bims-mitmed 2025-07-13 papers

bims-mitmed

Biomed News

on Mitochondrial medicine

Issue of 2025–07–13
25 papers selected by
Dario Brunetti, Fondazione IRCCS Istituto Neurologico

Transabdominal ultrasound guided AAV9-GFP delivery in fetal pigs: a translational and minimally invasive model for in utero fetal gene therapy.
MitoRUSH as a tool to study the efficiency of mitochondrial import in complex I-deficient cells.
Extremely low-frequency electromagnetic field (ELF-EMF) enhances mitochondrial energy production in NARP cybrids.
FASTKD5 processes mitochondrial pre-mRNAs at noncanonical cleavage sites.
Leber's hereditary optic neuropathy-associated ND1 3733G> C mutation ameliorates the mitochondrial quality control and cellular homeostasis.
Clu1/Clu form mitochondria-associated granules upon metabolic transitions and regulate mitochondrial protein translation via ribosome interactions.
Altered endothelial mitochondrial Opa1-related fusion in mouse accelerates age-associated vascular and kidney damage.
Super-resolution microscopy of mitochondrial mRNAs.
The xenobiotic detoxification pathway - glycine conjugation - is downregulated in a mouse model of Leigh syndrome.
The Role of Estrogen in Mitochondrial Disease.
Preclinical models of mitochondrial dysfunction: mtDNA and nuclear-encoded regulators in diverse pathologies.
Coenzyme Q headgroup intermediates can ameliorate a mitochondrial encephalopathy.
Autophagic stress activates distinct compensatory secretory pathways in neurons.
Combining phenomics with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion.
A guide to characterizing the dynamic mitochondria-endoplasmic reticulum contact sites.
Muscle AMP deaminase activity was lower in Neandertals than in modern humans.
Oocyte and dietary supplements: a mini review.
Revitalizing Donor Organs: The Potential of Mitochondrial Transplantation in Heart and Lung Transplantation.
Remyelination of chronic demyelinated lesions with directly induced neural stem cells.
Oxidative Phosphorylation in Uncoupled Mitochondria.
Evolution of growth factor signaling to the TSC complex to regulate mTORC1.
A porin-like protein used by bacterial predators defines a wider lipid-trapping superfamily.
Age and sex-specific changes in mitochondrial quality control in skeletal and cardiac muscle.
Neuroimaging characteristics of single Large-Scale mitochondrial DNA deletion syndromes.
Modulation of mitochondrial quality control through autophagic pathway in familial Alzheimer's disease.

Gene Ther. 2025 Jul 11.

Transabdominal ultrasound guided AAV9-GFP delivery in fetal pigs: a translational and minimally invasive model for in utero fetal gene therapy.

Alessia Di Donfrancesco, Alessia Adelizzi, Anastasia Giri, Roberto Duchi, Simona Boito, Maria Barandalla, Giulia Massaro, Chiara Santanatoglia, Enrica Cappellozza, Andrea Perota, Ivano Di Meo, Valeria Tiranti, Emanuela Bottani, Cesare Galli, Nicola Persico, Dario Brunetti.

In utero fetal gene therapy (IUFGT) has the potential to correct severe monogenic disorders before irreversible damage occurs. Despite promising results in small and large animal models, its translation to clinical practice remains limited by technical challenges, safety concerns, and the lack of standardized protocols in relevant disease models species. We established and validated a minimally invasive, ultrasound-guided approach for systemic gene delivery in fetal pigs using a self-complementary AAV9 vector encoding GFP under a CAG promoter. Injections were performed at different gestational ages (GA 80 and GA 108) via intracardiac or umbilical venous routes. Postnatal outcomes were monitored, and transgene biodistribution and expression were assessed by qPCR, ddPCR, immunofluorescence, and Western blotting. Inflammatory response, toxicity, and maternal safety were evaluated through cytokine profiling and histological analyses. The procedure was well tolerated, with no significant maternal morbidity or adverse obstetric outcomes beyond one preterm delivery. Biodistribution analysis revealed widespread vector presence in peripheral tissues, with robust GFP expression in liver and heart. Importantly, there was no evidence of significant tissue toxicity, necrosis, or fibrosis in any of the organs analyzed. Mild increases in pro-inflammatory cytokines (GM-CSF, GRO-α, IFN-γ) were observed but were not associated with histopathological changes. No anti-AAV9 capsid antibodies were detected in sera from piglets or sows, suggesting a minimal immune response to the vector. These findings demonstrate the safety, feasibility, and efficacy of ultrasound-guided IUFGT in pigs, supporting its potential as a translational platform for therapeutic gene delivery in fetuses affected by severe congenital diseases. This model offers a valuable framework for further preclinical development of prenatal interventions, particularly for disorders with early onset, such as mitochondrial diseases.

DOI: https://doi.org/10.1038/s41434-025-00551-8
J Cell Sci. 2025 Jul 01. pii: jcs263701. [Epub ahead of print]138(13):

MitoRUSH as a tool to study the efficiency of mitochondrial import in complex I-deficient cells.

Michal Wasilewski, Karthik Mohanraj, Maciej Zakrzewski, Remigiusz A Serwa, Agnieszka Chacinska.

  Most mitochondrial proteins are imported through the actions of the presequence translocase of the inner membrane, the TIM23 complex, which requires energy in the form of the electrochemical potential of the inner membrane and ATP. Conversions of energy in mitochondria are disturbed in mitochondrial disorders that affect oxidative phosphorylation. Despite the widely accepted dependence of protein import into mitochondria on mitochondrial bioenergetics, effects of mitochondrial disorders on biogenesis of the mitochondrial proteome are poorly characterized. Here, we describe molecular tools that can be used to explore mitochondrial protein import in intact cells, the mitoRUSH assay, and a novel method based on labeling of nascent proteins with an amino acid analog and click chemistry. Using these orthogonal approaches, we discovered that defects in the electron transport chain and manipulating the expression of TIMM23, as well as the TIMM17A or TIMM17B paralogs, in human cells are associated with a decrease in protein import into mitochondria. We postulate that in the absence of a functional electron transfer chain, the mechanisms that support electrochemical potential of the inner membrane and ATP production are insufficient to sustain the import of proteins to mitochondria.

