bims-auttor 2025-09-07 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2025–09–07
37 papers selected by
Viktor Korolchuk, Newcastle University

ATG conjugation-dependent/independent mechanisms underlie lysosomal stress-induced TFEB regulation.
Sequestering sequestosome 1 via S-acylation in autophagy, Huntington disease, and beyond.
Reconstitution of autophagic-like membrane tethering reveals that Atg11 can bind and cluster vesicles on cargo mimetics.
Amino acid-dependent TSC2 dephosphorylation by lysosome-PP2A regulates mTORC1 signaling transduction.
Artificial Peptides as Autophagy Modulators.
Autophagy and Bacterial infections.
RNF126 suppresses amino acid-mediated mTORC1 signaling pathway by ubiquitinating ILF3 in HEK293T cells.
KFERQ-selective protein autophagy in Caenorhabditis elegans depends on LMP-1.
Peri-mitochondrial actin filaments inhibit Parkin assembly by disrupting ER-mitochondria contacts.
VAMP8 stabilization by DRAM1 enables autophagosome-lysosome fusion and promotes metastatic extravasation.
The endoplasmic reticulum autophagy receptor TEX264 drives epidermal differentiation and is dysregulated in Darier disease.
The multifaceted roles of autophagy in plant immunity.
Role of mTORC1 signaling in postnatal microglia activation preceding neurodegeneration in a mouse model for Niemann-Pick disease Type C.
Optineurin deficiency disrupts phosphorylated tau proteostasis and clusterin expression in human neurons.
PPA2 activates MTFP1-DNM1L fission signaling to govern mitochondrial proliferation and mitophagy.
Autophagy and exosomes play different roles in the disposal of unwanted cellular materials.
Newly identified properties of known pharmaceuticals and myxobacterial small molecules revealed by screening for autophagy modulators.
Super-Resolution Imaging Captures Mitophagy Dynamics: Tricolor Fluorescence Labels Mitochondria, Autophagosomes, and Lysosomes.
Evidence that mitochondria in macrophages are destroyed by microautophagy.
Salmonella Typhimurium exploits the reticulophagy/ERphagy receptor RETREG1 to promote infection.
Potential of phytochemicals in the treatment of Alzheimer disease by modulating lysosomal dysfunction: a systematic review.
Rapamycin alleviates neurodegeneration in a Drosophila model of spinocerebellar ataxia type 51.
Mitochondrial Quality Control.
Mitophagy as a pivotal axis in non‑alcoholic fatty liver disease: From pathogenic mechanisms to therapeutic strategies (Review).
Autophagy controls the hippocampal postsynaptic organization and affects cognition in a mouse model of Fragile X syndrome.
HDAC6 and TDP-43 promote autophagy impairment in amyotrophic lateral sclerosis.
The Proteostasis Network in Proteinopathies: Mechanisms and Interconnections.
Conserved LIR-specific interaction of Sigma-1 receptor and GABARAP.
Differential cell survival outcomes in response to diverse amino acid stress.
Impaired MAPT/tau-secretory lysosomes are linked to cognitive vulnerability in Alzheimer patients.
N-degron-mediated ATG8 isoform switching controls plant thermotolerance.
Processing bodies promote lysosomal quality control and cell survival during recovery from lysosomal damage.
Lysosomal reduced thiols are essential for mouse embryonic development.
Asparaginase and Autophagy Inhibitors Effectively Remove Senescent Cells by Synergistically Limiting Asparagine Supply.
Stage-specific regulation by autophagy-related transcription factors drives hematopoietic stem cell formation.
The aging factor EPS8 induces disease-related protein aggregation through RAC signaling hyperactivation.
Molecular mechanisms of mitochondrial quality control.

J Cell Biol. 2025 Oct 06. pii: e202307079. [Epub ahead of print]224(10):

ATG conjugation-dependent/independent mechanisms underlie lysosomal stress-induced TFEB regulation.

Shiori Akayama, Takayuki Shima, Tatsuya Kaminishi, Mengying Cui, Jlenia Monfregola, Kohei Nishino, Andrea Ballabio, Hidetaka Kosako, Tamotsu Yoshimori, Shuhei Nakamura.

TFEB, a master regulator of autophagy and lysosomal biogenesis, is activated by several cellular stresses including lysosomal damage, but its underlying mechanism is unclear. TFEB activation during lysosomal damage depends on the ATG conjugation system, which mediates lipidation of ATG8 proteins. Here, we newly identify ATG conjugation-independent TFEB regulation that precedes ATG conjugation-dependent regulation, designated Modes I and II, respectively. We reveal unique regulators of TFEB in each mode: APEX1 in Mode I and CCT7 and/or TRIP6 in Mode II. APEX1 interacts with TFEB independently of the ATG conjugation system, and is required for TFEB stability, while both CCT7 and TRIP6 accumulate on lysosomes during lysosomal damage, and interact with TFEB mainly in ATG conjugation system-deficient cells, presumably blocking TFEB activation. TFEB activation by several other stresses also involves either Mode I or Mode II. Our results pave the way for a unified understanding of TFEB regulatory mechanisms from the perspective of the ATG conjugation system under a variety of cellular stresses.

DOI: https://doi.org/10.1083/jcb.202307079
Autophagy Rep. 2025 ;4(1): 2547975

Sequestering sequestosome 1 via S-acylation in autophagy, Huntington disease, and beyond.

Y Alshehabi, F Abrar, D D O Martin.

  Protein mislocalization and aggregation are hallmark features in neurodegeneration. As proteins mislocalize, proteostasis deficiency and protein aggregation typically follow. Autophagy is a crucial pathway for the removal of protein aggregates to maintain neuronal health, but is impaired in various neurodegenerative diseases, including Huntington disease (HD). We identified S-acylation, a reversible lipid modification of proteins, as an important regulator in protein trafficking and autophagy. SQSTM1 (sequestosome 1/p62) is an essential selective autophagy receptor for the sequestration of ubiquitinated cargoes within autophagosomes and subsequent delivery into lysosomes for degradation. Recently, we reported that S-acylation of SQSTM1 at the di-cysteine motif C289,290 directs SQSTM1 to lysosomes. We further showed that SQSTM1 S-acylation is significantly reduced in brains from both HD patients and mouse HD model, which may result in the cargo sequestration defect within autophagosomes in HD. Treatment with palmostatin B, a deacylation inhibitor, significantly increases SQSTM1 localization to lysosomes. Our work highlights SQSTM1 S-acylation as a novel potential therapeutic strategy in HD. As a crucial autophagy component, our work suggests S-acylation of SQSTM1 may have a broader role in neurodegeneration.

Keywords:  Autophagy; Huntington disease; S-acylation; fasting; huntingtin; localization; mouse model; palmitoylation; palmostatin B; sequestosome 1

DOI:  https://doi.org/10.1080/27694127.2025.2547975
Autophagy. 2025 Sep 03. 1-20

Reconstitution of autophagic-like membrane tethering reveals that Atg11 can bind and cluster vesicles on cargo mimetics.

Devika Andhare, Sarah Katzenell, Sarah I Najera, Sylvie C Mauras, Katherine M Bauer, Michael J Ragusa.

  Macroautophagy (hereafter, autophagy) is essential for the degradation of mitochondria from yeast to humans. Mitochondrial autophagy in yeast is initiated when the selective autophagy scaffolding protein Atg11 is recruited to mitochondria through its interaction with the selective autophagy receptor Atg32. This also results in the recruitment of small 30-nm vesicles that fuse to generate the initial phagophore membrane. We demonstrate that Atg11 can bind to autophagic-like membranes in vitro in a curvature-dependent manner in part via a predicted amphipathic helix. Deletion of the amphipathic helix from Atg11 results in a delay in the formation of mitophagy initiation sites in yeast. Furthermore, using a novel biochemical approach, we demonstrate that the interaction between Atg11 and Atg32 results in the tethering of autophagic-like vesicles in clusters to giant unilamellar vesicles containing a lipid composition designed to mimic the outer mitochondrial membrane. We also demonstrate that the N-terminal region of Atg11 is an important mediator of vesicle tethering to cargo mimetics and that clustering of autophagic-like vesicles requires the C-terminal region of Atg11. Taken together, our results reveal that Atg11 clusters into high-order oligomers, can tether autophagic-like membranes and due to its ability to oligomerize can cluster vesicles on the surface of cargo mimetics. This work provides new insight into the mechanisms of protein and membrane clustering by Atg11. Given the increasing importance of protein oligomerization and clustering in autophagy, these results have important implications in the initiation of mitochondrial autophagy.Abbreviations Atg11: autophagy related 11; Atg11-Cterm: C-terminal region of Atg11; Atg11-Nterm: N-terminal region of Atg11; Atg32: autophagy related 32; COV: coefficient of variance; DOPC: 1,2-dioleoyl-sn-glycero-3-phosphocholine; DOPE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine; DOPS: 1,2-dioleoyl-sn-glycero-3-phospho-L-serine; FRAP: fluorescence recovery after photobleaching; GLT: GUV and liposome tethering; GUV: giant unilamellar vesicle; MKO: multiple knockout; OMM: outer mitochondrial membrane; PC: phosphatidylcholine; PE: phosphatidylethanolamine; PtdIns: phosphatidylinositol; PtdIns3P: phosphatidylinositol-3-phosphate; RhPE: rhodamine phosphatidylethanolamine; SAR: selective autophagy receptor; SEC: size-exclusion chromatography; SLB: supported lipid bilayers; SMrT: supported membrane templates; YPL: yeast polar lipids.

