bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2025–02–23
sixty papers selected by
Viktor Korolchuk, Newcastle University



  1. Proc Natl Acad Sci U S A. 2025 Feb 25. 122(8): e2415422122
      The cGAS-STING pathway mediates innate immune responses to cytosolic DNA. In addition to its well-established role in inducing inflammatory cytokines, activation of the cGAS-STING pathway also induces noncanonical autophagy, a process involving the conjugation of the ATG8 family of ubiquitin-like proteins to membranes of the endolysosomal system. The mechanisms and functions of STING-induced autophagy remain poorly understood. In this study, we demonstrated that STING activation induced formation of pH-elevated Golgi-derived vesicles that led to ATG16L1 and V-ATPase-dependent noncanonical autophagy. We showed that STING-induced noncanonical autophagy resulted in activation of the MiT/TFE family of transcription factors (TFEB, TFE3, and MITF), which regulate lysosome biogenesis. We found that lipidation of the ATG8 proteins, particularly GABARAPs, inhibited phosphorylation of MiT/TFE transcription factors by mTORC1. The lipidated GABARAPs bound to the Folliculin-interacting proteins (FNIPs), thereby sequestering the FNIP-folliculin protein complexes from activating mTORC1, resulting in dephosphorylation and nuclear translocation of MiT/TFE transcription factors. Furthermore, we found that STING-induced autophagy activated Leucine-rich repeat kinase 2 (LRRK2), a protein implicated in Parkinson's disease, through GABARAPs lipidation. We further showed that STING-induced autophagy induced ALIX-mediated ESCRT machinery recruitment to mitigate endolysosomal perturbation. These results reveal the multifaceted functions of STING-induced noncanonical autophagy in regulating endolysosomal homeostasis.
    Keywords:  ESCRT; STING; TFEB; autophagy; cGAS
    DOI:  https://doi.org/10.1073/pnas.2415422122
  2. J Vis Exp. 2025 Jan 31.
      Macroautophagy, commonly referred to as autophagy, is a highly conserved cellular process responsible for the degradation of cellular components. This process is particularly prominent under conditions such as fasting, cellular stress, organelle damage, cellular damage, or aging of cellular components. During autophagy, a segment of the cytoplasm is enclosed within double-membrane vesicles known as autophagosomes, which then fuse with lysosomes. Following this fusion, the contents of autophagosomes undergo non-selective bulk degradation facilitated by lysosomes. However, autophagy also exhibits selective functionality, targeting specific organelles, including mitochondria, peroxisomes, lysosomes, nuclei, and lipid droplets (LDs). Lipid droplets are enclosed by a phospholipid monolayer that isolates neutral lipids from the cytoplasm, protecting cells from the harmful effects of excess sterols and free fatty acids (FFAs). Autophagy is implicated in various conditions, including neurodegenerative diseases, metabolic disorders, and cancer. Specifically, lipophagy -- the autophagy-dependent degradation of lipid droplets -- plays a crucial role in regulating intracellular FFA levels across different metabolic states. This regulation supports essential processes such as membrane synthesis, signaling molecule formation, and energy balance. Consequently, impaired lipophagy increases cellular vulnerability to death stimuli and contributes to the development of diseases such as cancer. Despite its significance, the precise mechanisms governing lipid droplet metabolism regulated by lipophagy in cancer cells remain poorly understood. This article aims to describe confocal imaging acquisition and quantitative imaging analysis protocols that enable the investigation of lipophagy associated with metabolic changes in cancer cells. The results obtained through these protocols may shed light on the intricate interplay between autophagy, lipid metabolism, and cancer progression. By elucidating these mechanisms, novel therapeutic targets may emerge for combating cancer and other metabolic-related diseases.
    DOI:  https://doi.org/10.3791/67287
  3. mSphere. 2025 Feb 21. e0082924
      Macroautophagy is an important cellular process involving lysosomal degradation of cytoplasmic components, facilitated by autophagy-related proteins. In the protozoan parasite Toxoplasma gondii, autophagy has been demonstrated to play a key role in adapting to stress and the persistence of chronic infection. Despite limited knowledge about the core autophagy machinery in T. gondii, two PROPPIN family proteins (TgPROP1 and TgPROP2) have been identified with homology to Atg18/WIPI. Prior research in acute-stage tachyzoites suggests that TgPROP2 is predominantly involved in a non-autophagic function, specifically apicoplast biogenesis, while TgPROP1 may be involved in canonical autophagy. Here, we investigated the distinct roles of TgPROP1 and TgPROP2 in chronic stage T. gondii bradyzoites, revealing a critical role for TgPROP1, but not TgPROP2, in bradyzoite autophagy. Conditional knockdown of TgPROP2 did not impair bradyzoite autophagy. In contrast, TgPROP1 KO parasites had impaired autolysosome formation, reduced cyst burdens in chronically infected mice, and decreased viability. Together, our findings clarify the indispensable role of TgPROP1 to T. gondii autophagy and chronic infection.
    IMPORTANCE: It is estimated that up to a third of the human population is chronically infected with Toxoplasma gondii; however, little is known about how this parasite persists long term within its hosts. Autophagy is a self-eating pathway that has recently been shown to play a key role in parasite persistence, yet few proteins that carry out this process during T. gondii chronic infection are known. Here, we provide evidence for a non-redundant role of TgPROP1, a protein important in the early steps of the autophagy pathway. Genetic disruption of TgPROP1 resulted in impaired autophagy and chronic infection of mice. Our results reveal a critical role for TgPROP1 in autophagy and underscore the importance of this pathway in parasite persistence.
    Keywords:  Toxoplasma gondii; autophagy; bradyzoite; persistance
    DOI:  https://doi.org/10.1128/msphere.00829-24
  4. Autophagy. 2025 Feb 19. 1-3
      Stress granules (SGs) are transient, non-membrane-bound cytoplasmic condensates that form in response to environmental stresses, serving as protective reservoirs for mRNAs and proteins. In plants, SGs play a crucial role in stress adaptation, but their relationship with macroautophagy/autophagy, a key process for degrading damaged organelles and misfolded proteins, remains poorly understood. In a recent study, we revealed that key autophagy proteins, including components of the ATG1-ATG13 kinase complex, the class III phosphatidylinositol 3-kinase (PtdIns3K) complex, and the ATG8-PE system, translocate to SGs during heat stress (HS) in Arabidopsis thaliana. Using biochemical, cell biological and genetic approaches, we demonstrated that ATG proteins accumulate on HS-induced SGs and are released to the cytosol upon SG disassembly during the post-HS recovery stage. This process facilitates rapid autophagy activation. Notably, a SG-deficient mutant (ubp1abc) exhibits delayed autophagy activation and impaired clearance of ubiquitinated protein aggregates, highlighting the importance of SGs in regulating autophagy. Our findings uncover a novel mechanism by which SGs sequester autophagy proteins during stress, ensuring their rapid availability for stress recovery, and provide new insights into the interplay between SGs and autophagy in plant stress responses.Abbreviation: ATG, autophagy related; HS, heat stress; PtdIns3K, phosphatidylinositol 3-kinase; RBP47B, RNA-binding protein 47B; SG, stress granule; UBP1, ubiquitin-specific protease 1.
    Keywords:  ATG8; Arabidopsis thaliana; UBP1; autophagy; heat stress; stress granules
    DOI:  https://doi.org/10.1080/15548627.2025.2465395
  5. Neurosci Biobehav Rev. 2025 Feb 19. pii: S0149-7634(25)00069-7. [Epub ahead of print] 106069
      While many individuals with anorexia nervosa (AN) undergo remission of the disorder, a significant proportion will experience relapse and/or persistent symptoms. The persistence of AN is thought to be driven by changes in neural circuits that underline treatment-resistant symptoms (maladaptive plasticity). Recent evidence about the biology of AN suggests it extends beyond psychiatric symptoms to involve also systemic metabolic dysfunction, which is based on alterations of the mechanistic Target Of Rapamycin Complex 1 (mTORC1). In this review, we propose that AN's maladaptive plasticity and mTORC1 alterations involve norepinephrine (NE) nuclei, which spread neurobiological alterations concomitantly to the forebrain as well as to peripheral organs through the autonomic nervous system. In this review, we will present current evidence supporting this new perspective about the role of NE neurons in producing the psycho-metabolic dysfunction occurring in AN and discuss how it may inform more effective treatments for AN in the future.
    Keywords:  Autophagy; Brainstem; Hypothalamus; Metabolic syndrome; Norepinephrine; Reticular Formation; mTORC1
    DOI:  https://doi.org/10.1016/j.neubiorev.2025.106069
  6. Mol Biol Cell. 2025 Feb 19. mbcE24120535
      Cytoplasmic K63-linked polyubiquitin signals have well-established roles in endocytosis and selective autophagy. However, how these signals help to direct different cargos to different intracellular trafficking routes is unclear. Here we report that, when the K63-polyubiquitin signal is blocked by intracellular expression of a high-affinity sensor (named Vx3), many proteins originating from the plasma membrane are found trapped in clusters of small vesicles that co-localize with ATG9A, a transmembrane protein that plays an essential role in autophagy. Importantly, whereas ATG9A is required for cluster formation, other core autophagy machinery as well as selective autophagy cargo receptors are not required. Although the cargos are sequestered in the vesicular clusters in an ATG9-dependent manner, additional signals are needed to induce LC3 conjugation. Upon removal of the Vx3 block, K63-polyubiquitylated cargos are rapidly delivered to lysosomes. These observations suggest that ATG9A plays an unexpected role in the trafficking of K63-polyubiquitin modified membrane proteins. [Media: see text] [Media: see text] [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E24-12-0535
  7. Autophagy. 2025 Feb 14. 1-17
      Macroautophagy/autophagy plays a crucial role in maintaining cellular and organismal health, making the measurement of autophagy flux in vivo essential for its study. Current tools often depend on the overexpression of autophagy probes. In this study, we developed a knock-in mouse model, termed tfLC3-KI, by inserting a tandem fluorescent tag coding sequence into the native Map1lc3b gene locus. We found that tfLC3-KI mice exhibit optimal expression of mRFP-eGFP-LC3B, allowing for convenient measurement of autophagic structures and flux at single-cell resolution, both in vivo and in primary cell cultures. Additionally, we compared autophagy in neurons and glial cells across various brain regions between tfLC3-KI mice and CAG-tfLC3 mice, the latter overexpressing the probe under the strong CMV promoter. Finally, we used tfLC3-KI mice to map the spatial and temporal dynamics of basal autophagy activity in the reproductive system. Our findings highlight the value of the tfLC3-KI mouse model for investigating autophagy flux in vivo and demonstrate the feasibility of tagging endogenous proteins to visualize autophagic structures and flux in both bulk and selective autophagy research in vivo.Abbreviation: BafA1: bafilomycin A1; CQ: chloroquine; EBSS: Earle's balanced salt solution; Es: elongating spermatids; HPF: hippocampalformation; HY: hypothalamus; LCs: leydig cells; OLF: olfactory areas; PepA: pepstatin A; Rs: round spermatids; SCs: sertoli cells; Spc: spermatocytes; Spg: spermatogonia; tfLC3: tandem fluorescently tagged mRFP-eGFP-LC3; TH: thalamus.
    Keywords:  Autophagy flux; endogenous LC3B; in vivo; knock-in; tandem fluorescence protein
    DOI:  https://doi.org/10.1080/15548627.2025.2457910
  8. Autophagy. 2025 Feb 19.
      Healthy cells need functional lysosomes to degrade cargo delivered by autophagy and endocytosis. Defective lysosomes can lead to severe conditions such as lysosomal storage diseases (LSDs) and neurodegeneration. To maintain lysosome integrity and functionality, cells have evolved multiple quality control pathways corresponding to different types of stress and damage. These can be divided into five levels: regulation, reformation, repair, removal, and replacement. The different levels of lysosome quality control often work together to maintain the integrity of the lysosomal network. This review summarizes the different quality control pathways and discusses the less-studied area of lysosome membrane protein regulation and degradation, highlighting key unanswered questions in the field.