Keywords:  Bioenergetics; Mitochondria; Mitochondrial diseases; Protein import; TIM23; Translocase; mitoRUSH

DOI:  https://doi.org/10.1242/jcs.263701
Sci Rep. 2025 Jul 08. 15(1): 24369

Extremely low-frequency electromagnetic field (ELF-EMF) enhances mitochondrial energy production in NARP cybrids.

Mikako Ito, Zhizhou Huang, Kosaku Nomura, Masaki Teranishi, Fei Zhao, Hiroyuki Mino, Makoto Yoneda, Masashi Tanaka, Kinji Ohno.

  A mutation (m.8993T > G) in MT-ATP6 in mitochondrial DNA (mtDNA) causes the neuropathy, ataxia, retinitis pigmentosa (NARP) syndrome by impairing mitochondrial energy production. Extremely low-frequency electromagnetic field (ELF-EMF) suppresses mitochondrial oxidative phosphorylation (OXPHOS) Complex II and induces mitohormetic activation of mitochondrial OXPHOS activities. We examined the effects of ELF-EMF on normal cybrids carrying 100% wild-type mtDNA (2SA cybrids) and NARP cybrids carrying 40% wild-type and 60% mutant mtDNA (NARP3-2 cybrids). We found that ELF-EMF had no effect on the copy number of mtDNA either in 2SA or NARP3-2 cybrids, or the ratio of wild-type-to-mutant mtDNA in NARP3-2 cybrids. Instead, ELF-EMF increased the transcription of mtDNA and the transcription ratio of wild-type-to-mutant mtDNA in NARP3-2 cybrids. In addition, ELF-EMF increased the expression of mitochondrial OXPHOS proteins and the mitochondrial OXPHOS Complex V activity in NARP3-2 cybrids. ELF-EMF upregulated fission-promoting phosphorylation of DRP1, as well as the expression of fusion-promoting MFN1 and MFN2, in NARP3-2 cybrids. ELF-EMF also increased ATP production estimated by oxygen consumption rates (OCR) and by a biochemical assay in NARP3-2 cybrids. Hormetic activation of mitochondria by ELF-EMF is likely to be effective to ameliorate defective mitochondrial energy production in NARP and other mitochondrial diseases.

Keywords:  And mitohormesis; Extremely low-frequency electromagnetic field (ELF-EMF); Mitochondrial DNA; Mitochondrial biogenesis; Mitophagy; Neuropathy, ataxia, retinitis pigmentosa (NARP) syndrome

DOI:  https://doi.org/10.1038/s41598-025-10536-7
Nucleic Acids Res. 2025 Jul 08. pii: gkaf665. [Epub ahead of print]53(13):

FASTKD5 processes mitochondrial pre-mRNAs at noncanonical cleavage sites.

Hana Antonicka, Ana Vučković, Woranontee Weraarpachai, Seungwoo Hong, Michele Brischigliaro, Ahram Ahn, Antoni Barrientos, Hauke S Hillen, Eric A Shoubridge.

The first post-transcriptional step in mammalian mitochondrial gene expression, required for the synthesis of the 13 polypeptides encoded in mitochondrial DNA (mtDNA), is endonucleolytic cleavage of the primary polycistronic transcripts. Excision of the mtDNA-encoded transfer RNAs (tRNAs) releases most mature RNAs; however, processing of three noncanonical messenger RNAs (mRNAs) not flanked by tRNAs (CO1, CO3, and CYB) requires FASTKD5. To investigate the molecular mechanism involved, we created knockout human cell lines to use as assay systems. The absence of FASTKD5 produced a severe OXPHOS assembly defect due to the inability to translate two unprocessed noncanonical mRNAs and predicted altered folding patterns specifically at the 5'-end of the CO1 coding sequence. Structural features 13-15 nt upstream of the CO1 and CYB cleavage sites suggest FASTKD5 recognition mechanisms. Remarkably, a map of essential FASTKD5 amino acid residues revealed RNA substrate specificity; however, a key, putative active site residue was required for processing all three noncanonical pre-RNAs. Mutating this site did not significantly alter the binding of any client RNA substrate. A reconstituted in vitro system showed that wild-type, but not mutant, FASTKD5, was able to cleave client substrates correctly. These results establish FASTKD5 as the missing piece of biochemical machinery required to completely process the primary mitochondrial transcript.

DOI: https://doi.org/10.1093/nar/gkaf665
J Biol Chem. 2025 Jul 08. pii: S0021-9258(25)02314-2. [Epub ahead of print] 110464

Leber's hereditary optic neuropathy-associated ND1 3733G> C mutation ameliorates the mitochondrial quality control and cellular homeostasis.

Meiheriayi Yasheng, Yanchun Ji, Yunfan He, Qiuzi Yi, Huanhuan Zhang, Wenqi Shan, Kai Wang, Juanjuan Zhang, Ya Li, Feilong Meng, Minglian Zhang, Jun Qin Mo, Shihui Wei, Min-Xin Guan.

Leber's hereditary optic neuropathy (LHON) is a paradigm for mitochondrial retinopathy due to mitochondrial DNA (mtDNA) mutations. However, the mechanism underlying LHON-linked mtDNA mutations, especially their impact on mitochondrial and cellular integrity, is not well understood. Recently, the ND1 3733G>C (p.E143Q) mutation was identified in three Chinese pedigrees with suggestively maternal inheritance of LHON. In this study, we investigated the pathogenic mechanism of m.3733G>C mutation using cybrids generated by fusing mtDNA-less ρ0 cells with enucleated cells from a Chinese patient carrying the m.3733G>C mutation and control subject. Molecular dynamics simulations showed that p.E143Q mutation destabilized these interactions between residues E143 and S110/Y114, or between S141 and W290 in the ND1. Its impact of ND1 structure and function was further evidenced by reduced levels of ND1 in mutant cells. The m.3733G>C mutation caused defective assembly and activity of complex I, respiratory deficiency, diminished mitochondrial ATP production, and increased production of mitochondrial ROS in the mutant cybrids carrying the m.3733G>C mutation. These mitochondrial dysfunctions regulated mitochondrial quality control via mitochondrial dynamics and mitophagy. The m.3733G>C mutation-induced dysfunction yielded elevating mitochondrial localization of DRP1, decreasing network connectivity and increasing fission with abnormal morphologies. Furthermore, the m.3733G>C mutation downregulated ubiquitin-dependent mitophagy pathway, evidenced by decreasing the levels of Parkin and Pink, but not ubiquitin-independent mitophagy pathway. The m.3733G>C mutation-induced deficiencies reshaped the cellular homeostasis via impairing autophagy process and promoting intrinsic apoptosis. Our findings provide new insights into pathophysiology of LHON arising from the m.3733G>C mutation-induced mitochondrial dysfunctions and reprograming organellular and cellular homeostasis.