Keywords:  Biochemistry; membrane tethering; mitophagy; reconstitution; selective autophagy; yeast

DOI:  https://doi.org/10.1080/15548627.2025.2551678
Life Sci Alliance. 2025 Nov;pii: e202503206. [Epub ahead of print]8(11):

Amino acid-dependent TSC2 dephosphorylation by lysosome-PP2A regulates mTORC1 signaling transduction.

Takanori Nakamura, Shigeyuki Nada, Masaki Matsumoto, Nuha Loling Othman, Hidetaka Kosako, Kazuki Ikeda, Naohiko Koshikawa, Junya Masumoto, Tatsuya Sawasaki, Mutsuhiro Takekawa, Takashi Suzuki, Masato Okada.

The mammalian target of rapamycin complex 1 (mTORC1) signaling pathway, composed of amino acid (AA)-sensing (Ragulator/LAMTOR-Rag) and growth factor (GF)-sensing (AKT-TSC1/2-Rheb) axes, pivotally regulates intracellular anabolism and catabolism. mTORC1 deregulation is associated with various metabolic diseases, including cancer and diabetes. As a key regulator of nutrient signaling, mTORC1 integrates a variety of nutrient signals. However, signal integration and crosstalk in the mTORC1 pathway remain incompletely understood. Therefore, in this study, we aimed to understand the complex mTORC1 signaling cascade by constructing an integrated mathematical model of temporal mTORC1 regulation using two AA-sensing and GF-sensing axes. Mathematical simulations and experimental data revealed robust AKT phosphorylation (P-T308/P-S473) after insulin stimulation, regardless of the intracellular AA levels. Conversely, AKT-mediated inhibitory TSC2 phosphorylation (P-T1462) substantially diminished during AA deprivation compared with AA treatment. Furthermore, we highlighted PP2A-mediated TSC2 dephosphorylation during AA removal, ensuring complete mTORC1 activation only upon concurrent AA and GF sensing. Thus, we elucidated mTORC1 signaling dynamics, revealing the complex interplay between AAs and GFs and offering insights into metabolic regulation.

DOI: https://doi.org/10.26508/lsa.202503206
Chembiochem. 2025 Sep 02. e202500432

Artificial Peptides as Autophagy Modulators.

Yuhai Cai, Ling Qiu, Boyu Zhang, Guanya Yang, Jin Cui.

  Autophagy is a highly conserved lysosomal degradation pathway for maintaining cellular homeostasis. Its dysregulation is implicated in various diseases, including cancer, neurodegeneration, and infections, making precise modulation of autophagy a potentially promising therapeutic strategy. Artificial peptide-based autophagy modulators have emerged as a promising alternative to conventional small molecules, offering several advantages in terms of specificity, biocompatibility, and functional versatility. This review summarizes recent advances in artificial peptide-based autophagy monitoring tools, autophagy inducers, and autophagy inhibitors.

Keywords:  autophagy regulator; cancer; chemical modification; drug development; peptide

DOI:  https://doi.org/10.1002/cbic.202500432
Autophagy Rep. 2025 ;4(1): 2542904

Autophagy and Bacterial infections.

Ken Cadwell, Clara Abraham, Shai Bel, Santosh Chauhan, Jörn Coers, María I Colombo, Jacob R Davis, Daniel Hofius, Hang Thi Thu Nguyen, Michinaga Ogawa, Craig R Roy, Feng Shao, Sayaka Shizukuishi, Christina L Stallings, Magdalena Szczesna, Gergory Taylor, Teresa Lm Thurston, Robert Watson, Thomas Wileman, Yue Xu, Dario S Zamboni.

  Autophagy is an evolutionarily conserved cellular process that is prominent during bacterial infections. In this review article, we discuss how direct pathogen clearance via xenophagy and regulation of inflammatory products represent dual functions of autophagy that coordinate an effective antimicrobial response. We detail the molecular mechanisms of xenophagy, including signals that indicate the presence of an intracellular pathogen and autophagy receptor-mediated cargo targeting, while highlighting pathogen counterstrategies, such as bacterial effector proteins that inhibit autophagy initiation or exploit autophagic membranes for replication. Pathways that are related to autophagy, including LC3-associated phagocytosis (LAP) and conjugation of ATG8 to single membranes (CASM), are expanding the role of autophagy in antimicrobial defense beyond traditional double-membrane autophagosomes. Examination of Crohn disease-associated genes links impaired autophagy to inflammation and defective bacterial handling. We propose emerging concepts, such as effector-triggered immunity, where autophagy inhibition by pathogens triggers inflammatory defenses and discusses the therapeutic potential of modulating autophagy in infectious and inflammatory diseases.

Keywords:  Autophagy; CASM; Crohn disease; LC3 associated phagocytosis; bacteria; xenophagy

DOI:  https://doi.org/10.1080/27694127.2025.2542904
Cell Signal. 2025 Sep 02. pii: S0898-6568(25)00525-X. [Epub ahead of print] 112110

RNF126 suppresses amino acid-mediated mTORC1 signaling pathway by ubiquitinating ILF3 in HEK293T cells.

Bin Hu, Meng-Di Shang, Xi Wang, Xiao-Gang Zhang, Meng-Hua Dong, Qi Cao, Xiao-Dan Wei, Yan-Chun Han, Fan Li, Zhen-Lin Yang, Lu-Ying Liu, Jiu-Qiang Wang.

  The mammalian Target of Rapamycin Complex 1 (mTORC1) serves as a metabolic hub that integrates external nutrients to promote cell growth and metabolism, with its activation closely associated with accelerated cancer progression. Interleukin enhancer-binding factor 3 (ILF3) has been identified as a negative regulator of mTORC1 by tethering GATOR1/2 to the lysosomal membrane during amino acid sensing. However, the regulatory mechanisms of the ILF3-mediated mTORC1 signaling pathway remain unclear. In this study, we demonstrate that RNF126 negatively regulates mTORC1 signaling by promoting the K63-linked ubiquitination of ILF3 in HEK293T cells. Silencing RNF126 significantly attenuated the interaction between ILF3 and the GATOR2 complex. Notably, RNF126 depletion in MCF7 cells suppressed breast cancer progression in preclinical models, highlighting its potential as a therapeutic target.

Keywords:  Amino acid; ILF3; RNF126; mTORC1

DOI:  https://doi.org/10.1016/j.cellsig.2025.112110
PLoS One. 2025 ;20(9): e0330339

KFERQ-selective protein autophagy in Caenorhabditis elegans depends on LMP-1.

María Gallardo-Campos, Alicia N Minniti, Juan Hormazabal, Gonzalo Núñez, Carlos F Lagos, Tomás Perez-Acle, Rebeca Aldunate, Iván E Alfaro.

Mammalian cells exhibit three autophagy mechanisms: macroautophagy, microautophagy (MIA), and chaperone-mediated autophagy (CMA), each employing unique mechanisms for transporting cellular material to the lysosome for degradation. MIA involves the engulfment of proteins via lysosomes/late endosomes through membrane invagination, while CMA directly imports cytosolic proteins into lysosomes, selectively targeting those harboring the KFERQ pentapeptide motif, helped by the chaperone HSC70. Despite the identification of several genetic markers of these pathways, our understanding of the underlying mechanisms, particularly in MIA and CMA, remains limited. To study CMA in vivo we designed a photoactivatable CMA reporter consisting of a plasmid encoding the KFERQ consensus signal for CMA targeting. We generated transgenic C. elegans strains with diverse genetic backgrounds to analyze the role of known molecular components of CMA in mammals. Additionally, we conducted an in-silico analysis of the structural interaction between C. elegans LMP-1 or LMP-2 proteins with the HSP-1 chaperone. Results: Our study shows a significant alteration in the distribution pattern of the KFERQ reporter in muscle cells upon induction of selective autophagy (CMA or MIA). We found that the reporter localized into lysosomes only during starvation, which abrogated in the absence of LMP-1. This study validates CMA in C. elegans and provides the development of a new tool for understanding selective autophagy mechanisms and their potential implications in various organisms.

