stem cells; MAPT; lysosomal trafficking; neurons; tauopathy
    DOI:  https://doi.org/10.1080/15548627.2026.2669685
  5. Int J Mol Sci. 2026 Apr 14. pii: 3488. [Epub ahead of print]27(8):
      Autophagy is a tightly regulated catabolic process essential for cellular homeostasis, stress adaptation, and regeneration. In the nematode Caenorhabditis elegans, with its short lifespan, transparent body, and well-defined genetics, the process can be investigated in a tissue- and age-specific manner, making it an excellent model to study the connection between autophagy and longevity. While autophagy is generally protective-promoting cellular maintenance and longevity-its dysregulation or hyperactivation during aging can be deleterious, leading to cellular stress, tissue damage, and cell death. In this context, autophagy can act as a double-edged sword: its beneficial effects can become harmful if hyperactivated or improperly controlled, particularly in post-reproductive or stressed tissues. Here, we review studies in C. elegans that link autophagy to lifespan regulation, with a focus on unexpected, context-dependent, or harmful effects of modulating autophagy-related genes during aging. We highlight how age- and tissue-specific regulation of autophagy can optimize its protective role and discuss the implications of these findings for designing strategies to promote healthy aging, potentially providing insights for the therapeutic targeting of autophagy in humans.
    Keywords:  Caenorhabditis elegans; aging; autophagy; lifespan regulation; proteostasis; stress response
    DOI:  https://doi.org/10.3390/ijms27083488
  6. Transl Neurodegener. 2026 May 07. pii: 21. [Epub ahead of print]15(1):
      Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuron loss and the accumulation of misfolded α-synuclein, yet the underlying mechanisms remain incompletely understood. Over the past two decades, genetic discoveries have highlighted the convergence of multiple familial PD genes on the autophagy-lysosome pathway (ALP), a key cellular system responsible for the degradation and recycling of intracellular components. Recent studies have further revealed that components of the ALP not only mediate the clearance of α-synuclein aggregates but also, under certain pathological conditions, contribute to their propagation via lysosomal exocytosis or secretory autophagy. The precise functions of autophagy are highly context-dependent, with neuronal and glial cells exhibiting distinct ALP dynamics that shift with development, stress, and aging. In this review, we summarize current knowledge on the physiological regulation of autophagy in the brain and critically examine its involvement in PD pathogenesis, incorporating mechanistic insights from familial models and emerging evidence from sporadic PD. We also explore translational implications, focusing on efforts to identify ALP-related biomarkers in cerebrospinal fluid and urine, and on the therapeutic potential of modulating ALP activity. Although the causality between ALP dysfunction and PD remains elusive, mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking. Future research should aim to define cell type-specific ALP alterations, clarify the bidirectional interactions between α-synuclein and autophagic machinery, and develop in vivo tools to monitor autophagy activity and secretory signatures. A deeper understanding of these processes will be crucial for refining PD models, discovering robust fluid biomarkers, and designing targeted therapies capable of modifying disease trajectory.
    Keywords:  Autophagy-lysosome pathway; Lysosomal homeostasis; Parkinson’s disease; Secretory autophagy; α-Synuclein
    DOI:  https://doi.org/10.1186/s40035-026-00555-3
  7. Antioxidants (Basel). 2026 Apr 09. pii: 465. [Epub ahead of print]15(4):
      Gaucher disease (GD) is characterized by the accumulation of glucosylceramide within lysosomes due to mutations in the GBA1 gene, which encodes the enzyme glucocerebrosidase. Current treatments are ineffective for patients suffering from severe neuronopathic forms of the disease. In this context, new therapeutic approaches for neuronopathic GD forms are needed. Lysosomal and mitochondrial dysfunction associated with increased oxidative stress and disturbances in the autophagic process have been described in GD. Here, we address c-Abl-RIPK3 signaling and its contribution to the accumulation of dysfunctional mitochondria in GD. Fibroblasts from patients with GBA1 mutations and neurons treated with the glucocerebrosidase inhibitor CBE exhibited alterations in the ΔΨm and mitochondrial morphology, as well as reduced capacity to form autophagosomes. Pharmacological inhibition of c-Abl or RIPK3 restored mitochondrial function and promoted autophagosome formation, along with an increase in autophagic engulfment of mitochondria in both GD models. In conclusion, the c-Abl-RIPK3 signaling pathway contributes to mitochondrial dysfunction and blockade of autophagy components in the mitochondria, both of which are altered in the neuronopathic forms of GD.
    Keywords:  Gaucher disease; RIPK3; autophagy; c-Abl; lysosomal storage disorders; mitochondrial dysfunction; mitophagy; oxidative stress
    DOI:  https://doi.org/10.3390/antiox15040465
  8. Front Cell Dev Biol. 2026 ;14 1818512
      Oligodendrocytes generate and maintain myelin, a highly specialized membrane system essential for efficient signal propagation and long-term white matter integrity. The extreme biosynthetic demands and unique architecture of myelinating oligodendrocytes place exceptional pressure on intracellular quality control pathways. In this context, autophagy-lysosome networks have emerged as central regulators of oligodendrocyte biology, operating beyond bulk degradation to coordinate membrane remodeling, organelle homeostasis, and selective protein turnover. Here, we synthesize current evidence demonstrating that autophagy is dynamically regulated across the oligodendrocyte lineage and fulfills stage-specific roles, from precursor maintenance and differentiation-associated remodeling to long-term maintenance of compact myelin. We highlight advances revealing selective autophagic degradation of myelin proteins, the spatial distribution of autophagy within myelinating cells, and functional interactions between autophagy, endo-lysosomal trafficking, and myelin integrity. We also discuss emerging concepts of functional heterogeneity within autophagy-related compartments and context-dependent routing of myelin-associated cargo. Finally, we outline key open questions that define current gaps in our understanding of oligodendroglial autophagy. By framing autophagy as an integrated regulatory network rather than a single pathway, this review provides a conceptual foundation for understanding myelin biology under physiological conditions and establishes a basis for future studies on white matter vulnerability.
    Keywords:  autophagy; lysosome; membrane trafficking; myelin; myelin integrity; oligodendrocytes; proteostasis
    DOI:  https://doi.org/10.3389/fcell.2026.1818512
  9. J Neurosci. 2026 May 07. pii: e1224252026. [Epub ahead of print]
      Midbrain dopamine (mDA) neurons play a wide range of brain functions, but the molecular mechanisms driving the formation of mDA circuits remain largely unknown. Here, we show that autophagy, the main cellular recycling pathway, is present in the growth cones of developing mDA neurons, and its level changes dynamically in response to guidance cues. To characterize the role of autophagy in mDA axon growth and guidance, we knocked out essential autophagy genes (Atg12, Atg5) specifically in mDA neurons in mice of either sex. Autophagy-deficient mDA axons exhibit axonal swellings and reduced branching both in vitro and in vivo. Strikingly, deletion of autophagy-related genes completely blunted the response of mDA neurons to both chemorepulsive and chemoattractive guidance cues. Our data demonstrate that autophagy plays a central role in regulating mDA neuron development by orchestrating axonal growth and guidance.Significance Statement Midbrain dopaminergic neurons form circuits essential for movement, motivation, and cognition, yet the intracellular mechanisms controlling their axon growth and guidance remain poorly understood. Here we show that autophagy, a major cellular recycling pathway, operates locally in dopaminergic growth cones and is dynamically regulated by guidance cues. Using neuron-specific deletion of core autophagy genes, we demonstrate that autophagy is required for proper axonal morphology, branching, and responsiveness to both chemoattractive and chemorepulsive signals. These findings identify autophagy as a key regulator of dopaminergic circuit formation and reveal a previously unrecognized mechanism linking intracellular degradation pathways to axon guidance during brain development.