DOI: https://doi.org/10.1016/j.jbc.2025.110464
PLoS Genet. 2025 Jul 07. 21(7): e1011773

Clu1/Clu form mitochondria-associated granules upon metabolic transitions and regulate mitochondrial protein translation via ribosome interactions.

Leonor Miller-Fleming, Wing Hei Au, Laura Raik, Pedro Rebelo-Guiomar, Jasper Schmitz, Ha Yoon Cho, Aron Czako, Alexander J Whitworth.

Mitochondria perform essential metabolic functions and respond rapidly to changes in metabolic and stress conditions. As the majority of mitochondrial proteins are nuclear-encoded, intricate post-transcriptional regulation is crucial to enable mitochondria to adapt to changing cellular demands. The eukaryotic Clustered mitochondria protein family has emerged as an important regulator of mitochondrial function during metabolic shifts. Here, we show that the Drosophila melanogaster and Saccharomyces cerevisiae Clu/Clu1 proteins form dynamic, membraneless, mRNA-containing granules adjacent to mitochondria in response to metabolic changes. Yeast Clu1 regulates the translation of a subset of nuclear-encoded mitochondrial proteins by interacting with their mRNAs while these are engaged in translation. We further show that Clu1 regulates translation by interacting with polysomes, independently of whether it is in a diffuse or granular state. Our results demonstrate remarkable functional conservation with other members of the Clustered mitochondria protein family and suggest that Clu/Clu1 granules isolate and concentrate ribosomes engaged in translating their mRNA targets, thus, integrating metabolic signals with the regulation of mitochondrial protein synthesis.

DOI: https://doi.org/10.1371/journal.pgen.1011773
Physiol Rep. 2025 Jul;13(13): e70451

Altered endothelial mitochondrial Opa1-related fusion in mouse accelerates age-associated vascular and kidney damage.

Carlotta Turnaturi, Loïck L'Hoste, Coralyne Proux, Linda Grimaud, Emilie Vessieres, Antonio Zorzano, Anne Teissier, Pascal Reynier, Raffaella Sorrentino, Guy Lenaers, Laurent Loufrani, Daniel Henrion.

  Cardiovascular diseases are the major cause of death worldwide, and their frequency increases with age in association with kidney damage. As a reduction in fusion protein optic atrophy type 1 (Opa1) level in endothelial cells (ECs) decreases the vascular response to flow and increases oxidative stress in perfused kidneys, we hypothesized that reduced Opa1 expression contributes to vascular aging. We used male and female mice with ECs specific Opa1 knock-out (EC-Opa1), and littermate wild-type (EC-WT) mice aged 6 (young) and 20 months (old). Mesenteric resistance arteries (MRA) and kidneys were collected for vascular reactivity and western-blot analysis. In old EC-Opa1 mice, blood urea was greater than in EC-WT mice, and MRA showed reduced endothelium-dependent relaxation. In kidneys, the mitochondria fission protein fission-1 (Fis-1) and the peroxisome proliferator-activated receptor gamma coactivator-1 alpha (Pgc-1α) were increased in old EC-Opa1 mice. The level of caveolin-1 expression was greater in old EC-Opa1 mice. Moreover, in kidneys from EC-Opa1 old mice, NADPH-oxidase subunit gp91 expression was greater than in age-matched EC-WT mice. Thus, reduced mitochondrial fusion in mouse ECs altered mesenteric vascular reactivity and increased markers of oxidative stress in aging kidneys. Thus, Opa1 might protect the vascular tree in target organs such as the kidney.

Keywords:  aging; arteries; endothelial cell; kidney; mitochondrial fusion

DOI:  https://doi.org/10.14814/phy2.70451
Nat Commun. 2025 Jul 10. 16(1): 6391

Super-resolution microscopy of mitochondrial mRNAs.

Stefan Stoldt, Frederike Maass, Michael Weber, Sven Dennerlein, Peter Ilgen, Jutta Gärtner, Aysenur Canfes, Sarah V Schweighofer, Daniel C Jans, Peter Rehling, Stefan Jakobs.

Mitochondria contain their own DNA (mtDNA) and a dedicated gene expression machinery. As the mitochondrial dimensions are close to the diffraction limit of classical light microscopy, the spatial distribution of mitochondrial proteins and in particular of mitochondrial mRNAs remains underexplored. Here, we establish single-molecule fluorescence in situ hybridization (smFISH) combined with STED and MINFLUX super-resolution microscopy (nanoscopy) to visualize individual mitochondrial mRNA molecules and associated proteins. STED nanoscopy reveals the spatial relationships between distinct mRNA species and proteins such as the RNA granule marker GRSF1, demonstrating adaptive changes in mRNA distribution and quantity in challenged mammalian cells and patient-derived cell lines. Notably, STED-smFISH shows the release of mRNAs during apoptosis, while MINFLUX reveals the folding of the mRNAs into variable shapes, as well as their spatial proximity to mitochondrial ribosomes. These protocols are transferable to various cell types and open new avenues for understanding mitochondrial gene regulation in health and disease.

DOI: https://doi.org/10.1038/s41467-025-61577-5
Biochem Biophys Res Commun. 2025 Jul 01. pii: S0006-291X(25)00993-3. [Epub ahead of print]777 152278

The xenobiotic detoxification pathway - glycine conjugation - is downregulated in a mouse model of Leigh syndrome.