    Keywords:  ESCRT; Lysophagy; lysosome membrane protein regulation; lysosome membrane repair; lysosome quality control
    DOI:  https://doi.org/10.1080/15548627.2025.2469206
  9. Aging Cell. 2025 Feb 17. e70018
      The mechanistic target of rapamycin (mTOR) complexes 1 and 2 (mTORC1/2) are crucial for various physiological functions. Although the role of mTORC1 in retinal pigmented epithelium (RPE) homeostasis and age-related macular degeneration (AMD) pathogenesis is established, the function of mTORC2 remains unclear. We investigated both complexes in RPE health and disease. Therefore, in this study, we have attempted to demonstrate that the specific overexpression of mammalian lethal with Sec13 protein 8 (mLST8) in the mouse RPE activates both mTORC1 and mTORC2, inducing epithelial-mesenchymal transition (EMT)-like changes and subretinal/RPE deposits resembling early AMD-like pathogenesis. Aging in these mice leads to RPE degeneration, causing retinal damage, impaired debris clearance, and metabolic and mitochondrial dysfunction. Inhibition of mTOR with TORIN1 in vitro or βA3/A1-crystallin in vivo normalized mTORC1/2 activity and restored function, revealing a novel role for the mTOR complexes in regulating RPE function, impacting retinal health and disease.
    Keywords:  RPE; epithelial–mesenchymal transition; mLST8; mTOR complex 1; mTOR complex 2; metabolic/mitochondrial changes
    DOI:  https://doi.org/10.1111/acel.70018
  10. Exp Cell Res. 2025 Feb 18. pii: S0014-4827(25)00068-0. [Epub ahead of print] 114472
      Hypoxia-induced apoptosis and mitochondrial dysfunction in cardiomyocytes are involved in the mechanisms of heart failure. Our previous studies have confirmed that NRF-1 alleviates hypoxia-induced injury by promoting mitochondrial function and inhibiting apoptosis in cardiomyocytes. However, the mechanism by which NRF-1 attenuates hypoxia-induced injury in cardiomyocytes is still unclear. Mitophagy, a selective autophagy, has recently shown a remarkable correlation with hypoxia-induced cardiomyocyte injury. In this study, we evaluated whether NRF-1 protects cardiomyocytes from hypoxia-induced injury by regulating mitophagy. The findings indicate that hypoxia prevents H9C2 cells from growing, encourages mitochondrial dysfunction, and triggers mitophagy. In addition, promoting mitophagy by rapamycin reduces hypoxia-induced injury in H9C2 cells. Overexpression of NRF-1 in hypoxia-induced H9C2 cells promotes mitophagy and alleviates cell injury, and this effect can be inhibited by 3-MA. Further study found that NRF-1 promotes the expression of FUNDC1 by binding to its promoter region. Knockdown of FUNDC1 in NRF-1 over-expression H9C2 cells inhibited mitophagy and aggravated hypoxia-induced injury. In conclusion, our study suggests that NRF-1 protects against hypoxia-induced injury by regulating FUNDC1-mediated mitophagy in cardiomyocytes.
    Keywords:  FUNDC1; H9c2 cardiomyocytes; Heart failure; NRF-1; hypoxia; mitophagy
    DOI:  https://doi.org/10.1016/j.yexcr.2025.114472
  11. Chin Med J (Engl). 2025 Feb 18.
       BACKGROUND: Disruption of hepatic lipid homeostasis leads to excessive hepatic triglyceride accumulation and the development of metabolic dysfunction-associated steatotic liver disease (MASLD). Autophagy, a critical process in liver lipid metabolism, is impaired in MASLD pathogenesis. Irisin, a skeletal muscle-driven myokine, regulates lipid metabolism, but its impact on hepatic lipid metabolism is not well understood. Here, we aimed to explore the role of irisin in hepatic steatosis and the underlying mechanisms involved.
    METHODS: A high-fat diet (HFD)-induced MASLD mouse model was used, and the recombinant irisin protein, herein referred to as "Irisin", was intraperitoneally administered for 4 weeks to evaluate the effects of irisin on hepatic lipid accumulation. Liver tissues were stained with Oil red O (ORO), and triglyceride (TG) and total cholesterol (TC) contents were measured in serum and liver homogenates. The expression of the autophagosome marker microtubule-associated protein 1 light chain 3 (LC3), the autophagy receptor protein sequestosome-1 (SQSTM1/p62), autophagy initiation complex unc-51-like kinase 1 (ULK1) and the lysosomal functional protein cathepsin B was measured via Western blotting, and the expression of the transcription factor EB (TFEB) was analyzed via immunofluorescence to explore autophagic changes. The effect of irisin on autophagic flux was further evaluated in palmitic acid-induced HepG2 cells by measuring autophagic degradation with chloroquine (CQ), and analyzing the colocalization of LC3 and lysosome-associated protein 1 (LAMP1). The possible mechanism was examined by measuring the expression of the autophagic sirtuin 3 (SIRT3) pathway and further validated using overexpression of SIRT3 with plasmid transfection or siRNA-mediated knockdown. Student's t-test was utilized for statistical analysis.
    RESULTS: Irisin significantly reduces hepatic lipid accumulation in mice fed with HFD, accompanied by enhanced hepatocyte autophagy and upregulation of the SIRT3 pathway. In HepG2 cells, Irisin attenuated palmitic acid-induced lipid accumulation, which was partially dependent on SIRT3 levels. Mechanistically, Irisin treatment upregulated SIRT3 and phosphorylated AMP-activated protein kinase (AMPK), inhibited mammalian target of rapamycin (mTOR) activity, promoted TFEB nucleus translocation, increased cathepsin B expression, enhanced autophagic degradation, and alleviated hepatic steatosis. No significant changes in phosphorylation of ULK1 in the hepatocytes were observed. However, when siRNA was used to knock down SIRT3, the changes of those protein were partially reversed, and hepatic steatosis was further exacerbated.
    CONCLUSIONS: Our findings highlight irisin as a potential therapeutic for hepatic steatosis by modulating autophagy and lipid metabolism, potentially providing a novel therapeutic target for the management of MASLD. Further research is needed to elucidate the underlying mechanisms and explore the potential clinical applications of this approach in the treatment of MASLD.
    DOI:  https://doi.org/10.1097/CM9.0000000000003427
  12. Autophagy. 2025 Feb 17.
      Lysosomes are essential membrane-bound organelles that integrate intracellular needs and external signals through multiple functions, including autophagy-mediated degradation and MTORC1 signaling. The integrity of the lysosomal membrane is therefore crucial for maintaining cellular homeostasis. Various endogenous and exogenous factors can damage lysosomes, contributing to diseases such as infections, cancer, and neurodegeneration. In response, cells mount defensive mechanisms to cope with such stress, including the formation of stress granules (SGs) - membraneless organelles composed of RNAs and protein complexes. While SGs have emerged as key players in repairing damaged lysosomes, how lysosomal damage triggers their formation and influences cell fate remains unclear. Here we report that the calcium signal from damaged lysosomes mediates SG formation and protects cells from lysosomal damage-induced cell death. Mechanistically, calcium leakage from damaged lysosomes signals the recruitment of calcium-activating protein PDCD6IP/ALIX and its partner PDCD6/ALG2. This complex recruits protein kinase EIF2AK2/PKR and its activator PRKRA/PACT, which phosphorylates translation initiator factor EIF2S1, stalling global translation initiation. This translation arrest leads to the accumulation of inactive messenger ribonucleoprotein complexes (mRNPs), resulting in SG formation. Cells deficient in SG formation show increased cell death when exposed to lysosomal damage from disease-associated factors including SARS-CoV-2ORF3a, adenovirus, malarial pigment, proteopathic MAPT/tau, or environmental hazards. Collectively, this study reveals how damaged lysosomes signal through calcium to trigger SG assembly, promoting cell survival. This establishes a novel link between membrane-bound and membraneless organelles, with implications for diseases involving lysosomal damage and SG dysfunction.
    Keywords:  Calcium signaling; cell survival; lysosomal damage; stress granules
    DOI:  https://doi.org/10.1080/15548627.2025.2468910
  13. Autophagy. 2025 Feb 19.
      The occurrence of necrosis during Mycobacterium bovis (M. bovis) infection is regarded as harmful to the host because it promotes the spread of M. bovis. Ferroptosis is a controlled type of cell death that occurs when there is an excessive buildup of both free iron and harmful lipid peroxides. Here, we demonstrate that the mammalian cell entry (Mce) 4 family protein Mb3523c triggers ferroptosis to promote M. bovis pathogenicity and dissemination. Mechanistically, Mb3523c, through its Y237 and G241 site, interacts with host HSP90 protein to stabilize the LAMP2A on the lysosome to promote the chaperone-mediated autophagy (CMA) pathway. Then, GPX4 is delivered to lysosomes for destruction via the CMA pathway, eventually inducing ferroptosis to promote M. bovis transmission. In summary, our findings offer novel insights into the molecular mechanisms of pathogen-induced ferroptosis, demonstrating that targeting the GPX4-dependent ferroptosis through blocking the M. bovis Mb3523c-host HSP90 interface represents a potential therapeutic strategy for tuberculosis (TB).
    Keywords:  Chaperone-mediated autophagy; Mb3523c protein; cell death, innate immunity, infection disease; ferroptosis; mycobacterium bovis
    DOI:  https://doi.org/10.1080/15548627.2025.2468139
  14. Biosens Bioelectron. 2025 Feb 07. pii: S0956-5663(25)00120-4. [Epub ahead of print]276 117246
      Mitophagy is a key pathway for regulating mitochondrial quality and quantity which is essential for the preservation of cellular homeostasis. Mitophagy process may be accompanied by changes of the mitochondrial microenvironments. The multifunctional fluorescent probe is crucial for the precise detection of multiple microenvironments, which is vital for the visualization of mitophagy. Herein, a mitochondria-immobilized fluorescent probe DPP was designed and fabricated to visualize mitophagy by monitoring polarity and viscosity in dual-channel. The DPP is characterized by "D-π-A″ structure, which provides the basis for the intramolecular charge transfer (ICT) and twisted intramolecular charge transfer (TICT) platform, enabling dual-channel responses to polarity and viscosity at emission wavelengths of 487 nm and 656 nm, respectively. The significant wavelength gap (169 nm) between the above channels prevents signal crosstalk. Additionally, the incorporation of 1, 4-dibenzyl chloride grants the probe mitochondrial immobilization capabilities, avoiding the leak of probe due to mitochondrial depolarization during autophagy. The DPP accumulates in mitochondria and monitors polarity and viscosity changes in green and red channels, respectively. Notably, the investigation of the relationship between polarity and viscosity revealed that an increase in viscosity is accompanied by a decrease in polarity. The mitophagy was effectively observed through the induction of DPP by rapamycin, with a particular emphasis on the increase in viscosity and decrease in polarity. Thus, DPP offers a powerful tool for a deeper understanding of the physiological and pathological processes associated with mitophagy and are regulated by various microenvironmental parameters.
    Keywords:  Fluorescent probe; Mitochondria; Polarity; Viscosity
    DOI:  https://doi.org/10.1016/j.bios.2025.117246
  15. J Clin Invest. 2025 Feb 17. pii: e188507. [Epub ahead of print]135(4):
      Lysosome storage dysfunction plays a central role in numerous human diseases, but a lack of appropriate tools has hindered lysosomal content profiling in clinical settings. In this issue of the JCI, Saarela et al. introduce a method called tagless LysoIP that enabled rapid isolation of intact lysosomes from blood and brain cells via immunoprecipitation of the endogenous protein TMEM192. Applied to the neurodegenerative lysosomal storage disorder known as Batten disease (caused by mutations in the CLN3 gene), tagless LysoIP revealed substantial accumulation of glycerophosphodiesters (GPDs) in patient lysosomes. These findings highlight the role of CLN3 in GPD clearance and present an innovative method that will enable biomarker discovery and therapeutic advancement in lysosomal diseases.