    DOI:  https://doi.org/10.1523/JNEUROSCI.1224-25.2026
  10. Nat Commun. 2026 05 07. pii: 4195. [Epub ahead of print]17(1):
      The accumulation of protein aggregates has been causatively linked to the pathogenesis of neurodegenerative diseases. Here, we conduct a genome-wide CRISPR-Cas9 screen to identify cellular factors that regulate the degradation of an aggregation-prone reporter. Genes encoding proteins involved in mitochondrial homeostasis, including the translation factor eIF5A, are enriched among suppressors of the degradation of the reporter. Genetic or chemical inhibition of eIF5A leads to dissociation of the aggregation-prone substrate from mitochondria, which is accompanied by enhanced ubiquitin-dependent proteasomal degradation. The presence of an aggregation-prone, amphipathic helix that localizes the reporter to mitochondria is crucial for the stimulatory effect of eIF5A inhibition on proteasomal degradation. Additionally, inhibition of eIF5A also enhances degradation of mutant huntingtin and α-synuclein, two disease-associated proteins that contain amphipathic helices and mislocalize to mitochondria. We propose that mitochondria serve as a holdout compartment for aggregation-prone proteins. Therefore, preventing mitochondrial localization of aggregation-prone proteins may offer a viable therapeutic strategy for reducing disease-associated proteins in neurodegenerative disorders.
    DOI:  https://doi.org/10.1038/s41467-026-72783-0
  11. EMBO J. 2026 May 05.
      p62/SQSTM1 self-assembles with polyubiquitin into liquid-like condensates ("p62 bodies") that function as stress-signaling hubs and selective autophagy cargo. We show that TBK1-dependent phosphorylation at Ser403 acts as a threshold-dependent modulator of a condensate's physical properties and promotes their rapid autophagic clearance. Phosphorylation within p62 bodies drives a transition from large, fluid droplets to compact, gel-like condensates that efficiently capture LC3-positive isolation membranes and accelerate the autophagic removal of ubiquitinated proteins. PP2A holoenzymes containing PPP2R5A/B/E, recruited via a KEAP1 bridge, counteract TBK1 by dephosphorylating Ser403. Homozygous p62S403E/S403E knock-in embryonic stem cells differentiate into post-mitotic neurons enriched in miniaturized, gel-like p62 bodies. Consistently, phosphorylation-mimetic knock-in mice show similar remodeling of p62 condensates in vivo, demonstrating that this phosphorylation-driven mechanism maintains proteostasis across scales. We propose that Ser403 phosphorylation functions as a molecular switch that couples the material state of p62 condensates to their stability and serves as a central control point for p62-mediated protein degradation.
    DOI:  https://doi.org/10.1038/s44318-026-00785-1
  12. Life Metab. 2026 Jun;5(3): loag005
      The central nervous system is highly sensitive to energy supply, and the hippocampus operates under sustained metabolic load due to continuous synaptic activity and information processing. Lysosomes couple nutrient status to cellular energetics through the mechanistic target of rapamycin complex 1 (mTORC1) and the autophagy-lysosome pathway, yet their -subcellular contribution to neuronal metabolic profiles remains unclear. To address this, we established an in vivo AAV-LysoTag/Lyso-IP workflow combined with metabolomics to quantify metabolites within mouse hippocampal lysosomes. An in vitro Lyso-IP platform and immunofluorescence provided cell-based validation. Under every-other-day fasting, hippocampal lysosomes exhibited reprogramming: small-molecule substrates derived from amino acids and fatty acids accumulated; bis(monoacylglycero)phosphate was upregulated, indicating enhanced intraluminal vesicle formation and lipid degradation/sorting; -sphingolipids and cardiolipin increased, consistent with selective mitophagy. Notably, high basal lysosomal levels of malic acid and α-ketoglutarate (α-KG) suggested additional sources beyond the mitochondria. Immunofluorescence further showed lysosomal localization of isocitrate dehydrogenase and fumarate hydratase, suggesting partial residency of these enzymes. The oxoglutarate carrier (SLC25A11) signals were observed in LAMP1+ compartments, suggesting potential transmembrane exchange of α-KG and malic acid. Together, our data indicate that lysosomal tricarboxylic acid -related metabolites are maintained by three parallel routes: mitochondrial delivery to lysosomes, local production by resident enzymes, and transporter-mediated exchange. These metabolites supplement and reshape neuronal carbon flux and metabolic resilience at the subcellular level. Our findings elevate lysosomes from degradative endpoints to mobilizable metabolic hubs in the brain and provide both methodological and conceptual frameworks for neurometabolic adaptation under energy scarcity.
    Keywords:  Lyso-IP; TCA cycle; lysosome; metabolomics; mouse hippocampus
    DOI:  https://doi.org/10.1093/lifemeta/loag005
  13. Mech Ageing Dev. 2026 May 03. pii: S0047-6374(26)00040-0. [Epub ahead of print]231 112188
      Autophagy is a core cellular mechanism that preserves tissue homeostasis by removing damaged proteins and organelles. In skeletal muscle, proper regulation of autophagic flux is essential for maintaining metabolic and structural integrity, whereas its disruption contributes to muscle atrophy, metabolic dysfunction, and age-related functional decline. Increasing evidence identifies polyamines, particularly spermidine (Spd), as important modulators of autophagy and cellular resilience, with beneficial effects on stress responses, metabolic regulation, and lifespan extension. Physical exercise likewise acts as a physiological inducer of autophagy, promoting muscle remodelling, mitochondrial quality control, and adaptive responses to stress. Within this framework, spermine oxidase (SMOX) has emerged as a relevant regulator of muscle homeostasis. SMOX expression is maintained in healthy muscle but declines in atrophic conditions. By converting spermine into spermidine, SMOX may help sustain autophagy-related pathways and support muscle mass under physiological conditions. This review explores the interplay between exercise, spermidine, and SMOX, highlighting autophagy as a unifying regulatory axis. We summarize current evidence on their individual and combined roles in preserving muscle function and discuss their potential relevance for promoting healthy muscle aging and counteracting sarcopenia.
    Keywords:  Atrophy; Autophagy; Polyamine metabolism; Skeletal muscle; Spermidine
    DOI:  https://doi.org/10.1016/j.mad.2026.112188
  14. Autophagy. 2026 May 06.
      Lipophagy, a selective form of macroautophagy/autophagy, degrades lipid droplets (LDs) to provide energy and is implicated in metabolic disorders. The molecular mechanism underlying lipophagy induction remains incompletely understood. This study explored the role of SETDB1 in starvation-induced autophagy and lipophagy. We demonstrate that SETDB1 deficiency exacerbates starvation-induced hepatic lipid accumulation by inhibiting lipophagy. Mechanistically, starvation promotes ATM-mediated phosphorylation of SETDB1, which enhances its interaction with and methylation of the RNA helicase DDX5. In SETDB1-knockout hepatocytes, hypomethylation of DDX5 facilitates the formation of the DDX5-METTL3-METTL14 complex, increasing m6A modification of BECN1 and TFEB mRNAs. This modification promoted YTHDF2-mediated decay of these transcripts, thereby inhibiting starvation-induced autophagy and lipophagy. Furthermore, administration of the SETDB1 activator (R, R)-59 significantly enhances lipophagy and attenuates starvation-induced hepatic steatosis. Collectively, our findings reveal a novel pathway in which SETDB1 deficiency drives m6A-mediated mRNA degradation to suppress lipophagy, thereby contributing to hepatic steatosis.