Belinda R Fouché, Zander Lindeque, Francois van der Westhuizen, Marianne Venter, Rencia van der Sluis.

  Leigh syndrome (LS), a primary mitochondrial disease frequently caused by complex I (CI) deficiency, has been associated with hepatic dysfunction and impaired metabolic homeostasis. Despite this, the impact of mitochondrial dysfunction on hepatic xenobiotic detoxification pathways remains poorly understood. This study investigated the glycine conjugation pathway-central to the metabolism of dietary xenobiotics such as benzoate, salicylate, and medium-chain fatty acids (MCFAs)-in a whole-body Ndufs4 knockout (Ndufs4-/-) mouse model of LS. Transcriptomic analysis revealed a significant downregulation of the xenobiotic/medium chain fatty acid: CoA ligases (Acsm1 and Acsm2) and glycine N-acyltransferase (Glyat) in the livers of Ndufs4-/- mice, suggesting impaired activation and conjugation of xenobiotics. This was corroborated by reduced GLYAT (EC2.3.1.13) enzymatic activity and a marked decrease in hepatic hexanoylglycine levels. These findings imply that CI deficiency attenuates glycine conjugation capacity, potentially compromising the liver's ability to metabolise xenobiotic and dietary substrates. Given the role of glycine conjugation in detoxification, our data highlight a metabolic vulnerability in LS that may influence dietary and pharmacological interventions. Adjusting dietary intake of conjugation substrates may therefore be crucial in the clinical management of mitochondrial disease.

Keywords:  ACSM; GLYAT; Glycine N-Acyltransferase; Glycine conjugation; Leigh syndrome; Xenobiotic detoxification; Xenobiotic/medium chain fatty acid: CoA ligases

DOI:  https://doi.org/10.1016/j.bbrc.2025.152278
Cell Mol Neurobiol. 2025 Jul 11. 45(1): 68

The Role of Estrogen in Mitochondrial Disease.

Xi Huang, Cun-Hui Pan, Fei Yin, Jing Peng, Li Yang.

  This review aims to investigate the potential role of estrogen in various mitochondrial diseases, such as Leber's Hereditary Optic Neuropathy and Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like Episodes, focusing on its effects on aging, oxidative stress, mitochondrial biogenesis, and mitophagy. Mitochondrial diseases have become important in modern medical research due to their complex genetic background and diverse clinical manifestations. Studies in recent years have shown that estrogen plays an essential role in physiological regulation and may also affect the health status of cells by regulating mitochondrial function, which in turn affects the occurrence and development of diseases. However, there is still a lack of systematic review of estrogen's specific mechanisms and roles in these diseases. This review will synthesize the relevant literature to explore the association between estrogen and mitochondrial diseases and its possible therapeutic prospects, aiming to provide a theoretical basis and reference for future research.

Keywords:  Aging; Estrogen; Mitochondrial biogenesis; Mitochondrial disease; Mitophagy; Oxidative stress

DOI:  https://doi.org/10.1007/s10571-025-01592-8
Front Aging. 2025 ;6 1585508

Preclinical models of mitochondrial dysfunction: mtDNA and nuclear-encoded regulators in diverse pathologies.

Dalia M Miller, Stephen L Archer, Kimberly J Dunham-Snary.

  Mitochondrial-driven diseases encompass a diverse group of single-gene and complex disorders, all linked to mitochondrial dysfunction, with significant impacts on human health. While there are rare mitochondrial diseases in which the primary defect resides in mutations in mitochondrial DNA, it is increasingly clear that acquired mitochondrial dysfunction, both genetically- and epigenetically-mediated, complicates common complex diseases, including diabetes, cardiovascular disease and ischemia reperfusion injury, cancer, pulmonary hypertension, and neurodegenerative diseases. It is also recognized that mitochondrial abnormalities not only act by altering metabolism but, through effects on mitochondrial dynamics, can regulate numerous cellular processes including intracellular calcium handling, cell proliferation, apoptosis and quality control. This review examines the crucial role of preclinical models in advancing our understanding of mitochondrial genetic contributions to these conditions. It follows the evolution of models of mitochondrial-driven diseases, from earlier in vitro and in vivo systems to the use of more innovative approaches, such as CRISPR-based gene editing and mitochondrial replacement therapies. By assessing both the strengths and limitations of these models, we highlight their contributions to uncovering disease mechanisms, identifying therapeutic targets, and facilitating novel discoveries. Challenges in translating preclinical findings into clinical applications are also addressed, along with strategies to enhance the accuracy and relevance of these models. This review outlines the current state of the field, the future trajectory of mitochondrial disease modeling, and its potential impact on patient care.

Keywords:  CRISPR/Cas9; conplastic mouse; cybrid; mitochondrial replacement therapy (MRT); mitochondrial-driven diseases; mitochondrial-nuclear eXchange (MNX) mice; organoid; preclinical models

DOI:  https://doi.org/10.3389/fragi.2025.1585508
Nature. 2025 Jul 09.

Coenzyme Q headgroup intermediates can ameliorate a mitochondrial encephalopathy.

Guangbin Shi, Claire Miller, Sota Kuno, Alejandro G Rey Hipolito, Salsabiel El Nagar, Giulietta M Riboldi, Megan Korn, Wyatt C Tran, Zixuan Wang, Lia Ficaro, Tao Lin, Quentin Spillier, Begoña Gamallo-Lana, Drew R Jones, Matija Snuderl, Soomin C Song, Adam C Mar, Alexandra L Joyner, Roy V Sillitoe, Robert S Banh, Michael E Pacold.

