bims-auttor 2025-10-12 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2025–10–12
27 papers selected by
Viktor Korolchuk, Newcastle University

CRISPR-Cas9 screening reveals G2E3 as a novel ubiquitin-linked factor controlling autophagosome-lysosome fusion and cancer cell progression.
Atg2/TRAPPIII-Ypt1 axis: deciphering the phagophore-ERES connection.
Compromised autophagy in the aging epididymis: Evidence and relevance to male fertility.
PPP2/PP2A-mediated dephosphorylation of LC3B links PINK1-PRKN/Parkin-mediated mitophagy to SCA12 pathogenesis.
The autophagy-specific exocyst subcomplex contributes to phagophore assembly site integrity by promoting phagophore expansion.
Transcriptional Dysregulation of Autophagy in Aging and Potential Interventions: Insights Into TFEB and FOXOs.
PEX14 acts as a molecular link between optineurin and the autophagic machinery to induce pexophagy.
Molecular bases of the interactions of ATG16L1 with FIP200 and ATG8 family proteins.
Structural insight into GPR155-mediated cholesterol sensing and signal transduction.
Endosome transcriptomics reveal trafficking of Cajal bodies into multivesicular bodies.
Hijacking a cellular highway: non-lipidated LC3 proteins and PCNT (pericentrin) drive influenza a virus uncoating.
TRAF6 integrates innate immune signals to regulate glucose homeostasis via Parkin-dependent and Parkin-independent mitophagy.
Ubiquitin-mediated mitophagy regulates the inheritance of mitochondrial DNA mutations.
Reoviruses hijack the SMARCB1-MYC transcriptional regulation complex to activate autophagy for persistent viral infection in leafhopper vector.
MYT1L promotes autophagy to ameliorate amyloid-β pathology and cognitive deficits in Alzheimer's disease via Notch signaling pathway.
ATG4B is required for mTORC1-mediated anabolic activity and is associated with clinical outcomes in non-small cell lung cancer.
Mycobacterium bovis induces macrophage mitochondrial release of hexokinase 2 to enhance intracellular survival.
STAR/STARD1: A mitochondrial intermembrane space cholesterol shuttle degraded through mitophagy.
A novel lncRNA FAM151B-DT regulates degradation of aggregation prone proteins.
Fas apoptotic inhibitor molecule 2 mitigates metabolic dysfunction-associated fatty liver disease through autophagic CRTC2 degradation.
A secretory protein from "candidatus Liberibacter asiaticus" targets SNARE protein CsVTI13 to suppress autophagosome-vacuole fusion and promote bacterial infection.
Histone H4K16 acetylation modification regulated autophagy and apoptosis in neuron after spinal cord injury.
Mutations in the Key Autophagy Tethering Factor EPG5 Link Neurodevelopmental and Neurodegenerative Disorders Including Early-Onset Parkinsonism.
UFM1 at the endoplasmic reticulum: linking ER stress, ribosome quality control, and ER-phagy.
The integrated stress response suppresses antiviral RNA interference by autophagy-mediated degradation of the RNA-induced silencing complex.
Activating PIK3CA mutation promotes overgrowth of adipose tissue via inhibiting lipophagy in macrodactyly.
EIPR1 variants cause a neurodevelopmental disorder with endolysosomal and dense core vesicle defects.

Cell Death Discov. 2025 Oct 09. 11(1): 455

CRISPR-Cas9 screening reveals G2E3 as a novel ubiquitin-linked factor controlling autophagosome-lysosome fusion and cancer cell progression.

Yumei Gong, Marc Leon, Huaqing Mo, Premkamol Pengpaeng, Hai Yang, Yanxi Lu, Zhiqiang Yin, Alan Benard, Yong Zhou, Robert Grützmann, Christian Pilarsky.

Autophagy is a tightly regulated process essential for cellular homeostasis, with ubiquitination playing a crucial role in its regulation. However, the specific ubiquitin related factors involved in autophagic flux remain largely unexplored. Identifying these regulators is essential for advancing the mechanistic understanding of autophagy and its broader implications in cellular function. This study aimed to identify novel ubiquitination-associated regulators of autophagy. To achieve this, we conducted a CRISPR-Cas9 loss-of-function screen targeting 660 ubiquitination-related genes in pancreatic cancer cells expressing the mCherry-GFP-LC3 autophagy flux reporter system. Among the top candidates, we identified G2E3, a G2/M-phase-specific E3 ubiquitin ligase, as a previously unrecognized autophagy regulator. Subsequent functional analyses revealed that G2E3 knock out led to a significant accumulation of LC3B-II and GABARAPs, indicative of impaired autophagic flux. Further confocal imaging demonstrated that the co-localization of LC3B with LAMP1-positive lysosomes was significantly reduced in G2E3 knock out cells, suggesting defective autophagosome-lysosome fusion. Mechanistically, G2E3 directly interacts with GABARAP and GABARAPL1, but not LC3B, positioning it as a key regulator of late-stage autophagy. Additionally, G2E3 knock out cells exhibited reduction in migration and invasion capability, suggesting its role in cancer progression. These findings establish G2E3 as a novel ubiquitin-related regulator of autophagy, specifically facilitating autophagosome-lysosome fusion via a GABARAPs-dependent mechanism. This study reveals a previously unrecognized role of G2E3 in late-stage autophagy and suggests that targeting G2E3 could provide a potential therapeutic approach for modulating autophagy-dependent cellular processes, including cancer progression.

DOI: https://doi.org/10.1038/s41420-025-02717-0
Autophagy. 2025 Oct 08. 1-3

Atg2/TRAPPIII-Ypt1 axis: deciphering the phagophore-ERES connection.

Rubén Gómez-Sánchez, J Christopher Fromme, Christian Ungermann, Fulvio Reggiori.

  De novo generation of membrane contact sites (MCSs) between the nascent phagophore and the endoplasmic reticulum (ER), particularly the ER exit sites (ERES), are crucial for autophagy as they provide the lipids necessary for the phagophore expansion into an autophagosome. Our recent study provides insights into the mechanism involved in the formation of phagophore-ERES MCSs and uncovers how this event synchronizes the factors involved in phagophore expansion. We revealed that the TRAPPIII complex, the guanine nucleotide exchange factor of the Rab GTPase Ypt1, and the lipid transfer protein Atg2 participate in the phagophore-ERES association. We also show that establishment of phagophore-ERES MCSs leads to TRAPPIII activation and subsequent Ypt1 recruitment onto the phagophore. The presence of active Ypt1 on the growing phagophore enhances local biosynthesis of phosphatidylinositol-3-phosphate (PtdIns3P), triggering the recruitment of the PtdIns3P-effectors Atg18 and Atg21, which play a central role in phagophore expansion. These findings suggest that generation of phagophore-ERES MCSs is one of the signals initiating phagophore expansion.Abbreviations: Atg, autophagy related; ER, endoplasmic reticulum; ERES, ER exit sites; GEF, guanine nucleotide exchange factor; MCS, membrane contact site; PAS, phagophore assembly site; PtdIns3P, phosphatidylinositol-3-phosphate; PtdIns3K, phosphatidylinositol 3-kinase; SNARE, soluble NSF attachment protein receptor; TOR, Target of Rapamycin; WIPI, WD-repeat domain, phosphoinositide interacting.