DOI: https://doi.org/10.1371/journal.pone.0330339
EMBO Rep. 2025 Aug 29.

Peri-mitochondrial actin filaments inhibit Parkin assembly by disrupting ER-mitochondria contacts.

Tak Shun Fung, Amrapali Ghosh, Maite R Zavala, Zuzana Nichtova, Dhavalkumar Shukal, Marco Tigano, Gyorgy Csordas, Henry N Higgs, Rajarshi Chakrabarti.

  Mitochondrial damage represents a dramatic change in cellular homeostasis, necessitating metabolic adaptation and clearance of the damaged organelle. One rapid response to mitochondrial damage is peri-mitochondrial actin polymerization within 2 min, which we term ADA (Acute Damage-induced Actin). ADA is vital for a metabolic shift from oxidative phosphorylation to glycolysis upon mitochondrial dysfunction. In the current study, we investigated the effect of ADA on Pink1/Parkin mediated mitochondrial quality control. We show that inhibition of proteins involved in the ADA pathway significantly accelerates Parkin recruitment onto depolarized mitochondria. Addressing the mechanism by which ADA resists Parkin recruitment onto depolarized mitochondria, we found that ADA disrupts ER-mitochondria contacts in an Arp2/3 complex-dependent manner. Interestingly, overexpression of ER-mitochondria tethers overrides the effect of ADA, allowing rapid recruitment of not only Parkin but also LC3 after mitochondrial depolarization. During chronic mitochondrial dysfunction, Parkin and LC3 recruitment are completely blocked, which is reversed rapidly by inhibiting ADA. Taken together we show that ADA acts as a protective mechanism, delaying mitophagy following acute damage, and blocking mitophagy during chronic mitochondrial damage.

Keywords:  Actin; Arp2/3 Complex; ER; LC3; Parkin

DOI:  https://doi.org/10.1038/s44319-025-00561-y
Autophagy. 2025 Sep 02. 1-3

VAMP8 stabilization by DRAM1 enables autophagosome-lysosome fusion and promotes metastatic extravasation.

Rui Zhang, Vincenzo Torraca, Chaojun Yan, Hao Lyu, Shuai Xiao, Dong Guo, Qi Zhang, Cefan Zhou, Jingfeng Tang.

  Autophagosome-lysosome fusion, essential for macroautophagy/autophagy completion, requires the STX17-SNAP29-VAMP8 SNARE complex. While VAMP8 is crucial, its regulatory mechanisms remain incompletely understood. Here, we identify DRAM1 (DNA damage regulated autophagy modulator 1) as a key interactor and stabilizer of VAMP8 on lysosomes. In this study, we demonstrated that DRAM1 directly binds VAMP8, and this interaction is enhanced during autophagy induction. Mechanistically, DRAM1 inhibits ubiquitin-mediated degradation of lysosomal VAMP8 by the E3 ligase STUB1/CHIP to enhance autolysosome formation. DRAM1 competitively binds VAMP8 within residues 66-100 aa, shielding lysines 68, 72, and 75 from STUB1-mediated ubiquitination. This stabilization promotes assembly of the STX17-SNAP29-VAMP8 complex, enhancing autophagosome-lysosome fusion. Functionally, DRAM1-mediated VAMP8 stabilization and autophagic flux promote the extravasation and metastasis of hepatocellular carcinoma (HCC) cells in vitro and in vivo (mouse and zebrafish models). Depletion of core autophagy genes (ATG5 or ATG7) abolishes DRAM1's pro-metastatic effects. Our findings reveal a novel DRAM1-VAMP8 axis that regulates autophagic flux and identify DRAM1 as a potential therapeutic target for inhibiting autophagy-dependent HCC metastasis. Here, we summarize our findings and discuss their implications for our understanding of autophagy regulation.

Keywords:  Autophagosome-lysosome fusion; DRAM1; STUB1; VAMP8; extravasation; ubiquitination

DOI:  https://doi.org/10.1080/15548627.2025.2554794
bioRxiv. 2025 Aug 07. pii: 2025.08.05.668774. [Epub ahead of print]

The endoplasmic reticulum autophagy receptor TEX264 drives epidermal differentiation and is dysregulated in Darier disease.

Christopher J Johnson, Afua Tiwaa, Arti Parihar, Edwin Antonio, Brooke D Lorenz, Reeteka Kudallur, Aaron Ramonett, Anthony Coon, Mrinal K Sarkar, Johann E Gudjonsson, Cory L Simpson.

Differentiating keratinocytes break down their organelles and nuclei to become the compacted cornified layers of the epidermal barrier in a poorly understood catabolic process. Live confocal imaging of stratified human organotypic epidermis revealed endoplasmic reticulum (ER) fragmentation and lysosomal engulfment in the cornifying layers, where we found up-regulation of TEX264, a receptor that mediates selective autophagy of the ER (reticulophagy). TEX264 expression was increased by ER stress, which caused precocious cornification of organotypic epidermis. In undifferentiated keratinocytes, ectopic TEX264 was sufficient to fragment the ER, while in highly differentiated keratinocytes, it accelerated ER elimination and induced nuclear shrinkage; these effects were abolished by mutating the LC3 interacting region required for its autophagic function. Knockout of TEX264 or inhibiting its activation disrupted maturation of organotypic cultures, pointing to a critical role for reticulophagy in cornification. Finally, in patient biopsies and an organotypic model of Darier disease, a genetic cornification disorder linked to ER dysfunction, we found increased TEX264 in areas of premature cornification (dyskeratosis). Our results identified TEX264 as a key driver of epidermal differentiation and led us to propose a novel model of cornification in which keratinocytes activate selective autophagy receptors to orchestrate orderly organelle elimination during cutaneous barrier formation.
GRAPHICAL ABSTRACT:

DOI: https://doi.org/10.1101/2025.08.05.668774
Curr Opin Plant Biol. 2025 Aug 30. pii: S1369-5266(25)00095-0. [Epub ahead of print]87 102781

The multifaceted roles of autophagy in plant immunity.

Hwi Seong Jeon, Eunjeong Jang, Ohkmae K Park.

Autophagy is a highly conserved trafficking pathway that mediates selective degradation of intracellular components via the vacuole or lysosome. Although its roles in cellular homeostasis and stress adaptation are well characterized, the specific functions of autophagy in plant immunity remain incompletely understood. Emerging evidence reveals that autophagy dynamically modulates plant immune responses, contributing to both resistance and susceptibility to a broad spectrum of pathogens. In this review, we explore recent advances in understanding the multifaceted roles of autophagy in plant immunity, with an emphasis on its mechanistic contributions to plant-microbe interactions.

DOI: https://doi.org/10.1016/j.pbi.2025.102781
PLoS One. 2025 ;20(9): e0330437

Role of mTORC1 signaling in postnatal microglia activation preceding neurodegeneration in a mouse model for Niemann-Pick disease Type C.

Caroline E Murray, David S Betancourt-Trompa, Michael S Martinez, Julia M Carson, Lindsay J Walsh, Will C Remillard, Kayla B Fordyce, Rohan Reddy, Ileana Soto.

