bims-tofagi 2025-11-02 papers

Issue of 2025–11–02
six papers selected by
Michele Frison, University of Cambridge

Brain. 2025 Oct 30. pii: awaf414. [Epub ahead of print]

VPS35 mutation inhibits PINK1/parkin-mediated mitophagy via increased LRRK2 kinase activity.

Liselot Manders, Thibaut Heyninck, Dorien Imberechts, Bjørn Holst, Rejko Krüger, Wim Vandenberghe.

The p.D620N mutation in VPS35 causes an autosomal dominant form of Parkinson's disease via mechanisms that are poorly understood. PINK1 and parkin, two proteins whose loss of function underlies autosomal recessive Parkinson's disease, cooperate to mediate mitophagy, a quality control pathway for selective elimination of damaged mitochondria. PINK1/parkin-mediated mitophagy is disrupted by LRRK2 mutations, which are the most prevalent cause of autosomal dominant Parkinson's disease. Here, we investigated whether the p.D620N VPS35 mutation has an effect on PINK1/parkin-mediated mitophagy. We identified a novel family with autosomal dominant Parkinson's disease caused by a p.D620N VPS35 mutation. We cultured skin fibroblasts and iPSC-derived dopaminergic neurons from the proband and from a second, unrelated Parkinson's disease patient with the p.D620N VPS35 mutation, and compared them with isogenic and non-isogenic control cells. PINK1/parkin-mediated mitophagy was severely impaired in VPS35 mutant fibroblasts and neurons, while non-selective, starvation-induced autophagy and lysosomal degradative capacity were preserved. siRNA-mediated VPS35 knockdown rescued the mitophagy defect in VPS35 mutant cells, whereas overexpression of wild-type VPS35 did not, suggesting a gain-of-function mechanism of the mutation. The VPS35 mutation did not interfere with activation of PINK1 or parkin after mitochondrial depolarization, but impaired mitochondrial recruitment of the autophagy receptor optineurin. LRRK2 kinase activity was increased in the VPS35 mutant cells, as shown by enhanced levels of the T73-phosphorylated form of the LRRK2 substrate RAB10. The enhanced level of phosphorylated RAB10 in VPS35 mutant cells was decreased by treatment with LRRK2 kinase inhibitors and by VPS35 knockdown. Importantly, the mitophagy defect of VPS35 mutant fibroblasts and neurons was fully rescued by LRRK2 kinase inhibitors as well as by overexpression of PPM1H, a phosphatase that dephosphorylates multiple RAB substrates of LRRK2. Finally, in situ proximity ligation experiments revealed that endogenous VPS35 and LRRK2 are proximity partners in human dopaminergic neurons and that this proximity relationship is enhanced by the VPS35 mutation. In conclusion, the VPS35 mutation impairs PINK1/parkin-mediated mitophagy via a gain-of-function mechanism that involves stimulation of LRRK2 kinase activity. Thus, a VPS35/LRRK2 axis linked to dominant Parkinson's disease intersects with a pathway mediated by proteins encoded by the recessive Parkinson's disease genes.

Keywords: Parkinson’s disease; RAB; autophagy; induced pluripotent stem cell; lysosome; mitochondrion

DOI: https://doi.org/10.1093/brain/awaf414

J Biol Chem. 2025 Oct 27. pii: S0021-9258(25)02712-7. [Epub ahead of print] 110860

Substrate recognition by the human mitochondrial processing peptidase and its processing of PINK1.

Andrew N Bayne, Danielle M Simons, Naoto Soya, Karl Grenier, Gergely L Lukacs, Edward A Fon, Jean-François Trempe.