    Keywords:  Autophagy; SETDB1; hepatic steatosis; lipophagy; m6A modification
    DOI:  https://doi.org/10.1080/15548627.2026.2669984
  15. Autophagy. 2026 May 04.
      Proteasome inhibition remains the frontline therapy in multiple myeloma, yet its efficacy is attenuated by adaptive stress responses. Central to these is the transcription factor NRF1, which transcriptionally upregulates proteasome subunits and components of the autophagy-lysosomal machinery, restoring proteostasis and sustaining tumor cell survival. The anti-apoptotic protein Mcl1 has independently emerged as a dominant mediator of resistance to proteasome inhibitors. In our recent work, we report a first-in-class Mcl1-targeting autophagy-targeting chimera (AUTAC) that selectively degrades Mcl1 via the lysosomal pathway through K63-linked ubiquitination by TRAF6 and UBC13, and recognition by the cargo receptor p62/SQSTM1. Proteasome inhibition with carfilzomib markedly potentiates AUTAC activity, and this potentiation is abolished in NRF1-deficient cells, establishing NRF1 as the licensing factor that couples proteotoxic stress to enhanced lysosomal targeted protein degradation. The combination produces synergistic tumor cell death across proteasome inhibitor-sensitive and resistant multiple myeloma and lung cancer models in vitro and significantly suppresses tumor growth in a U266B1 multiple myeloma xenograft model. These findings reframe cytoprotective autophagy not as a resistance liability to be inhibited, but as an inducible degradation capacity that can be redirected to eliminate oncogenic survival factors, suggesting a generalizable strategy for amplifying lysosomal targeted protein degradation through controlled proteostasis stress.
    Keywords:  AUTAC; Mcl1; NRF1; autophagy; proteotoxic stress; resistance
    DOI:  https://doi.org/10.1080/15548627.2026.2669686
  16. Chem Biol Interact. 2026 May 05. pii: S0009-2797(26)00231-0. [Epub ahead of print] 112123
      Pyrrolidinophenones (PPs), a class of synthetic cathinones, have emerged as hazardous new psychoactive substances due to their high lipophilicity and potent neurotoxicity. However, the mechanisms underlying PPs-induced neuronal damage, particularly the roles of mitochondrial reactive oxygen species (ROS) and mitophagy, remain unclear. In this study, we investigated the interplay among ROS overproduction, mitochondrial dysfunction, mitophagy, and apoptosis in human neuronal cells exposed to representative PPs. Treatment with PPs induced neuronal cell toxicity in a manner dependent on the elongation of the alkyl chain, with α-pyrrolidinooctanophenone (POP) exhibiting the strongest effects. The treatment also facilitated the production of intracellular and mitochondrial ROS, including superoxide, hydrogen peroxide, and hydroxyl radical. Furthermore, the cytotoxicity was remarkably attenuated by pretreating with antioxidant, N-acetyl-L-cysteine, indicating a critical role of ROS in PPs-induced cytotoxicity. Subcellular fractionation analysis revealed an accumulation of highly lipophilic PPs such as α-pyrrolidinoheptanophenone (PHPP) and POP in mitochondria, and the treatment with PHPP or POP resulted in an increase in Bax/Bcl2 ratio, caspase-9 activation, and mitochondrial lipid peroxidation, presumably due to an activation of mitochondria-dependent apoptotic signaling. Notably, POP induced mitophagy via activation of the PINK1/Parkin pathway. Additionally, pharmacological inhibition of autophagy or mitophagy exacerbated both ROS production and cytotoxicity, suggesting a protective role of mitophagy through the removal of damaged mitochondria. Collectively, these findings demonstrate that mitochondrial accumulation of PPs promotes ROS-dependent apoptosis, while mitophagy functions as an adaptive cytoprotective mechanism. This study provides new insights into mitochondrial quality control in PPs-induced neurotoxicity and highlights mitophagy as a potential therapeutic target.
    Keywords:  Apoptosis; Mitophagy; Neuronal SK-N-SH cell; Pyrrolidinophenones; Reactive oxygen species
    DOI:  https://doi.org/10.1016/j.cbi.2026.112123
  17. Adv Biol (Weinh). 2026 May;10(5): e00274
      Parkinson's disease (PD) is a common neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta and the formation of Lewy bodies, abnormal protein aggregates primarily composed of α-synuclein. Copper, an essential trace element, plays a role in α-synuclein aggregation and PD pathogenesis. This study examines the effects of copper overload on α-synuclein clearance pathways, focusing on autophagy and the ubiquitin-proteasome system (UPS) in dopaminergic SH-SY5Y neuroblastoma cells. Copper exposure enhances autophagosome formation, as indicated by increased Beclin-1 and LC3-II levels, and impairs autophagic flux, evidenced by LC3-II accumulation in the presence of chloroquine. Concurrently, copper increases polyubiquitinated proteins, suggesting UPS dysfunction, which is confirmed through MG132 treatment. These disruptions lead to the accumulation and aggregation of α-synuclein, particularly in its phosphorylated form. Immunofluorescence reveals neurite-localized α-synuclein aggregates, consistent with copper's role in α-synuclein pathology. This study highlights copper dyshomeostasis as a contributor to impaired α-synuclein clearance through autophagy and UPS dysfunction, advancing the understanding of PD's molecular basis.
    Keywords:  Parkinson's disease; alpha‐synuclein; autophagy; copper
    DOI:  https://doi.org/10.1002/adbi.202500274
  18. Autophagy. 2026 May 04.
      Pathological accumulation of toxic SNCA species and loss of E3-ligase function of PRKN are two key features observed in Parkinson disease (PD). Here, we established the contribution of an E3-ligase-independent transcriptional function of PRKN in SNCA regulation. PRKN depletion decreased SNCA and GBA1 (glucosylceramidase beta 1) mRNA levels and reduced CMA-driven degradation of SNCA, thereby triggering the accumulation of its phosphorylated aggregation-prone toxic species. We established that PRKN controls the CMA player LAMP2A but not HSPA8/HSC70 in isolated lysosomal fractions prepared from human neuronal and mouse fibroblastic cells. Further, we showed that PRKN-associated regulation of LAMP2 is isoform specific. We showed that PRKN-mediated control of SNCA, GBA1 and LAMP2A occurs in vivo and is impaired in the paraquat-treated PD mice model. We showed that the levels of phosphorylated SNCA and PRKN are correlated in sporadic PD human brain samples and that fibroblasts of patients carrying pathogenic PRKN mutations exhibit impaired CMA activity. Our study decrypts a new molecular mechanism linking three PD major therapeutic targets. It enriches the portfolio of transcriptional targets of PRKN and establishes PRKN as a novel CMA regulator. Further, it shows that PRKN controls both direct and indirect (GBA1-dependent) transcriptional regulation of SNCA. This novel molecular cascade opens potential new avenues in PD treatment.
    Keywords:  GBA1 and SNCA gene regulation; PRKN role in CMA; PRKN transcription factor function and transcriptional regulation; in vivo studies
    DOI:  https://doi.org/10.1080/15548627.2026.2669458
  19. NPJ Dement. 2026 ;2(1): 35
      Lysosomes, central to protein and organelle homeostasis in all cells, have more recently been recognized as critical to other cellular processes, including nutrient sensing, cell metabolism, immune response, and programmed cell death. Tied into these varied functions, their composition as well as location within cells, lysosomes are now recognized to be made of heterogeneous subpopulations. Mechanisms that build and help maintain lysosome heterogeneity, its role in cell physiology, and links to pathologies are only now being worked out. Lysosome dysfunction has been associated with the pathogenesis of several neurodegenerative diseases. Neurons, which are particularly sensitive to lysosome dysfunction, are perhaps where lysosome biogenesis and transport, as well as its heterogeneity, are best studied in the nervous system. However, there is a growing interest in understanding lysosomal biogenesis and trafficking in other cell types of the nervous system, including microglia. In this review, we focus on key studies that have shed insight into microglial lysosome biology: its regulation, composition, and function, and how these properties are linked to immune activation, aging, and certain disease pathologies.