    DOI:  https://doi.org/10.1172/JCI188507
  16. Acta Neuropathol Commun. 2025 Feb 20. 13(1): 37
      Maintaining cellular homeostasis by removing damaged and senescent mitochondria, a process termed mitophagy, is crucial in preventing Alzheimer's disease (AD) and represents a promising therapeutic target. Our previous research revealed altered mitophagy biomarkers, such as increased CSF and serum PINK1 and serum BNIP3L and decreased serum TFEB levels, indicating impaired autophagy-lysosomal degradation in the AD continuum. However, the role of autophagy/mitophagy in frontotemporal lobar degeneration (FTLD) remains unclear. This study investigated the biomarkers of autophagy/mitophagy and lysosomal biogenesis (PINK1, ULK1, BNIP3L, and TFEB) in biofluids (CSF and serum) from 308 biomarker-defined individuals across the FTLD continuum (FTLD-dementia, n = 29; FTLD-MCI, n = 33) and compared them with those across the AD continuum (MCI-AD, n = 100; AD-dementia, n = 100) and cognitively unimpaired (CU) controls (n = 46) recruited from Czech Brain Aging Study. Additionally, we compared the mitophagy biomarkers across different FTLD clinical subtypes (frontal, semantic and nonfluent variant) with CU, and explored the association between mitophagy biomarkers and clinical phenotypes of FTLD (biomarkers of tau, biomarkers of neurodegeneration, cognition and ATN profile).Our findings indicated a significantly lower CSF PINK1 and ULK1 levels in FTLD compared to AD, with FTLD dementia showing particularly low CSF PINK1 levels compared to AD-dementia. Conversely, CSF ULK1 levels were higher in FTLD-MCI compared to AD-dementia. Serum analyses revealed lower PINK1 and higher TFEB levels in FTLD dementia compared to AD dementia. This study provides compelling evidence of distinct alterations in autophagy/mitophagy biomarkers between FTLD and AD, indicating that these neurodegenerative diseases may affect the cellular waste disposal system through different pathways. This is the first study to explore mitophagy biomarkers in human CSF and serum in FTLD, opening avenues for further research and potential clinical applications.
    Keywords:  Autophagy; Frontotemporal lobar degeneration; MAPT; Neurocognitive impairment; PINK1, TDP-43, TFEB
    DOI:  https://doi.org/10.1186/s40478-025-01954-9
  17. Nat Commun. 2025 Feb 16. 16(1): 1690
      Systemic lipid homeostasis requires hepatic autophagy, a major cellular program for intracellular fat recycling. Here, we find melanocortin 3 receptor (MC3R) regulates hepatic autophagy in addition to its previously established CNS role in systemic energy partitioning and puberty. Mice with Mc3r deficiency develop obesity with hepatic triglyceride accumulation and disrupted hepatocellular autophagosome turnover. Mice with partially inactive human MC3R due to obesogenic variants demonstrate similar hepatic autophagic dysfunction. In vitro and in vivo activation of hepatic MC3R upregulates autophagy through LC3II activation, TFEB cytoplasmic-to-nuclear translocation, and subsequent downstream gene activation. MC3R-deficient hepatocytes had blunted autophagosome-lysosome docking and lipid droplet clearance. Finally, the liver-specific rescue of Mc3r was sufficient to restore hepatocellular autophagy, improve hepatocyte mitochondrial function and systemic energy expenditures, reduce adipose tissue lipid accumulation, and partially restore body weight in both male and female mice. We thus report a role for MC3R in regulating hepatic autophagy and systemic adiposity.
    DOI:  https://doi.org/10.1038/s41467-025-56936-1
  18. Nucleic Acids Res. 2025 Feb 08. pii: gkaf074. [Epub ahead of print]53(4):
      Rett syndrome (RTT) is a severe neurodevelopmental disorder primarily caused by loss-of-function mutations in the MECP2 gene, resulting in diverse cellular dysfunctions. Here, we investigated the role of the long noncoding RNA (lncRNA) NEAT1 in the context of MeCP2 deficiency using human neural cells and RTT patient samples. Through single-cell RNA sequencing and molecular analyses, we found that NEAT1 is markedly downregulated in MECP2 knockout (KO) cells at various stages of neural differentiation. NEAT1 downregulation correlated with aberrant activation of the mTOR pathway, abnormal protein metabolism, and dysregulated autophagy, contributing to the accumulation of protein aggregates and impaired mitochondrial function. Reactivation of NEAT1 in MECP2-KO cells rescued these phenotypes, indicating its critical role downstream of MECP2. Furthermore, direct RNA-RNA interaction was revealed as the key process for NEAT1 influence on autophagy genes, leading to altered subcellular localization of specific autophagy-related messenger RNAs and impaired biogenesis of autophagic complexes. Importantly, NEAT1 restoration rescued the morphological defects observed in MECP2-KO neurons, highlighting its crucial role in neuronal maturation. Overall, our findings elucidate lncRNA NEAT1 as a key mediator of MeCP2 function, regulating essential pathways involved in protein metabolism, autophagy, and neuronal morphology.
    DOI:  https://doi.org/10.1093/nar/gkaf074
  19. Liver Res. 2023 Dec;7(4): 304-320
      Autophagy is a physiological process that is ubiquitous and essential to the disposal or recycling of damaged cellular organelles and misfolded proteins to maintain organ homeostasis and survival. Its importance in the regulation of liver function in normal and pathological conditions is increasingly recognized. This review summarizes how autophagy regulates epithelial cell- and non-epithelial cell-specific function in the liver and how it differentially participates in hepatic homeostasis, hepatic injury response to stress-induced liver damage such as cholestasis, sepsis, non-alcoholic and alcohol-associated liver disease, viral hepatitis, hepatic fibrosis, hepatocellular and cholangiocellular carcinoma, and aging. Autophagy-based interventional studies for liver diseases that are currently registered in clinicatrials.gov are summarized. Given the broad and multidirectional autophagy response in the liver, a more refined understanding of the liver cell-specific autophagy activities in a context-dependent manner is necessary.
    Keywords:  Autophagy; Biliary epithelial cell; Hepatic stellate cell; Hepatitis; Hepatocellular carcinoma; Hepatocyte
    DOI:  https://doi.org/10.1016/j.livres.2023.12.001
  20. Cell Signal. 2025 Feb 15. pii: S0898-6568(25)00076-2. [Epub ahead of print] 111663
       BACKGROUND: WIPI1 is a member of the WD-repeat protein family that interacts with phosphoinositides and plays a crucial role in autophagy. This study investigated how WIPI1-mediated mitophagy dysfunction contributes to ventricular remodeling in rat and mouse models of diabetes mellitus.
    METHODS: The study utilized a 32-weeks diabetic animal model to simulate long-term diabetic conditions. AAV9-cTNT-WIPI1 vectors were employed to overexpress WIPI1 in the myocardium. Cardiac function was assessed by echocardiography. Mitochondrial membrane potential was assessed using JC-1 dye. Oxygen consumption rates were quantified using an Oxygraph-O2K high-resolution respirometry.
    RESULTS: Long-term diabetes led to decreased ejection fraction and fractional shortening associated with a marked increase in ventricular fibrosis and elevated expression of fibrotic markers such as collagen type I and periostin. Expression of autophagy markers such as LC3b-II and SQSTM1 was reduced, and colocalization with mitochondria was disrupted, suggesting failures in autophagosome formation and maturation. This impairment was further supported by decreased levels of mitophagy-related proteins (PINK and Parkin), indicating impaired mitophagy. WIPI1 knockdown led to mitochondrial dysfunction, characterized by loss of membrane potential and reduced respiratory capacity.
    CONCLUSION: WIPI1 is essential for proper mitophagy function. Its downregulation produces ventricular remodeling and dysfunction. These findings suggest that targeting WIPI1-mediated pathways could be a potential therapeutic strategy for treating diabetic cardiomyopathy by improving mitochondrial health and mitophagic processes.
    Keywords:  Diabetic cardiomyopathy; Mitochondrial dysfunction; Mitophagy
    DOI:  https://doi.org/10.1016/j.cellsig.2025.111663
  21. Biochem Biophys Res Commun. 2025 Feb 09. pii: S0006-291X(25)00182-2. [Epub ahead of print]752 151468
      Atg1/ULK1 protein kinase induces macroautophagy, but not microautophagy, after nutrient starvation and inactivation of target of rapamycin complex 1 (TORC1) protein kinase. Microautophagy is also induced by TORC1 inactivation, but a TORC1-downstream protein kinase responsible for microautophagy induction remains obscure. Here, we show that the Greatwall kinase Rim15, a downstream protein kinase of TORC1, promotes bulk microautophagy induction after TORC1 inactivation. In addition, Rim15 was required for proper induction of microlipophagy (microautophagic degradation of lipid droplet). Endosomal sorting complex required for transport (ESCRT) machinery is recruited onto the vacuolar membrane after TORC1 inactivation for microautophagy. Loss of Rim15 reduced protein levels of subunits (Vps27 and Hse1) of ESCRT-0, a primary ESCRT subcomplex. Consistently, the recruitment of ESCRT-0 onto the vacuolar membrane after rapamycin was reduced in rim15Δ cells. On the other hand, Rim15 was dispensable for ESCRT function in multivesicular body formation. This study reveals that Rim15 specifically regulates function of ESCRT-0 in microautophagy under the control of TORC1 and provides a new insight into lipophagy-related human diseases.
    Keywords:  Autophagy; ESCRT; Lipophagy; Microautophagy; Rim15; TORC1
    DOI:  https://doi.org/10.1016/j.bbrc.2025.151468
  22. bioRxiv. 2025 Feb 03. pii: 2025.02.01.636045. [Epub ahead of print]
      The quality of inherited mitochondria determines embryonic viability 1 , metabolic health during adulthood and future generation endurance. The oocyte is the source of all zygotic mitochondria 2 , and mitochondrial health is under strict developmental regulation during early oogenesis 3-5 . Yet, fully developed oocytes exhibit the presence of deleterious mitochondrial DNA (mtDNA) 6,7 and mitochondrial dysfunction from high levels of endogenous reactive oxygen species 8 and exogenous toxicants 9 . How fully developed oocytes prevent transmission of damaged mitochondria to the zygotes is unknown. Here we discover that the onset of oocyte-to-zygote transition (OZT) developmentally triggers a robust and rapid mitophagy event that we term mitophagy at OZT (MOZT). We show that MOZT requires mitochondrial fragmentation, activation of the macroautophagy system and the mitophagy receptor FUNDC1, but not the prevalent mitophagy factors PINK1 and BNIP3. Oocytes upregulate expression of FUNDC1 in response to diverse mitochondrial insults, including mtDNA mutations and damage, uncoupling stress, and mitochondrial dysfunction, thereby promoting selection against damaged mitochondria. Loss of MOZT leads to increased inheritance of deleterious mtDNA and impaired bioenergetic health in the progeny, resulting in diminished embryonic viability and the extinction of descendent populations. Our findings reveal FUNDC1-mediated MOZT as a mechanism that preserves mitochondrial health during the mother-to-offspring transmission and promotes species continuity. These results may explain how mature oocytes from many species harboring mutant mtDNA give rise to healthy embryos with reduced deleterious mtDNA.