Keywords:  Atg2; Atg9; TRAPPIII; Ypt1; autophagy; membrane contact sites; phagophore

DOI:  https://doi.org/10.1080/15548627.2025.2571682
Exp Gerontol. 2025 Oct 05. pii: S0531-5565(25)00249-9. [Epub ahead of print]211 112920

Compromised autophagy in the aging epididymis: Evidence and relevance to male fertility.

Nabil Eid.

  Impaired autophagy and increased cellular senescence in the aging epididymis may lead to cellular stress, inflammation, and epithelial dysfunction. This reduction in autophagy can be identified using light and electron microscopy, as well as molecular biology techniques. Autophagy, which may be selective or non-selective, is tightly regulated by genes such as LC3 and LAMP-2. Decreased autophagic activity in the epididymis results in reduced sperm quality and male fertility. These findings highlight autophagy as a potential therapeutic target in age-related male reproductive decline.

Keywords:  Autophagy; Epididymis; LC3-associated phagocytosis; Mitophagy; Senescence; Sperm

DOI:  https://doi.org/10.1016/j.exger.2025.112920
Autophagy. 2025 Oct 08.

PPP2/PP2A-mediated dephosphorylation of LC3B links PINK1-PRKN/Parkin-mediated mitophagy to SCA12 pathogenesis.

Ningning Li, Hongyu Hou, Dan Su, Bojun Yang, Rui Ni, Guoqiang Ma, Shan Sun, Qilian Ma, Qiang Peng, Siqian Chen, Kin Yip Tam, Hongfeng Wang, Zheng Ying.

  Atg8-family proteins are autophagosome-associated proteins and play important roles in macroautophagy/autophagy, a conserved process for degrading defective or excessive cellular components. Post-translational modifications of mammalian Atg8-family proteins, including phosphorylation, regulate multiple steps in the autophagic process. In this context, several Atg8-family protein-associated kinases have been found to regulate autophagy, yet the phosphatases in the dephosphorylation of Atg8-family proteins remain unknown. Here, we report that the heterotrimeric PPP2/PP2A (protein phosphatase 2) is a novel regulator in modulating LC3B dephosphorylation. Mechanistically, we find that PPP2-mediated LC3B dephosphorylation reduces the interaction between LC3B and the mitophagy receptor OPTN, thereby impeding the mitochondrial recruitment of phagophores during PINK1-PRKN/Parkin-mediated mitophagy. Interestingly, we find that overexpression of the β2 isoform of PPP2R2B (protein phosphatase 2 regulatory subunit Bbeta; PPP2R2Bβ2), which mimics the spinocerebellar ataxia type 12 (SCA12) pathological condition, harms neuronal survival by enhancing PPP2-mediated LC3B dephosphorylation and reducing mitochondrial recruitment of phagophores upon mitochondrial damage. Importantly, pharmacological induction of mitophagy by the small molecule compound deferiprone (DFP) relieves PPP2R2Bβ2-mediated neuronal toxicity. Overall, our results not only uncover a mechanism by which protein dephosphorylation negatively regulates mitophagy but also provide insights into the pathogenesis of PPP2R2Bβ2-mediated SCA12.

Keywords:  LC3B; PINK1-PRKN/Parkin-mediated mitophagy; PPP2/PP2A; PPP2R2Bβ2; dephosphorylation; mitochondrial quality control

DOI:  https://doi.org/10.1080/15548627.2025.2572528
Proc Natl Acad Sci U S A. 2025 Oct 14. 122(41): e2426476122

The autophagy-specific exocyst subcomplex contributes to phagophore assembly site integrity by promoting phagophore expansion.

Ruchika Kumari, Titikhya Nath, Jeremy Pflaum, Inchara R, Sannannagari Vinay, Florian Wilfling, Ravi Manjithaya.

  Autophagy is a crucial intracellular pathway for maintaining cellular homeostasis. It involves forming double-membrane vesicles called autophagosomes, which deliver cytosolic cargoes to the lysosomes/vacuoles for degradation. Biogenesis of autophagosomes is a membrane-intensive process wherein the membrane expansion steps are poorly understood. The tethering complex, exocyst, canonically implicated in secretion, also participates in autophagosome biogenesis in yeast, plants, and mammals. However, the contribution of the exocyst complex in autophagosome biogenesis is unclear. In this study, using yeast temperature-sensitive mutants of the exocyst, we observed the accumulation of multiple abortive PAS incapable of autophagosome biogenesis. These dysfunctional abortive structures were enriched with core autophagy proteins involved in initiation and membrane expansion. However, the membrane expansion ability required for cargo capture was severely compromised in these mutants. Further investigations, including a comprehensive epistasis analysis, revealed that the exocyst plays a role downstream of the Atg1 complex. However, it was required at a stage before phosphatidylinositol 3-kinase (PI3K complex I), Atg2-Atg18, and Atg12-Atg5-Atg16 complexes. Taken together, we show that productive PAS formation and membrane expansion during autophagosome biogenesis are exquisitely orchestrated by the autophagy-specific exocyst subcomplex, which excludes Exo70.

Keywords:  PAS; autophagy; exocyst; membrane expansion; phagophore

DOI:  https://doi.org/10.1073/pnas.2426476122
Front Biosci (Landmark Ed). 2025 Sep 28. 30(9): 38730

Transcriptional Dysregulation of Autophagy in Aging and Potential Interventions: Insights Into TFEB and FOXOs.

Cheng-Ju Kuo, Denisa M Manastireanu, Jose L Nieto-Torres, Caroline Kumsta.

  Autophagy is a highly conserved cellular degradation and recycling process essential for maintaining cellular homeostasis. However, autophagic activity declines with age, contributing to the accumulation of damaged organelles and protein aggregates. The decline in autophagic activity is considered a primary hallmark of aging, as it contributes to cellular dysfunction and the onset of age-associated diseases, including neurodegenerative disorders and metabolic dysfunction. Sustaining autophagy with age requires transcriptional regulation, which may become impaired with age. In this review, we summarize current understanding of transcriptional regulation of autophagy during aging, with a specific focus on transcription factor EB (TFEB) and forkhead box O (FOXO) transcription factors. We integrate mechanistic insights from both mammalian systems and model organisms to highlight how their regulatory activity declines with age through changes in expression, post-translational modifications, nuclear transport, and transcriptional efficiency. We further explore pharmacological and lifestyle interventions aimed at restoring autophagic function to mitigate cellular decline. Given the pivotal role of autophagy in promoting cellular resilience and disease prevention, targeting autophagy-regulating transcription factors holds promise as a therapeutic strategy to counteract age-related functional decline and extend healthspan.

Keywords:  aging/genetics; autophagy/genetics; drug effects/therapeutic use; forkhead box O (FOXO) transcription factors/forkhead transcription factors; transcription factor EB (TFEB)/microphthalmia-associated transcription factors (MITFs)

DOI:  https://doi.org/10.31083/FBL38730
J Cell Biol. 2025 Nov 03. pii: e202411184. [Epub ahead of print]224(11):

PEX14 acts as a molecular link between optineurin and the autophagic machinery to induce pexophagy.