    Keywords:  Cell biology; Immunology; Neuroscience
    DOI:  https://doi.org/10.1038/s44400-026-00086-8
  20. Front Immunol. 2026 ;17 1732775
      This review systematically summarizes the central roles and molecular mechanisms of the cytoskeletal system-including actin filaments, microtubules (MT), intermediate filaments, and the Septin family-in the regulation of autophagy. The cytoskeleton not only provides a structural framework and facilitates transport for the autophagic process but also acts as a dynamic signaling hub, participating in every stage from autophagosome formation and cargo recognition to targeted trafficking and autophagosome-lysosome fusion. Actin filaments regulate the initiation of autophagy through dynamic assembly, Arp2/3-mediated nucleation, and mechanosensing. Microtubules drive the transport and localization of autophagosomes by relying on "dynamic instability" and the "tubulin code". Intermediate filaments-such as vimentin-and septins influence autophagy flux by maintaining organelle integrity, forming molecular scaffolds, and establishing diffusion barriers on membranes. This review further discusses the functional implications of this regulatory network in diverse physiological and pathological neuroimmune contexts, including neurodegeneration and aging. Finally, we highlight that targeting the cytoskeleton-autophagy interaction axis may offer novel therapeutic strategies for related diseases.
    Keywords:  actin filaments; autophagy; intermediate filaments; microtubules; septins
    DOI:  https://doi.org/10.3389/fimmu.2026.1732775
  21. Mol Genet Metab. 2026 Apr 16. pii: S1096-7192(26)00413-0. [Epub ahead of print]148(2): 110130
      Deficiency of tripeptidyl-peptidase 1 (TPP1; EC 3.4.14.9), a lysosomal enzyme encoded by the CLN2 gene, is associated with the lysosomal storage disorder - classic late infantile neuronal ceroid lipofuscinosis (CLN2 disease). The classic form of CLN2 disease leads to the accumulation of autofluorescent lysosomal storage and a massive loss of neurons with gliosis in the brain. The major component of the storage is subunit c of mitochondrial ATP synthase, a highly hydrophobic, 75-aminoacid polypeptide. We developed an in vitro model of CLN2 disease by knocking out CLN2 in the human neuroblastoma cells SH-SY5Y by using CRISPR/cas9 technology. We focused on defining the pattern of deposition of subunit c, factors contributing to subunit c accumulation, and subcellular morphometry to identify differences between the model cells knockout (KO) and controls. Implementation of acetone for cell fixation allowed us to: i. identify higher levels of subunit c in the mitochondria of KO cells than controls; ii. characterize in detail subunit c inclusions, also present in controls; iii. identify other mitochondrial proteins colocalizing with subunit c in inclusions; and iv. detect mitochondrial pathology in degenerating cells often accompanied by deposition of subunit c. Differentiation of cells with retinoic acid and brain-derived neurotrophic factor led to a substantial increase in the levels of subunit c and to significant differences in the levels of autophagy-related proteins between KO and control cells. Inhibition of induced autophagy by bafilomycin A1 (Baf.A1) decreased subunit c levels in controls but not in KO cells, whereas the levels of subunit c were unaffected by Baf.A1 treatment upon basal autophagy. Finally, subcellular morphometry showed differences in the number and size of vesicular structures immunostained for autophagy-related proteins between KO cells and controls upon both induced and basal autophagy, further supporting the association of TPP1 deficiency with autophagy.
    Keywords:  Autophagy; Bafilomycin A1; CLN2 disease model; Human neuroblastoma SH-SY5Y cells; RA/BDNF; Subunit c of mitochondrial ATP synthase
    DOI:  https://doi.org/10.1016/j.ymgme.2026.110130
  22. Acta Neuropathol. 2026 May 03. pii: 52. [Epub ahead of print]151(1):
      Lipofuscin is an autofluorescent material that accrues in brain tissues with age and in Neuronal Ceroid Lipofuscinosis (NCL), a neurodegenerative disease with pediatric onset. The distribution, composition, and organellar origin of lipofuscin have remained unclear despite its widespread presence in aged tissues and involvement in neurodegeneration. Here, we elucidate lipofuscin composition in mouse and human brain and assemble a reference neuroanatomical atlas of lipofuscin accumulation with age and NCL (Type 1; CLN1) progression across 425 fine brain regions. We identify a primary role of the lysosomal-mitochondrial axis in the formation of lipofuscin pathology via multimodal mass spectrometry, ultrastructural analyses, and assays of cellular and enzymatic metabolism. We find the protein and lipid composition of lipofuscin in the aged and CLN1 brain to be remarkably similar. Dissection of implicated molecular pathways reveals protein S-acylation and unsaturated lipid homeostasis as central processes involved in lipofuscin deposition during aging and CLN1. Notably, > 95% of lipofuscin resident proteins can be S-acylated and many are substrates of the enzyme PPT1, validating a seminal hypothesis that CLN1 lipofuscin contains these lipid-modified proteins. Further, we discover deficient de-S-acylation is correlated with lipofuscin load in healthy aging, as the specific de-S-acylation enzyme activity of PPT1 is found to decline with advancing age. Finally, we identify lipid metabolite biomarkers of lipofuscin, including long-chain polyunsaturated fatty acids, bis(monoacylglycerol)phosphate (BMP), and oxidized phosphatidylethanolamine (OxPE) lipid species. Overall, we provide a comprehensive redefinition of lipofuscin neuropathology and a resource for studying aging, lysosomal storage disorders, and neurodegeneration.
    Keywords:   CLN1 ; Aging; Autofluorescence; Lipid homeostasis; Lipofuscin; Lysosomal storage disorder; Mitochondria-lysosome axis; Neurodegeneration; Neuronal Ceroid Lipofuscinosis; Palmitoyl protein thioesterase 1; S-acylation
    DOI:  https://doi.org/10.1007/s00401-026-03012-7
  23. Biomedicines. 2026 Apr 02. pii: 812. [Epub ahead of print]14(4):
      Background/Objectives: Autophagy is an evolutionarily conserved degradation and recycling pathway through which cells deliver cytoplasmic components, including toxic or damaged proteins and organelles, to lysosomes for clearance. In neurons, which are largely post-mitotic, degradative pathways are essential to prevent the accumulation of cellular waste and to maintain nutrient and energy homeostasis. Increasing evidence suggests that autophagy plays a critical role during early brain development, when neuronal circuits are established, synaptic connections are refined, and activity-dependent mechanisms shape network architecture. However, the developmental regulation of autophagy-related genes and the composition of the autophagic machinery at synapses remain poorly understood. This study aimed to characterize the maturation-dependent dynamics of autophagy-lysosomal genes and to investigate the synaptic autophagy-associated proteome during cortical development. Methods: Genome-wide transcriptomic analyses were performed in the cortical brain region across developmental stages to assess changes in the expression of autophagy-lysosomal genes. In parallel, synaptosomes were isolated and subjected to proteomic analysis to identify autophagy-related proteins associated with synaptic compartments. Results: Transcriptomic profiling revealed stage-dependent regulation of autophagy-lysosomal genes during cortical maturation. Proteomic analysis of synaptosomes identified multiple autophagy-associated proteins enriched at synaptic sites, suggesting that components of the autophagic machinery are present at synapses and may participate in synaptic remodeling and function during key phases of neuronal network formation. Conclusions: These findings provide new insights into the developmental regulation of autophagy in the brain and highlight the potential contribution of synaptic autophagy to neuronal circuit maturation. Understanding these mechanisms may help identify novel therapeutic targets for neurological disorders associated with impaired synaptic and cellular homeostasis.
