bims-mitdis 2025-10-26 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2025–10–26
35 papers selected by
Catalina Vasilescu, Helmholz Munich

The mitochondrial disulphide relay substrate FAM136A safeguards IMS proteostasis and cellular fitness.
Clinical utility of the ATP hydrolysis assay for the diagnosis of complex V deficiency in cultured skin fibroblasts.
Newborn screening for fatty acid oxidation disorders: epidemiological and genetic findings in Southeastern China.
Nanomaterial-induced mitochondrial biogenesis enhances intercellular mitochondrial transfer efficiency.
Delayed protein translocation protects mitochondria against toxic CAT-tailed proteins.
The IQ-compete assay for measuring mitochondrial protein import efficiencies in living yeast cells.
Macular OCT inner retinal changes reflect CNS involvement in m.3243A>G disease.
In situ characterization of mitochondrial Hsp60-Hsp10 chaperone complex under folding stress.
An optimized variant prioritization process for rare disease diagnostics: recommendations for Exomiser and Genomiser.
Disrupting mitochondrial β-oxidation by depletion of HADHA impairs primary ciliogenesis.
Tuning the Hsp70 chaperone cycle: emerging roles of GrpE-like NEFs in proteostasis and organelle function.
Pathogenic UNC13A variants cause a neurodevelopmental syndrome by impairing synaptic function.
Increased Intermembrane Space [Ca2+] Drives Mitochondrial Structural Damage in CPVT.
Mitochondrial dysfunction in age-related sarcopenia: mechanistic insights, diagnostic advances, and therapeutic prospects.
A crucial role of the malate aspartate shuttle in metabolic reprogramming in TNF-induced SIRS.
Progesterone receptor membrane component 1 (PGRMC1) regulates Heme trafficking through mitochondria-ER junctions.
PHB1 attenuates triptolide-induced cardiotoxicity by regulating mitochondrial dynamics in cultured newborn mice cardiomyocytes.
ZC3H4, a novel regulator of mitochondrial complex I, impacts prostate stromal cell senescence, attachment, adhesion and anoikis resistance.
Development of Two In Vitro ND1-LHON Models for Evaluating Gene Therapy Efficacy.
Mic60/Mitofilin inhibitor, Miclxin, induces rat H9C2 cardiomyoblast death by inhibiting the removal of damaged mitochondria.
High-resolution native electrophoresis in-gel activity assay reveals biological insights of medium-chain fatty acyl-CoA dehydrogenase deficiency.
Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes.
Development of an AAV-Based Gene Therapy for the Ocular Phenotype of Friedreich's Ataxia.
Human dental pulp stem cell-derived mitochondria restore mitochondrial function and promote neuroregeneration in a cellular model of Parkinson's disease.
Nuclear hormone-sensitive lipase regulates adipose tissue mass and adipocyte metabolism.
The gut microbiome promotes mitochondrial respiration in the brain of a Parkinson's disease mouse model.
Label-free robotic mitochondrial biopsy.
TCA-cycle metabolites in the nucleus: drivers of chromatin and epigenetic control.
Structural dynamics of the mitochondrial ADP/ATP carrier support an asymmetric transport mechanism.
Google AI aims to make best-in-class scientific software even better.
Protocol for image-based monitoring of de novo RNA synthesis at DNA double-strand breaks in human cell lines.
Analytical Validation of a Genomic Newborn Screening Workflow.
FUNDC1 deficiency aggravates endothelial senescence and retinal dysfunction.
Hypercontractility and Oxidative Stress Drive Creatine Kinase Dysfunction in Hypertrophic Cardiomyopathy.
Ribonucleic acid and gene therapies in cardiovascular disease: clinical applications, delivery challenges and emerging precision tools.

Redox Biol. 2025 Oct 08. pii: S2213-2317(25)00397-0. [Epub ahead of print]87 103884

The mitochondrial disulphide relay substrate FAM136A safeguards IMS proteostasis and cellular fitness.

Christine Zarges, Hanna Fieler, Robin Alexander Rothemann, Simon Poepsel, Lucas T Jae, Jan Riemer.