Decreased brain levels of coenzyme Q10 (CoQ10), an endogenously synthesized lipophilic antioxidant1,2, underpin encephalopathy in primary CoQ10 deficiencies3,4 and are associated with common neurodegenerative diseases and the ageing process5,6. CoQ10 supplementation does not increase CoQ10 pools in the brain or in other tissues. The recent discovery of the mammalian CoQ10 headgroup synthesis pathway, in which 4-hydroxyphenylpyruvate dioxygenase-like protein (HPDL) makes 4-hydroxymandelate (4-HMA) to synthesize the CoQ10 headgroup precursor 4-hydroxybenzoate (4-HB)7, offers an opportunity to pharmacologically restore CoQ10 synthesis and mechanistically treat CoQ10 deficiencies. To test whether 4-HMA or 4-HB supplementation promotes CoQ10 headgroup synthesis in vivo, here we administered 4-HMA and 4-HB to Hpdl-/- mice, which model an ultra-rare, lethal mitochondrial encephalopathy in humans. Both 4-HMA and 4-HB were incorporated into CoQ9 and CoQ10 in the brains of Hpdl-/- mice. Oral treatment of Hpdl-/- pups with 4-HMA or 4-HB enabled 90-100% of Hpdl-/- mice to live to adulthood. Furthermore, 4-HB treatment stabilized and improved the neurological symptoms of a patient with progressive spasticity due to biallelic HPDL variants. Our work shows that 4-HMA and 4-HB can modify the course of mitochondrial encephalopathy driven by HPDL variants and demonstrates that CoQ10 headgroup intermediates can restore CoQ10 synthesis in vivo.

DOI: https://doi.org/10.1038/s41586-025-09246-x
Proc Natl Acad Sci U S A. 2025 Jul 15. 122(28): e2421886122

Autophagic stress activates distinct compensatory secretory pathways in neurons.

Sierra D Palumbos, Jacob Popolow, Juliet Goldsmith, Erika L F Holzbaur.

  Autophagic dysfunction is a hallmark of neurodegenerative disease, leaving neurons vulnerable to the accumulation of damaged organelles and aggregated proteins. However, the late onset of diseases suggests that compensatory quality control mechanisms may be engaged to delay these deleterious effects. Neurons expressing common familial Parkinson's disease-associated mutations in the leucine-rich repeat kinase 2 (LRRK2) exhibit defective autophagy. Here, we demonstrate that both primary murine neurons and human induced Pluripotent Stem Cells (iPSC)-derived neurons harboring pathogenic LRRK2 upregulate the secretion of extracellular vesicles. We used unbiased proteomics to characterize the secretome of LRRK2G2019S neurons and found that autophagic cargos including mitochondrial proteins were enriched. Based on these observations, we hypothesize that autophagosomes are rerouted toward secretion when cell-autonomous degradation is compromised to mediate clearance of undegraded cellular waste. Immunoblotting confirmed the release of autophagic cargos and live-cell imaging demonstrated that secretory autophagy is upregulated in LRRK2G2019S neurons. We also found that LRRK2G2019S neurons upregulate the release of exosomes containing microRNAs. Live-cell imaging confirmed that this upregulation of exosomal release is dependent on hyperactive LRRK2 activity, while pharmacological experiments indicate that this release staves off apoptosis. Finally, we show that markers of both vesicle populations are upregulated in plasma from mice expressing pathogenic LRRK2. In sum, we find that neurons expressing pathogenic LRRK2 upregulate secretory autophagy and the compensatory release of exosomes to mediate waste disposal and transcellular communication, respectively. We propose that this increased secretion contributes to the maintenance of cellular homeostasis, delaying neurodegenerative disease progression over the short term while potentially contributing to neuroinflammation over the longer term.

Keywords:  Parkinson’s disease; autophagy; neurodegeneration; secretion

DOI:  https://doi.org/10.1073/pnas.2421886122
Nat Commun. 2025 Jul 09. 16(1): 6332

Combining phenomics with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion.

Matthew Tegtmeyer, Dhara Liyanage, Yu Han, Kathryn B Hebert, Ruifan Pei, Gregory P Way, Pearl V Ryder, Derek Hawes, Callum Tromans-Coia, Beth A Cimini, Anne E Carpenter, Shantanu Singh, Ralda Nehme.

Neuropsychiatric disorders remain difficult to treat due to complex and poorly understood mechanisms. NeuroPainting is a high-content morphological profiling assay based on Cell Painting and optimized for human stem cell-derived neural cell types, including neurons, progenitors, and astrocytes. The assay quantifies over 4000 features of cell structure and organelle organization, generating a dataset suitable for phenotypic screening in neural models. Here, we show that, in studies of the 22q11.2 deletion-a strong genetic risk factor for schizophrenia-we observe cell-type-specific effects, particularly in astrocytes, including mitochondrial disruption, altered endoplasmic reticulum organization, and cytoskeletal changes. Transcriptomic analysis shows reduced expression of cell adhesion genes in deletion astrocytes, consistent with post-mortem brain data. Integration of RNA and morphology data suggests a link between adhesion gene dysregulation and mitochondrial abnormalities. These results illustrate how combining image-based profiling with gene expression analysis can reveal cellular mechanisms associated with genetic risk in neuropsychiatric disease.

DOI: https://doi.org/10.1038/s41467-025-61547-x
FEBS J. 2025 Jul 07.

A guide to characterizing the dynamic mitochondria-endoplasmic reticulum contact sites.

Antigoni Diokmetzidou, Luca Scorrano.

  Organelles were once regarded as discrete entities, but it is now established that they interact through specialized membrane contacts maintained by protein tethers and lipid interactions. Among these, mitochondria-endoplasmic reticulum contact sites (MERCS) emerged as hubs for calcium signaling, lipid metabolism, and mitochondrial dynamics. Here, we critically appraise current methodologies for MERC visualization and quantification, survey the molecular toolbox for their selective perturbation, and highlight common experimental pitfalls. We also discuss key conceptual issues-defining MERCs on structural and functional grounds, addressing redundancy among tethering factors, and distinguishing primary MERC-mediated effects from secondary cellular responses. Finally, we propose that an integrative strategy combining imaging, precise biochemical isolation, proteomics, and functional assays will be essential to resolve outstanding questions about MERC dynamics in physiology and pathology.

Keywords:  endoplasmic reticulum; imaging; membrane contact sites; mitochondria; mitochondria–ER contact sites

DOI:  https://doi.org/10.1111/febs.70184
Nat Commun. 2025 Jul 10. 16(1): 6371

Muscle AMP deaminase activity was lower in Neandertals than in modern humans.