    Keywords:  autophagy; cortical development; lysosome; proteomic; synapsis; transcriptomic
    DOI:  https://doi.org/10.3390/biomedicines14040812
  24. Cell Commun Signal. 2026 May 07.
       BACKGROUND: The amyloid β (Aβ) precursor C99 (or APP-βCTF) accumulates in Alzheimer's disease and has been proposed to display Aβ-independent toxicity, notably by affecting the endosomal-lysosomal-autophagic (ELA) network. Our previous findings suggested that some ELA-associated C99 could correspond to dimeric and oligomeric species, but the intracellular sites of C99 dimerization, as well as the toxicity linked to it, remains unknown.
    METHODS: We here developed a bimolecular fluorescence complementation (BiFC) probe to visualize de novo C99 dimerization and dimer trafficking, as well as to identify possible cellular responses specifically linked to C99 dimerization. Moreover, to confirm dimer localizations and toxicities, the localization and cellular effects of the dimerization mutant C99G29L/G33L was compared to that of wildtype C99. The C99 constructs were transfected into HeLa cells and dimer localizations, expression levels and intracellular toxicities were evaluated by Western blot and immunocytochemistry.
    RESULTS: BiFC-C99 dimers were first detected within the TGN, in which monomers initially accumulate. The proteasomal inhibitor MG-132 led to increased dimer formation, indicating that the proteasomal activity status is a key determinant of C99 dimerization. Conversely, TGN-associated C99 dimerization had a negative impact on both the ubiquitin-proteasome system (UPS) and the TGN, as highlighted by the appearance of p62/SQSTM1-positive aggresomes and fragmented Golgi, then suggesting a two-way relationship between UPS function and C99 dimerization. Dimerization also led to lysosome repositioning and to the accumulation of LC3B-positive autophagy vesicles, agreeing with the well-known interplay between autophagy and proteasome in protein turnover. P62/SQSTM1 and LC3B accumulation could similarly be observed in cells expressing C99G29L/G33L, a mutant favoring dimerization, while this was not the case in wildtype C99 expressing cells, confirming the dimerization-specific effect. While proteasomal inhibition caused TGN-associated dimer formation, repression of γ-secretase-mediated C99 proteolysis instead led to a redistribution of monomers to EEA1-positive endosomes, whereas already existing C99 dimers remained unaffected by this treatment. These new endosome-associated monomers were found also to dimerize, resulting in dimers destined for either secretion via small extracellular vesicles or autophagy-lysosomal degradation.
    CONCLUSIONS: Taken together, our findings indicate that the cellular status of UPS, autophagy and γ-secretase activities are all determinant for C99 expression levels, and are thus crucial for both the level of C99 dimerization and for the fate of the dimers. Moreover, our data show that C99 dimerization itself negatively affects these activities thereby indicating a two-way relationship between C99 dimerization, proteostasis disruption and organelle dysfunction.
    Keywords:  Aggresomes; Autophagy; BiFC; C99 dimerization; C99 dimerization mutant; Endosome-lysosome-autophagy compartments; Golgi fragmentation; Small extracellular vesicles; Ubiquitin-proteasome
    DOI:  https://doi.org/10.1186/s12964-026-02928-7
  25. Mol Brain. 2026 May 08.
      Cohen syndrome (CS) is a rare autosomal recessive neurodevelopmental disorder characterized by intellectual disability, microcephaly, retinal dystrophy, and neutropenia. We previously demonstrated that VPS13B mediates phosphatidylinositol 4-phosphate (PI4P) transport to promote mitochondrial fission. Here, we identify VPS13B as a regulator of lysosomal homeostasis. VPS13B knockout (KO) HeLa cells exhibited aberrant lysosomal distribution and reduction in LAMP1-positive lysosomes. Bulk RNA sequencing revealed coordinated downregulation of lysosome-related genes, including genes required for acidification and lysosome biogenesis, which was confirmed by quantitative RT-PCR. Consistent with these transcriptional changes, VPS13B KO significantly reduced the abundance of LysoTracker-positive acidic compartments. Induced neurons derived from CS patient iPSCs recapitulated the loss of acidic lysosomal compartments, supporting disease relevance. Mechanistically, VPS13B KO altered TFEB mRNA levels and modestly increased the basal nuclear-to-cytoplasmic (N/C) ratio of endogenous TFEB, but blunted its further increase upon Torin1 treatment. Together, these findings identify VPS13B as a regulator of lysosomal homeostasis and provide insight into how VPS13B deficiency may contribute to Cohen syndrome pathology.
    Keywords:  Cohen syndrome; Lysosomal acidification; Lysosome; Neurodevelopmental disorder; TFEB; VPS13B
    DOI:  https://doi.org/10.1186/s13041-026-01309-y
  26. bioRxiv. 2026 Apr 25. pii: 2026.04.22.720209. [Epub ahead of print]
      How protein quality control is maintained during acute metabolic stress remains poorly understood. In budding yeast, abrupt glucose depletion rapidly lowers ATP levels and leads to the formation of chaperone-containing inclusions, suggesting that ATP-dependent degradation of misfolded proteins may be compromised when energy becomes limiting. Here we find that selective degradation of misfolded proteins remains active during acute glucose starvation despite reduced cellular ATP levels. Using model misfolded substrates in yeast Saccharomyces cerevisiae , we show that misfolded proteins continue to be efficiently degraded throughout both early and late phases of acute glucose depletion. This degradation requires the proteasome and depends on its functional 19S regulatory particle, indicating that ATP-dependent proteasomal activity persists during metabolic stress. We further find that nucleus-vacuole junctions (NVJs) promote efficient degradation during prolonged glucose starvation, revealing a role for organelle contact sites in supporting proteostasis under energy limitation. Together, these findings indicate that cells preserve proteasome-mediated proteostasis during acute glucose starvation, while NVJ membrane contact sites help sustain degradation capacity when metabolic resources are scarce.
    DOI:  https://doi.org/10.64898/2026.04.22.720209
  27. Int J Biol Macromol. 2026 May 01. pii: S0141-8130(26)02158-6. [Epub ahead of print] 152231
       BACKGROUND: Autophagy and apoptosis co-regulate the fate of cardiomyocytes after myocardial infarction (MI). OPTN is a well-characterized autophagy inducer, while FABP3 promotes apoptosis. However, the functional interaction between the two in MI remained unclear.
    METHOD: A rat MI model was established by left anterior descending coronary artery ligation, with electrocardiography for model validation and echocardiography for cardiac function assessment. Molecular expression was analyzed via immunofluorescence. AC16 cardiomyocytes were subjected to oxygen-glucose deprivation (OGD), with plasmid transfection to modulate OPTN and expression. Rapamycin (RAPA) and Baf A1 were used for autophagy modulation. Cell viability, apoptosis, protein expression, intracellular reactive oxygen species (ROS), and mitochondrial membrane potential (MMP) were measured by cellular assays.
    RESULT: MI caused significant downregulation of OPTN and upregulation of FABP3 in cardiac tissue. OPTN overexpression improved cardiac function, increased left ventricular ejection fraction (LVEF) and fractional shortening (LVFS), reduced infarct size, attenuated myocardial fibrosis and oxidative stress, and suppressed cardiomyocyte apoptosis. OPTN overexpression enhanced autophagic activity, manifested by elevated Beclin-1 and LC3I/II, alongside decreased p62. FABP3 overexpression inhibited autophagy and promoted apoptosis, counteracting the OPTN-mediated cardioprotective effect. RAPA reversed FABP3-induced injury, while Baf A1 attenuated OPTN-mediated protection. In vitro, OPTN protected cardiomyocytes by enhancing autophagic flux through reducing ROS and maintaining MMP in OGD-exposed cells.