In Npc1 deficient mice, postnatal developmental alterations in cerebellar microglia and Purkinje cells (PCs) are followed by early-onset neurodegeneration. Even in the absence of PC loss, microglia in Npc1nmf164 mice display hallmark features of activation during early postnatal development, including increased proliferation, enhanced phagocytic activity, and morphological changes indicative of an activated state. In this study, we investigated whether mammalian target of rapamycin complex 1 (mTORC1) drives postnatal activation of cerebellar microglia in Npc1nmf164 mice. We found that elevated CLEC7A (Dectin-1) expression and phosphorylation of S6 ribosomal protein (pS6R), a downstream target of mTORC1, co-occurred in microglial precursors within the developing white matter region (dWMR) of wild-type (WT) mice at postnatal day 7 (P7), as well as in neurodegeneration-associated microglia located in the molecular layer (ML) of Npc1nmf164 mice at P60. In contrast, microglia in the WMR of Npc1nmf164 mice at P60 did not show evidence of CLEC7A expression or increased mTORC1 activation. Interestingly, microglial precursors in the dWMR of Npc1nmf164 mice did not exhibit increased mTORC1 activation at P7 but instead showed delayed increased activation at P10. Inhibiting mTORC1 signaling with rapamycin from P10 to P21 reduced both microglial proliferation and soma size in Npc1nmf164 mice. Additionally, rapamycin treatment preserved VGLUT2⁺ presynaptic terminals/axons that innervate PC dendrites and decreased the total volume of CD68⁺ phagosomes per microglial cell, suggesting a reduction in phagocytic activity. However, the volume of VGLUT2⁺ synaptic material per phagosome remained unchanged between vehicle- and rapamycin-treated groups. While rapamycin enhanced myelination in Npc1nmf164 mice, it did not alter microglial phenotypes in the cerebellar WMR, suggesting that mTORC1 signaling does not mediate WMR microglial activation in this model. Together, our findings demonstrate that mTORC1 activation contributes to the aberrant activation of postnatal ML microglia and to early cerebellar pathology in Npc1nmf164 mice.

DOI: https://doi.org/10.1371/journal.pone.0330437
Acta Neuropathol Commun. 2025 Sep 02. 13(1): 188

Optineurin deficiency disrupts phosphorylated tau proteostasis and clusterin expression in human neurons.

Zachary M Augur, Garrett M Fogo, Mason R Arbery, Andrew M Stern, Courtney R Benoit, Yi-Chen Hsieh, Tracy L Young-Pearse.

  Optineurin (OPTN) is an autophagy adaptor protein involved in selective autophagy, including aggrephagy and mitophagy. Pathogenic mutations in OPTN have also been linked to amyotrophic lateral sclerosis, frontotemporal dementia, and glaucoma, supporting its role in the etiology of neurodegenerative diseases. Despite its established biological roles, knowledge about its potential contribution to Alzheimer's disease (AD) pathology and neuronal functioning is lacking. AD is characterized by the accumulation of extracellular amyloid-β plaques and intracellular phosphorylated tau (pTau) tangles, with dysfunction in the autophagy-lysosomal pathway exacerbating tau pathology and impairing proteostasis. To investigate the role of OPTN in neuronal proteostasis and AD, we utilized induced pluripotent stem cell-derived neuron (iN) and astrocyte (iA) models. Analyses revealed a significant negative correlation between OPTN and specific pTau epitopes in neurons, as well as a decrease in OPTN protein abundance in brain tissues of individuals with AD. Given these findings, we generated OPTN knockout (KO), heterozygous, and wildtype iNs and iAs using CRISPR/Cas9 editing of iPSCs in two genetic backgrounds. Loss of OPTN in iNs increased specific pTau proteoforms without substantially affecting autophagy processes or mitochondrial respiration. Despite no clear effect on mitochondrial function, several mitochondrial proteins, including OXCT1, were enriched in an unbiased analysis of the OPTN interactome in iNs, as well as proteins involved in intracellular trafficking. Proteomic analyses further identified intracellular clusterin, an AD risk gene, as significantly upregulated in OPTN KO iNs, suggesting OPTN may influence its intracellular processing. Our model system demonstrates modest roles for OPTN in certain neuronal biological processes and potential implications for AD pathogenesis. These findings also suggest that OPTN may exhibit functional redundancy with other autophagy adaptor proteins in human neurons, leading to relatively mild phenotypic changes with complete loss of OPTN.

Keywords:  Alzheimer’s disease; Autophagy; Clusterin; Optineurin; Tau

DOI:  https://doi.org/10.1186/s40478-025-02103-y
Autophagy. 2025 Aug 27.

PPA2 activates MTFP1-DNM1L fission signaling to govern mitochondrial proliferation and mitophagy.

Soumya Ranjan Mishra, Priyadarshni Mishra, Kewal Kumar Mahapatra, Bishnu Prasad Behera, Gajanan Kendre, Moureq Rashed Alotaibi, Vijay Pandey, Birija Sankar Patro, Daniel J Klionsky, Sujit Kumar Bhutia.

  The inorganic pyrophosphatase PPA2, a matrix-localized protein, maintains mitochondrial function. Here, we identified the role of PPA2 in activating mitochondrial fission signaling. We found that PPA2 overexpression promotes mitochondrial fission by upregulating the mitochondrial translocation of phosphorylated DNM1L S616. Moreover, PPA2 interacts with MTFP1, a mitochondrial inner membrane protein, to induce fission signaling; cells knocked down for MTFP1 and overexpressing PPA2 failed to induce DNM1L activation and subsequent mitochondrial fission. Furthermore, in physiological conditions, PPA2 directed mitochondrial fission at the midzone through MFF-DNM1L, leading to mitochondrial proliferation. Interestingly, during mitochondrial stress following CCCP treatment, PPA2 triggers peripheral fission through FIS1 and DNM1L to segregate parts of damaged mitochondria, which is essential for mitophagy. In addition, PPA2 utilized the C-terminal LC3-interacting region (LIR) of MTFP1 for mitophagy-mediated clearance of damaged mitochondria. In conclusion, PPA2 activates mitochondrial fission signaling through MTFP1-DNM1L and is essential in defining the site of mitochondrial fission, leading to mitochondrial proliferation or mitophagy for maintaining mitochondrial homeostasis.

Keywords:  MTFP1; Mitochondria; PPA2; mitochondrial fission; mitophagy

DOI:  https://doi.org/10.1080/15548627.2025.2552900
FEBS J. 2025 Sep 02.

Autophagy and exosomes play different roles in the disposal of unwanted cellular materials.

Kedan Mao, Lin Wei, Fangfang Huo, Sidong Xiong, Yuxuan Fu.

  Degradative autophagy supplies a source of nutrients and energy by digesting cytoplasmic components. Additionally, it eliminates toxic protein aggregates and defective organelles from cells. Exosomes are small vesicles that are released by cells into the extracellular environment and are also involved in maintenance of homeostasis by removing unwanted materials and intracellular pathogens. Nevertheless, it remains unclear how these two processes may differ or are alike in their roles in maintaining intracellular homeostasis. In this study, we found that secretory exosomes served as a quality control mechanism, maintaining intracellular RNA homeostasis by facilitating both the selective packaging of endogenous and exogenous RNA species. Conversely, autophagic degradation primarily functions to dispose of both endogenous and exogenous proteins, resulting in controlling intracellular proteostasis. The depletion of exosome secretion resulted in prolonged accumulation of exogenous RNA within the cells, whereas it had no significant effect on the accumulation of exogenous proteins. Viral infection not only induced the host autophagy response, but also impacted secretion of exosomes. Our data showed that secretory exosomes contributed to the clearing of increased intracellular microRNAs induced by enterovirus infection, thereby weakening viral replication. Furthermore, the secretory exosomes were essential for the disposal of viral RNA replicon rather than autophagic degradation, thereby facilitating host survival. Our results collectively revealed that both secretory exosome and autophagic degradation were crucial for maintaining cellular homeostasis, but that they operate through distinct mechanisms and dispose of different types of unwanted materials.

Keywords:  ESCRT pathway; autophagic degradation; exosomes; homeostasis; virus infection

DOI:  https://doi.org/10.1111/febs.70244
FEBS J. 2025 Aug 28.

Newly identified properties of known pharmaceuticals and myxobacterial small molecules revealed by screening for autophagy modulators.

Janine Fichtner, Yan Yan Beer, H G Mauricio Ramm, Sabrina Mühlen, Frank Surup, Jennifer Herrmann, Toni Luise Meister, Stephanie Pfaender, Ursula Bilitewski, Mark Brönstrup, Rolf Müller, Manfred Wirth, Eeva-Liisa Eskelinen, Ingo Schmitz.

  Autophagy is a cellular degradation and recycling process important for maintaining cellular health and function. It is constitutively active at a low level in eukaryotic cells and can be induced by conditions of cellular stress, such as nutrient starvation. Moreover, autophagy plays an important role in diverse processes such as immunobiology, pathogen infection, ageing, and neurodegenerative and other diseases. Using a high-content fluorescence assay for microtubule-associated protein 1 light chain 3 beta (LC3B), a major player in the autophagic pathway, we screened a library of commercial drugs and natural products for activators and inhibitors of LC3B-positive vesicle accumulation. Positive hits for known autophagy modulators included anisomycin, amphotericin B, carbonyl cyanide m-chlorophenylhydrazone (CCCP) and cytochalasin D. Importantly, we identified several new autophagy modulators, such as aciclovir and myxobacterial vioprolides. Anisomycin, aciclovir and vioprolides promoted intracellular growth of Staphylococcus aureus, a bacterium that is known to be a target of autophagy. In contrast, anisomycin strongly inhibited influenza A virus and SARS-CoV-2 replication. Subsequently, we investigated the influence of these autophagy modulators in a cellular disease model of neuronal vacuolation and spinocerebellar degeneration (NVSD), which is associated with cysteine protease ATG4D mutations. We provide evidence that anisomycin and famciclovir, an aciclovir analogue, can normalise the elevated amount of LC3-positive vesicles in mutant fibroblasts, highlighting their potential for the treatment of NVSD. Thus, the screening method enabled the identification of autophagy-modulating compounds with therapeutic potential.