Dominik Macak, Shin-Yu Lee, Tomas Nyman, Henry Ampah-Korsah, Emilia Strandback, Svante Pääbo, Hugo Zeberg.

The enzyme AMPD1 is expressed in skeletal muscle and is involved in ATP production. All available Neandertal genomes carry a lysine-to-isoleucine substitution at position 287 in AMPD1. This variant, which occurs at an allele frequency of 0-8% outside Africa, was introduced to modern humans by gene flow from Neandertals. Here, we show that the catalytic activity of the purified Neandertal AMPD1 is ~25% lower than the ancestral enzyme, and when introduced in mice, it reduces AMPD activity in muscle extracts by ~80%. Among present-day Europeans, another AMPD1 variant encoding a stop codon occurs at an allele frequency of 9-14%. Individuals heterozygous for this variant are less likely to be top-performing athletes in various sports, but otherwise reduced AMPD1 activity is well tolerated in present-day humans. While being conserved among vertebrates, AMPD1 seems to have become less functionally important among Neandertals and modern humans.

DOI: https://doi.org/10.1038/s41467-025-61605-4
Front Cell Dev Biol. 2025 ;13 1619758

Oocyte and dietary supplements: a mini review.

Hao Chen, Shuoqi Wang, Meiying Song, Dongxia Yang, Hongmei Li.

  Rising rates of infertility have stimulated interest in dietary supplements to improve oocyte quality through mitochondrial function, antioxidant activity, and epigenetically regulated metabolic pathways. Mitochondria provides adenosine triphosphate for oocyte maturation, with Coenzyme Q10 (CoQ10) demonstrating efficacy in animal models by alleviating oxidative damage and enhancing blastocyst formation. In aged mice, CoQ10 restored mitochondrial activity and reduced chromosomal abnormalities, while preliminary human studies noted improved embryo quality in poor responders, though randomized controlled trials (RCTs) remain inconclusive. Antioxidants like melatonin counter reactive oxygen species (ROS)-induced spindle defects and mitochondrial dysfunction, showing benefits in murine oocyte maturation and blastocyst development. Resveratrol enhanced bovine oocyte quality through metabolic modulation. Human trials on antioxidants show reduced granulosa cell stress but lack robust evidence. Epigenetically, folate supports DNA methylation critical for embryonic gene expression, with deficiencies linked to hyperhomocysteinemia and developmental defects in animal models. Human observational studies associate folate-rich diets with lower aneuploidy and better assisted reproductive technology outcomes, while omega-3 fatty acids aid chromatin remodeling via histone deacetylase regulation. Despite compelling preclinical data, human trials face inconsistencies due to variable designs and confounders. Standardized RCTs are urgently needed to translate mechanistic insights into clinical guidelines, addressing the disconnect between animal studies and human reproductive outcomes.

Keywords:  clinical trials; dietary supplements; lifestyle changes; oocyte process; quality ovary

DOI:  https://doi.org/10.3389/fcell.2025.1619758
J Heart Lung Transplant. 2025 Jul 05. pii: S1053-2498(25)02107-2. [Epub ahead of print]

Revitalizing Donor Organs: The Potential of Mitochondrial Transplantation in Heart and Lung Transplantation.

Aybuke Celik, Sandra Lindstedt, David C McGiffin, Jacky Y Suen, John F Fraser, Pedro J Del Nido, Sitaram M Emani, James D McCully.

  Heart and lung transplantation remain the primary treatments for end-stage organ failure; yet organ shortages and ischemia-reperfusion injury (IRI) limit their success. Extended criteria donors (ECDs) have expanded the donor pool; however, prolonged cold ischemia times increase the risk of primary graft dysfunction (PGD). Static cold storage (SCS), the standard organ preservation method, is suboptimal, leading to mitochondrial dysfunction, ATP depletion, and oxidative stress. Recent advancements in organ storage show promise in maintaining graft viability. Mitochondria are key regulators of cellular homeostasis, and their dysfunction exacerbates IRI, contributing to inflammation and graft failure. Mitochondrial transplantation (MTx) has emerged as a novel therapeutic strategy to restore cellular bioenergetics, reduce oxidative stress, and improve graft function. Further research is needed to optimize MTx protocols and integrate them into current preservation techniques to enhance transplant success and long-term graft survival.

Keywords:  heart transplantation; ischemia reperfusion injury; lung transplantation; mitochondria; mitochondrial transplantation; primary graft dysfunction

DOI:  https://doi.org/10.1016/j.healun.2025.07.002
Brain. 2025 Jul 07. pii: awaf208. [Epub ahead of print]

Remyelination of chronic demyelinated lesions with directly induced neural stem cells.

Luca Peruzzotti-Jametti, Nunzio Vicario, Giulio Volpe, Sandra Rizzi, Cheek Kwok, Ivan Lombardi, Mads S Bergholt, Lucas Barea-Moya, Andrea D'Angelo, Alexandra M Nicaise, Giuseppe D'Amico, Grzegorz Krzak, Cory M Willis, Sara Gil-Perotin, Olena Hruba, Alice Braga, Molly M Stevens, José M Garcia-Verdugo, Kourosh Saeb-Parsy, Chao Zhao, Robin J M Franklin, Frank Edenhofer, Stefano Pluchino.

  The limited ability of CNS progenitor cells to differentiate into oligodendrocytes limits the repair of demyelinating lesions and contributes to the disability of people with progressive multiple sclerosis (PMS). Neural stem cell (NSC) transplantation has emerged as a safe therapeutic approach in people with PMS, where it holds the promise of healing the injured CNS. However, the mechanisms by which NSC grafts could promote CNS remyelination need to be carefully assessed before their widespread clinical adoption. In this study, we used directly induced NSCs (iNSCs) as a novel transplantation source to boost remyelination in the CNS. Using a mouse model of focal lysophosphatidylcholine (LPC)-induced demyelination, we found that mouse iNSCs promote remyelination by enhancing endogenous oligodendrocyte progenitor cells differentiation and by directly differentiating into mature oligodendrocytes. Transplantation of mouse iNSCs in LPC-lesioned Olig1-/- mice, which exhibits impaired remyelination, confirmed the direct remyelinating ability of grafts and the formation of new exogenous myelin sheaths. We also demonstrated that the xenotransplantation of human iNSCs (hiNSCs) is safe in mice, with hiNSCs persisting long-term in demyelinating lesions where they can produce graft-derived human myelin. Our findings support the use of NSC therapies to enhance remyelination in chronic demyelinating disorders, such as PMS.