Nuclear-encoded mitochondrial proteins rely on N-terminal targeting sequences (N-MTS) for their import. Most N-MTSs are cleaved in the matrix by the mitochondrial processing peptidase (MPP), a heterodimeric metalloprotease composed of (α) and catalytic (β) subunits, essential for the maturation of imported proteins. Import and processing of PINK1, a kinase implicated in Parkinson's disease, govern its ability to sense mitochondrial damage. The current paradigm suggests PINK1 undergoes two sequential processing steps: first, MPP removes the PINK1 N-MTS in the matrix; second, the inner mitochondrial membrane protease PARL cleaves the PINK1 transmembrane domain, leading to PINK1 degradation. Upon depolarization, PINK1 escapes proteolysis and accumulates on mitochondria to initiate mitophagy. However, the MPP cleavage site on PINK1, the role of MPP in PINK1 signalling, and the mechanisms of substrate recognition by human MPP remain unclear. Here, we define the MPP cleavage site on PINK1 between Ala28-Tyr29 and show it is inefficiently processed compared to canonical N-MTSs. In cells, MPP cleavage is dispensable for both PARL processing and PINK1 function, decoupling PINK1 import and damage sensing from its N-MTS removal. However, in vitro, the PINK1 N-MTS binds potently to MPP, inhibits the cleavage of other substrates, and traps MPP in a slowly processing complex. Exploiting PINK1 as a mechanistic probe, we use hydrogen-deuterium exchange mass spectrometry to map the PINK1 binding site on MPPα. We identify a two-step mechanism involving MPPα lid rearrangement followed by active site engagement, providing key insight into PINK1's unique import pathway and fundamental MPP processing mechanisms.

Keywords: PTEN-induced putative kinase 1 (PINK1); Parkinson disease; hydrogen-deuterium exchange; mitochondria; mitochondrial processing peptidase (MPP); protein import; protein processing

DOI: https://doi.org/10.1016/j.jbc.2025.110860

EMBO J. 2025 Oct 30.

Mechanism of autophagy initiation by transmembrane selective autophagy receptors.

Elias Adriaenssens, Sascha Martens.

Selective autophagy ensures the targeted degradation of damaged or surplus cellular components, including organelles, thereby safeguarding cellular homeostasis. This process relies on selective autophagy receptors (SARs) that link specific cargo to the autophagy machinery. These receptors exist in two distinct forms: soluble SARs that are recruited to the cargo on demand, and transmembrane SARs that are stably embedded in the membranes of organelles they target. While both receptor types converge on the same autophagy core machinery, they differ in how they recognize cargo, are regulated, and recruit this machinery to the site of degradation. In this review, we explore the unique challenges and strategies associated with transmembrane SARs, including how their activity is suppressed under basal conditions and activated in response to stress. We compare their mode of action with that of soluble SARs, highlight key differences in kinase regulation, including the roles of TBK1, ULK1, CK2, and Src, and discuss emerging models of autophagy initiation. We further highlight fundamental principles of organelle-selective autophagy and identify open questions that will guide future research.

Keywords: Autophagosome; ER-phagy; Mitophagy; Quality Control; Selective Autophagy

DOI: https://doi.org/10.1038/s44318-025-00615-w

Cell Metab. 2025 Oct 24. pii: S1550-4131(25)00395-X. [Epub ahead of print]

Quercetin-derived microbial metabolite DOPAC potentiates CD8+ T cell anti-tumor immunity via NRF2-mediated mitophagy.

Penghu Han, Shuzheng Chu, Jing Shen, Lixiang Li, Yan Zhang, Shiguan Wang, Yatai Chen, Yangchun Ma, Xiaolong Tang, Chao Gao, Xiangyun Zheng, Bowen Xu, Qiong Wang, Detian Yuan, Shiyang Li.

Quercetin, a dietary flavonol, shows promise in cancer prevention, though its effects on the immune compartment within the tumor microenvironment are not fully understood. Here, we identify 3,4-dihydroxyphenylacetic acid (DOPAC), a microbial metabolite of quercetin, as a critical mediator of its anti-tumor effects in a CD8+ T cell-dependent manner. Mechanistically, DOPAC directly binds to Kelch-like epichlorohydrin-associated protein 1 (KEAP1), disrupting its interaction with nuclear factor erythroid 2-related factor 2 (NRF2) and preventing KEAP1-mediated degradation of NRF2 in CD8+ T cells. Elevated NRF2 transcriptionally enhances the expression of B cell lymphoma 2-interacting protein 3, promoting mitophagy and mitochondrial functionality, which improves CD8+ T cell fitness within the tumor microenvironment. Furthermore, DOPAC synergizes with immune checkpoint blockade to suppress tumor growth. Our findings underscore the role of microbial metabolites of dietary nutrients in modulating anti-tumor immune responses, positioning DOPAC as a promising candidate for cancer immunotherapy.

Keywords: BNIP3; CD8(+) T cells; DOPAC; NRF2; anti-tumor immunity; microbiota; mitophgagy; quercetin

DOI: https://doi.org/10.1016/j.cmet.2025.09.010

Nat Aging. 2025 Oct 31.

Effect of the mitophagy inducer urolithin A on age-related immune decline: a randomized, placebo-controlled trial.