  The mitochondrial disulphide relay is the key machinery for import and oxidative protein folding in the mitochondrial intermembrane space. Among IMS proteins with unknown function, we identified FAM136A as a new substrate of the mitochondrial disulphide relay. We demonstrate a transient interaction between FAM136A and MIA40, and that MIA40 introduces four disulphide bonds in two twin-CX3C motifs of FAM136A. Consequently, IMS import of FAM136A requires these cysteines and its steady state levels in intact cells are strongly dependent on MIA40 and AIFM1 levels. Furthermore, we show that FAM136A forms non-covalent homodimers as a mature protein. Acute deletion of FAM136A curtails cellular proliferation capacity and elicits a robust induction of the integrated stress response, coincident with the aggregation and/or depletion of selected IMS proteins including HAX1 and CLPB. Together, this establishes FAM136A as a pivotal component of the IMS proteostasis network, with implications for overall cellular function and health.

Keywords:  FAM136A; Integrated stress response; MIA40; Oxidative protein folding

DOI:  https://doi.org/10.1016/j.redox.2025.103884
Mol Genet Metab. 2025 Oct 06. pii: S1096-7192(25)00249-5. [Epub ahead of print]146(3): 109257

Clinical utility of the ATP hydrolysis assay for the diagnosis of complex V deficiency in cultured skin fibroblasts.

Marisa W Friederich, Johan L K Van Hove.

  Complex V catalyzes the formation of ATP from ADP and Pi through the dissipation of the proton gradient generated during the process of oxidative phosphorylation. Most complex V genetic disorders are caused by missense mutations in the mtDNA-encoded subunits, a (MT-ATP6) and A6L (MT-ATP8). Nuclear DNA-encoded gene mutations are increasingly recognized as causes of complex V defects and exhibited both autosomal recessive and autosomal dominant inheritance. Most identified variants are novel and confirmation by functional assays is important especially for variants demonstrating autosomal dominant inheritance. A kinetic spectrophotometric assay of the Complex V enzymatic hydrolysis activity has been reported. Here we report the clinical utility of this assay for the diagnosis of complex V deficiency after optimization and validation for the diagnosis of isolated complex V disorders due to both nuclear and mitochondrial DNA encoded variants and also for use in combined respiratory chain deficiencies. This assay was able to identify all nuclear DNA-encoded complex V deficiencies, whereas a decrease in complex V activity was observed in some patient cell lines with combined deficiencies. However, this assay only identified 50% of the mitochondrial DNA-encoded complex V deficiencies due to pathogenic variants in MT-ATP6/8. In conclusion, the enzymatic assay of complex V has best clinical utility for nuclear DNA-encoded complex V defects.

Keywords:  ATP synthase; Clinical utility; Complex V; Enzyme assay; Sensitivity

DOI:  https://doi.org/10.1016/j.ymgme.2025.109257
BMC Pediatr. 2025 Oct 24. 25(1): 863

Newborn screening for fatty acid oxidation disorders: epidemiological and genetic findings in Southeastern China.

Suping Zhang, Xintong Li, Sheng Ye, Weiting Song, Hong Chen.

  Fatty acid oxidation disorders (FAODs) are a group of rare diseases caused by deficiencies in the function of enzymes or proteins involved in the mitochondrial oxidation of fatty acids. This study aimed to analyze the incidence, disease spectrum, gene profile, and clinical phenotypes of FAODs in the southeastern coastal region of China. Between January 2016 and June 2024, acylcarnitine, genetic mutation, and clinical manifestation data were collected from patients diagnosed with FAOD through newborn screening. A total of 210,913 newborns were screened, identifying 36 cases of FAODs, with an overall incidence of 1 in 5,859. Primary carnitine deficiency (PCD) was the most prevalent FAOD, with an incidence of 1 in 9,587, followed by multiple acyl-CoA dehydrogenase deficiency (MADD). Moreover, we identified 32 mutations, including 5 novel variants. Patients with PCD who carried homozygous variants (R254*) of the SLC22A5 gene demonstrated significantly lower average free acylcarnitine levels than those with compound heterozygous variants (2.45 ± 1.27 µmol/L versus 4.42 ± 1.13 µmol/L, p < 0.05). In patients with MADD, rescreening revealed lower levels of characteristic acylcarnitines (C6, C8, C10, C12, and C14) compared with initial screening values, with 42.3% returning to normal levels. During long-term follow-up (approximately 6 years), all patients remained under clinical surveillance initiated based on their NBS diagnosis. One patient with PCD developed severe retinal detachment at age 5. Three patients with long-chain FAOD (two VLCADD, one CPT-IID) died following infections that triggered metabolic crises (ages 5 and 8 months, respectively). These fatal outcomes occurred despite early diagnosis and initiation of standard management protocols prompted by the NBS results. No other severe complications were observed in the surviving cohort. Our findings highlight the importance of developing screening protocols and clinical management strategies to improve outcomes for affected newborns.