    DOI:  https://doi.org/10.1101/2025.02.01.636045
  23. medRxiv. 2025 Jan 24. pii: 2025.01.22.25320997. [Epub ahead of print]
      Neurodegenerative diseases share common features of protein aggregation along with other pleiotropic traits, including shifts in transcriptional patterns, neuroinflammation, disruptions in synaptic signaling, mitochondrial dysfunction, oxidative stress, and impaired clearance mechanisms like autophagy. However, key regulators of these pleotropic traits have yet to be identified. Here, we discovered a novel long non-coding RNA (lncRNA), FAM151B-DT , that is reduced in a stem cell model of frontotemporal dementia with tau inclusions (FTLD-tau) and in brains from FTLD-tau, progressive supranuclear palsy, Alzheimer's disease, and Parkinson's disease patients. We show that silencing FAM151B-DT in vitro is sufficient to enhance tau aggregation. To begin to understand the mechanism by which FAM151B-DT mediates tau aggregation and contributes to several neurodegenerative diseases, we deeply characterized this novel lncRNA and found that FAM151B-DT resides in the cytoplasm where it interacts with tau, α-synuclein, HSC70, and other proteins enriched in protein homeostasis. When silenced, FAM151B-DT blocks autophagy, leading to the accumulation of tau and α-synuclein. Importantly, we discovered that increasing FAM151B-DT expression is sufficient to promote autophagic flux, reduce phospho-tau and α-synuclein, and reduce tau aggregation. Overall, these findings pave the way for further exploration of FAM151B-DT as a promising molecular target for several neurodegenerative diseases.
    DOI:  https://doi.org/10.1101/2025.01.22.25320997
  24. Cell Death Differ. 2025 Feb 17.
      Fanconi Anemia (FA) is an autosomal recessive disorder characterized by diverse clinical manifestations such as aplastic anemia, cancer predisposition, and developmental defects including hypogonadism, microcephaly, organ dysfunction, infertility, hyperpigmentation, microphthalmia, and skeletal defects. In addition to the well-described defects in DNA repair, mitochondrial dysfunction due to defects in mitochondrial autophagy (mitophagy) is also associated with FA, although its contribution to FA phenotypes is unknown. This study focused on the FANCC gene, which, alongside other FA genes, is integral to DNA repair and mitochondrial quality control. In the present study, we created a FANCC mutant mouse model, based on a human mutation (FANCC c.67delG) that is defective in DNA repair but proficient in mitophagy. We found that the FANCC c.67delG mutant mouse model recapitulates some phenotypes observed in FA patients, such as cellular hypersensitivity to DNA cross-linking agents and hematopoietic defects. In contrast, FA phenotypes such as microphthalmia, hypogonadism, and infertility, present in FANCC-deficient mice, were absent in the FANCC c.67delG mice, suggesting that the N-terminal 55 amino acids of FANCC are dispensable for these developmental processes. Furthermore, the FANCC c.67delG mutation preserved mitophagy, and unlike the FANCC null mutation, did not lead to the accumulation of damaged mitochondria in cells or tissues. This study highlights the multifaceted nature of the FANCC protein, with distinct domains responsible for DNA repair and mitophagy. Our results suggest that developmental defects in FA may not solely stem from DNA repair deficiencies but could also involve other functions, such as mitochondrial quality control.
    DOI:  https://doi.org/10.1038/s41418-025-01461-3
  25. Nucleic Acids Res. 2025 Feb 08. pii: gkaf062. [Epub ahead of print]53(4):
      Genetic screens using CRISPR (Clustered Regularly Interspaced Palindromic Repeats) provide valuable information about gene function. Nearly all pooled screening technologies rely on the cell to link genotype to phenotype, making it challenging to assay mechanistically informative, biochemically defined phenotypes. Here, we present CRISPuRe-seq (CRISPR PuRification), a novel pooled screening strategy that expands the universe of accessible phenotypes through the purification of ribonucleoprotein complexes that link genotypes to expressed RNA barcodes. While screening for regulators of the integrated stress response (ISR), we serendipitously discovered that the ISR represses transfer RNA (tRNA) production under conditions of reduced protein synthesis. This regulation is mediated through inhibition of mTORC1 and corresponding activation of the RNA polymerase III inhibitor MAF1. These data demonstrate that coherent downregulation of tRNA expression and protein synthesis is achieved through cross-talk between the ISR and mTOR, two master integrators of cell state.
    DOI:  https://doi.org/10.1093/nar/gkaf062
  26. Mol Biotechnol. 2025 Feb 20.
      The Yes-associated protein (YAP) is a key regulator in the pathogenesis of gastric cancer (GC), yet its role in modulating autophagy remains unclear. This study investigated the effects of YAP modulation on autophagy and tumor progression using the SNU-484 and MKN-74 gastric cancer cell lines. YAP overexpression led to increased B-cell lymphoma-2 (BCL-2) transcription, reducing autophagy and enhancing cell survival, while YAP knockdown resulted in elevated autophagic activity. In vivo experiments with nude mice confirmed that YAP overexpression promotes tumor growth, whereas YAP silencing inhibits it. Further analysis revealed that YAP directly binds to the BCL-2 promoter, driving its transcription and thereby inhibiting autophagy-induced cell death. Importantly, silencing BCL-2 mitigated the autophagy inhibition caused by YAP without affecting YAP expression itself. These findings indicate that YAP, by upregulating BCL-2, suppresses autophagy and contributes to gastric cancer progression, suggesting a potential therapeutic strategy targeting the YAP-BCL-2 axis in GC treatment.
    Keywords:  Autophagy; BCL2; Gastric cancer; YAP
    DOI:  https://doi.org/10.1007/s12033-024-01354-9
  27. Life Sci. 2025 Feb 17. pii: S0024-3205(25)00106-7. [Epub ahead of print] 123473
      Premature ovarian failure (POF) is a condition where the ovaries lose their function before the age of 40, leading to significant impacts on reproductive health and overall well-being. Current treatment options are limited and often ineffective at restoring ovarian function. This review explores the role of autophagy- a cellular process that helps maintain homeostasis by recycling damaged components-in the development and potential treatment of POF. Autophagy is crucial for the survival of follicle cells and can be disrupted by various stressors associated with POF, such as oxidative damage and mitochondrial dysfunction. We review several key molecular pathways involved in autophagy, including the PI3K/AKT/mTOR, PINK1-Parkin, JAK2/STAT3, MAPK and AMPK/FOXO3a pathways, which have been implicated in POF. Each pathway offers unique insights into how autophagy can be modulated to counteract POF-related damage. Additionally, we discuss emerging therapeutic strategies that target these pathways, including chemical compounds, peptides, hormones, RNA therapy, extracellular vesicles and traditional Chinese medicine. These approaches aim to restore autophagic balance, promote follicle survival and improve ovarian function. By targeting autophagy, new treatments may offer hope for better management and potential reversal of POF, thus improving the quality of life for affected individuals.
    Keywords:  Autophagy; Follicle; Granulosa cells; Molecular pathways; Premature ovarian failure; Therapeutic strategies
    DOI:  https://doi.org/10.1016/j.lfs.2025.123473
  28. Cell Stress Chaperones. 2025 Feb 19. pii: S1355-8145(25)00010-0. [Epub ahead of print]
      Acute kidney injury (AKI) is a common and serious complication resulting from ischemia and hypoxia, leading to significant morbidity and mortality. Autophagy, a cellular process for degrading damaged components, plays a crucial role in kidney protection. The unfolded protein response (UPR) pathway, particularly the IRE1α/XBP1 signaling cascade, is implicated in regulating autophagy during renal stress. To elucidate the role of the IRE1α/XBP1 pathway in autophagy during hypoxia/reoxygenation (H/R) and ischemia/reperfusion (I/R) injury, renal tubular epithelial cells (TECs) were subjected to H/R conditions, and I/R injury was induced in mice. The expression of autophagy-related and ER stress markers (IRE1α, XBP1, GRP78, Beclin1, LC3I/II, and P62) was assessed using immunoblotting and immunofluorescence. Additionally, the impacts of IRE1α overexpression and pharmacological agents, IXA6 (IRE1α agonist) and STF083010 (IRE1α inhibitor), were evaluated on autophagy regulation. H/R injury significantly increased mitochondrial damage and the formation of autophagic vesicles in TECs. Key markers of autophagy were elevated in response to H/R and I/R injury, with activation of the IRE1α/XBP1 pathway enhancing autophagic processes. IXA6 treatment improved renal function and reduced injury in I/R models, while STF083010 exacerbated kidney damage. The IRE1α/XBP1 pathway is a critical regulator of autophagy in renal TECs during ischemic stress, suggesting that pharmacological modulation of this pathway may offer therapeutic avenues for preventing or mitigating AKI. Enhanced understanding of these mechanisms may lead to novel strategies for kidney disease management.
    Keywords:  Autophagy; Endoplasmic reticulum stress; Ischemia-reperfusion; XBP1s; chronic kidney disease
    DOI:  https://doi.org/10.1016/j.cstres.2025.02.004
  29. Cell Rep. 2025 Feb 14. pii: S2211-1247(25)00087-7. [Epub ahead of print]44(2): 115316
      Macroautophagy/autophagy is crucial for cell survival during nutrient starvation. Autophagy requires the coordinated function of several Atg proteins, including the Atg1 kinase, for efficient induction and execution. Recently, several RNA-binding proteins (RBPs) have been shown to post-transcriptionally regulate ATG1. However, a comprehensive understanding of autophagy regulation by RBPs via ATG1 is yet to be elucidated. Here, we utilize an in vitro approach to identify RBPs that specifically interact with ATG1 untranslated regions. We show that Npl3 and Pub1 interact with the ATG1 5' and 3' untranslated regions during nitrogen starvation. Furthermore, Npl3 and Pub1 coordinate to facilitate ATG1 mRNA export to the cytoplasm and its subsequent interaction with the translational machinery. Significantly, in non-small cell lung cancer cell lines, mammalian Pub1, TIA1, also positively regulates ULK1 protein expression and autophagy during serum starvation. Overall, our study highlights the regulatory landscape that fine-tunes Atg1 protein expression to sustain autophagy during nutrient starvation.
    Keywords:  CP: Cell biology; CP: Molecular biology; RBPs; autophagy; mRNA metabolism; macroautophagy; mammalian cells; post-transcriptional regulation; stress; translation; yeast
    DOI:  https://doi.org/10.1016/j.celrep.2025.115316
  30. Nat Commun. 2025 Feb 14. 16(1): 1628
      During infection and cancer, mTORC1-mediated metabolic regulation impacts CD8+ T cell effector expansion and memory development. However, the mechanisms by which CD8+ T cells regulate mTORC1 to support their unique metabolic requirements remain unknown. Here we show that NKG7, a lysosomal protein whose expression is restricted to cytotoxic lymphocytes, negatively regulates mTORC1 recruitment and activation by inhibiting assembly and function of the lysosomal proton pump, vacuolar ATPase (v-ATPase). Human and mouse CD8+ T cells lacking NKG7 show more acidic lysosomes and increased activation of mTORC1 signaling, which could be reversed by inhibition of v-ATPase activity. In mice responding to LCMV infection, NKG7-deleted effector CD8+ T cells are less durable and generate fewer memory precursors, whereas induced expression of NKG7 in CD8+ T cells results in increased presence of intra-tumoral T cells. Overall, our work identifies NKG7 as a CD8+ T cell-specific regulator of mTORC1 activity, required for optimal immune responses.
    DOI:  https://doi.org/10.1038/s41467-025-56931-6
  31. bioRxiv. 2025 Feb 02. pii: 2025.02.01.635992. [Epub ahead of print]
      Disruption of endolysosomal acidification is a hallmark of several neurodevelopmental and neurodegenerative disorders. Impaired acidification causes accumulation of toxic protein aggregates and disrupts neuronal homeostasis, yet the molecular mechanisms regulating endolysosomal pH in neurons remain poorly understood. A critical regulator of lumenal acidification is the vacuolar ATPase (V-ATPase), a proton pump whose activity depends on dynamic assembly of its V0 and V1 subdomains. In this study, we identify transmembrane protein 184B (TMEM184B) as a novel regulator of endolysosomal acidification in neurons. TMEM184B is an evolutionarily conserved 7-pass transmembrane protein required for synaptic structure and function, and sequence variation in TMEM184B causes neurodevelopmental disorders, but the mechanism for this effect is unknown. We performed proteomic analysis of TMEM184B-interacting proteins and identified enrichment of components involved in endosomal trafficking and function, including the V-ATPase. TMEM184B localizes to early and late endosomes, further supporting a role in the endosomal system. Loss of TMEM184B results in significant reductions in endolysosomal acidification within cultured mouse cortical neurons. This alteration in pH is associated with impaired assembly of the V-ATPase V0 and V1 subcomplexes in the TMEM184B mutant mouse brain, suggesting a mechanism by which TMEM184B promotes flux through the endosomal pathway. Overall, these findings identify a new contributor in maintaining endosomal function and provide a mechanistic basis for disrupted neuronal function in human TMEM184B-associated nervous system disorders.