Hongli Li, Suyuan Chen, Celien Lismont, Bram Vandewinkel, Mohamed A F Hussein, Cláudio F Costa, Dorien Imberechts, Yiyang Liu, Jorge E Azevedo, Wim Vandenberghe, Steven Verhelst, Hans R Waterham, Pieter Vanden Berghe, Myriam Baes, Marc Fransen.

Pexophagy, the selective degradation of peroxisomes, is essential for removing excess or dysfunctional peroxisomes, and its dysregulation has been linked to various diseases. Although optineurin (OPTN), an autophagy receptor involved in mitophagy, aggrephagy, and xenophagy, has also been implicated in pexophagy in HEK-293 cells, the underlying mechanisms remain unclear. Using proximity labeling, we identified PEX14, a peroxisomal membrane protein, as a neighboring partner of OPTN. Microscopy analyses revealed that clustering of peroxisomes with OPTN is a key feature of OPTN-mediated pexophagy. Biochemical studies demonstrated that PEX14 and OPTN interact through their coiled-coil and ubiquitin-binding domains, respectively. Further analyses showed that the C-terminal half of overexpressed OPTN triggers pexophagy, likely by oligomerizing with endogenous OPTN. The colocalization of PEX14-OPTN complexes with LC3, together with the suppression of OPTN-mediated peroxisome degradation by bafilomycin A1, supports a model in which PEX14 acts as a docking site for OPTN on the peroxisomal membrane, enabling the recruitment of the autophagic machinery for OPTN-mediated pexophagy.

DOI: https://doi.org/10.1083/jcb.202411184
Nat Commun. 2025 Oct 10. 16(1): 9035

Molecular bases of the interactions of ATG16L1 with FIP200 and ATG8 family proteins.

Xinyu Gong, Yuqian Zhou, Yingli Wang, Yubin Tang, Haobo Liu, Xindi Zhou, Yuchao Zhang, Hanbo Guo, Zhenpeng Guo, Lifeng Pan.

Macroautophagy maintains cellular and organismal homeostasis, and entails de novo synthesis of double-membrane autophagosome. The effective formation of autophagosome requires the recruitment of the ATG12~ATG5-ATG16L1 complex to the pre-autophagosomal structure by relevant ATG16L1-binding autophagic factors including FIP200. However, the molecular mechanism governing the specific interaction of ATG16L1 with FIP200 remains elusive. Here, we uncover that ATG16L1 contains a FIP200-interacting region (FIR), which not only can directly bind FIP200 Claw domain, but also can serve as an atypical ATG8-interacting motif to selectively recognize mammalian ATG8 family proteins (ATG8s). We determine the high-resolution crystal structures of ATG16L1 FIR in complex with FIP200 Claw and GABARAPL1, respectively, and elucidate the molecular mechanism underlying the interactions of ATG16L1 with FIP200 and ATG8s. To distinguish the precise contribution of FIP200 from ATG8s for binding to ATG16L1 FIR in autophagy, we develop a ATG16L1 mutant that can exclusively interact with ATG8s but not FIP200. Finally, using relevant cell-based functional assays, we demonstrate that the interaction of ATG16L1 with FIP200 is indispensable for the effective autophagic flux. In conclusion, our findings provide mechanistic insights into the interactions of ATG16L1 with FIP200 and ATG8s, and are valuable for further understanding the function of ATG16L1 in autophagy.

DOI: https://doi.org/10.1038/s41467-025-64097-4
Sci Bull (Beijing). 2025 Sep 10. pii: S2095-9273(25)00925-9. [Epub ahead of print]

Structural insight into GPR155-mediated cholesterol sensing and signal transduction.

Delin Li, Xiaokang Zhang, Jie Feng, Yufeng Xie, Pu Han, Ming He, Lin Hao, Tianling Guo, Xiaoyi Bai, Kai Yuan, Junqing Sun, Xuefei Pang, Yan Wu, Yingxia Liu, George Fu Gao, Niu Huang, Haixia Xiao, Feng Gao.

  Cholesterol (CHL) serves as a building block for membrane biogenesis and a precursor to oxysterols, steroid hormones, bile acids, and vitamin D. The lysosome serves as a major sorting station for low-density lipoproteins (LDLs), which carry dietary CHL, and it is also the cellular site where the master growth regulator, the protein kinase mechanistic Target of Rapamycin Complex 1 (mTORC1), is activated. Recently, the lysosomal transmembrane protein GPR155 was reported to signals CHL sufficiency to mTORC1 through sequestration of the GTPase-activating protein towards the Rags 1 (GATOR1). Although the recently reported structures of GPR155 have revealed the CHL binding site, how the signal is transduced from the CHL binding site to the soluble parts of GPR155 and GATOR1 remains unknown. Here, with our three cryo-EM structures of GPR155 captured in different conformations in complex with CHL, complemented by long-time scale molecular dynamics simulations, the dynamic rearrangement of different domains was observed. CHL binding induces a widening of the crevice between the transporter and GPCR domains. The extending helix preceding transmembrane helix (TM) 16, which was unresolved in other structures, acts as a linkage lever that transmits the rotation of the GPCR domain to the soluble parts of GPR155 in response to CHL binding. This work not only answers the question of how CHL is sensed by GPR155, but also addresses a more profound question: how the signal perceived by the TMs regions is transduced to the LED and DEP domains.

Keywords:  Cholesterol; GATOR1; GPCR; LYCHOS; Transporter; mTORC1

DOI:  https://doi.org/10.1016/j.scib.2025.09.012
Proc Natl Acad Sci U S A. 2025 Oct 14. 122(41): e2511840122

Endosome transcriptomics reveal trafficking of Cajal bodies into multivesicular bodies.

Jasleen Singh, Justin Krish Williams, Quinn Elliott, Rohit Jhawar, Lucas Ferguson, Kathleen Collins, Randy Schekman.

  All eukaryotic cells secrete exosomes, a type of extracellular vesicles derived from the endocytic compartments known as multivesicular bodies (MVBs), or late endosomes (LEs). Exosomes contain a diverse range of cargo such as nucleic acids, proteins, lipids, and small molecules but whether these contents have a biological function remains an area of intense investigation. Over the last decade, numerous studies have described the transcriptome of exosomes but very little is known about the RNA content of the MVBs, the source compartment for exosome biogenesis. Here, we determine the small-RNA transcriptome of highly purified MVBs and report that various classes of nuclear small regulatory RNAs such as small-Cajal body associated RNAs, small-nucleolar RNAs, and small-nuclear RNAs traffic to MVBs. We show that this RNA-trafficking requires the function of endosomal sorting complexes required for transport (ESCRT) machinery but is independent of canonical LC3 lipidation mediated selective autophagy. Furthermore, blocking the activity of a PI3K Class 3 enzyme, VPS34, required for recruitment of the ESCRT machinery to the endosome, prevents the turnover of these nuclear RNAs in MVBs. Our results provide a mechanism for targeting nuclear ribonucleoprotein complexes, such as Cajal bodies, for degradation and turnover by the cytoplasmic endo-lysosomal pathway.

Keywords:  RNA-trafficking; RNPs; endosomes; exosomes; intraluminal vesicles (ILVs)

DOI:  https://doi.org/10.1073/pnas.2511840122
Autophagy. 2025 Oct 08.