Keywords:  ATG4D; LC3; anti‐infectives; autophagy; drug repurposing; drug screening; natural products

DOI:  https://doi.org/10.1111/febs.70243
Anal Chem. 2025 Sep 05.

Super-Resolution Imaging Captures Mitophagy Dynamics: Tricolor Fluorescence Labels Mitochondria, Autophagosomes, and Lysosomes.

Weikang Peng, Mei Li, Wenwen Li, Yuanjuan Wang, Cheng Tian, Zhilong Zhao, Min Gao, Lei Yang.

Mitophagy is a vital lysosome-dependent process in which damaged mitochondria exhibiting elevated H2O2 production are selectively engulfed by autophagosomes and delivered to lysosomes for degradation, thereby maintaining intracellular homeostasis. Consequently, monitoring mitophagy holds significant potential for disease diagnosis and therapeutic development. In this study, H2O2-activated lysosome-targeted fluorescent probe, PLM, was developed for the super-resolution imaging of the mitophagic process. The initiation of mitophagy induces the significant production of autophagosomes. Red-stained mitochondria are engulfed by blue-stained autophagosomes and subsequently fuse with lysosomes, leading to an increase in the H2O2 concentration within the lysosomes. This activates the green fluorescence signal of PLM. The entire mitophagic process can be visualized and monitored by observing changes in the fluorescence intensity of the autophagosomes and lysosomes as well as the overlap of fluorescence signals. Super-resolution imaging enables the triple-signal nanoscale visualization of the dynamic processes in three organelles. This probe was successfully applied to monitor rapamycin- and starvation-induced mitophagy and was further utilized to assess the role of mitophagy inhibition in enhancing antitumor activity.

DOI: https://doi.org/10.1021/acs.analchem.5c03247
Nat Commun. 2025 Aug 30. 16(1): 8123

Evidence that mitochondria in macrophages are destroyed by microautophagy.

Shiou-Ling Lu, Siyu Chen, Kazuya Noda, Yangjie Li, Chao-Yuan Tsai, Hiroko Omori, Yumiko Kato, Zidi Zhang, Bohan Chen, Kanako Tokuda, Tongxin Zheng, Masahiro Wakita, Eiji Hara, Mitsunori Fukuda, Yoh Wada, Eiji Morita, Narikazu Uzawa, Shinya Murakami, Takeshi Noda.

Microautophagy is an intracellular degradation process in which degradatory organelles, such as the lysosome, directly take up substrates by invagination and/or protrusion of their membranes. Here, we provide evidence that Rab32-positive, lysosome-related organelles in macrophages incorporate various other organelles, including endosomes and mitochondria. Our data indicates that, upon exposure to a mitochondria-damaging reagent, mitochondria can be directly engulfed by the lysosome-like organelles independently of macroautophagy or ESCRT machinery. Rab32 GTPase, phosphatidylinositol 3,5-bisphosphates, ubiquitination, and p62/SQSTM1 are crucial for this degradation. Furthermore, the degree of M1 polarization of macrophages, which is facilitated by metabolic reprogramming into increased glycolysis via mitochondrial elimination, is significantly reduced in Rab32/38 double-knockout macrophages. Thus, microautophagy plays a role in the physiological regulation of macrophages.

DOI: https://doi.org/10.1038/s41467-025-63531-x
Autophagy. 2025 Aug 27. 1-3

Salmonella Typhimurium exploits the reticulophagy/ERphagy receptor RETREG1 to promote infection.

Damian Gatica, Reham Alsaadi, Ryan C Russell.

  Macroautophagy/autophagy is a key catabolic-recycling pathway that can selectively target damaged organelles or invading pathogens for degradation. The selective autophagic degradation of the endoplasmic reticulum, called reticulophagy/ERphagy, controls ER size and degradation of misfolded protein aggregates. RETREG1/FAM134B is an ERphagy receptor that acts by inducing ER membrane curvature and scission through oligomerization. Interestingly, RETREG1 has also been implicated in the cellular response against pathogen infection. Multiple microbes have developed strategies to inhibit ERphagy by targeting RETREG1. In a recent study, we characterized an unidentified mechanism of bacterial-mediated inhibition of ERphagy. Specifically, we found that Salmonella enterica Serovar Typhimurium, a well-known intracellular pathogen that continues to be a major cause of foodborne infections worldwide, inhibits ERphagy by specifically targeting the activity of RETREG1, leading to a pronounced increase in Salmonella burden. We show that Salmonella prevents RETREG1 oligomerization, which is required for efficient ERphagy. Conversely, Salmonella-mediated ERphagy blockage can be bypassed by promoting RETREG1 oligomerization, which recovers ERphagy levels. Salmonella infection also decreases RETREG1 phosphorylation and acetylation, previously reported to be requisite steps in RETREG1-driven ERphagy. Furthermore, in vivo analysis of retreg1 knockout mice infected with Salmonella reveals increased intestinal damage and bacterial levels. Our results provide insights into the interplay between ERphagy and bacterial infection, highlighting a key role for RETREG1 in innate immunity.

Keywords:  Bacteria; FAM134B; SopF; endoplasmic reticulum; xenophagy

DOI:  https://doi.org/10.1080/15548627.2025.2551672
Chin Med. 2025 Sep 01. 20(1): 138

Potential of phytochemicals in the treatment of Alzheimer disease by modulating lysosomal dysfunction: a systematic review.

Man Yuan, Trinh Thach Thi Nguyen, Alasdair J Gibb, Yan-Fang Xian, Hong-Xi Xu.

  Alzheimer disease (AD) is a primary international health dilemma, especially in elderly populations, due to its progressive nature and its adverse cognitive impact. The dysfunction of lysosomes, which impairs protein degradation and leads to toxic accumulation in neurons, is a pivotal factor in AD. We explore phytochemicals that specifically target lysosomal dysfunction via the activation of autophagy, phagocytosis, and lysosome function, exhibiting anti-inflammatory and antioxidant properties. This study involves extracting and evaluating phytochemicals by exploring multiple databases, Google Scholar, PubMed, the Science Citation Index Expanded (SCIE), and the China National Knowledge Infrastructure (CNKI), integrating contemporary biochemical evidence with TCM principles-highlighting the interconnected roles of deficiency, stasis, and phlegm-to provide a comprehensive therapeutic framework. Key phytochemicals-magnolol, trehalose, and salidroside- demonstrate notable promise in enhancing lysosomal function, reducing amyloid beta accumulation, and improving cognitive outcomes. Addressing traditional theory and modern science, we underline the potential for future research by clarifying the mechanisms of compounds and their effectiveness, which may delay the disease process.

Keywords:  Alzheimer disease; Autophagy; Lysosomes; Phagocytosis; Phytochemicals

DOI:  https://doi.org/10.1186/s13020-025-01204-z
J Genet Genomics. 2025 Aug 29. pii: S1673-8527(25)00232-2. [Epub ahead of print]

Rapamycin alleviates neurodegeneration in a Drosophila model of spinocerebellar ataxia type 51.

Cuijie Wei, Taoyun Ji, Jin Xu, Yilei Zheng, Fuze Zheng, Suxia Wang, Chao Gao, Yalan Wan, Zhenyu Li, Jianwen Deng, Hui Xiong.