Keywords:  demyelination; iNSC grafts; multiple sclerosis; oligodendrocyte progenitor cells; remyelination; transplantation

DOI:  https://doi.org/10.1093/brain/awaf208
Bioessays. 2025 Jul 06. e70038

Oxidative Phosphorylation in Uncoupled Mitochondria.

Henver S Brunetta, Marcelo A Mori, Alexander Bartelt.

  Mitochondrial membrane potential is highly dependent on coupled as well as uncoupled respiration. While brown adipose tissue (BAT) mediates non-shivering thermogenesis (NST), a highly adaptive bioenergetic process critical for energy metabolism, the relationship of coupled and uncoupled respiration in thermogenic adipocytes remains complicated. Uncoupling protein 1 (UCP1)-mediated proton leak is the primary driver of NST, but recent studies have shown that oxidative phosphorylation may be an underappreciated contributor to UCP1-dependent NST. Here, we highlight the role of ATP synthase for BAT thermogenesis and discuss the implications of fine-tuning adrenergic signaling in brown adipocytes by the protein inhibitory factor 1 (IF1). We conclude by hypothesizing future directions for mitochondrial research, such as investigating the potential role of IF1 for mitochondrial substrate preference, structural dynamics, as well as its role in cell fate decision and differentiation.

Keywords:  UCP1; adipocytes; bioenergetics; metabolism; mitochondria; obesity; thermogenesis

DOI:  https://doi.org/10.1002/bies.70038
Sci Signal. 2025 Jul 08. 18(894): eadw4165

Evolution of growth factor signaling to the TSC complex to regulate mTORC1.

Kun Wang, Sophie E Lockwood, Brendan D Manning.

The mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) integrates signals from factors that both stimulate (exogenous growth factors) and are essential for (intracellular nutrients and energy) cellular growth. Activation of the protein kinase mTOR within mTORC1 results in the phosphorylation of downstream substrates that collectively stimulate biomass accumulation to drive cell growth. Many upstream signals, especially growth factors, regulate mTORC1 by inducing the phosphorylation of the tuberous sclerosis complex 2 (TSC2) subunit of the TSC protein complex, a conserved brake on mTORC1 activation and its promotion of cell growth. Cryo-electron microscopy studies of the TSC protein complex have revealed that this phosphoregulation of TSC2 occurs almost exclusively on residues in loops that are outside of the evolutionarily conserved core structural elements and that did not resolve in these structures. These phosphorylation-rich unstructured loops evolved with metazoans, suggesting that the regulation of mTORC1 by diverse growth factors likely evolved with the emergence of complex body plans and diverse cell types to coordinate cell growth and metabolism within and across distinct tissues. Unlike the core structure of TSC2, these loops lack disease-associated missense mutations. These features suggest that the regulatory loops on TSC2 are more amenable to evolutionary changes that enable diverse signals to converge on the TSC protein complex to regulate mTORC1.

DOI: https://doi.org/10.1126/scisignal.adw4165
Nat Commun. 2025 Jul 05. 16(1): 6213

A porin-like protein used by bacterial predators defines a wider lipid-trapping superfamily.

Rebecca J Parr, Yoann G Santin, Giedrė Ratkevičiūte, Simon G Caulton, Paul Radford, Dominik Gurvič, Matthew Jenkins, Matthew T Doyle, Liam Mead, Augustinas Silale, Bert van den Berg, Timothy J Knowles, R Elizabeth Sockett, Phillip J Stansfeld, Géraldine Laloux, Andrew L Lovering.

Outer membrane proteins (OMPs) define the surface biology of Gram-negative bacteria, with roles in adhesion, transport, catalysis and signalling. Specifically, porin beta-barrels are common diffusion channels, predominantly monomeric/trimeric in nature. Here we show that the major OMP of the bacterial predator Bdellovibrio bacteriovorus, PopA, differs from this architecture, forming a pentameric porin-like superstructure. Our X-ray and cryo-EM structures reveal a bowl-shape composite outer β-wall, which houses a central chamber that encloses a section of the lipid bilayer. We demonstrate that PopA, reported to insert into prey inner membrane, causes defects when directed into Escherichia coli membranes. We discover widespread PopA homologues, including likely tetramers and hexamers, that retain the lipid chamber; a similar chamber is formed by an unrelated smaller closed-barrel family, implicating this as a general feature. Our work thus defines oligomeric OMP superfamilies, whose deviation from prior structures requires us to revisit existing membrane-interaction motifs and folding models.

DOI: https://doi.org/10.1038/s41467-025-61633-0
Front Aging. 2025 ;6 1606110

Age and sex-specific changes in mitochondrial quality control in skeletal and cardiac muscle.

Catherine B Springer-Sapp, Olayinka Ogbara, Maria Canellas Da Silva, AbryAnna Henderson, Yuan Liu, Steven J Prior, Sarah Kuzmiak-Glancy.