Hijacking a cellular highway: non-lipidated LC3 proteins and PCNT (pericentrin) drive influenza a virus uncoating.

Yingying Cong, Fulvio Reggiori.

  MAP1LC3/LC3 (microtubule associated protein 1 light chain 3) proteins have long been thought to carry out their cellular and organismal functions, including macroautophagy/autophagy, exclusively in their lipidated form, also referred to as Atg8ylation. They are anchored mainly to the phosphatidylethanolamine present in membranes through the action of two ubiquitin-like conjugation systems. Our recent work, however, uncovered a role of non-lipidated LC3s during influenza A virus (IAV) infection. We revealed that LC3s, together with the centrosomal scaffold protein PCNT (pericentrin), form a dynein adaptor complex that facilitates IAV uncoating at late endosomes (LEs). We also showed that co-opting the LC3s-PCNT complex is an alternative strategy to aggresome processing machinery (APM) hijacking via HDAC6, allowing IAV to exploit the force generated by dynein-dependent motors for virion uncoating and genome delivery in the host cytoplasm. Notably, the function of LC3s in IAV uncoating does not require their Atg8ylation or the core autophagy machinery, and PCNT's role is independent from its centrosomal localization. These findings redefine LC3s as multifunctional adaptor proteins and reveal how viruses can co-opt centrosome assembly machinery components for host invasion.

Keywords:  Atg8ylation; IAV cell entry; LC3-I; centrosome; dynein

DOI:  https://doi.org/10.1080/15548627.2025.2572527
Sci Adv. 2025 Oct 10. 11(41): eadw4153

TRAF6 integrates innate immune signals to regulate glucose homeostasis via Parkin-dependent and Parkin-independent mitophagy.

Elena Levi-D'Ancona, Emily M Walker, Jie Zhu, Yamei Deng, Vaibhav Sidarala, Ava M Stendahl, Emma C Reck, Belle A Henry-Kanarek, Anne C Lietzke, Biaoxin Chai, Mabelle B Pasmooij, Dre L Hubers, Venkatesha Basrur, Sankar Ghosh, Linsey Stiles, Alexey I Nesvizhskii, Orian S Shirihai, Scott A Soleimanpour.

Innate immune signaling is activated in immunometabolic diseases, including type 2 diabetes, yet its impact 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 pancreatic β cell function at baseline, TRAF6 was pivotal for insulin secretion, mitochondrial respiration, and mitophagy following metabolic stress in mouse and human islets. TRAF6 was critical for the recruitment and function of the ubiquitin-mediated (Parkin-dependent) mitophagy machinery. Glucose intolerance induced by TRAF6 deficiency following metabolic stress was reversed by concomitant Parkin deficiency by relieving obstructions in receptor-mediated (Parkin-independent) mitophagy. Our results establish that TRAF6 is vital for traffic through Parkin-mediated mitophagy and implicates TRAF6 in the cross-regulation of ubiquitin- and receptor-mediated mitophagy. Together, we illustrate that β cells engage innate immune signaling to adaptively respond to a diabetogenic environment.

DOI: https://doi.org/10.1126/sciadv.adw4153
Science. 2025 Oct 09. 390(6769): 156-163

Ubiquitin-mediated mitophagy regulates the inheritance of mitochondrial DNA mutations.

Michele Frison, Brandon S Lockey, Yu Nie, Zoe Golder, Eleni Theiaspra, Cameron D Ryall, Camilla Lyons, Stephen P Burr, Malwina Prater, Lyuba V Bozhilova, Angelos Glynos, James B Stewart, Nick S Jones, Marcos R Chiaratti, Patrick F Chinnery.

Mitochondrial synthesis of adenosine triphosphate is essential for eukaryotic life but is dependent on the cooperation of two genomes: nuclear and mitochondrial DNA (mtDNA). mtDNA mutates ~15 times as fast as the nuclear genome, challenging this symbiotic relationship. Mechanisms must have evolved to moderate the impact of mtDNA mutagenesis but are poorly understood. Here, we observed purifying selection of a mouse mtDNA mutation modulated by Ubiquitin-specific peptidase 30 (Usp30) during the maternal-zygotic transition. In vitro, Usp30 inhibition recapitulated these findings by increasing ubiquitin-mediated mitochondrial autophagy (mitophagy). We also found that high mutant burden, or heteroplasmy, impairs the ubiquitin-proteasome system, explaining how mutations can evade quality control to cause disease. Inhibiting USP30 unleashes latent mitophagy, reducing mutant mtDNA in high-heteroplasmy cells. These findings suggest a potential strategy to prevent mitochondrial disorders.

DOI: https://doi.org/10.1126/science.adr5438
PLoS Pathog. 2025 Oct;21(10): e1013569

Reoviruses hijack the SMARCB1-MYC transcriptional regulation complex to activate autophagy for persistent viral infection in leafhopper vector.

Hui Wang, Runfa Liu, Guangming Xiao, Yanan Li, Bozhong Li, Qian Chen, Taiyun Wei.

Autophagy plays a crucial role in virus-host interactions, as viral components and particles can be degraded by the host's autophagic machinery. Additionally, some viruses can hijack autophagy for their own benefit. However, the mechanisms underlying the transcriptional regulation of autophagy by arboviruses in insect vectors remain largely unexplored. In this study, we found that rice dwarf virus (RDV) infection activates the autophagy pathway in the leafhopper vector, Nephotettix cincticeps, and this autophagy activation also facilitates viral infection in the leafhopper. We identified that MYC transcription factor regulates the expression of autophagy proteins ATG5 and ATG8 by directly targeting their promoters. A transcription regulator SMARCB1 binds to MYC and impedes its recognition of the ATG5 and ATG8 promoters, thus negatively regulating their expression. Moreover, NcSMARCB1 negatively regulates ATG5 expression by directly binding to its promoter. RDV major outer capsid protein P8 blocks the nuclear translocation of SMARCB1, disrupting the SMARCB1-MYC interaction and thereby relieving the transcriptional inhibition of ATG5 and ATG8, which leads to autophagy activation. Furthermore, major outer capsid protein P8 of rice gall dwarf virus (RGDV), same to RDV belonging to plant reoviruses, also interacts with SMARCB1 in leafhopper Recilia dorsalis, preventing its nuclear translocation. Similarly, suppression of SMARCB1 expression enhances autophagy formation and promotes RGDV infection. These findings highlight the critical role of insect vector SMARCB1 and MYC in regulating autophagy in response to arbovirus infection.

DOI: https://doi.org/10.1371/journal.ppat.1013569
Exp Neurol. 2025 Oct 06. pii: S0014-4886(25)00357-7. [Epub ahead of print] 115492

MYT1L promotes autophagy to ameliorate amyloid-β pathology and cognitive deficits in Alzheimer's disease via Notch signaling pathway.

Meiyan Zhang, Shuangshuang Hai, Xiaoyan Gao, Zhiqiang Cui, Tuo Yang, Aiming Wang, Jianwen Lin, Xiaohong Sun.