    Significance Statement: Endolysosomal acidification is essential for neuronal protein homeostasis, yet its regulation in neurons remains poorly understood. Here, we identify TMEM184B as a key regulator of this process, establishing its first known cellular role. We show that TMEM184B interacts with vacuolar ATPase (V-ATPase) components and promotes the assembly of its V0 and V1 subdomains, facilitating lumenal acidification. Loss of TMEM184B disrupts endolysosomal pH in neurons, potentially impairing proteostasis. These findings reveal a critical function for TMEM184B in neuronal maintenance and provide mechanistic insight into its link to neurological disorders. This work advances our understanding of endolysosomal regulation and suggests TMEM184B regulation could improve outcomes in diseases involving lysosomal dysfunction.
    DOI:  https://doi.org/10.1101/2025.02.01.635992
  32. J Cachexia Sarcopenia Muscle. 2025 Feb;16(1): e13725
       BACKGROUND: Few researches have investigated the molecular mechanism responsible for the age-related loss of the pelvic floor muscle (PFM) mass and functionality-a pivotal contributor to pelvic organ prolapse and diminished physical well-being. ADP ribosylation factor GTPase activating protein 3 (ArfGAP3) is a member of ArfGAPs, which regulates the vesicular trafficking pathway and intracellular proteins transporting. However, its effects on skeletal muscle ageing remain largely unknown.
    METHODS: Mouse models of natural ageing and D-gal (D-galactose)-induced ageing were subject to analyse the structure, function and pathological alterations of the PFM and the expression of ArfGAP3. Stable ArfGAP3 knockdown and overexpression C2C12 cell lines were established to investigate the anti-senescence effects of ArfGAP3 and the underlying mechanisms in ageing process, complemented by Rab5a genetic intervention and mRFP-GFP-LC3 adenoviral particles transfection. In vivo experiments entailed ArfGAP3 overexpression in mice alongside autophagy inhibitor treatment, with assessments encompassing tissue mass, bladder leak point pressure (BLPP), submicroscopic structure, antioxidative stress system and muscle regeneration.
    RESULTS: Aged (24-month-old) mice exhibited significant physiological alterations in PFMs, including decreased muscle mass, diminished cross-sectional area (CSA), deteriorated supporting function (as evidenced by reduced BLPP), impaired autophagy and increased levels of oxidative stress (p < 0.001). Utilizing ageing C2C12 model, we observed a dose-dependent relationship between D-gal induction and cellular senescence, impaired differentiation and mitochondrial damage. Remarkably, the expression levels of ArfGAP3 were markedly downregulated in both in vitro and in vivo ageing models. Knockdown of ArfGAP3 exacerbated impaired differentiation potential and induced aberrant mitochondrial morphology and functional dysfunction in ageing C2C12 myoblasts, whereas ArfGAP3 overexpression largely mitigated these effects. Mechanistically, our findings revealed an interplay between ArfGAP3 and Rab5a, indicating their coordinated regulation. ArfGAP3-mediated activation of Rab5a-associated autophagy and IRS1-AKT-mTOR signalling pathways during cellular senescence and myogenesis was identified, leading to enhanced autophagic flux and improved resistance to oxidative stress. In vivo, ArfGAP3 overexpression ameliorated D-gal-induced loss of muscle mass and function, while promoting antioxidant responses and muscle regeneration in mice. However, these protective effects of ArfGAP3 overexpression were extinguished by autophagy inhibition.
    CONCLUSIONS: Our study uncovers the significant role of ArfGAP3 in enhancing differentiation capacity and mitochondrial function through mediating Rab5a expression to activate IRS1-AKT-mTOR signalling pathways and promote autophagy during the ageing process. These findings underscore the potential of ArfGAP3 as a promising therapeutic target for ameliorating the decline in skeletal muscle function associated with ageing.
    Keywords:  ArfGAP3; Rab5a; ageing; autophagy; pelvic floor muscle
    DOI:  https://doi.org/10.1002/jcsm.13725
  33. Sci Rep. 2025 Feb 18. 15(1): 5943
      Autophagy is a fundamental cellular activity involved in the renewal of cellular components, occurring primarily in cells subjected to physiological remodeling or pathological stimuli. The occurrence of autophagy is closely related to the endoplasmic reticulum (ER), and ER stress (ERS) occurs when ER homeostasis is disrupted. The current study aimed to analyze the molecular mechanisms underlying the effects of ERS on autophagy in goat endometrial epithelial cells (gEECs). We found that rapamycin (an autophagy inducer) induced autophagy and ERS in a time-dependent manner in gEECs which was accompanied by significantly increased expression of the autophagy-related genes ATG5, the LC3II/LC3I and ERS-related genes GRP78, IRE1, ATF6, and XBP1s. PI3K and AKT protein phosphorylation was significantly reduced during gEECs autophagy. Interestingly, TG (ERS activator) significantly inhibited the expression of ATG5 and the LC3II/LC3I and significantly promoted expression of SQSTM1, whereas the ERS inhibitor 4-PBA showed the opposite results. Surprisingly, XBP1s knockdown inhibited the effects of TG. Furthermore, XBP1s overexpression significantly inhibited autophagy whereas XBP1s knockdown increased ATG5 expression and the LC3II/LC3I and decreased SQSTM1 expression in gEECs. Specifically, XBP1s overexpression significantly promoted PI3K and AKT protein phosphorylation while treatment with LY294002 (PI3K/AKT pathway inhibitor) significantly reversed the effect. Similarly, PI3K/AKT pathway activation was significantly inhibited following XBP1s knockdown whereas treatment with SC79 (PI3K/AKT pathway activator) showed the opposite results. Taken together, our data suggest that interactions between ERS and autophagy exist in gEECs. XBP1s, the key effector of ERS, inhibits autophagy in gEECs by promoting the PI3K/AKT pathway in gEECs. These results may contribute to the treatment and prevention of uterine diseases.
    Keywords:  Autophagy; Endometrial epithelium cell; Endoplasmic reticulum stress; PI3K/AKT pathway; XBP1s
    DOI:  https://doi.org/10.1038/s41598-024-84461-6
  34. Biochim Biophys Acta Mol Basis Dis. 2025 Feb 16. pii: S0925-4439(25)00081-X. [Epub ahead of print] 167736
      Variants in the CRB1 gene cause retinal degeneration and subsequent vision impairment in patients of retinitis pigmentosa (RP). No treatments are currently available to cure or impede the progression of CRB1-associated retinopathy. Previous studies have revealed alterations in the endolysosomal systems and autophagy in the absence of CRB1, but their roles in the pathogenesis of CRB1 retinopathy are unclear. Here, we examined the disease mechanism of CRB1 retinopathy using loss-of-function mutants of the crumbs (crb), the Drosophila homolog of CRB1. We found that the loss of crb results in overactivation of autophagy in the eye. We also discovered that the dihydroceramide desaturase (encoded by infertile crescent (ifc), was up-regulated in crb mutants. Overexpression of ifc inhibited autolysosomes and alleviated Atg1-induced autophagic cell death. Mechanistically, ifc enhanced the binding of Rac1 to Atg8 and increased the autophagosomal localization of active Rac1, thus inhibiting autophagy. Importantly, autophagy inhibitions achieved through ifc overexpression, chloroquine treatment, or Beclin-1 RNAi all ameliorated the neurodegeneration of crb mutant eyes. Together, these findings highlighted the mechanism of dihydroceramide desaturase in modulating autolysosome functions in crb mutants, providing new insights for developing treatments against CRB1 retinopathy.
    Keywords:  Autophagic cell death; CRB1 retinopathy; Dihydroceramide desaturase; Retinitis pigmentosa
    DOI:  https://doi.org/10.1016/j.bbadis.2025.167736
  35. Cancer Metastasis Rev. 2025 Feb 15. 44(1): 33
      The multidomain protein cargo adaptor p62, also known as sequestosome 1, serves as a shuttling factor and adaptor for the degradation of substrates via the proteasome and autophagy pathways. Regarding its structure, p62 is composed of several functional domains, including the N-terminal Phox1 and Bem1p domains, a ZZ-type zinc finger domain, a LIM protein-binding domain that contains the tumor necrosis factor receptor-associated factor 6 (TRAF6) binding region, two nuclear localization signals (NLS 1/2), a nuclear export signal (NES), the LC3-interacting region (LIR), a Kelch-like ECH-associated protein 1 (KEAP1)-interacting region, and a ubiquitin-associated (UBA) domain. Recent studies have highlighted the critical role of p62 in the development and progression of various malignancies. Overexpression and/or impaired degradation of p62 are linked to the initiation and progression of numerous cancers. While p62 is primarily localized in the cytosol and often considered a cytoplasmic protein, most of the existing literature focuses on its cytoplasmic functions, leaving its nuclear roles less explored. However, an increasing body of research has uncovered p62's involvement in the cellular response to DNA damage. In this review, we summarize the current understanding of p62's molecular functions in malignancies, with particular emphasis on its role in DNA damage repair, highlighting the latest advances in this field.
    Keywords:  DDR; Modular structures; P62/SQSTM1; Tumorigenesis
    DOI:  https://doi.org/10.1007/s10555-025-10250-w
  36. Proc Natl Acad Sci U S A. 2025 Feb 25. 122(8): e2414738122
      G protein-coupled receptors (GPCRs) modulate various physiological functions by rewiring cellular gene expression in response to extracellular signals. Control of gene expression by GPCRs has been studied almost exclusively at the transcriptional level, neglecting an extensive amount of regulation that takes place translationally. Hence, little is known about the nature and mechanisms of gene-specific posttranscriptional regulation downstream of receptor activation. Here, we apply an unbiased multiomics approach to delineate an extensive translational regulatory program initiated by the prototypical beta2-adrenergic receptor (β2-AR) and provide mechanistic insights into how these processes are orchestrated. Using ribosome profiling (Ribo-seq), we identify nearly 120 gene targets of adrenergic receptor activity for which expression is exclusively regulated at the level of translation. We next show that all translational changes are induced selectively by endosomal β2-ARs and report that this proceeds through activation of the mammalian target of rapamycin (mTOR) pathway. Specifically, within the set of translational GPCR targets, we find significant enrichment of genes with 5' terminal oligopyrimidine (TOP) motifs, a gene class classically known to be translationally regulated by mTOR. We then demonstrate that endosomal β2-ARs are required for mTOR activation and subsequent mTOR-dependent TOP mRNA translation. This site-selective crosstalk between the pathways is observed in multiple cell models with native β2-ARs, across a range of endogenous and synthetic adrenergic agonists, and for other GPCRs with intracellular activity. Together, this comprehensive analysis of drug-induced translational regulation establishes a critical role for location-biased GPCR signaling in fine-tuning the cellular protein landscape.