    CONCLUSION: OPTN and FABP3 formed a functional antagonistic axis in MI. OPTN exerted cardioprotective effects by enhancing autophagy, whereas FABP3 suppressed autophagy and promoted apoptosis, thereby counteracting OPTN's protective effects. Targeting OPTN/FABP3 axis to restore autophagy-apoptosis balance might be a novel therapeutic strategy.
    Keywords:  Apoptosis; Autophagy; FABP3; Myocardial infarction; OPTN; Oxidative stress
    DOI:  https://doi.org/10.1016/j.ijbiomac.2026.152231
  28. Front Immunol. 2026 ;17 1720544
      Autophagy functions as a context-dependent stress adaptation pathway in T cells; however, its role in sustaining chimeric antigen receptor (CAR)-T cell function within solid tumor environments remains insufficiently defined. In this study, we investigated whether ATG5-mediated autophagy regulation contributes to CAR-T cell functional durability under tumor-associated stress conditions. ATG5 overexpression (OE) CAR-T cells did not increase basal autophagy activity but instead selectively enhanced autophagy flux in response to inducible stimuli. Under tumor-mimicking immunosuppressive conditions, ATG5 OE CAR-T cells maintained cytotoxic activity during prolonged antigen exposure and exhibited preserved effector cytokine production together with reduced oxidative stress. Consistent with these in vitro findings, ATG5 OE CAR-T cells exhibited enhanced antitumor efficacy in vivo under IR-preconditioned settings, characterized by improved tumor control and survival, which was associated with sustained effector function of tumor-infiltrating CAR-T cells. Collectively, these findings demonstrate that reinforcing inducible autophagy capacity through ATG5 promotes the maintenance of CAR-T cell function under tumor-associated challenges, highlighting a targeted strategy to enhance CAR-T cell persistence in solid tumor immunotherapy.
    Keywords:  ATG5 overexpression; CAR-T cell therapy; CAR-T persistence; autophagy; tumor microenvironment
    DOI:  https://doi.org/10.3389/fimmu.2026.1720544
  29. Life Sci Alliance. 2026 Jul;pii: e202503536. [Epub ahead of print]9(7):
      ER stress underlies numerous severe pathologies. We have metabolically perturbed normal fibroblasts to study the biological roles of microRNAs (miRs) under mild and extended ER stress. We now report that miR-4488 quenches inflammation-associated gene expression in such metabolically perturbed cells. Remarkably, generation of miR-4488 is Drosha-independent. Furthermore, we define miR-4488 as a noncanonical miRNA derived from the expansion segment ES7L of the 28S ribosomal RNA. Moreover, its generation involves the autophagy-lysosome route and is inhibited when this pathway is blocked, thus unveiling an anti-inflammatory role for ribosomal RNA and lysosomes, engaged at the onset of stress. Mechanistically, miR-4488 suppresses the expression of NFKB2 and RELB, whose mRNAs specifically associate with miR-4488 exclusively upon stress. This selectivity suggests that miR-4488 may bear promise for treating mild ER stress-associated diseases.
    DOI:  https://doi.org/10.26508/lsa.202503536
  30. Pharmacology. 2026 May 08. 1-25
       INTRODUCTION: Diabetic cardiomyopathy (DCM) involves myocardial injury under hyperglycemia, where impaired autophagy and oxidative stress play critical roles. This study explores whether Sappanone A (a natural compound) alleviates DCM by activating TFEB-mediated lysosomal autophagy.
    METHODS: In vitro: H9c2 cardiomyocytes were injured with high glucose and treated with Sappanone A. Cell viability (CCK-8), apoptosis (flow cytometry), ROS (DCFHDA), and autophagy markers (LC3-II/I, p62, LAMP1 via WB/qPCR) were assessed. In vivo: STZ-induced DCM mice received Sappanone A (10 mg/kg/day, 8 weeks). Cardiac function (echocardiography), serum ANP/BNP (ELISA), histopathology (H&E/Masson), and autophagy flux (TFEB/LAMP1) were analyzed. TFEB-knockout models and chloroquine (CQ, autophagy inhibitor) validated mechanistic links.
    RESULTS: Sappanone A dose-dependently enhanced HG-injured cardiomyocyte survival, reduced apoptosis and ROS, while upregulating TFEB nuclear translocatiandlysosomal function.In DCM mice, it improved ejection fraction, reduced fibrosis, and restored autophagic flux.These effects were abolished in TFEB-knockout models or with CQ co-treatment, confirming TFEB-dependent autophagy as the core mechanism.
    CONCLUSION: Sappanone A protects against DCM by activating TFEB-driven lysosomal autophagy, mitigating oxidative stress, and preserving cardiac function. It represents a novel therapeutic candidate for DCM.
    DOI:  https://doi.org/10.1159/000551971
  31. bioRxiv. 2026 Apr 23. pii: 2026.04.20.719647. [Epub ahead of print]
      The cellular environment plays a critical role in shaping protein conformations, including aggregated states implicated in disease. One challenge to studying this relationship is that most techniques offering high-resolution insight into the nature of these aggregates cannot be deployed in living cells. Systematic mutagenesis presents an opportunity to bridge this gap but requires general and robust methods to detect protein aggregation across large numbers of variants. Here, we use clickable protein tags to generate FRET pairs in situ that can report protein aggregation in high throughput in living cells. We applied this strategy to probe the nature of cellular inclusions of α-synuclein in a popular yeast model. Our results demonstrate that cellular aggregates of α-synuclein in yeast are likely dominated by protein-membrane interactions, making the aggregation pathway in this cellular model very different than in many in vitro experiments. Furthermore, our comprehensive mutational data reveal the molecular determinants of membrane-induced aggregation. For example, residues that control membrane affinity have a profound effect on membrane-induced aggregation both in vitro and in cells. Furthermore, we discovered that glycine residues, particularly in the central region of the protein, act as gatekeepers to reduce membrane-induced aggregation. Mutational scanning with a clickable protein tag therefore provides high-resolution insights into cellular protein aggregates.
    DOI:  https://doi.org/10.64898/2026.04.20.719647
  32. Free Radic Biol Med. 2026 May 05. pii: S0891-5849(26)00478-8. [Epub ahead of print]252 132-149
      TAR DNA-binding protein 43 (TDP43) aggregation is a well-established pathological hallmark of amyotrophic lateral sclerosis (ALS) and related neurodegenerative disorders, contributing significantly to oxidative stress and neuronal injury. Here, we report that the M337V mutation in TDP43 exacerbates its proteotoxicity relative to the wild-type protein. Concurrently, multi-omics analysis revealed a pronounced downregulation of TRIM16 in motor neuron-like cells expressing either wild-type or M337V mutant TDP43. Functional studies demonstrated that TRIM16 overexpression effectively mitigated oxidative stress, restored mitochondrial integrity, and suppressed ferroptosis. Mechanistically, TRIM16 promoted the ubiquitination and degradation of Keap1, thereby facilitating the activation of Nrf2-mediated antioxidant genes. Furthermore, we identified the iron import receptor TFR1 as a novel ubiquitination substrate of TRIM16. TRIM16 mediated the ubiquitination of TFR1 and targeted it for p62-dependent autophagic degradation, which in turn reduced iron accumulation and lipid peroxidation. Collectively, our findings establish TRIM16 as a pivotal suppressor of TDP43-induced toxicity by orchestrating dual cytoprotective pathways to enhance cellular resilience, highlighting its promising therapeutic potential for TDP43 proteinopathy.