Dominic Denk, Anurag Singh, Herbert G Kasler, Davide D'Amico, Julia Rey, Lucía Alcober-Boquet, Johanna M Gorol, Christoph Steup, Ritesh Tiwari, Ryan Kwok, Rafael J Argüello, Julie Faitg, Kathrin Sprinzl, Stefan Zeuzem, Valentina Nekljudova, Sibylle Loibl, Eric Verdin, Chris Rinsch, Florian R Greten.

Mitochondrial dysfunction and stem cell exhaustion contribute to age-related immune decline, yet clinical interventions targeting immune aging are lacking. Recently, we demonstrated that urolithin A (UA), a mitophagy inducer, expands T memory stem cells (TSCM) and naive T cells in mice. In this randomized, double-blind, placebo-controlled trial, 50 healthy middle-aged adults received oral UA (1,000 mg day-1) or placebo for 4 weeks; time points of analysis were baseline and day 28. Primary outcomes were phenotypical changes in peripheral CD3+ T cell subsets and immune metabolic remodeling. UA expanded peripheral naive-like, less terminally exhausted CD8+ cells (treatment difference 0.50 percentage points; 95% CI = 0.16 to 0.83; P = 0.0437) while also increasing CD8+ fatty acid oxidation capacity (treatment difference = 14.72 percentage points; 95% confidence interval (CI) = 6.46 to 22.99; P = 0.0061). Secondary outcomes included changes in plasma cytokine levels (IL-6, TNF, IL-1β, IL-10), immune populations assessed via flow cytometry, immune cell function, and mitochondrial content. Analysis revealed augmented mitochondrial biogenesis in CD8+ cells, increased peripheral CD56dimCD16bright NK cells, and nonclassical CD14loCD16hi monocytes in UA-treated participants, as well as improved activation-elicited TNF secretion in T cells and bacterial uptake by monocytes. Exploratory single-cell RNA sequencing demonstrated UA-driven transcriptional shifts across immune populations, modulating pathways linked to inflammation and metabolism. These findings indicate that short-term UA supplementation modulates human immune cell composition and function, supporting its potential to counteract age-related immune decline and inflammaging. ClinicalTrials.gov registration number: NCT05735886 .

DOI: https://doi.org/10.1038/s43587-025-00996-x

Int Immunopharmacol. 2025 Oct 30. pii: S1567-5769(25)01711-4. [Epub ahead of print]167 115723

Urolithin A promotes peripheral nerve regeneration via TFEB-mediated mitophagy and NLRP3 inflammasome suppression.

Zhe Zhang, Shanying Xiao, Dongbu Tian, Tao Lin, Kongmei Luo, Dong Peng, Yixin Bo, Anhao Guo, Yujie Hu, Long Wu, Hede Yan.

BACKGROUND: Peripheral nerve injury (PNI) often results in incomplete recovery due to persistent neuroinflammation and mitochondrial dysfunction. Here, we investigated the therapeutic potential of Urolithin A (UA), a gut microbiota-derived metabolite, in promoting nerve regeneration by modulating mitophagy and inflammasome activation.
OBJECTIVE: To evaluate whether UA enhances peripheral nerve regeneration by activating TFEB-mediated mitophagy and inhibiting NLRP3 inflammasome activation.
METHODS: In a rat sciatic nerve crush injury model and Schwann cell cultures, UA effects were evaluated using behavioral tests, histological analysis, transmission electron microscopy, immunofluorescence, Western blotting, and molecular docking.
RESULTS: UA administration significantly improved sciatic functional index, reduced muscle atrophy, and enhanced axonal regeneration and remyelination. Mechanistically, UA promoted transcription factor EB (TFEB) nuclear translocation, upregulated autophagy-lysosomal genes, and facilitated clearance of damaged mitochondria, leading to reduced ROS levels and suppression of NLRP3 inflammasome activation. These effects were abolished by TFEB knockdown or autophagy inhibition, indicating a TFEB-dependent mechanism. Molecular docking suggested direct binding between UA and TFEB.
CONCLUSION: UA facilitates peripheral nerve repair by coupling TFEB-mediated mitophagy with NLRP3 inflammasome inhibition. This dual action provides a promising non-invasive therapeutic strategy for PNI and warrants further translational research.

Keywords: Mitophagy; NLRP3 inflammasome; Peripheral nerve regeneration; Urolithin A

DOI: https://doi.org/10.1016/j.intimp.2025.115723