  Spinocerebellar ataxia (SCA) type 51 is a neurodegenerative disease caused by CAG repeat expansions in exon 1 of the THAP11 gene. These repeats are translated into a glutamine-rich protein, THAP11-polyQ, which forms protein aggregates and exhibits toxicity in cell models; however, the underlying mechanism remains unclear. In this study, we generate transgenic Drosophila models expressing varying lengths of THAP11-polyQ using the UAS-GAL4 system and assess neurodegeneration through pathological and behavioral analyses. Our results demonstrate that expression of THAP11-polyQ in transgenic flies leads to progressive neuronal cell loss, locomotor deficiency, and reduced survival. RNA sequencing of patient-derived skin fibroblasts reveals significant enrichment of the PI3K-Akt-mTOR pathway, and electron microscopy of transgenic flies shows an increase in multilamellar bodies, suggesting involvement of autophagy in SCA51. Consequently, we treat the fly model with rapamycin, an mTOR inhibitor known to enhance autophagy. This treatment reduces toxic THAP11-polyQ protein aggregates, significantly alleviates neuronal degeneration, and improves locomotor function, consistent with the rescue effects observed upon overexpression of Atg8a. Overall, these findings suggest that the Drosophila model, which recapitulates the neurodegenerative features of SCA51, can be used to investigate pathogenic mechanisms, and that rapamycin holds promising potential as a therapeutic approach for this disease.

Keywords:  Drosophila model; PolyQ disease; Rapamycin; Spinocerebellar ataxia type 51; THAP11 gene

DOI:  https://doi.org/10.1016/j.jgg.2025.08.010
Adv Exp Med Biol. 2025 ;1478 51-60

Mitochondrial Quality Control.

Yuntian Guan, Zhen Yan.

  Mitochondria, the power plants of cells, are essential for various cellular functions. In skeletal muscle, mitochondria form a network, called mitochondrial reticulum, which fuels muscle contractile and metabolic functions. The high degree of structure-to-function specialization of mitochondria in skeletal muscle implies that it is closely gauged and regulated to maintain energy production capacity to match the functional demands. The processes that regulate the overall structure and function of mitochondrial reticulum are collectively referred to as mitochondrial quality control. Mitochondrial quality control consists of mitochondrial biogenesis, dynamics (i.e., fission and fusion), and selective degradation via proteolysis and mitophagy. In this chapter, we will discuss different aspects of contemporary understanding of mitochondrial quality control, their respective mechanisms, and their adaptability to exercise training.

Keywords:  Adaptation; Exercise; Mitochondrial biogenesis; Mitochondrial fission; Mitochondrial fusion; Mitochondrial reticulum; Mitophagy; Skeletal muscle

DOI:  https://doi.org/10.1007/978-3-031-88361-3_3
Mol Med Rep. 2025 Nov;pii: 299. [Epub ahead of print]32(5):

Mitophagy as a pivotal axis in non‑alcoholic fatty liver disease: From pathogenic mechanisms to therapeutic strategies (Review).

Yushu Huang, Xueqing Xia, Jingyang Xu, Zihan Wang, Yanting You, Qingfeng Du.

  Non‑alcoholic fatty liver disease (NAFLD), characterized by excessive lipid accumulation in hepatocytes, has emerged as the leading cause of chronic liver disorders globally. As the central metabolic organ, the liver critically depends on mitochondrial integrity. Mitophagy, a selective form of autophagy, plays a pivotal role in sustaining mitochondrial homeostasis by eliminating dysfunctional mitochondria. Dysregulated mitophagy contributes to the progression of NAFLD, while its restoration mitigates disease severity. The present review outlines the tripartite axis of mitophagy, namely, the PTEN‑induced putative kinase 1/Parkin, PI3K/AKT/mTOR and AMP‑activated protein kinase pathways, in NAFLD pathogenesis across the various stages of disease development, including steatosis, nonalcoholic steatohepatitis and fibrosis, and explores their therapeutic potential. Additionally, emerging regulators, including FUN14 domain‑containing protein 1, prohibitin 2, ceramide signaling and non‑coding RNAs, which fine‑tune mitophagy in NAFLD are highlighted. By integrating evidence from pharmacological and natural agents, including traditional Chinese medicines, mitophagy‑centric strategies to promote hepatic lipid metabolism, mitigate disease progression and inform novel NAFLD therapeutics are discussed. This exploration of the mechanisms that govern mitochondrial‑autophagic crosstalk not only advances mechanistic insights but also opens new avenues for precision medicine in the treatment of metabolic liver diseases.

Keywords:  mechanisms; mitophagy; non‑alcoholic fatty liver disease; therapies

DOI:  https://doi.org/10.3892/mmr.2025.13664
Res Sq. 2025 Aug 27. pii: rs.3.rs-4415392. [Epub ahead of print]

Autophagy controls the hippocampal postsynaptic organization and affects cognition in a mouse model of Fragile X syndrome.

Jingqi Yan, Ziyan Zhang, Cameron Keyser, Yaxin Li, Breandan Rosolia, Peng Jiang, Bin Su, Wen Zhang, Morgan Porch, R Suzanne Zukin.

Dysregulated spine morphology is a common feature in pathology of many neurodevelopmental and neuropsychiatric disorders. Overabundant immature dendritic spines in the hippocampus are causally related to cognitive deficits of Fragile X syndrome (FXS), the most common form of heritable intellectual disability. Recent findings from us and others indicate autophagy plays important roles in synaptic stability and morphology, and autophagy is downregulated in FXS neurons. However, the mechanism remains unclear. In this study, we identified that activated autophagy degrades the eukaryotic initiation factor 4G1 (eIF4G1) and postsynaptic density protein-95 (PSD-95) in hippocampal neurons of Fmr1 KO mice and FXS neurons from patients, which subsequently corrected the dysregulated postsynaptic organization and actin assembly, the critical processes determining synaptic maturation and density. Centrally activating autophagy in hippocampus degrades eIF4G1 and PSD-95, restores actin dynamics, and improves cognition of Fmr1 KO mice. In human neurons derived from patients diagnosed with both FXS and intellectual disability, activating autophagy corrected the aberrant actin assembly. Thus, our findings revealed a previously unappreciated mechanism through which autophagy affects actin assembly and synaptic organization, suggesting a critical role of autophagy in regulating structural synaptic plasticity in healthy and diseased conditions.

DOI: https://doi.org/10.21203/rs.3.rs-4415392/v1
Neurobiol Dis. 2025 Sep 03. pii: S0969-9961(25)00296-7. [Epub ahead of print] 107079

HDAC6 and TDP-43 promote autophagy impairment in amyotrophic lateral sclerosis.

Matteo Bordoni, Eveljn Scarian, Emanuela Jacchetti, Camilla Viola, Luca Diamanti, Francesca Dragoni, Rosalinda Di Gerlando, Bartolo Rizzo, Manuela Teresa Raimondi, Stella Gagliardi, Orietta Pansarasa.

  TDP-43 is known to bind the mRNA of histone deacetylase 6 (HDAC6), influencing its RNA translation. Many studies suggest that HDAC6 participates in the regulation of autophagy, which we found impaired in sporadic ALS (sALS) patients. Aim of this work is to evaluate the interaction between TDP-43 and HDAC6 mRNA and to evaluate the effect of the up- and down-regulation of HDAC6 on autophagy in SH-SY5Y cells. Protein level of HDAC6 and TDP-43 binding with HDAC6 mRNA by RNA immunoprecipitation were studied on sALS peripheral blood mononuclear cells (PBMCs). Initially, we observed increased level of HDAC6 protein and increased binding of its mRNA with TDP-43 in sALS PBMCs. We observed that TDP-43 transfection and aggregation in SH-SY5Y cells leads to overexpression of HDAC6. Our results indicate that the autophagy pathway is sensitive to both extremes of α-tubulin acetylation. Indeed, a marked reduction due to HDAC6 overexpression, as well as an excessive increase following HDAC6 downregulation, both result in autophagic dysfunction. This work supports the hypothesis that dysregulation of HDAC6 is a key factor in the disruption of the autophagy pathway previously detected in sALS PBMCs. Our work suggests for the first time that TDP-43 influences autophagy by binding and modulating HDAC6 mRNA. This new pathway suggests that in ALS the aggregation of TDP-43 leads to the overexpression of HDAC6 which impairs autophagy pathway. Thus, our work suggest that in sALS HDAC6 should be tuned and these findings could be exploited in the future as possible therapeutic target.

Keywords:  ALS; HDAC6; Neuroblastoma; Peripheral blood mononuclear cells; TDP-43

DOI:  https://doi.org/10.1016/j.nbd.2025.107079
Am J Pathol. 2025 Aug 26. pii: S0002-9440(25)00300-1. [Epub ahead of print]

The Proteostasis Network in Proteinopathies: Mechanisms and Interconnections.

Dariusz Pytel, Jody Fromm Longo.