    Keywords:  Autophagy; Ferroptosis; Mitochondrial dysfunction; Nrf2; Oxidative stress; TDP43; TRIM16; Transferrin receptor 1
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2026.05.014
  33. Sci Adv. 2026 May 08. 12(19): eadz0196
      Noncanonical conjugation of ATG8 proteins, including LC3, to single membranes implicates the autophagy machinery in cell functions unrelated to metabolic stress. One such pathway is LC3-associated phagocytosis (LAP), which aids in phagosome maturation and subsequent signaling upon cargo uptake mediated by certain innate immunity-associated receptors. Here, we show that a specific isoform of RAB5 GTPases, the molecular switches controlling early endosome traffic, is necessary for LAP. We demonstrate that RAB5c regulates phagosome recruitment and function of complexes required for phosphatidylinositol 3-phosphate [PI(3)P] and reactive oxygen species (ROS) generation by macrophages. RAB5c facilitates phagosome translocation of the V-ATPase transmembrane core, which is needed for ATG16L1 binding and consequent LC3 conjugation. RAB5c depletion impaired macrophage elimination of the fungal pathogen Aspergillus fumigatus and disruption of the V-ATPase-ATG16L1 axis increased susceptibility in vivo. Thus, early endosome-to-phagosome trafficking can be selectively engaged to promote pathogen elimination by directing phagosomal maturation toward LAP.
    DOI:  https://doi.org/10.1126/sciadv.adz0196
  34. bioRxiv. 2026 Apr 25. pii: 2026.04.24.719390. [Epub ahead of print]
      Parkinson's disease (PD) is commonly associated with dysfunctional mitochondrial homeostasis. PINK1, a S/T kinase mutated in early-onset PD, generates phosphoserine 65 ubiquitin (pS65Ub) on damaged mitochondria facilitating their removal. Here, we show that pS65Ub translocates into the nucleus after generation at damaged mitochondria and is directly attached to substrates by resident E3 ligases. Histone H2A is a major substrate and is modified at lysine 119 (H2AK119) by the polycomb silencer, E3 ligase RING1B. At nucleosomes, pS65Ub simultaneously suppresses RING1B and potentiates H2A deubiquitinases USP16 and USP21. Epigenetic profiling and RNA sequencing reveal that pS65Ub is enriched at the promoters of poorly expressed yet dynamically regulated genes and is associated with H2AK119ub depletion. Functionally, we show that pS65Ub enrichment drives polycomb target gene expression, which accelerates the maturation of dopaminergic neurons. Importantly, post-mortem PD brains exhibit elevated nuclear pS65Ub, potentially linking nuclear pS65Ub accumulation with disease pathogenesis. Together, these data indicate that pS65Ub generated at damaged mitochondria regulates fundamental cellular processes at distant sites.
    DOI:  https://doi.org/10.64898/2026.04.24.719390
  35. J Neural Transm (Vienna). 2026 May 04.
      Retinal degenerative diseases range from rare inherited forms to common multifactorial disorders such as age-related macular degeneration, which is the leading cause of blindness in developed countries. Recent evidence identifies impaired autophagy as a key pathogenetic mechanism. In the disease process alterations of the outer retina start from the retinal pigment epithelium (RPE), to progress downstream in the inner retina leading to widespread whole retinal degeneration. Recent studies indicate that among autophagy-related proteins Beclin1 plays a relevant effect in sustaining retinal integrity, since it is induced by light exposure and it is placed at the intersection between mitophagy, lipophagy, and glycophagy, which are involved during retinal degeneration. The present study was carried out by profiting of BECN1 heterozygous aged mice (BECN+/-), where RT-PCR and western blotting analysis confirmed the loss of both the primary transcript (BECN1) and protein (Beclin1) in the whole retina. Multiple converging techniques indicate a marked degeneration of RPE and photoreceptor layer, where a dismantling of proteins forming tight junction was documented. Inner retinal degeneration was extended within outer and inner nuclear layer. In the inner retina the expression of the detrimental protein alpha synuclein was increased concomitantly with a defect of autophagy markers. The study indicates a seminal role of Beclin1 in maintaining retinal integrity and it defines the vulnerability of various retinal layers in the spreading of Beclin1-dependent retinal degeneration. The potential of increasing the expression of Beclin1 through photobiomodulation is discussed, since it supports retinal integrity when amber/red light-induced stimulation occurs.
    Keywords:  AMD; Beclin1; Photobiomodulation; RPE65; Retinal degenerative disorders; ZO1
    DOI:  https://doi.org/10.1007/s00702-026-03166-4
  36. Biochim Biophys Acta Proteins Proteom. 2026 May 06. pii: S1570-9639(26)00026-9. [Epub ahead of print] 141149
      Chronic infection with hepatitis B virus (HBV) remains a global health issue, leading to liver diseases such as chronic hepatitis B, cirrhosis, and hepatocellular carcinoma. The HBV X protein (HBx) promotes viral replication and disease progression by interacting with various host proteins. One of its functions involves binding to microtubule-associated protein 1 light chain 3B (LC3B), which mediates selective autophagy and facilitates the removal of the immune-related protein TNFRSF10B (tumor necrosis factor receptor superfamily 10B). However, even the mechanism by which HBx interacts with LC3B remained unclear. In this study, we focused on the HBx-LC3B interaction as a first step and identified a conserved LC3-interacting region motif (Trp120-X-X-Leu123) within the Bcl-2 homology 3 (BH3)-like domain of HBx that directly binds to LC3B. This interaction was characterized using isothermal titration calorimetry and nuclear magnetic resonance (NMR) spectroscopy. We present the first NMR structure of LC3B in complex with the HBx BH3-like peptide, revealing that it adopts an extended conformation upon binding and that Trp120 and Leu 123 are essential for LC3B recognition. Notably, the same portion forms an α-helix when binding to B-cell lymphoma 2 (Bcl-2) and B-cell lymphoma extra-large (Bcl-xL), suggesting that HBx uses different conformations to interact with distinct targets. This structural plasticity may underlie the multifunctional roles of HBx.
    Keywords:  Autophagy; Complex structure; HBx; LC3B; NMR
    DOI:  https://doi.org/10.1016/j.bbapap.2026.141149
  37. EMBO J. 2026 May 02.
      Lysosomes and peroxisomes are essential for cellular homeostasis, yet how their activities are coordinated remains poorly understood. Here, we identify peroxisome-derived ether lipids as key regulators of lysosomal function. A genome-wide CRISPR/Cas9 screen in LYSET-deficient mucolipidosis V cells revealed that disruption of ether lipid synthesis genes or peroxins markedly reduces lysosome accumulation and restores degradative capacity. Genetic or pharmacological inhibition of ether lipid synthesis enhanced lysosomal exocytosis and promoted the clearance of undigested material independently of mannose-6-phosphate trafficking. Conversely, supplementation with the ether lipid precursor hexadecylglycerol increased lysosome abundance, while reducing their degradative capacity. These findings uncover a peroxisome-lysosome metabolic axis, in which ether lipids act as bidirectional regulators of lysosomal number and function independently of the lysosomal master regulator TFEB. Our findings reveal how peroxisome-localized lipid metabolism modulates lysosomal homeostasis, and suggest potential new strategies to combat lysosomal and peroxisomal disorders.