  Autophagy is essential in the growth and advancement of Alzheimer's disease (AD). Myelin transcription factor 1-like (MYT1L) has been reported to have neuroprotective properties; however, its precise role in AD is still unclear. This study identified a reduction in MYT1L expression in the hippocampal neurons of AD model mice. Interestingly, increasing MYT1L expression in these neurons helped alleviate cognitive impairments in APP/PS1 mice. Additionally, MYT1L overexpression reduced the amyloid-beta (Aβ) burden, promoted autophagy, and provided neuroprotection in the hippocampus of these mice. Further investigation of the mechanisms revealed that MYT1L overexpression downregulated the Notch signaling pathway in Aβ25-35-induced SH-SY5Y cells, which in turn promoted autophagy and protected neuronal health. These results highlight previously unrecognized roles of MYT1L in neuronal protection, suggesting that MYT1L could be an intriguing therapeutic target for AD.

Keywords:  Alzheimer's disease; MYT1L; Notch signaling pathway; autophagy; β-amyloid protein

DOI:  https://doi.org/10.1016/j.expneurol.2025.115492
FEBS Open Bio. 2025 Oct 09.

ATG4B is required for mTORC1-mediated anabolic activity and is associated with clinical outcomes in non-small cell lung cancer.

Patrick J Ryan, Bethany C Guerra, Selina Uranga, Jessica M Cardin, Steven E Riechman, Mariana Janini Gomes, James D Fluckey.

  The complex interplay of metabolic signaling networks is critical to the pathophysiology of lung cancer. The anabolic mTORC1 kinase and catabolic process of autophagy are key among these regulatory pathways. While their relationship has long been viewed as a matter of simple inhibition, with mTORC1 as a negative regulator of autophagy, new evidence suggests that this relationship may be more nuanced than previously described. Here, we demonstrate that an autophagy-related, ATG4B, is required for mTORC1 activity and is associated with negative clinical outcomes in non-small cell lung cancer (NSCLC). Targeting ATG4B in vitro suppresses cell proliferation, protein synthesis rates, and mTORC1 signaling in NSCLC cell lines. In contrast, overexpressing the ATG4B protease in healthy models of lung tissue increased mTORC1 kinase activity in healthy lung cell models, indicating that an increase in ATG4B is sufficient to drive cellular anabolic signaling. Finally, we found that ATG4B expression is high in NSCLC patient tumors, is elevated in early-stage cancer, and predicts survival in lung adenocarcinoma patients. Taken together, our results demonstrate that ATG4B is required for anabolic behavior in NSCLC, indicating that the autophagic cascade may be a required input for mTORC1 activity and cellular anabolism in lung cancer. These results have implications for the field of cancer biology more broadly, as they indicate that the far from being a simple target of mTORC1, the autophagic cascade may serve as a requisite input for anabolic signaling, casting new light on the relationship between these processes in cancer pathophysiology.

Keywords:  autophagy; cell signaling; mTORC1; metabolism; non‐small cell lung cancer

DOI:  https://doi.org/10.1002/2211-5463.70138
Cell Rep. 2025 Oct 08. pii: S2211-1247(25)01192-1. [Epub ahead of print]44(10): 116421

Mycobacterium bovis induces macrophage mitochondrial release of hexokinase 2 to enhance intracellular survival.

Lin Li, Yulan Chen, Yuanzhi Wang, Yuhui Dong, Haoran Wang, Ziyi Liu, Xin Ge, Puxiu Shen, Yue Li, Dingpu Liu, Xiangmei Zhou.

  Hexokinases (HKs) are essential enzymes in sugar metabolism, but their mitochondrial release also reflects cellular status in disease. Mycobacterium bovis (M. bovis), the causative agent of bovine and human tuberculosis, infects macrophages and induces mitophagy, yet the role of HKs in this process remains unclear. We find that M. bovis infection induces the release of HK2 from mitochondria, where it dissociates from voltage-dependent anion channel (VDAC). This dissociation promotes VDAC oligomerization, pore formation in the outer mitochondrial membrane, and mitochondrial damage. Damaged mitochondria subsequently undergo mitophagy, which enhances the intracellular survival of M. bovis. Consistent with this mechanism, we show that ESAT6-mediated phagosome membrane rupture is critical for HK2 release and subsequent mitochondrial events. Our study identifies a pathway by which M. bovis manipulates host cell processes to promote survival, providing insights into the host-pathogen interaction and potential avenues for tuberculosis prevention and therapy.

Keywords:  CP: Microbiology; Mycobacterium bovis; VDAC; autophagy; hexokinase; macrophage; mitochondria; mitophagy; tuberculosis

DOI:  https://doi.org/10.1016/j.celrep.2025.116421
Proc Natl Acad Sci U S A. 2025 Oct 14. 122(41): e2508809122

STAR/STARD1: A mitochondrial intermembrane space cholesterol shuttle degraded through mitophagy.

Prasanthi P Koganti, Amy H Zhao, Michael C Kern, Auriole C R Fassinou, Vimal Selvaraj.

  The import of cholesterol to the inner mitochondrial membrane by the steroidogenic acute regulatory protein (STAR/STARD1) is essential for de novo steroid hormone biosynthesis and the alternate pathway of bile acid synthesis. This robust system, evolved to start and stop colossal cholesterol movement, ensures pulsatile yet rapid mitochondrial steroid metabolism in cells. Nonetheless, the proposed mechanism and components involved in this process have remained a topic of ongoing debate. In this study, we elucidate the mitochondrial import machinery and structural aspects of STAR, revealing its role as an intermembrane space cholesterol shuttle that subsequently undergoes rapid degradation by mitophagy. This mechanism illuminates a fundamental process in cell biology and provides precise interpretations for the full range of human STAR mutation-driven lipoid congenital adrenal hyperplasia in patients.

Keywords:  cholesterol; intermembrane space; lipoid congenital adrenal hyperplasia; mitochondria; steroidogenesis

DOI:  https://doi.org/10.1073/pnas.2508809122
Mol Psychiatry. 2025 Oct 06.

A novel lncRNA FAM151B-DT regulates degradation of aggregation prone proteins.

Arun Renganathan, Miguel A Minaya, Matthew Broder, Isabel Alfradique-Dunham, Rebecca L Miller, Dhruva D Dhavale, Michelle Moritz, Reshma Bhagat, Jacob Marsh, Anthony Verbeck, Grant Galasso, Emma Starr, David A Agard, Paul T Kotzbauer, Carlos Cruchaga, Celeste M Karch.

Neurodegenerative diseases share common features of protein aggregation along with other pleiotropic traits, including shifts in transcriptional patterns, neuroinflammation, disruption in synaptic signaling, mitochondrial dysfunction, oxidative stress, and impaired clearance mechanisms like autophagy. However, key regulators of these pleiotropic traits have yet to be identified. Here, we used transcriptomics, mass spectrometry, and biochemical assays to define the role of a novel lncRNA on tau pathophysiology. We discovered a long non-coding RNA (lncRNA), FAM151B-DT, that is reduced in a stem cell model of frontotemporal lobar 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 and α-synuclein 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 involved 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 clearance of phosphorylated tau and α-synuclein, and reduce tau and α-synuclein 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/10.1038/s41380-025-03277-6
Exp Mol Med. 2025 Oct 07.