  Proteinopathies are neurodegenerative disorders that are characterized by accumulation of misfolded toxic protein aggregates that lead to synaptic and neuronal dysfunction. Though genetically, clinically and pathologically distinct, a common feature of these diseases is disruption of protein homeostasis (proteostasis), which causes accumulation of misfolded proteins. The machinery mediating proteostasis exquisitely balances and interlaces protein synthesis, protein folding and trafficking, and protein degradation processes within the proteostasis network to maintain homeostasis. The proteostasis network governs a functional and dynamic proteome by modulating the timing, location, and stoichiometry of protein expression, surveillance and maintenance of protein folding and removal of misfolded or excess proteins. Although a functional proteome is essential for the health of all cell types, this is especially true for neurons which are prone to enhanced cellular stress. Aging is the most important risk factor for proteostasis decline and the development of proteinopathies. However, germline and somatic mutations can also functionally impair components of the proteostasis network. Post-mitotic cells, particularly neurons, are rendered further susceptible to proteostasis dysfunction due to their extended lifespan. This review discusses the interconnections between the functional components mediating proteostasis in neuronal cells and how aberrations in proteostasis contribute to neuronal dysfunction and disease.

Keywords:  Alzheimer’s Disease; Amyotrophic Lateral Sclerosis; ER stress; ERAD; Frontotemporal Dementia; Huntington’s Disease; Parkinson’s Disease; UPR; aggregates; autophagy; protein homeostasis; proteinopathies

DOI:  https://doi.org/10.1016/j.ajpath.2025.07.011
iScience. 2025 Sep 19. 28(9): 113287

Conserved LIR-specific interaction of Sigma-1 receptor and GABARAP.

Marius Wilhelm Baeken, Maximilian Christ, Daniel Schmitt, Wencke Trein, Heike Nagel, Albrecht Martin Clement, Hagen Körschgen, Christian Behl.

  Among its various functions, the sigma-1 receptor (σ1R) has been reported to modulate macroautophagy. It is currently unknown how this activity is mediated. We phylogenetically, structurally, and biochemically analyzed σ1R regarding its function in autophagy. We identified several putative LC3-interacting-regions (LIRs) that may mediate interactions with ATG8 proteins, which are known to promote autophagosome biogenesis, autophagic cargo reception, and lysosome fusion. Human σ1R comprises a LIR motif (hLIR5) typical for interaction with a specific ATG8, GABARAP. Biochemically, we uncovered a GABARAP-σ1R interaction depending on this motif via peptide array analysis and confirmed this via immunoprecipitation, co-localization, and proximity ligation assays. In addition, we verified a LIR-dependent presence of σ1R in isolated native autophagic vesicles. Excitingly, two point mutations within this LIR that have previously been reported to be associated with autosomal-recessive distal spinal muscular atrophy lack the ability to interact with GABARAP, highlighting the physiological relevance of the hLIR5-mediated σ1R-GABARAP interaction.

Keywords:  Biochemistry; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2025.113287
Life Sci Alliance. 2025 Nov;pii: e202503324. [Epub ahead of print]8(11):

Differential cell survival outcomes in response to diverse amino acid stress.

Marion Russier, Alessandra Fiore, Ana Bici, Annette Groß, Maria Tanzer, Assa Yeroslaviz, Matthias Mann, Peter J Murray.

Amino acid (AA) detection is fundamental for cellular function, balancing translation demands, biochemical pathways, and signaling networks. Although the GCN2 and mTORC1 pathways are known to regulate AA sensing, the global cellular response to AA deprivation remains poorly understood, particularly in non-transformed cells, which may exhibit distinct adaptive strategies compared with cancer cells. Here, we employed murine pluripotent embryonic stem (ES) cells as a model system to dissect responses to AA stress. Using multi-omics analyses over an extended time course, we examined the effects of arginine (Arg) and leucine (Leu) deprivation. We uncovered a broad array of proteomic, phosphoproteomic, transcriptomic, and metabolomic adaptations, including an increase in lysosome production, all occurring without lethality. We found that Arg or Leu starvation induces reversible cell cycle exit, promoting a quiescent state that enhances resistance to cytotoxic stressors. In contrast, cysteine (Cys) and threonine (Thr) deprivation led to cell death via distinct pathways: ferroptosis for Cys starvation, whereas Thr deprivation triggered a previously uncharacterized form of cell death, which could be entirely suppressed by methionine (Met) co-starvation, and mTOR or translational inhibition. These findings suggest that ES cells implement specialized survival strategies in response to different AA limitations, highlighting their ability to reprogram cellular biochemistry under nutrient stress.

DOI: https://doi.org/10.26508/lsa.202503324
Autophagy. 2025 Sep 02. 1-15

Impaired MAPT/tau-secretory lysosomes are linked to cognitive vulnerability in Alzheimer patients.

Preeti Sharma, Anuma Pallavi, Ananya Chatterjee, Vidya Mangala Prasad, Nikhil R Gandasi, Sivaprakasam R Saroja.

  MAPT/tau proteins propagate between brain regions in a prion-like manner, driving the onset and progression of dementia in Alzheimer disease (AD). However, the basis for variability in dementia progression among AD patients remains poorly understood. Here, we demonstrate that cognitively resilient AD patients, characterized by reduced MAPT/tau pathology, maintain lysosomal integrity, whereas cognitively vulnerable patients, exhibiting greater MAPT/tau burden, display lysosomal dysfunction. Lysosomes in cognitively vulnerable AD brains contain partially digested, seed-competent MAPT/tau species composed mainly of the amyloidogenic core with degraded peripheral regions. These pathogenic MAPT/tau forms are secreted via lysosomal exocytosis, facilitating MAPT/tau propagation and contributing to cognitive decline. Cognitively vulnerable female AD patients show increased lysosome-mediated MAPT/tau secretion relative to their male counterparts. Our findings suggest that lysosomal dysfunction, marked by altered protein expression, pH dysregulation, and MAPT/tau accumulation, underlies the heterogeneity in dementia severity. Targeting lysosomal exocytosis and the amyloidogenic core of MAPT/tau fibrils offer a promising therapeutic avenue to mitigate MAPT/tau pathology and promote cognitive resilience in AD and related dementias.Abbreviation: AD: Alzheimer disease, LAMP1; lysosomal associated membrane protein 1, NFT: neurofibrillary tangles; MAPT: microtubule associated protein tau; PHF: paired helical filaments; TIRF: total internal reflection fluorescence; TARDBP/TDP-43:TAR DNA binding protein.

Keywords:  Alzheimer’s disease; cognitive resilience; cognitive vulnerability; lysosome; sex differences; tau pathology

DOI:  https://doi.org/10.1080/15548627.2025.2552905
Autophagy. 2025 Aug 30. 1-3

N-degron-mediated ATG8 isoform switching controls plant thermotolerance.

Seu Ha Kim, Ohkmae K Park.

  Macroautophagy/autophagy is a highly conserved catabolic pathway in eukaryotes that mediates the selective degradation and recycling of cellular components through the formation of double-membrane autophagosomes. ATG8 is a core component of autophagy and determines cargo selectivity through interactions with specific cargo receptors. Higher plants harbor multiple ATG8 isoforms, implying potential functional diversification; however, the biological significance of this isoform expansion remains largely unexplored. In a recent study, we identified UBR7 (UBIQUITIN PROTEIN LIGASE E3 COMPONENT N-RECOGNIN 7) as a novel N-recognin that targets ATG8a for proteasomal degradation via the Arg/N-degron pathway. This selective degradation triggers isoform switching by enabling the replacement of ATG8a with alternative ATG8 isoforms. Notably, this process occurs specifically during the recovery phase following heat stress and plays a critical role in enhancing thermotolerance. Our findings provide new insights into the functional specialization and dynamic regulation of ATG8 isoforms in plants and suggest new directions for improving crop resilience under climate-associated temperature fluctuations.Abberivations HS, heat stress: HSP, heat shock protein; RBP, RNA-binding protein; UTR, untranslated region.

Keywords:  ATG8 isoforms; Arabidopsis; N-degron; UBR7; heat stress; thermotolerance

DOI:  https://doi.org/10.1080/15548627.2025.2552904
bioRxiv. 2025 Aug 30. pii: 2025.08.27.672666. [Epub ahead of print]

Processing bodies promote lysosomal quality control and cell survival during recovery from lysosomal damage.

Jingyue Jia, Jacob Duran, Li Chen, Jing Pu, Pavel Ivanov.