    Keywords:  GPCR; PKA; cAMP; gene translation; mTOR
    DOI:  https://doi.org/10.1073/pnas.2414738122
  37. Mol Psychiatry. 2025 Feb 14.
      Phosphatase and Tensin Homolog (PTEN) is a dual-specific protein and lipid phosphatase that regulates AKT and downstream signaling of the mechanistic target of rapamycin (mTOR). PTEN functions as a tumor suppressor gene whose mutations result in PTEN Hamartoma Tumor Syndrome (PHTS) characterized by increased cancer risk and neurodevelopmental comorbidity. Here, we generated a novel neuron-specific Pten knock-out mouse model (Syn-Cre/Pten HOM) to test the ability of pharmacologic mTOR inhibition to rescue Pten mutation-associated disease phenotypes in vivo and in vitro. We found that treatment with the mTOR inhibitor, everolimus, increased the survival of Syn-Cre/Pten HOM mice while some neurologic phenotypes persisted. Transcriptomic analyses revealed that in contrast to mice harboring a neuron-specific deletion of the Tuberous Sclerosis Complex 2 gene (Syn-Cre/Tsc2 KO), genes that are under AKT regulation were significantly increased in the Syn-Cre/Pten HOM mice. In addition, genes associated with synapse, extracellular matrix, and myelination were broadly increased in Syn-Cre/Pten HOM mouse neocortex. These findings were confirmed by immunostaining of cortical sections in vivo, which revealed excessive immunoreactivity of myelin basic protein and perineuronal nets (PNN), the specialized extracellular matrix surrounding fast-spiking parvalbumin (PV) interneurons. We also detected increased expression of Synapsin I/PSD95 positive synapses and network hyperactivity phenotypes in Syn-Cre/Pten HOM mice neurons compared to wild-type (WT) neurons in vitro. Strikingly, everolimus treatment rescued the number of synapses and network hyperactivity in the Syn-Cre/Pten HOM mice cortical neuron cultures. Taken together, our results revealed in vivo and in vitro molecular and neuronal network mechanisms underlying neurological phenotypes of PHTS. Notably, pharmacologic mTOR inhibition by everolimus led to successful downstream signaling rescue, including mTOR complex 1 (mTORC1) site-specific suppression of S6 phosphorylation, correlating with phenotypic rescue found in our novel neuron-specific Syn-Cre/Pten HOM mice.
    DOI:  https://doi.org/10.1038/s41380-025-02916-2
  38. bioRxiv. 2025 Feb 02. pii: 2025.02.02.636110. [Epub ahead of print]
      Adipose tissue dysfunction leads to a variety of deleterious systemic consequences including ectopic lipid deposition and impaired insulin sensitivity. PPARγ is a major regulator of adipocyte differentiation and functionality and is thus a determinant of systemic metabolic health. We recently reported that deletion of adipocyte fatty acid synthase (AdFasnKO) impairs autophagy in association with a striking upregulation of genes controlled by PPARγ, including thermogenic uncoupling protein 1 (Ucp1). In this present study, screening for PPARγ coactivators regulated by autophagy revealed a protein denoted as Nuclear receptor coactivator 4 (Ncoa4), known to mediate ferritinophagy and interact with PPARγ and other nuclear receptors. Indeed, we found Ncoa4 is upregulated in the early phase of adipocyte differentiation and is required for adipogenesis. Ncoa4 is also elevated in FasnKO adipocytes and necessary for full upregulation of Ucp1 expression in vitro , even in response to norepinephrine. Consistent with these findings, adipose-selective knockout of Ncoa4 (AdNcoa4KO mice) impairs Ucp1 expression in brown adipose tissue and cold-induced thermogenesis. Adipose-selective double KO of Fasn plus Ncoa4 (AdFasnNcoa4DKO mice) prevents the upregulation of classic PPARγ target genes normally observed in the white adipose tissue of AdFasnKO mice, but not thermogenic Ucp1 expression. These findings reveal Ncoa4 is a novel determinant of adipocyte PPARγ activity and regulator of white and brown adipocyte biology and suggest that manipulation of autophagy flux modulates PPARγ activity and key adipocyte functions via Ncoa4 actions.
    DOI:  https://doi.org/10.1101/2025.02.02.636110
  39. bioRxiv. 2025 Feb 01. pii: 2025.01.31.634950. [Epub ahead of print]
      Proteasome inhibitor drugs are currently used in the clinic to treat multiple myeloma and mantle cell lymphoma. These inhibitors cause accumulation of undegraded proteins, thus inducing proteotoxic stress and consequent cell death. However, cancer cells counteract this effect by activating an adaptive response through the transcription factor Nuclear factor erythroid 2-related factor 1 (NRF1, also known as NFE2L1). NRF1 induces transcriptional upregulation of proteasome and autophagy/lysosomal genes, thereby reducing proteotoxic stress and diminishing the effectiveness of proteasome inhibition. While suppressing this protective autophagy response is one potential strategy, here we investigated whether this heightened autophagy could instead be leveraged therapeutically. To this end, we designed an autophagy-targeting chimera (AUTAC) compound to selectively degrade the anti-apoptotic protein Mcl1 via the lysosome. Our results show that this lysosome-mediated targeted degradation is significantly amplified in the presence of proteasome inhibition, in a NRF1-dependent manner. The combination of the proteasome inhibitor carfilzomib and Mcl1 AUTAC synergistically promoted cell death in both wild-type and proteasome inhibitor-resistant multiple myeloma and lung cancer cells. Thus, our work offers a novel strategy for enhancing proteasome inhibitor efficacy by exploiting the adaptive autophagy response. More broadly, our study establishes a framework for amplifying lysosome-mediated targeted protein degradation, with potential applications in cancer therapeutics and beyond.
    DOI:  https://doi.org/10.1101/2025.01.31.634950
  40. Epilepsy Behav. 2025 Feb 19. pii: S1525-5050(25)00052-6. [Epub ahead of print]165 110313
      Tuberous sclerosis complex (TSC) is typically associated with epilepsy, but patients also present with a myriad of comorbid neuropsychiatric disorders. TSC is caused by mutations in the tuberous sclerosis complex genes 1 or 2 (TSC1, TSC2). This TSC1/2 complex serves as a negative regulator of the mammalian target of rapamycin (mTOR) signaling pathway, which plays a crucial role in regulating neuronal function, including cell proliferation, survival, growth, and protein synthesis. Mutations result in hyperactivation of the pathway. Animal models with mutations in Tsc1 or Tsc2 consistently exhibit epilepsy and behavioral phenotypes. Additionally, abnormal neuronal populations can impact the broader network, leading to deficits in learning and memory, anxiety-like behaviors, deficits in social behaviors, and perseverative and repetitive behaviors. This review aims to synthesize the existing animal literature linking TSC models to epileptogenesis and behavioral impairments, with insights on how modifications in TSC signaling influence both the structure and function of neurons and behavior. Understanding these relationships may provide valuable insights into potential therapeutic targets for managing epilepsy and neuropsychiatric disorders associated with TSC dysregulation.
    Keywords:  Epilepsy; Seizures; TAND; Tuberous Sclerosis Complex; mTOR
    DOI:  https://doi.org/10.1016/j.yebeh.2025.110313
  41. bioRxiv. 2025 Feb 14. pii: 2025.02.09.637107. [Epub ahead of print]
      The pathological hallmark of neurodegenerative disease is the aberrant post-translational modification and aggregation of proteins leading to the formation of insoluble protein inclusions. Genetic factors like APOE4 are known to increase the prevalence and severity of tau, amyloid, and α-Synuclein inclusions. However, the human brain is largely inaccessible during this process, limiting our mechanistic understanding. Here, we developed an iPSC-based 3D model that integrates neurons, glia, myelin, and cerebrovascular cells into a functional human brain tissue (miBrain). Like the human brain, we found pathogenic phosphorylation and aggregation of α-Synuclein is increased in the APOE4 miBrain. Combinatorial experiments revealed that lipid-droplet formation in APOE4 astrocytes impairs the degradation of α-synuclein and leads to a pathogenic transformation that seeds neuronal inclusions of α-Synuclein. Collectively, this study establishes a robust model for investigating protein inclusions in human brain tissue and highlights the role of astrocytes and cholesterol in APOE4 -mediated pathologies, opening therapeutic opportunities.
    DOI:  https://doi.org/10.1101/2025.02.09.637107
  42. Nat Aging. 2025 Feb 21.
      Blood-borne factors are essential to maintain neuronal synaptic plasticity and cognitive resilience throughout life. One such factor is osteocalcin (OCN), a hormone produced by osteoblasts that influences multiple physiological processes, including hippocampal neuronal homeostasis. However, the mechanism through which this blood-borne factor communicates with neurons remains unclear. Here we show the importance of a core primary cilium (PC) protein-autophagy axis in mediating the effects of OCN. We found that the OCN receptor GPR158 is present at the PC of hippocampal neurons and mediates the regulation of autophagy machinery by OCN. During aging, autophagy and PC core proteins are reduced in neurons, and restoring their levels is sufficient to improve cognitive impairments in aged mice. Mechanistically, the induction of this axis by OCN is dependent on the PC-dependent cAMP response element-binding protein signaling pathway. Altogether, this study demonstrates that the PC-autophagy axis is a gateway to mediate communication between blood-borne factors and neurons, and it advances understanding of the mechanisms involved in age-related cognitive decline.
    DOI:  https://doi.org/10.1038/s43587-024-00791-0
  43. Free Radic Biol Med. 2025 Feb 19. pii: S0891-5849(25)00096-6. [Epub ahead of print]
      Lipid metabolism has been identified as a potential target for the treatment of doxorubicin-induced cardiomyopathy (DIC). Mitochondria, as a central regulator of energy production and utilization, plays a crucial role in this process, and enhancing mitophagy holds promise in mitigating myocardial damage in DIC. However, the relationship between mitophagy and lipid metabolism remains unclear, and the key molecules mediating this connection remain to be elucidated. Among these candidates, heterogeneous nuclear ribonucleoprotein K (hnRNPK) emerges as a potential regulator of mitophagy and metabolism. However, its specific role in DIC remains unclear. In this study, we established chronic DIC models both in vivo and in vitro to assess the relationship between hnRNPK levels, mitophagy, and lipid metabolism, as well as to evaluate the impact of hnRNPK on cardiac function. Our findings revealed that hnRNPK expression is significantly reduced in the hearts and cardiomyocytes of doxorubicin (DOX)-treated mice. Notably, hnRNPK overexpression improves cardiac function and effectively reduces lipid accumulation by enhancing mitophagy. Mechanistically, hnRNPK expression was found to be downregulated in DIC, accompanied by its translocation from the nucleus to the cytoplasm, thereby reducing the transcriptional regulation of PINK1. Overexpression of hnRNPK and inhibition of its cytoplasmic translocation alleviates DOX-induced lipid accumulation by regulating the PINK1/Parkin pathway. These findings underscore a previously unrecognized role of hnRNPK in inhibiting lipid accumulation to prevent DIC.
    Keywords:  Doxorubicin-induced cardiomyopathy; Lipid metabolism; Mitophagy; PINK1/Parkin; Therapeutic target; hnRNPK
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2025.02.021
  44. Autophagy. 2025 Feb 20.
      The endosomal sorting complex required for transport (ESCRT) machinery is a membrane abscission system that mediates various intracellular membrane remodeling processes, including macroautophagy/autophagy. In our recent study, we established the unique requirement of the ubiquitin E2 variant-like (UEVL) domain of the ESCRT-I subunit VPS37A in phagophore closure, the final step in autophagosome biogenesis, and determined the physiological impact of systemically inhibiting closure by targeting this region in mice. While the mutant mice exhibited phenotypes similar to those reported in mice deficient in generating ATG8 (mammalian Atg8 homologs)-conjugated (ATG8ylated) phagophores, certain phenotypes, such as neonatal lethality and liver injury, were found to be notably milder. Further investigation revealed that ATG8ylated phagophores promote TBK1-dependent SQSTM1 phosphorylation and droplet formation, leading to the formation of large insoluble aggregates upon closure inhibition. These findings suggest potential roles for ATG8ylated membranes in mitigating proteotoxicity by efficiently concentrating and sequestering soluble, reactive microaggregates and converting them into less reactive, insoluble large aggregates. The study highlights VPS37A UEVL mutant mice as a model for investigating the physiological and pathological roles of phagophores that extend beyond degradation.