Fas apoptotic inhibitor molecule 2 mitigates metabolic dysfunction-associated fatty liver disease through autophagic CRTC2 degradation.

Yongjie Yu, Sha Hu, Tuo Zhang, Hongjie Shi, Dajun Li, Yongping Huang, Yu Zhang, Haitao Wang, Yufeng Hu, Hong Yu, Guang-Nian Zhao, Peng Zhang.

Lysosomal membrane proteins play fundamental roles in the lysosomal degradation of proteins and are attractive drug targets for metabolic dysfunction-associated fatty liver disease (MAFLD). Fas apoptotic inhibitory molecule 2 (FAIM2), a lysosomal membrane protein, has been recognized as an inhibitor of apoptosis in a variety of diseases. Here we reveal that FAIM2 is an inhibitor of fatty acid synthesis and suppresses MAFLD. FAIM2 protein expression is decreased in MAFLD. Moreover, FAIM2 is degraded by the E3 ubiquitin ligase NEDD4L through the catalysis of K48-linked ubiquitination. High-fat and high-cholesterol diet-induced hepatic steatosis, inflammation and fibrosis are aggravated in Faim2-knockout mice and alleviated in mice with AAV8-mediated FAIM2 overexpression. Furthermore, in hepatocytes, FAIM2 knockout increases the expression of genes related to fatty acid synthesis, while overexpressing FAIM2 exhibits the opposite effect. Mechanistically, FAIM2 directly interacts with CREB-regulated transcription coactivator 2 (CRTC2), a prominent regulator of lipid metabolism, and mediates its degradation through autophagy. Specifically, we find that the N terminus of FAIM2, which interacts with CRTC2 and LC3, is required for autophagic degradation of CRTC2. Collectively, our findings reveal that FAIM2 acts as a fatty acid synthesis inhibitor in MAFLD by promoting the autophagic degradation of CRTC2 and that FAIM2-CRTC2 may be a promising therapeutic target.

DOI: https://doi.org/10.1038/s12276-025-01559-1
Autophagy. 2025 Oct 08. 1-17

A secretory protein from "candidatus Liberibacter asiaticus" targets SNARE protein CsVTI13 to suppress autophagosome-vacuole fusion and promote bacterial infection.

Xuejin Cui, Meixia Du, Xiyin Zheng, Li Ren, Yingzhe Yuan, Shimian Ma, Caifu Liu, Xiuping Zou, Shimin Fu, Changyong Zhou, Xuefeng Wang.

  Macroautophagy/autophagy functions in plant host immunity responses to pathogen infection. The molecular mechanisms and functions used by the citrus Huanglongbing (HLB)-associated intracellular bacterium "Candidatus Liberibacter asiaticus" (CLas) to manipulate autophagy are largely unknown. Here, we identified a CLas effector, SDE4580 (CLIBASIA_04580), which contributes to HLB progression. Transgenic SDE4405 in Wanjincheng orange (Citrus sinensis) promotes CLas proliferation and symptom expression, while inhibiting autophagosome-vacuole fusion. Further investigations revealed that SDE4580 interacts with the citrus SNARE protein CsVTI13, which positively regulates autophagosome-vacuole fusion and limits pathogen proliferation. CsVTI13 interacts with CsSYP22, which acts as a bridge connecting CsVTI13 to CsATG8g, a process that is critical for the CsVTI13-mediated promotion of autophagic flux. Additional analyses demonstrated that SDE4580 competitively disrupts the interaction between CsVTI13 and CsSYP22, thereby inhibiting CsVTI13-mediated autophagy. Our findings demonstrate the role of SDE4580 in manipulating SNARE proteins for disrupting autophagosome-vacuole fusion and impairing autophagy-mediated antimicrobial defenses, unraveling a novel pathogen strategy to counteract defense-related autophagy during plant-bacteria interaction.Abbreviations: ATG: autophagy related; BSMV: barley stripe mosaic virus; BiFC: bimolecular fluorescence complementation; BTH: benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester; CLas: Candidatus Liberibacter asiaticus; co-IP: co-immunoprecipitation; CsACD2: ACCELERATED CELL DEATH 2; HLB: Huanglongbing; N. benthamiana: Nicotiana benthamiana; PhoA: alkaline phosphatase; PtdIns3K: phosphatidylinositol 3-kinase; SNARE: soluble N-ethylmaleimide-sensitive factor attachment protein receptor; VPS34: vacuolar protein sorting 34; WT: wild-type; Y2H: yeast two-hybrid.

Keywords:  Autophagosome-vacuole fusion; CsSYP22; CsVTI13; Huanglongbing; SDE4580; SNARE protein

DOI:  https://doi.org/10.1080/15548627.2025.2569683
Sci Rep. 2025 Oct 06. 15(1): 34686

Histone H4K16 acetylation modification regulated autophagy and apoptosis in neuron after spinal cord injury.

Jie-Min Lin, Kun-Hui Li, Lin-Quan Zhou, De-Hui Chen, Xin Zhao, Wen-Wen Li, Wen-Ge Liu.

  Autophagy maintains the homeostasis of the internal environment by clearing misfolded proteins and damaged organelles, which can reduce neuronal apoptosis in the early stage of spinal cord injury (SCI) and promote neural function recovery. Previous studies have shown that decreased acetylation modification of histone H4 lysine16 acetylation (H4K16ac) induces the expression of downstream autophagy genes. However, the role of H4K16ac modification and its impact on autophagy and apoptosis in the early stage of SCI remains unclear. This study aimed to determine the relationship between H4K16ac and autophagy, apoptosis in the early stage of SCI, and the effects of regulating H4K16ac on autophagy and apoptosis. In this study, the state of nerve cells after spinal cord injury was simulated by the rat pheochromocytoma cell line (PC12 cells) injured by oxygen-glucose deprivation (OGD) Model. Using OGD model in NGF-differentiated PC12 cells, we assessed H4K16ac dynamics via Western blot, immunofluorescence, and qPCR. Autophagy and apoptosis were evaluated through transmission electron microscopy, LC3B/p62 analysis, TUNEL staining, and flow cytometry. Results showed that OGD reduced H4K16ac in a time-dependent manner, correlating with enhanced autophagy (increased LC3B-II/I, Beclin1, ATG5; decreased p62) and apoptosis (elevated Bax/Bcl-2, cleaved caspase-3). Pharmacological inhibition of deacetylases by Trichostatin A (TSA) restored H4K16ac, suppressed autophagy, and exacerbated apoptosis. Similarly, Sirtuin 1 (SIRT1) knockdown upregulated H4K16ac, inhibited autophagic flux, and promoted apoptosis via the Bax/Bcl-2/caspase-3 pathway. These findings reveal that H4K16ac downregulation post-SCI enhances autophagy as a protective response, while its restoration via SIRT1 inhibition disrupts this balance, aggravating neuronal apoptosis.

Keywords:  Apoptosis; Autophagy; H4K16ac; Spinal cord injury

DOI:  https://doi.org/10.1038/s41598-025-10352-z
Ann Neurol. 2025 Oct 06.

Mutations in the Key Autophagy Tethering Factor EPG5 Link Neurodevelopmental and Neurodegenerative Disorders Including Early-Onset Parkinsonism.