Lysosomes are essential for cell survival but are highly susceptible to diverse physical and pathological stressors. Thus, the ability to initiate an acute damage response and promote recovery after stressor resolution is critical for maintaining cellular homeostasis and viability. Although recent studies have advanced our understanding of acute responses to lysosomal injury, the molecular mechanisms governing the recovery stage and distinguishing it from the acute phase remain poorly defined. Here, we delineate a key difference between these two stages in translational regulation and uncover lysosomal recovery from acute damage as a novel trigger for processing body (PB) formation. PBs are membraneless biomolecular condensates involved in RNA metabolism and translational reprogramming. We provide the first evidence that PBs are critical for lysosomal quality control and cell survival during recovery. Mechanistically, PBs are induced selectively during the recovery phase, but not during the acute damage response, through interactions with stress granules (SGs), distinct membraneless biomolecular condensates formed upon acute injury to stabilize damaged lysosomal membranes for repair. Functional analyses reveal that PBs promote lysosomal quality control by collaborating with SG-mediated membrane stabilization, while independently recruiting released cathepsins, thereby collectively supporting cell survival. Together, these findings establish PBs as central effectors of the lysosomal recovery program and underscore the broader relevance of biomolecular condensates in cellular responses to lysosomal damage and related disease processes.

DOI: https://doi.org/10.1101/2025.08.27.672666
Proc Natl Acad Sci U S A. 2025 Sep 09. 122(36): e2427125122

Lysosomal reduced thiols are essential for mouse embryonic development.

Charles H Adelmann, Avanthika Venkatachalam, Lingjuan Huang, Michelle Liu, Sharon Germana, Stefan A Harry, Paul C Rosen, Joshua Herron, Pei-Chieh Tien, Liron Bar-Peled, David M Sabatini, David E Fisher.

  While it has been appreciated for decades that lysosomes can import cysteine, its significance for whole-organism physiology has remained uncertain. Recent work identified MFSD12 as a transmembrane protein required for cysteine import into lysosomes (and melanosomes), enabling genetic interrogation of this pathway. Here, we show that Mfsd12 knockout mice die between embryonic days 10.5 and 12.5, indicating that MFSD12 is essential for organogenesis. Mfsd12 loss results in the expression of genes involved in cellular stress and thiol metabolism and likely disproportionately affects the erythroid, myeloid, and neuronal lineages. Within lysosomes, imported cysteine is largely oxidized to cystine, which is exported to the cytosol by the cystinosin (CTNS) transporter. However, unlike Mfsd12, loss of Ctns is compatible with viability, suggesting that the essential role of MFSD12 lies not in supplying cystine to the cytosol, but in providing reduced cysteine within the lysosomal lumen. Supporting this model, maternal treatment with cysteamine-a lysosome-penetrant thiol-rescued the development of Mfsd12 knockout embryos, yielding viable adult offspring. These findings establish lysosomal thiol import as a critical metabolic pathway and provide genetic tools to further clarify its physiological and biochemical roles.

Keywords:  MFSD12; cysteine; lysosome; redox

DOI:  https://doi.org/10.1073/pnas.2427125122
Aging Cell. 2025 Sep 04. e70203

Asparaginase and Autophagy Inhibitors Effectively Remove Senescent Cells by Synergistically Limiting Asparagine Supply.

Zhihua Huang, Xinxin Liu, Xiaojia Zhou, Keyu Chen, Honglin Diao, Mingyue Wang, Jianlei Wei, Zeping Li, Yang Yang, Zebin Mao, Wenhua Yu.

  The accumulation of senescent cells (SNCs) contributes to tissue dysfunction and age-related diseases, creating an urgent need for effective senolytic strategies. We identified a metabolic vulnerability in SNCs characterized by marked downregulation of asparagine synthetase (ASNS), rendering them uniquely dependent on exogenous asparagine (Asn). This vulnerability was exploited through combined treatment with L-asparaginase (ASNase) and autophagy inhibitors, which synergistically deplete Asn via complementary mechanisms: ASNase degrades extracellular Asn pools, while autophagy inhibition blocks intracellular protein recycling as an alternative Asn source. This dual approach induced selective synthetic lethality across multiple SNC types in vitro. In aged mice, the combination therapy significantly reduced SNC burden in diverse tissues, improved physiological function, and attenuated progression of age-related conditions including osteoporosis, atherosclerosis, and non-alcoholic fatty liver disease. Our findings establish concurrent targeting of extracellular and intracellular Asn supplies as a potent, selective senolytic strategy with broad therapeutic potential for age-related disorders.

Keywords:  asparaginase; asparagine; asparagine synthetase; autophagy inhibitors; senescent cell

DOI:  https://doi.org/10.1111/acel.70203
Autophagy. 2025 Aug 28. 1-3

Stage-specific regulation by autophagy-related transcription factors drives hematopoietic stem cell formation.

Jia Chen, Jiayi Zheng, Xiaoya Chen, Gangjue Tang, Yan Huang.

  Macroautophagy/autophagy critically regulates hematopoietic stem cell (HSC) development and differentiation, yet the upstream transcriptional mechanisms governing autophagy during dynamic developmental processes remain poorly characterized. Here, we combined single-cell RNA sequencing (scRNA-seq) with metaTF to dissect six consecutive stages of murine HSC development, spanning the aorta-gonad-mesonephros (AGM) region at embryonic day (E) 10.5, the fetal liver at E12.5/E14.5, and adult bone marrow. Beyond transcript abundance alone, we found that the activity of autophagy-related transcription factors (TFs) more robustly characterized cell-type specificity, particularly distinguishing T1 and T2 pre-HSCs, and identified 32 cell-type-specific autophagy-related TFs. Stage-specific autophagy-related TF-target gene networks constructed for T1 and T2 revealed functional partitioning of the pre-HSC stage: an early T1 phase characterized by elevated autophagy activity, and a later T2 phase primarily involved in proliferation and maturation. These findings highlight the temporal regulation exerted by autophagy-related TFs during embryonic hematopoiesis and underscore the importance of autophagy in stem cell fate decision.Abbreviations: HSC: hematopoietic stem cell; TF: transcription factor.

Keywords:  Autophagy; TF activity; metaTF; mouse embryos; single cells

DOI:  https://doi.org/10.1080/15548627.2025.2551671
Nat Aging. 2025 Sep 03.

The aging factor EPS8 induces disease-related protein aggregation through RAC signaling hyperactivation.

Seda Koyuncu, Yaiza Dominguez-Canterla, Rafael Alis, Nassima Salarzai, Dunja Petrovic, Nuria Flames, David Vilchez.

Aging is a major risk factor for neurodegenerative diseases associated with protein aggregation, including Huntington's disease and amyotrophic lateral sclerosis (ALS). Although these diseases involve different aggregation-prone proteins, their common late onset suggests a link to converging changes resulting from aging. In this study, we found that age-associated hyperactivation of EPS8/RAC signaling in Caenorhabditis elegans promotes the pathological aggregation of Huntington's disease-related polyglutamine repeats and ALS-associated mutant FUS and TDP-43 variants. Conversely, knockdown of eps-8 or RAC orthologs prevents protein aggregation and subsequent deficits in neuronal function during aging. Similarly, inhibiting EPS8 signaling reduces protein aggregation and neurodegeneration in human cell models. We further identify the deubiquitinating enzyme USP4 as a regulator of EPS8 ubiquitination and degradation in both worms and human cells. Notably, reducing USP-4 upregulation during aging prevents EPS-8 accumulation, extends longevity and attenuates disease-related changes. Our findings suggest that targeting EPS8 and its regulatory mechanisms could provide therapeutic strategies for age-related diseases.

DOI: https://doi.org/10.1038/s43587-025-00943-w
Transl Neurodegener. 2025 Sep 01. 14(1): 45

Molecular mechanisms of mitochondrial quality control.

Wensheng Li, Yuran Gui, Cuiping Guo, Yuting Huang, Yi Liu, Xuan Yu, Huiliang Zhang, Jianzhi Wang, Rong Liu, Yacoubou Abdoul Razak Mahaman, Qiuhong Duan, Xiaochuan Wang.

  Mitochondria produce adenosine triphosphate (ATP), the main source of cellular energy. To maintain normal function, cells rely on a complex mitochondrial quality control (MQC) system that regulates mitochondrial homeostasis, including mitochondrial dynamics, mitochondrial dynamic localization, mitochondrial biogenesis, clearance of damaged mitochondria, oxygen radical scavenging, and mitochondrial protein quality control. The MQC system also involves coordination of other organelles, such as the endoplasmic reticulum, lysosomes, and peroxisomes. In this review, we discuss various ways by which the MQC system maintains mitochondrial homeostasis, highlight the relationships between these pathways, and characterize the life cycle of individual mitochondria under the MQC system.

Keywords:  Evidence-based therapies; Mitochondria; Mitochondrial diseases; Mitochondrial homeostasis; Mitochondrial quality control

DOI:  https://doi.org/10.1186/s40035-025-00505-5