Keywords:  Fatty acid oxidation disorders; Genetic variation; Multiple acyl-CoA dehydrogenase deficiency; Newborn screening; Primary carnitine deficiency; Tandem mass spectrometry

DOI:  https://doi.org/10.1186/s12887-025-06250-y
Proc Natl Acad Sci U S A. 2025 Oct 28. 122(43): e2505237122

Nanomaterial-induced mitochondrial biogenesis enhances intercellular mitochondrial transfer efficiency.

John Soukar, Kanwar Abhay Singh, Ari Aviles, Sarah Hargett, Harman Kaur, Samantha Foster, Shounak Roy, Feng Zhao, Vishal M Gohil, Irtisha Singh, Akhilesh K Gaharwar.

  Intercellular mitochondrial transfer, the spontaneous exchange of mitochondria between cells, is a recently described phenomenon crucial for cellular repair, regeneration, and disease management. Enhancing this natural process holds promise for developing novel therapies targeting diseases associated with mitochondrial dysfunction. Here, we introduce a nanomaterial-based approach employing molybdenum disulfide (MoS2) nanoflowers with atomic-scale vacancies to stimulate mitochondrial biogenesis in cells to make them mitochondrial biofactories. Upon cellular uptake, these nanoflowers result in a two-fold increase in mitochondrial mass and enhancing mitochondrial transfer to recipient cells by several-fold. This enhanced efficiency of transfer significantly improves mitochondrial respiratory capacity and adenosine triphosphate production in recipient cells under physiological conditions. In cellular models of mitochondrial and cellular damage, MoS2 enhanced mitochondrial transfer achieved remarkable restoration of cell function. This proof-of-concept study demonstrates that nanomaterial-boosted intercellular mitochondrial transfer can enhance cell survivability and function under diseased conditions, offering a promising strategy for treating mitochondrial dysfunction-related diseases.

Keywords:  biomaterials; cellular medicine; mitochondria; nanomaterials; regenerative medicine

DOI:  https://doi.org/10.1073/pnas.2505237122
Mol Cell. 2025 Oct 20. pii: S1097-2765(25)00815-9. [Epub ahead of print]

Delayed protein translocation protects mitochondria against toxic CAT-tailed proteins.

Nils Bertram, Toshiaki Izawa, Felix Thoma, Serena Schwenkert, Stéphane Duvezin-Caubet, Sae-Hun Park, Nikola Wagener, Anne Devin, Christof Osman, Walter Neupert, Dejana Mokranjac.

  Ribosome-associated protein quality control (RQC) protects cells against the toxic effects of faulty polypeptides produced by stalled ribosomes. However, mitochondria are vulnerable to C-terminal alanyl and threonyl (CAT)-tailed proteins that are generated in this process, and faulty nuclear-encoded mitochondrial proteins are handled by the recently discovered mitoRQC. Here, we performed a genome-wide screen in yeast to identify additional proteins involved in mitoRQC. We found that peptidyl-tRNA hydrolase 2 (Pth2), present in the mitochondrial outer membrane, influences aggregation of CAT-tailed proteins without majorly affecting the CAT-tailing process itself. Peptidyl-tRNA hydrolase activity is essential during this process, yet the activity of Pth2 can be substituted by another peptidyl-tRNA hydrolase upon proper localization. Our data suggest that Pth2 acts by modulating protein translocation and that the mitochondrial proteostasis network is relieved through increased access of CAT-tailed proteins to cytosolic chaperones. Other hits obtained in the screen show that, in general, delayed protein translocation protects mitochondria against toxic CAT-tailed proteins.

Keywords:  RQC; TOM complex; cellular homeostasis; mitoRQC; mitochondria; peptidyl-RNA hydrolase; protein translocation

DOI:  https://doi.org/10.1016/j.molcel.2025.09.030
FEBS Lett. 2025 Oct 25.

The IQ-compete assay for measuring mitochondrial protein import efficiencies in living yeast cells.

Yasmin Hoffman, Annika Egeler, Saskia Rödl, Johannes M Herrmann.