   Introduction: Skeletal and cardiac muscle mitochondria exist in a dynamic reticulum that is maintained by a balance of mitochondrial biogenesis, fusion, fission, and mitophagy. This balance is crucial for adequate ATP production, and alterations in skeletal muscle mitochondria have been implicated in aging-associated declines in mitochondrial function.
Methods: We sought to determine whether age and biological sex affect mitochondrial content [Complex IV (CIV)], biogenesis (PGC-1ɑ), fusion (MFN2, OPA1), fission (DRP1, FIS1), and mitophagy (Parkin, Pink1) markers in skeletal and cardiac muscle by assessing protein expression in tibialis anterior (TA) and ventricular tissue from 16 young (≤6 months) and 16 old (≥20 months) male and female Sprague-Dawley rats.
Results: In the TA, CIV expression was 40% lower in old vs. young rats (p < 0.001), indicating lower mitochondrial content, and coincided with higher expression of Parkin (+4-fold, p < 0.001). Further, MFN2 expression was higher (+2-fold, p < 0.005) and DRP1 expression was lower (-40%, p = 0.014) in older rats. In cardiac muscle, mitochondrial content was maintained in old vs. young rats, and this occurred concomitantly with higher expression of both PGC-1ɑ and Parkin. MFN2 and OPA1 expression were also 1.2-5-fold higher in older rats (p < 0.05 for all). Largely, protein expression did not differ between male and female rats, with the exception of Pink1 and FIS1 expression in the TA.
Discussion: Collectively, older skeletal and cardiac muscle demonstrated higher expression of fusion and mitophagy proteins, which indicates age alters the balance of biogenesis, fission, fusion, and mitophagy. This may, in turn, affect the ability to provide ATP to these metabolically active tissues.

Keywords:  biological sex; fission; fusion; mitophagy; muscle health

DOI:  https://doi.org/10.3389/fragi.2025.1606110
Neuroradiology. 2025 Jul 10.

Neuroimaging characteristics of single Large-Scale mitochondrial DNA deletion syndromes.

Tamer Sobeh, Tal Granek, Omer Bar-Yosef, Elad Jacoby, Chen Hoffmann, Shai Shrot.

   BACKGROUND AND PURPOSE: Single large-scale mitochondrial DNA deletion syndromes (SLSMDSs) are rare mitochondrial disorders that present a continuum of phenotypes, including Pearson syndrome, Kearns-Sayre syndrome, and progressive external ophthalmoplegia. Neuroimaging findings in SLSMDSs are underreported, and their role in diagnosis and disease monitoring remains inadequately defined. This study aims to characterize clinical features and analyze neuroimaging findings, including spectroscopy and diffusion imaging, in patients with SLSMDSs.
METHODS: A retrospective review of 11 patients diagnosed with SLSMDSs at a tertiary referral center between 2013 and 2024 was conducted. Clinical, genetic, and neuroimaging data were analyzed. MRI scans were reviewed for abnormalities in various brain regions, including white matter, basal ganglia, thalami, corpus callosum, cerebellum, and brainstem.
RESULTS: The cohort had a mean age of 8.3 years (63.6% female). MRI was normal in 4 patients. Among the remaining 7, symmetrical T2/FLAIR hyperintensities, with or without diffusion alterations, were frequently observed, involving the dorsal brainstem in 7/7 and the cerebellum in 6/7 of patients. Globi pallidi involvement was also present in 6 of 7 patients. MR basal ganglia spectroscopy demonstrated elevated lactate in 3 of 7 patients with available spectroscopy. Subcortical and deep white matter abnormalities were identified in 3 patients, sparing the periventricular regions. Imaging progression was noted in patients with serial studies (4 patients).
CONCLUSIONS: Neuroimaging in SLSMDSs typically demonstrates characteristic involvement of the dorsal brainstem, cerebellum, and basal ganglia, and may show diffusion alterations, a finding suggestive of metabolic injury. The observed pattern of subcortical white matter involvement with periventricular sparing may aid in differentiating this disorder from others. Normal imaging may be present in early or less severe disease. MRI, including diffusion imaging and spectroscopy, can support diagnosis and longitudinal monitoring.

Keywords:  Brainstem abnormalities; Diffusion MRI; Magnetic resonance spectroscopy; Single large-scale mitochondrial DNA deletion syndromes

DOI:  https://doi.org/10.1007/s00234-025-03689-9
Biochim Biophys Acta Mol Cell Res. 2025 Jul 07. pii: S0167-4889(25)00124-7. [Epub ahead of print] 120019

Modulation of mitochondrial quality control through autophagic pathway in familial Alzheimer's disease.

Adriana Limone, Clelia Di Napoli, Giusy De Rosa, Silvia Bagnoli, Antonella Izzo, Claudio Procaccini, Giuseppe Matarese, Benedetta Nacmias, Antonio Lavecchia, Daniela Sarnataro.

  Autophagy is a highly conserved cellular catabolic process recognized as an essential pathway for the maintenance of cellular homeostasis. Growing evidence implicates autophagic dysfunction in the pathogenesis of several neurodegenerative disorders, including Alzheimer's disease (AD), thus its modulation might represent an interesting therapeutic tool. Searching for a compound that stimulates autophagic pathway, led us to identify the inhibitor of RPSA receptor, NSC47924. In this study, we show that, NSC47924 down-modulated Akt-mTOR-axis pathway, the master regulator of autophagy, which was abnormally hyperactivated in fibroblasts from genetic AD-affected patients. Consistently, by monitoring the conversion of LC3, we found that inhibition of RPSA enhanced and restored the compromised autophagic flux. Moreover, by qRT-PCR analysis we found that inhibitor treatment upregulated the expression of autophagy-linked genes. Importantly, AD-affected fibroblasts exhibited massive mitochondrial network fragmentation and mitophagy defects, which were restored through the stimulation of autophagy induced by RPSA inhibition. Consistent with an efficient elimination of dysfunctional mitochondria, we found that the turnover of both the mitophagy regulators PINK1 and Parkin and the autophagic receptors p62, NDP52, OPTN, was modulated, thus restoring a highly interconnected organelle's network. In addition, the improvement of mitochondrial morphology correlated with a functional recovery, as assessed by Seahorse analysis and mitochondrial ROS production evaluation. Collectively, our findings suggest that RPSA inhibition stimulates an autophagic pathway promoting the efficient removal of damaged mitochondria, favouring the recovery of cellular homeostasis, and counteracting crucial AD pathogenic mechanisms.

Keywords:  37/67 kDa non-integrin laminin receptor; APP V717I mutant; Alzheimer's disease; Autophagy; Mitophagy; PS1 M146L mutant; RPSA

DOI:  https://doi.org/10.1016/j.bbamcr.2025.120019