    DOI:  https://doi.org/10.1038/s44318-026-00791-3
  38. Biomolecules. 2026 Mar 25. pii: 492. [Epub ahead of print]16(4):
      Neurodegenerative diseases feature diverse pathological protein aggregates, including Lewy bodies in Alzheimer's disease (AD) and skein-like filaments in amyotrophic lateral sclerosis (ALS). The physical mechanisms underlying this morphological diversity remain unclear. Here, we demonstrate that aggregation of the prion-like domain of hnRNPA1 (A1PrD), implicated in AD and ALS, is driven by solution composition and phase transition dynamics. Utilizing 3D timelapse and fluorescence lifetime imaging microscopy, we show that solution conditions modulate phase separation, gelation, and fibrillation, resulting in distinct structures such as fibril, gel, and starburst morphologies. Homotypic and heterotypic interactions between A1PrD and RNA were observed to shift the balance between pathological and physiological condensates. Importantly, amyloid-rich starbursts displayed prion-like infection capabilities toward amyloid-poor condensates. Our findings highlight how the interplay between solution composition and kinetic balances of liquid-liquid phase separation, gelation, and fibrillation shapes the diverse pathological aggregate morphologies characteristic of neurodegenerative diseases.
    Keywords:  ALS; Alzheimer’s disease; FLIM; LLPS; aggregation; biomolecular condensates; fibrillation; hnRNPA1; phase transitions; prion-like domain
    DOI:  https://doi.org/10.3390/biom16040492
  39. Biochem Biophys Rep. 2026 Jun;46 102613
      While pharmacological inducers of autophagy have been extensively studied, their systemic adverse effects may limit clinical use. Increasing preclinical evidence suggests that magnetic fields (MFs) can represent a non-invasive alternative for autophagy modulation. In this systematic review, we sought to evaluate preclinical evidence on MF-mediated autophagy activation, including intervention parameters, mechanistic pathways, and therapeutic outcomes, to guide future translational research. Following PRISMA guidelines, we searched (January 2010-August 2025) four structured electronic databases (PubMed, Scopus, Embase, and IEEE Xplore) for studies investigating MF effects on autophagy in preclinical models. Eligible reports included in vitro and animal investigations with clearly defined MF parameters and validated autophagy markers. Nine studies met inclusion criteria, covering diverse MF modalities such as repetitive transcranial magnetic stimulation, rotating fields, pulsed and power-frequency fields, and radiofrequency exposures. Across a wide range of frequencies (1-50 Hz) and intensities (20 mT-1.5 T), most studies reported autophagy activation, as evidenced by LC3-II accumulation, Beclin-1 upregulation, p62 degradation, and autophagic flux confirmation in select experimental models. Mechanistic analyses converged on PI3K/AKT/mTOR inhibition. Functionally, MF-induced autophagy conferred neuronal protection and drove behavioral recovery in models of Alzheimer's disease, vascular dementia, and stress, whereas it triggered autophagic cell death in cancer. Some studies reported incomplete flux or autophagosome accumulation. Risk of bias was generally unclear due to methodological heterogeneity. In summary, preclinical evidence indicates that MFs can act as versatile, non-pharmacological activators of autophagy. Defining optimal stimulation parameters, clarifying mechanistic pathways, and advancing translational studies will be essential for clinical application.
    Keywords:  Autophagy; Cancer; Magnetic fields; Neurodegenerative diseases; Preclinical models; Repetitive transcranial magnetic stimulation
    DOI:  https://doi.org/10.1016/j.bbrep.2026.102613
  40. Autophagy. 2026 May 06. 1-16
      Di(2-ethylhexyl) phthalate (DEHP) is a widely used industrial plasticizer, raising global concerns due to its potential endocrine-disrupting effects and environmental persistence. Human exposure to DEHP primarily occurs through the ingestion of contaminated food and water, inhalation of airborne particles, and dermal contact with products containing DEHP. Understanding the toxicological mechanisms of DEHP is essential for evaluating its health risks and developing effective strategies to mitigate its adverse effects. In this study, we conducted long-term exposure experiments to DEHP using both an animal model and in vitro system to investigate the complex interplay among DNA methylation, hyperactivation of macroautophagy/autophagy, mitochondrial dysfunction, and lipid accumulation induced by DEHP. The results revealed that DEHP exposure induced the degradation of DNMT1 (DNA methyltransferase 1) by enhancing its interaction with the autophagy-related protein SQSTM1 (sequestosome 1). DNMT1 degradation resulted in decreased methylation of the promoter regions of genes associated with autophagosome formation, subsequently increasing their expression. The resulting demethylation excessively activated autophagy, contributing to mitochondrial dysfunction and lipid accumulation in the liver. This study uncovered a previously unrecognized interplay among hyperactivation of autophagy, mitochondrial dysfunction, and lipid accumulation in the context of DEHP exposure. These findings enhanced our understanding of DEHP's toxicity and underscored concerns about the long-term health effects of environmental pollutants, particularly regarding metabolic diseases.Abbreviation: ATG5:autophagy related 5; ATG16L1: autophagy related 16 like 1; BECN1:beclin 1; COX4/COXIV: cytochrome c oxidase subunit 4; BS-seq:bisulfite sequencing; DCFH-DA: 2',7'-dichlorodihydrofluoresceindiacetate; DEHP: di(2-ethylhexyl) phthalate; DNMT1: DNAmethyltransferase 1; DNMT3A: DNA methyltransferase 3A; FABP4: fattyacid binding protein 4; FASN: fatty acid synthase; LPL: lipoproteinlipase; MAP1LC3/LC3: microtubule associated protein1 light chain 3; NAFLD: nonalcoholic fatty liver disease; NR1H3:nuclear receptor subfamily 1 group H member 3; PPARG: peroxisomeproliferator activated receptor gamma; RB1CC1: RB1 induciblecoiled-coil 1; SQSTM1: sequestosome 1; SREBF2: sterol regulatoryelement binding transcription factor 2; VDAC1: voltage dependentanion channel 1.
    Keywords:  Autophagy; DEHP; DNA methylation; lipid accumulation; mitochondrial dysfunction
    DOI:  https://doi.org/10.1080/15548627.2026.2668651
  41. Res Sq. 2026 Apr 30. pii: rs.3.rs-9337412. [Epub ahead of print]
      According to the prevalent 'Amyloid Hypothesis,' the underlying cause for neurodegeneration in Alzheimer Disease (AD) is attributed to the accumulation of misfolded Amyloid ß and tau protein in the form of extracellular sticky plaques and neurofibrillary tangles, respectively. These protein accumulations are thought to be caused by impaired waste removal. In an alternative hypothesis, we have proposed the existence of an extensive glial canal system that is likely formed by myelinated aquaporin-4 (AQP4)-expressing tanycytes and removes cellular waste from the hippocampal formation. Here, we demonstrate that tanycyte-derived waste-internalizing receptacles are immunoreactive for Aß and emanate from specialized nucleus-like organelles in the following referred to as 'tanysomes.' Utilizing RNA-scope in situ hybridization, we demonstrate that these receptacle-forming tanysomes express RNA for AQP4 and the Aß-related genes, amyloid precursor protein, and presenilin-1. These findings suggest that Aß is likely synthesized where receptacle formation is observed and that Aß may play an important structural role in receptacle formation. In AD-affected hippocampus, excessive amounts of Aß-immunoreactive waste receptacles emerge from tanysomes and have the appearance of plaques in Aß-immunolabeled hippocampus. Moreover, we demonstrate that the same receptacle-forming organelles exhibit strong immunolabeling for hyperphosphorylated tau protein in AD-affected tissue. We postulate that both proteins may play important structural roles in waste uptake and that hypertrophic swelling of impaired tanycytes in AD-affected brain may be due to obstructions of this extensive interconnected glial canal system.
    DOI:  https://doi.org/10.21203/rs.3.rs-9337412/v1