  Most mitochondrial proteins are synthesized in the cytosol and imported into the organelle. Here, we describe a novel Import and de-Quenching Competition (IQ-compete) assay which monitors the import efficiency of model proteins by fluorescence in living cells. For this method, the sequence of the tobacco etch virus (TEV) protease is fused to a mitochondrial precursor and coexpressed with a cytosolic reporter which becomes fluorescent upon TEV cleavage. Thus, inefficient import of the fusion protein leads to a fluorescent signal. With the IQ-compete assay, the import efficiency of proteins can be reliably analyzed in fluorescence readers, by flow cytometry, by microscopy, and by western blotting. We are convinced that the IQ-compete assay will be a powerful strategy for many different applications. Impact statement This article describes a novel method to monitor the mitochondrial import efficiency for a given protein in living yeast cells. With this IQ-compete assay, protein import efficiencies can be quantified by fluorescent microscopy, flow cytometry, fluorescence spectrometry or western blotting.

Keywords:  fluorescence quenching; genetically encoded sensors; mitochondria; presequences; protein targeting

DOI:  https://doi.org/10.1002/1873-3468.70206
BMJ Neurol Open. 2025 ;7(2): e001232

Macular OCT inner retinal changes reflect CNS involvement in m.3243A>G disease.

Hatem Jouda, Andrew C Browning, Akhunzada M Aftab, Ikhlas Mahmoud, Saima Bibi, Robert McFarland, Sarah J Pickett, Helen Devine.

   Background: The m.3243A>G mitochondrial DNA variant is the most common cause of adult mitochondrial disease and is associated with a heterogeneous clinical phenotype. The retina and optic nerve are among the most metabolically active tissues, making them vulnerable to mitochondrial dysfunction. Optical coherence tomography (OCT) studies have demonstrated retinal nerve fibre layer (RNFL) thinning in mitochondrial and other neurodegenerative diseases. We investigated whether temporal RNFL thinning is associated with central nervous system (CNS) involvement in individuals with the m.3243A>G variant.
Methods: High-resolution OCT was used to assess peripapillary RNFL thickness and perform macular segmentation. Participants were categorised into normal RNFL (n=14) or temporal RNFL thinning (n=15) groups. Demographic data, mean-corrected m.3243A>G heteroplasmy, Newcastle Mitochondrial Disease Adult Scale (NMDAS) scaled scores and NMDAS neurological traits were compared.
Results: Temporal RNFL thinning was significantly associated with neurological features (Fisher's exact test, p=0.027). In multivariable analysis, RNFL thinning and age were independent predictors of neurological involvement. Macular OCT revealed concomitant thinning of the ganglion cell-inner plexiform (GC-IPL) complex in the RNFL thinning group, with preservation of outer retinal layers, supporting primary retinal ganglion cell vulnerability. No significant associations were found between RNFL thinning and m.3243A>G heteroplasmy or NMDAS scaled scores.
Conclusion: Temporal RNFL thinning, accompanied by GC-IPL loss, is associated with neurological involvement in m.3243A>G-related mitochondrial disease, supporting its potential as a non-invasive biomarker of CNS dysfunction. Longitudinal studies are needed to determine whether these retinal changes are progressive and predictive of neurological decline.

Keywords:  CLINICAL NEUROLOGY; MITOCHONDRIAL DISORDERS; NEUROMUSCULAR; NEUROOPHTHALMOLOGY

DOI:  https://doi.org/10.1136/bmjno-2025-001232
Sci Adv. 2025 Oct 24. 11(43): eadw6064

In situ characterization of mitochondrial Hsp60-Hsp10 chaperone complex under folding stress.

Mingyu Jung, Minjung Kim, Su Jin Ham, Jongkyeong Chung, Soung-Hun Roh.