    Keywords:  ATG8ylation; ESCRT; SQSTM1; TBK1; VPS37A UEVL mutant mouse; phagophore closure
    DOI:  https://doi.org/10.1080/15548627.2025.2468907
  45. Nat Aging. 2025 Feb 19.
      Consequences of age-associated thymic atrophy include declining T-cell responsiveness to pathogens and vaccines and diminished T-cell self-tolerance. Cortical thymic epithelial cells (cTECs) are primary targets of thymic aging, and recent studies suggested that their maintenance requires mTOR signaling downstream of medullary TEC (mTEC)-derived growth factors. Here, to test this hypothesis, we generated a knock-in mouse model in which FGF21 and mCherry are expressed by most mTECs. We find that mTEC-derived FGF21 promotes temporally distinct patterns of mTORC1 and mTORC2 signaling in cTECs, promotes thymus and individual cTEC growth and maintenance, increases T-cell responsiveness to viral infection, and diminishes indicators of peripheral autoimmunity in older mice. The effects of FGF21 overexpression on thymus size and mTOR signaling were abrogated by treatment with the mTOR inhibitor rapamycin. These results reveal a mechanism by which paracrine FGF21 signaling regulates thymus size and function throughout the lifespan, as well as potential therapeutic targets for improving T-cell function and tolerance in aging.
    DOI:  https://doi.org/10.1038/s43587-024-00801-1
  46. bioRxiv. 2025 Feb 07. pii: 2025.02.05.636718. [Epub ahead of print]
      Failures of the lysosome-autophagy system are a hallmark of aging and many disease states. As a consequence, interventions that enhance lysosome function are of keen interest in the context of drug development. Throughout the biomedical literature, evolutionary biologists have discovered that challenges faced by humans in clinical settings have been resolved by non-model organisms adapting to wild environments. Here, we used a primary cell culture approach to survey lysosomal characteristics in selected species of the genus Mus. We found that cells from M. musculus, mice adapted to human environments, had weak lysosomal acidification and high expression and activity of the lysosomal enzyme β-galactosidase, a classic marker of cellular senescence. Cells of wild relatives, especially the Mediterranean mouse M. spretus, had more robustly performing lysosomes and dampened β-galactosidase levels. We propose that classic laboratory models of lysosome function and senescence may reflect characters that diverge from the phenotypes of wild mice. The M. spretus phenotype may ultimately provide a blueprint for interventions that ameliorate lysosome breakdown in stress and disease.
    DOI:  https://doi.org/10.1101/2025.02.05.636718
  47. Folia Med Cracov. 2024 Dec 26. 64(3): 17-35
      Melanoma treatments are necessary when surgically curable treatments are limited. The major challenge of targeted therapy for treating malignant melanoma is acquired drug resistance. Translation and autophagy pathways are interconnected and involved in developing cancer drug resistance. We hypothesized that coordinate inhibition of autophagy and translation would lead to a better anticancer effect. In the present study, we used chloroquine combined with two translation inhibitors (NVP-BEZ235 and CGP57380) acting at different signaling pathway levels, activating the translation. Our study was conducted for human melanoma cell lines with similar genomic alteration (BRAFV600E and PTEN loss). The combination of the drugs suppresses cell invasiveness and growth by inducing apoptosis. We showed multiple direct and indirect interactions, indicating the overlap and interaction between the translation machinery and autophagy. These data suggest that coordinated inhibition of translation and autophagy promotes apoptosis and may be a new therapeutic model for melanoma treatment.
    Keywords:  MNK; chloroquine; eIF2α; eIF4E; mTOR; melanoma
    DOI:  https://doi.org/10.24425/fmc.2024.152163
  48. Sci China Life Sci. 2025 Feb 17.
      Fabry disease is a monogenic disease characterized by a deficiency or loss of α-galactosidase A (GLA). Cardiomyopathy is the leading cause of death in Fabry patients; however, a lack of understanding of the pathological mechanism impedes the development of effective therapies. Here, we used a Gla knockout (KO) mouse model and investigated its impact on cardiomyopathy. We found that globotriaosylceramide (Gb3) increased the uptake and accumulation of fatty acids in KO hearts by increasing the expression levels of CD36 and ACC2. The augmented fatty acid metabolism further increased autophagy activity, leading to age-related late-onset cardiac hypertrophy. Additionally, increased autophagy facilitates disturbances in fatty acid metabolism. The inhibition of autophagy by supplementation with 3-methyladenine (3-MA) or the overexpression of GLA by the cardiomyocyte-specific adeno-associated virus for 2 months could rebalance abnormal fatty acid metabolism and ameliorate cardiac hypertrophy and dysfunction in KO hearts, suggesting a central role of autophagy in GLA deficiency-related cardiomyopathy.
    Keywords:  autophagy; cardiomyopathy; fabry disease; globotriaosylceramide; α-galactosidase A
    DOI:  https://doi.org/10.1007/s11427-023-2731-0
  49. Prog Biophys Mol Biol. 2025 Feb 15. pii: S0079-6107(25)00007-0. [Epub ahead of print]
      Chronic heart failure (CHF) is the final stage of heart disease and is caused by various factors. Unfortunately, CHF has a poor prognosis and a high mortality rate. Recent studies have found that aging is a significant risk factor for the development of CHF and that cellular senescence plays a vital role in its development. This article reviews different types of cellular senescence, mitochondrial dysfunction in senescent cells, autophagy in senescent cells,and senescence-associated secretory phenotype (SASP), and epigenetic regulation, to provide new perspectives on the research and treatment of CHF.
    Keywords:  autophagy; cellular senescence; chronic heart failure; senescence-associated secretory phenotype
    DOI:  https://doi.org/10.1016/j.pbiomolbio.2025.02.002
  50. bioRxiv. 2025 Feb 01. pii: 2025.01.31.635900. [Epub ahead of print]
      Activation of innate immune signaling occurs during the progression of immunometabolic diseases, including type 2 diabetes (T2D), yet the impact of innate immune signaling on glucose homeostasis is controversial. Here, we report that the E3 ubiquitin ligase TRAF6 integrates innate immune signals following diet-induced obesity to promote glucose homeostasis through the induction of mitophagy. Whereas TRAF6 was dispensable for glucose homeostasis and pancreatic β-cell function under basal conditions, TRAF6 was pivotal for insulin secretion, mitochondrial respiration, and increases in mitophagy following metabolic stress in both mouse and human islets. Indeed, TRAF6 was critical for the recruitment and function of machinery within both the ubiquitin-mediated (Parkin-dependent) and receptor-mediated (Parkin-independent) mitophagy pathways upon metabolic stress. Intriguingly, the effect of TRAF6 deficiency on glucose homeostasis and mitophagy was fully reversed by concomitant Parkin deficiency. Thus, our results implicate a role for TRAF6 in the cross-regulation of both ubiquitin- and receptor- mediated mitophagy through the restriction of Parkin. Together, we illustrate that β-cells engage innate immune signaling to adaptively respond to a diabetogenic environment.
    DOI:  https://doi.org/10.1101/2025.01.31.635900
  51. Biochem Pharmacol. 2025 Feb 19. pii: S0006-2952(25)00084-X. [Epub ahead of print] 116822
      Renal fibrosis is a common feature of chronic kidney disease, in which transforming growth factor-β1 (TGF-β1) plays an important role. Tripartite motif-containing 21 (TRIM21), an E3 ubiquitin ligase, has been studied for its role in acute kidney injury, but its role in renal fibrosis has not been reported. We analyzed public RNA-seq data of unilateral ureteral obstruction (UUO), ischemia-reperfusion injury (I/R), and aristolochic acid (AA)-induced renal fibrosis and found that TRIM21 expression was significantly elevated in fibrotic kidneys, which was verified by Western blot results corresponding to the mouse models. Similarly, TRIM21 expression was significantly elevated and negatively correlated with renal function in human fibrotic kidneys. We showed that TRIM21 knockout alleviated renal fibrosis in UUO mice. In vitro, TRIM21 knockout reduced TGF-β1-induced expression of mature TGF-β1 in HK-2 cells and primary renal tubular cells (PTECs), and this process was reversed by the autophagy inhibitor bafilomycin A1 (Baf-A1). Specifically, TRIM21 promoted K63-linked ubiquitination of p62, inhibited its oligomerization and thus its aggregation and segregation functions, and suppressed autophagic degradation of TGF-β1. Meanwhile, in the UUO mouse model, TRIM21 knockout promoted autophagy levels, and reduced the protein levels of mature TGF-β1 and the phosphorylation levels of SMAD2/3. In conclusion, our study demonstrates that TRIM21 knockdown alleviates renal fibrosis by promoting autophagic degradation of mature TGF-β1 and provides an insight into TRIM21 as a potential therapeutic target for the treatment of kidney fibrosis.
    Keywords:  Autophagy; P62; Renal fibrosis; TGF-β1; TRIM21
    DOI:  https://doi.org/10.1016/j.bcp.2025.116822
  52. BMC Biol. 2025 Feb 21. 23(1): 48
      ATG1 stimulates autophagy biogenesis and serves as a gatekeeper for classical autophagy. To obtain insight into the control of autophagy by ATG1 and determine whether ATG1 has broader processes, we performed a thorough proteomics analysis on the Col-0 wild-type and atg1abct mutant in Arabidopsis thaliana. Proteomic data analysis pointed out that ATG1 has an unidentified function within the inositol trisphosphate and fatty acid metabolism. We also discovered ATG1-dependent autophagy has an emerging connection with ER homeostasis and ABA biosynthesis. Moreover, Gene Ontology terms for abiotic and biotic stress were strongly enriched in differentially abundant proteins, consistent with the reported role of canonical autophagy in these processes. Additional physiological and biochemical analysis revealed that atg1abct exhibited stronger drought resistance under both PEG-simulated drought treatment and natural drought stress. Results from DAB staining also indicated that atg1abct accumulation fewer ROS than Col-0 following drought treatment. As a result, these results illuminate previously unknown functions for ATG1 and offers novel perspectives into the underlying processes of autophagy function.
    Keywords:  ATG1; Autophagy; Nitrogen deprivation; Plant stress; Proteomic
    DOI:  https://doi.org/10.1186/s12915-025-02149-3
  53. Clin Transl Med. 2025 Feb;15(2): e70197
       BACKGROUND: The integrity of brain function is at stake due to cerebral ischemia-reperfusion injury (CIRI), which encompasses mitochondrial dysfunction, autophagy, and neuroinflammation. The role of E2F1 in mediating these processes in microglia during CIRI remains unclear.
    METHODS: A CIRI mouse model was utilized for single-cell RNA transcriptome sequencing of brain tissues. The research comprised diverse gene expression, gene ontology (GO), and the enrichment of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Experimental techniques included oxygen-glucose deprivation (OGD/R) cell models, RT-qPCR, Western Blot, ChIP assays, and microglia-neuron co-cultures.
    RESULTS: A significant aspect highlighted in the study was the involvement of CDK5 in the induction of mitochondrial abnormalities associated with CIRI. Upregulation of E2F1 and CDK5 in post-CIRI microglia was observed. E2F1 facilitated CDK5 transcription, leading to DRP1 phosphorylation, exacerbating neurotoxic effects. Silencing E2F1 improved neurobehavioral outcomes in CIRI mice.
    CONCLUSIONS: Activation of E2F1-mediated CDK5 drives mitochondrial division while inhibiting mitophagy in microglia, triggering inflammation, neuronal apoptosis, and exacerbating CIRI damage. Targeting this pathway could offer novel therapeutic strategies for mitigating CIRI-induced brain injury.