Hormos Salimi Dafsari, Celine Deneubourg, Kritarth Singh, Reza Maroofian, Zita Suprenant, Ay Lin Kho, Neil J Ingham, Karen P Steel, Preethi Sheshadri, Franciska Baur, Lea Hentrich, Birgit Gerisch, Mina Zamani, Cesar Alves, Ata Siddiqui, Haidar S Dafsari, Mehri Salari, Anthony E Lang, Michael Harris, Alice Abdelaleem, Saeid Sadeghian, Reza Azizimalamiri, Hamid Galehdari, Gholamreza Shariati, Alireza Sedaghat, Jawaher Zeighami, Daniel Calame, Dana Marafi, Ruizhi Duan, Adrian Boehnke, Gary D Clark, Jill A Rosenfeld, Carrie A Mohila, Dora Steel, Saurabh Chopra, Suvasini Sharma, Nicolai Kohlschmidt, Steffi Patzer, Afshin Saffari, Darius Ebrahimi-Fakhari, Büşra Eser Çavdartepe, Irene J Chang, Erika Beckman, Renate Peters, Andrew Paul Fennell, Bernice Lo, Luisa Averdunk, Felix Distelmaier, Martina Baethmann, Frances Elmslie, Kairit Joost, Sheela Nampoothiri, Dhanya Yesodharan, Hanna Mandel, Amy Kimball, Antonie D Kline, Cyril Mignot, Boris Keren, Vincent Laugel, Katrin Õunap, Kalpana Devadathan, Frederique M C van Berkestijn, Arpana Silwal, Saskia Koene, Sumit Verma, Mohammed Yousuf Karim, Chahynez Boubidi, Majid Aziz, Gehad ElGhazali, Lauren Mattas, Mohammad Miryounesi, Farzad Hashemi-Gorji, Shahryar Alavi, Nayereh Nouri, Mehrdad Noruzinia, Saeideh Kavousi, Arveen Kamath, Sandeep Jayawant, Russell Saneto, Nourelhoda A Haridy, Pinar Ozkan Kart, Ali Cansu, Madeleine Joubert, Claire Beneteau, Kyra E Stuurman, Martina Wilke, Tahsin Stefan Barakat, Homa Tajsharghi, Annarita Scardamaglia, Sadeq Vallian, Semra Hız, Ali Shoeibi, Reza Boostani, Narges Hashemi, Meisam Babaei, Norah Saleh Alsaleh, Julie Porter, Tania Attié-Bitach, Pauline Marzin, Dorota Wicher, Jessica I Gold, Elisabeth Schuler, Amna Kashgari, Rakan F Alanazi, Wafaa Eyaid, Marc Engelen, Mirjam Langeveld, Burkhard Stüve, Yun Li, Gökhan Yigit, Bernd Wollnik, Mariana H G Monje, Dimitri Krainc, Niccolò E Mencacci, Somayeh Bakhtiari, Michael Kruer, Emanuela Argilli, Elliott Sherr, Yalda Jamshidi, Ehsan Ghayoor Karimiani, Yiu Wing Sunny Cheung, Ivan Karin, Giovanni Zifarelli, Peter Bauer, Wendy K Chung, James R Lupski, Manju A Kurian, Jörg Dötsch, Jürgen-Christoph von Kleist-Retzow, Thomas Klopstock, Matias Wagner, Calvin Yip, Andreas Roos, Rita Carsetti, Carlo Dionisi-Vici, Mathias Gautel, Michael R Duchen, Adam Antebi, Henry Houlden, Manolis Fanto, Heinz Jungbluth.

OBJECTIVE: Autophagy is a fundamental biological pathway with vital roles in intracellular homeostasis. During autophagy, defective cargoes including mitochondria are targeted to lysosomes for clearance and recycling. Recessive truncating variants in the autophagy gene EPG5 have been associated with Vici syndrome, a severe early-onset neurodevelopmental disorder with extensive multisystem involvement. Here, we aimed to delineate the extended, age-dependent EPG5-related disease spectrum.
METHODS: We investigated clinical, radiological, and molecular features from the largest cohort of EPG5-related patients identified to date, complemented by experimental investigation of cellular and animal models of EPG5 defects.
RESULTS: Through worldwide collaboration, we identified 211 patients, 97 of them previously unpublished, with recessive EPG5 variants. The phenotypic spectrum ranged from antenatally lethal presentations to milder isolated neurodevelopmental disorders. A novel Epg5 knock-in mouse model of a recurrent EPG5 missense variant featured motor impairments and defective autophagy in brain areas particularly relevant for the neurological disorders in milder presentations. Novel age-dependent neurodegenerative manifestations in our cohort included adolescent-onset parkinsonism and dystonia with cognitive decline, and myoclonus. Radiological features suggested an emerging continuum with brain iron accumulation disorders. Patient fibroblasts showed defects in PINK1-Parkin-dependent mitophagic clearance and α-synuclein overexpression, indicating a cellular basis for the observed neurodegenerative phenotypes. In Caenorhabditis elegans, EPG5 knockdown caused motor impairments, defective mitophagic clearance, and changes in mitochondrial respiration comparable to observations in C. elegans knockdown of parkinsonism-related genes.
INTERPRETATION: Our findings illustrate a lifetime neurological disease continuum associated with pathogenic EPG5 variants, linking neurodevelopmental and neurodegenerative disorders through the common denominator of defective autophagy. ANN NEUROL 2025 ANN NEUROL 2025.

DOI: https://doi.org/10.1002/ana.78013
Essays Biochem. 2025 Oct 09. pii: EBC20253054. [Epub ahead of print]

UFM1 at the endoplasmic reticulum: linking ER stress, ribosome quality control, and ER-phagy.

Masaaki Komatsu, Gaoxin Mao.

  Ubiquitin-fold modifier 1 (UFM1) is a small protein that functions as a ubiquitin-like modifier attached to other proteins to alter their behavior. Although less famous than ubiquitin, UFM1 has gained attention as a key regulator of proteostasis (protein homeostasis) in the cell. Notably, the endoplasmic reticulum (ER) has emerged as the central stage for UFM1's activity. UFM1 was initially recognized for its role in the ER stress response, and we now know it orchestrates two critical quality-control processes at the ER: ribosome-associated quality control and selective autophagy of the ER. Together, these mechanisms ensure that the cell can cope with misfolded proteins and stalled ribosomes, maintaining the health of the ER and the proteins it produces. In this review, we will explore how UFM1 works at the ER, how its components are regulated during stress, how it facilitates both immediate quality control and longer-term ER turnover, and how disruptions in this system lead to disease, especially in the nervous system.

Keywords:  encephalopathy; endoplasmic reticulum; proteostasis

DOI:  https://doi.org/10.1042/EBC20253054
Proc Natl Acad Sci U S A. 2025 Oct 14. 122(41): e2511857122

The integrated stress response suppresses antiviral RNA interference by autophagy-mediated degradation of the RNA-induced silencing complex.

Qiyu Wang, Lingyue Chen, Jiayin Wang, Zhijian Chen, Zixian Ma, Xuan Xie, Xiaohui Zeng, Yuanyuan Bie, Zhaowei Wang.