    KEY POINTS: Identification of the E2F1/CDK5/DRP1 Axis in CIRI This study reveals that the E2F1 transcription factor upregulates CDK5 expression, which in turn phosphorylates DRP1, promoting excessive mitochondrial fission and inhibiting mitophagy in microglia. This mechanism plays a critical role in cerebral ischemia-reperfusion injury (CIRI). Mitochondrial Dysfunction and Neuroinflammation The activation of DRP1 leads to mitochondrial fragmentation and excessive ROS accumulation, triggering microglial activation and inflammatory responses, exacerbating neuronal apoptosis and brain injury in CIRI. Therapeutic Potential of E2F1 Silencing Knockdown of E2F1 in microglia effectively reduces mitochondrial damage, restores mitophagy, suppresses inflammation, and improves neurological outcomes in a CIRI mouse model, highlighting a promising therapeutic target for ischemic stroke intervention.
    Keywords:  CDK5; DRP1; E2F1; cerebral ischemia‐reperfusion; microglia; mitochondrial division; mitophagy; single‐cell transcriptome sequencing
    DOI:  https://doi.org/10.1002/ctm2.70197
  54. EMBO Rep. 2025 Feb 20.
      Stimulator of interferon genes (STING) is essential for innate immune pathway activation in response to pathogenic DNA. Proper activation of STING signaling requires STING translocation and phosphorylation. Here, we show that dual serine/threonine and tyrosine protein kinase (DSTYK) directly phosphorylates STING Ser366 at late endosomes to promote the activation of STING signaling. We find that TBK1 promotes STING post-Golgi trafficking via its kinase activity, thereby enabling the interaction between DSTYK and STING. We also demonstrate that DSTYK and TBK1 can both promote STING phosphorylation at late endosomes. Using an in vivo Dstyk-knockout model, we showed that mice deficient in DSTYK demonstrate reduced STING signaling activation and are more susceptible to infection with a DNA virus. Together, we reveal the previously unknown cellular function of DSTYK in phosphorylating STING and our findings provide insights into the mechanism of STING signaling activation at late endosomes.
    Keywords:  DSTYK; Innate Immunity; Phosphorylation; STING; TBK1
    DOI:  https://doi.org/10.1038/s44319-025-00394-9
  55. J Mol Neurosci. 2025 Feb 17. 75(1): 23
      Radiation brain injury (RBI) is a complication of cranial tumor radiotherapy that significantly impacts patients' quality of life. Astrocyte-secreted vascular endothelial growth factor (VEGF) disrupts the blood-brain barrier (BBB) in RBI. However, further studies are required to elucidate the complex molecular mechanisms involved. Reactive oxygen species (ROS) are closely linked to VEGF pathway regulation, with excessive ROS potentially disrupting this pathway. Mitochondria, the primary ROS-producing organelles, play a crucial role under irradiation. Our findings suggest that irradiation activates astrocytes with altered polarity, generating both cellular and mitochondrial ROS. Concurrently, mitochondrial morphology and function are disrupted, leading to defective mitophagy and an accumulation of damaged mitochondria, which further exacerbates ROS damage. Urolithin A (UA) is a natural activator of mitophagy. We found that UA promoted mitophagy in irradiated astrocytes, reduced cellular and mitochondrial ROS, restored mitochondrial morphology and function, reversed VEGF overexpression, and attenuated the disruption of endothelial tight junction proteins in endothelial cells cultured with irradiated astrocyte supernatants. In conclusion, our study identifies a connection between impaired mitophagy and VEGF overexpression in radiation-induced astrocytes. We also demonstrated UA may serve as a therapeutic strategy for protecting the tight junction protein in RBI by enhancing mitophagy, reducing ROS accumulation, and downregulating VEGF expression.
    Keywords:  Astrocyte; Mitophagy; Radiation-induced brain injury; Urolithin A; VEGF
    DOI:  https://doi.org/10.1007/s12031-024-02302-7
  56. J Extracell Vesicles. 2025 Feb;14(2): e70042
      Histones are conserved nuclear proteins that function as part of the nucleosome in the regulation of chromatin structure and gene expression. Interestingly, extracellular histones populate biofluids from healthy individuals, and when elevated, may contribute to various acute and chronic diseases. It is generally assumed that most extracellular histones exist as nucleosomes, as components of extracellular chromatin. We analysed cell culture models under normal and stressed conditions to identify pathways of histone secretion. We report that core and linker histones localize to extracellular vesicles (EVs) and are secreted via the multivesicular body/exosome pathway. Upregulation of EV histone secretion occurs in response to cellular stress, with enhanced vesicle secretion and a shift towards a population of smaller EVs. Most histones were membrane associated with the outer surface of EVs. Degradation of EV-DNA did not impact significantly on EV-histone association. Individual histones  and histone octamers bound strongly to liposomes and EVs, but nucleosomes did not, showing histones do not require DNA for EV binding. Histones colocalized to tetraspanin positive EVs but using genetic or pharmacological intervention, we found that all known pathways of exosome biogenesis acted positively on histone secretion. Inhibition of autophagy and lysosomal degradation had a strong positive effect on EV histone release. Unexpectedly, EV-associated histones lacked the extensive post-translational modification of their nuclear counterparts, suggesting loss of PTMs may be involved in their trafficking or secretion. Our data does not support a significant role for EV-histones existing as nucleosomes. We show for the first time that histones are secreted from cells as membrane proteins via EVs/exosomes. This fundamental discovery provides support for further investigation of the biological activity of exosome associated histones and their role in disease.
    Keywords:  cellular stress; exosome; extracellular vesicles; histone; membrane associated proteins; posttranslational modification
    DOI:  https://doi.org/10.1002/jev2.70042
  57. Sci Rep. 2025 Feb 21. 15(1): 6347
      This study aimed to delineate the mechanistic target of the rapamycin (mTOR) pathway in the brain tissue of patients with Rasmussen encephalitis (RE) compared to individuals without epilepsy and those with focal cortical dysplasia (FCD) to identify unique pathogenic mechanisms and potential therapeutic targets. Experimental analysis was conducted using RE, control and FCD tissue samples obtained through surgical resection. Western blotting was performed to quantify the expression of established markers of mTOR upstream or downstream signaling. Moreover, immunohistochemistry (IHC) and immunofluorescence (IF) were used to assess cortical and white matter abnormalities and the cell-specific expression of distinct biomarkers. Samples from patients with FCD were utilized as positive controls. We found significantly increased levels of phospho-S6 (Ser240/244), phospho-AKT (Ser473), phospho-p44/42 MAPK (ERK1/2) and phospho-Stat3 (Tyr705) in RE samples compared to those in controls, consistent with the activation of both mTOR complex 1 (mTORC1) and mTORC2. Based on the results of the IHC and IF analyses, we observed strong expression of p-S6 and p-AKT in ectopic neurons and giant neurons. Additionally, we noted expression in perivascular microglia, astrocytes, and microglial nodules. p-MAPK was primarily expressed in astrocytes and blood vessels but was occasionally expressed in neurons; p-MAPK was not coexpressed in microglia. Phospho-ULK1 (Ser757) was expressed in apoptotic neurons, while beclin-1 was predominantly present in microglial nodules and atypical neurons, with no expression in astrocytes. P-Stat3 exhibited positive nuclear expression, while cytoplasmic positivity was observed in cortical cells with a morphology resembling that of astrocytes. The expression level of p-MAPK was significantly correlated with the progression of RE. Our experimental results demonstrate aberrant activation of mTORC1 and mTORC2 in RE patients. These findings offer novel insights into the pathogenic mechanisms of RE and might reveal new therapeutic targets for drug intervention in the treatment of RE.
    Keywords:  Epilepsy; MTOR; Neuropathology; Rasmussen encephalitis
    DOI:  https://doi.org/10.1038/s41598-025-89426-x
  58. Trends Neurosci. 2025 Feb 13. pii: S0166-2236(25)00019-0. [Epub ahead of print]
      Microglia are known to be involved in the modulation of amyloid-β (Aβ) plaques in Alzheimer's disease (AD). In a recent study, Jacquet et al. describe how microglia degrade larger Aβ aggregates by forming lysosomal synapses, further implicating the microglial release of lysosomal Aβ, amongst other processes, in the growth and spread of fibrillary Aβ.
    Keywords:  Alzheimer’s disease; amyloid-β; glia; neurodegeneration; neuroinflammation; plaques
    DOI:  https://doi.org/10.1016/j.tins.2025.01.005
  59. Cell Signal. 2025 Feb 13. pii: S0898-6568(25)00071-3. [Epub ahead of print]129 111658
       BACKGROUND AND PURPOSE: Cerebral ischemia/reperfusion (IR) after ischemic stroke causes deleterious microglial activation. Lysosomal associated membrane protein 3 (LAMP-3) has been indicated play a role in autophagy, yet the specific role of LAMP3 in microglia autophagy during cerebral ischemia and reperfusion (I/R) injury (CIRI) is unknown.
    METHODS: The oxygen-glucose deprivation/reperfusion (OGD/R) model and middle cerebral artery occlusion/reperfusion (MCAO/R) model were established. Changes in autophagy levels were detected through Western blot, immunohistochemistry, transmission electron microscopy, and laser scanning confocal microscopy. Oxidative stress damage in neurons was assessed using ROS and LDH assays. Cytokine levels (IL-6, IL-10, TNF-α, and IL-13) were measured using RT-qPCR and ELISA assays. HMC3, SH-SY5Y cell viability was evaluated using CCK8, EdU staining, Calcein/PI staining, and Transwell assays. Apoptosis was detected via TUNEL staining and flow cytometry. The role of LAMP3 in neuronal function post-cerebral ischemia-reperfusion was further investigated by administering rapamycin and BAY 11-7082.
    RESULTS: LAMP3 expression is decreased in IS, and negatively correlated with LC3B expression. In the HMC3 OGD/R model, LAMP3 inhibits microglial autophagy, and induces oxidative stress damage and inflammatory response in HMC3 cells through the NF-κB pathway. In co-culture system of HMC3 and SH-SY5Y cells, LAMP3 inhibits neuronal autophagy and activity through the NF-κB pathway under OGD/R conditions. In vivo, overexpression of LAMP3 inhibits autophagy and exacerbates brain tissue damage after MCAO/R.
    CONCLUSIONS: During cerebral ischemia-reperfusion, LAMP3 inhibits autophagy in microglia and neurons by activating the NF-κB pathway, thereby inducing oxidative stress and inflammatory factor release, promoting neuronal death. Treatment targeting microglial LAMP3 might be a potential therapeutic strategy for ischemic stroke treatment.
    Keywords:  Apoptosis; Autophagy; Cell co-culture; Cerebral ischemia-reperfusion; LAMP3
    DOI:  https://doi.org/10.1016/j.cellsig.2025.111658
  60. Biochem Biophys Res Commun. 2025 Feb 07. pii: S0006-291X(25)00161-5. [Epub ahead of print]752 151447
      Optineurin (OPTN) is a multifunctional adaptor protein involved in various cellular processes. One critical function is maintaining the Golgi complex, as OPTN depletion or its disease-associated mutations leads to Golgi fragmentation. On the other hand, OPTN is known to be phosphorylated by TBK1 to regulate specific cellular processes; however, its role in Golgi regulation remains unclear. Here, we show that expression of a phosphomimetic OPTN mutant, S177E, but not its phospho-deficient mutant, S177A, in HeLa cells effectively results in fragmentation of the Golgi apparatus. Although the effect of S177E appears similar to that of disease-associated OPTN mutations such as E50K, experiments using OPTN double mutants suggest that S177E induces Golgi fragmentation possibly through an E50K-independent pathway. Furthermore, we found that Ser177 phosphorylation in OPTN is enhanced by TBK1, and co-expression of TBK1 with wild-type OPTN induces Golgi fragmentation. Notably, Ser177 phosphorylation leads to the formation of cytoplasmic OPTN puncta, correlating with Golgi fragmentation. Taken together, our data suggest that OPTN phosphorylation by TBK1 induces ectopic OPTN accumulation, leading to Golgi disassembly, possibly via a novel pathway distinct from those associated with disease-related OPTN mutations.
    Keywords:  Golgi apparatus; Optineurin; Phosphorylation; TBK1
    DOI:  https://doi.org/10.1016/j.bbrc.2025.151447