  The small interfering RNA (siRNA) pathway is a highly conserved antiviral defense mechanism in vertebrates and invertebrates. Although the core components of this pathway are well characterized, its upstream regulatory networks remain poorly understood. Here, we identify the integrated stress response (ISR) as a negative regulator of the siRNA pathway, and demonstrate that the picorna-like virus CrPV (Cricket Paralysis Virus) exploits this mechanism for immune evasion. Mechanistically, the picorna-like virus triggers the ISR through transcriptional suppression of ppp1r15, a key regulator of eukaryotic initiation factor 2α (eIF2α) dephosphorylation. ISR activation subsequently induces the autophagy-lysosomal pathway by up-regulating Atg1 transcription in an ATF4-dependent manner. This process leads to selective degradation of Argonaute 2 (Ago2) and other core components of the RNA-induced silencing complex (RISC), thereby suppressing the host RNA interference (RNAi) machinery and enhancing viral replication. Our findings uncover an unconventional immune evasion strategy employed by a picorna-like virus and establish a previously unrecognized crosstalk between the ISR and siRNA pathways.

Keywords:  RNA interference; autophagy; integrated stress response; picorna-like virus

DOI:  https://doi.org/10.1073/pnas.2511857122
Cell Death Dis. 2025 Oct 06. 16(1): 686

Activating PIK3CA mutation promotes overgrowth of adipose tissue via inhibiting lipophagy in macrodactyly.

Yating Yin, Xiao Zhang, Shihui Lin, Zhibo Wang, Baoxing Tian, Xinyi Dai, Aiping Yu, Huixiao Li, Hailei Mao, Bin Wang.

Excessive proliferation and lipid accumulation of adipose tissue are the main pathological alterations in macrodactyly. Our previous studies found that macrodactyly exhibits abnormal lipid metabolism and inhibited autophagy, but the underlying mechanisms remain unclear. This study aims to investigate the regulatory mechanisms of autophagy in macrodactyly. The therapeutic impact and underlying mechanisms of autophagy on lipid accumulation, induced by a gain-of-function mutation of PIK3CA in macrodactyly, were assessed with respect to autophagy, lipid metabolism, oxidative stress, and deubiquitination. Autophagy deficiency resulting from PIK3CA mutation in macrodactyly led to excessive accumulation of adipose tissue. Lipid accumulation can be mitigated by inducing lipophagy of lipid droplets (LDs) in adipose derived stem cells of macrodactyly (Mac-ADSCs). The subsequent increase in free fatty acids (FFA) led to mitochondrial oxidative stress in Mac-ADSCs. Inducing autophagy exacerbated mitochondrial oxidative stress in Mac-ADSCs, thereby contributing to apoptosis. Additionally, the ablation of the deubiquitinase USP15 facilitated the degradation of LDs in Mac-ADSCs, through ubiquitin-dependent macrolipophagy. USP15 inhibitor reduced lipid accumulation in macrodactyly adipose tissue xenografts. In conclusion, activating PIK3CA mutation promotes excessive proliferation and lipid accumulation of Mac-ADSCs by inhibiting lipophagy. Targeted inhibition of USP15 may serve as a promising therapeutic approach for treating macrodactyly. A schematic illustrates that activating PIK3CA mutation promotes overgrowth of adipose tissue via inhibiting lipophagy in macrodactyly.

DOI: https://doi.org/10.1038/s41419-025-08024-x
Brain. 2025 Oct 07. pii: awaf371. [Epub ahead of print]

EIPR1 variants cause a neurodevelopmental disorder with endolysosomal and dense core vesicle defects.

Saikat Ghosh, Jaskaran Singh, Nadirah S Damseh, Mariasavina Severino, Raffaella De Pace, Adriana E Golding, Michal Jarnik, Poonam Thakran, Laurence Faivre, Jade Heitz, Anne-Sophie Denommé-Pichon, Antonio Vitobello, Lama AlAbdi, Firdous Abdulwahab, Safia Sumayli, Mashael Alqahtani, Huma Arshad Cheema, Iram Javed, JiHye Kim, Hanns Lochmuller, Hagar Mor-Shaked, Jennifer E Neil, Ganeshwaran H Mochida, Giovanni Zifarelli, Peter Bauer, Ehsan Barkhordari, Ehsan Ghayoor Karimiani, Henry Houlden, Bassam Abu-Libdeh, Shimon Edvardson, Orly Elpeleg, Reza Maroofian, Shunmoogum A Patten, Juan S Bonifacino.

  EIPR1 (EARP-interacting protein 1, formerly known as TSSC1) is a WD40-domain protein that interacts with the EARP (endosome-associated recycling protein) and GARP (Golgi-associated retrograde protein) complexes in the process of delivering endosome-derived transmembrane cargos to the plasma membrane and the trans-Golgi network (TGN), respectively. Additionally, EIPR1 cooperates with EARP in the biogenesis of dense core vesicles. While these properties of EIPR1 were established in cultured cells and model organisms, the physiological and pathological importance of EIPR1 in humans remains to be determined. Here we report the identification of five EIPR1 homozygous missense variants [NM_003310.5:c.835C>G p.(Arg279Gly), NM_003310.5:c.813C>G p.(His271Gln), NM_003310.5:c.694C>T p.(Arg232Trp), NM_003310.5:c.47G>A p.(Arg16His) and NM_003310.5:c.419T>A p.(Val140Asp)] in eight individuals from six unrelated families with a neurological disorder featuring a spectrum of global neurodevelopmental delay, microcephaly, ataxia, spasticity, delayed myelination, callosal hypoplasia, cerebellar atrophy, walking and speech impairments, dysmorphic facies, and neutropenia. Cellular studies using a heterologous transfection system demonstrate that these variants reduce EIPR1 protein levels and its physical interaction with EARP and GARP complexes. Furthermore, we show that the Arg279Gly and His271Gln variants reduce the ability of EIPR1 to promote EARP association with endosomes in non-neuronal cells and dense core vesicle biogenesis in iPSC-derived neurons. Additionally, skin fibroblasts from one of the Arg279Gly affected individuals shows reduced recycling of internalized transferrin to the plasma membrane (an EARP-deficiency phenotype) and impaired retrograde transport of internalized Shiga toxin B-subunit to the TGN (a GARP-deficiency phenotype) compared to fibroblasts from an unaffected parent. Moreover, these patient fibroblasts exhibit enlarged lysosomes, increased levels of the lysosomal membrane protein LAMP1, and increased levels of the autophagic markers LC3B-II and SQSTM1, all phenotypes previously associated with GARP deficiency. Knockout of the orthologous eipr1 in zebrafish results in neurodevelopmental and locomotor defects consistent with the clinical phenotype of the human patients. Injection of WT human EIPR1 mRNA into eipr1 KO zebrafish rescues these defects, whereas mRNAs encoding the human EIPR1 variants Arg279Gly or His271Gln fail to do so, confirming the impaired activity of these variants. These findings identify EIPR1 as a novel genetic locus associated with a neurodevelopmental disorder and underscore its critical role in endosomal recycling and dense core vesicle biogenesis, processes essential for the development and function of the nervous system.

Keywords:  EARP; GARP; Golgi; TSSC1; dense core vesicle; endosomes

DOI:  https://doi.org/10.1093/brain/awaf371