Mitochondrial proteostasis is critical for maintaining mitochondrial function, and its disruption induces mitochondrial unfolded protein response, which up-regulates chaperones to alleviate protein-folding stress. However, how these chaperones mitigate protein-folding stress remains unclear. Here, using correlated cryo-electron tomography, we show that folding stress triggers marked mitochondrial morphological changes, including the accumulation of amorphous protein aggregates and increased abundance and spatial clustering of the mitochondrial heat shock protein 60-heat shock protein 10 (mtHsp60-Hsp10) complex. Subtomogram analysis revealed the in situ architecture and conformational heterogeneity of mtHsp60-Hsp10 under stress, which retains its canonical double-ring structure while adopting distinct football, half-football, and bullet-like states. Notably, the mtHsp60-Hsp10 complex encapsulates unstructured substrates through conserved hydrophobic interactions. We further demonstrate that knockdown of the mtHsp60-Hsp10 complex exacerbates folding stress, as evidenced by elevated cellular stress responses and activation of mitophagy. Our study defines the in situ structural properties of the mtHsp60-Hsp10 complex and provides mechanistic insight into how it safeguards mitochondrial proteostasis under folding stress.

DOI: https://doi.org/10.1126/sciadv.adw6064
Genome Med. 2025 Oct 21. 17(1): 127

An optimized variant prioritization process for rare disease diagnostics: recommendations for Exomiser and Genomiser.

Undiagnosed Diseases Network

   BACKGROUND: Exome sequencing (ES) and genome sequencing (GS) are increasingly used as standard genetic tests to identify diagnostic variants in rare disease cases. However, prioritizing these variants to reduce the time and burden of manual interpretation by clinical teams remains a significant challenge. The Exomiser/Genomiser software suite is the most widely adopted open-source software for prioritizing coding and noncoding variants. Despite its ubiquitous use, limited data-driven guidelines currently exist to optimize its performance for diagnostic variant prioritization. Based on detailed analyses of Undiagnosed Diseases Network (UDN) probands, this study presents optimized parameters and practical recommendations for deploying the Exomiser and Genomiser tools. We also highlight scenarios where diagnostic variants may be missed and propose alternative workflows to improve diagnostic success in such complex cases.
METHODS: We analyzed 386 diagnosed probands from the UDN, including cases with coding and noncoding diagnostic variants. We systematically evaluated how tool performance was affected by key parameters, including gene:phenotype association data, variant pathogenicity predictors, phenotype term quality and quantity, and the inclusion and accuracy of family variant data.
RESULTS: Parameter optimization significantly improved Exomiser's performance over default parameters. For GS data, the percentage of coding diagnostic variants ranked within the top 10 candidates increased from 49.7% to 85.5%, and for ES, from 67.3% to 88.2%. For noncoding variants prioritized with Genomiser, the top 10 rankings improved from 15.0% to 40.0%. We also explored refinement strategies for Exomiser outputs, including using p-value thresholds and flagging genes that are frequently ranked in the top 30 candidates but rarely associated with diagnoses.
CONCLUSION: This study provides an evidence-based framework for variant prioritization in ES and GS data using Exomiser and Genomiser. These recommendations have been implemented in the Mosaic platform to support the ongoing analysis of undiagnosed UDN participants and provide efficient, scalable reanalysis to improve diagnostic yield. Our work also highlights the importance of tracking solved cases and diagnostic variants that can be used to benchmark bioinformatics tools. Exomiser and Genomiser are available at https://github.com/exomiser/Exomiser/ .

Keywords:  Diagnosis; Exome sequencing; Exomiser; Genome sequencing; Genomiser; HPO; Parameter optimization; Phenotype; Rare disease; Variant prioritization

DOI:  https://doi.org/10.1186/s13073-025-01546-1
Sci Rep. 2025 Oct 21. 15(1): 36544

Disrupting mitochondrial β-oxidation by depletion of HADHA impairs primary ciliogenesis.

Joon Bum Kim, Yong Hwan Kim, Seong Hyun Kim, Hyejin Hyung, Jun Hee So, Daeun Park, Na Yeon Park, Dong Kyu Choi, Ji-Eun Bae, Dong-Hyung Cho.

  Primary cilia are dynamic signaling hubs essential for cell homeostasis, and defects in ciliogenesis underpin various genetic disorders. Alpha-hydroxyacyl-CoA dehydrogenase (HADHA), a subunit of the mitochondrial trifunctional enzyme, is crucial for long-chain fatty acid β-oxidation and acetyl-CoA production. Although it was recently demonstrated that lipid metabolism modulates primary ciliogenesis, the connection between mitochondrial β-oxidation and primary cilia remains largely unexplored. Here, we report that HADHA dysfunction markedly impairs primary ciliogenesis and disrupts cilia-dependent signaling. Loss of HADHA reduces both ciliary frequency and length, accompanied by decreased levels of key ciliary signaling mediators. Reintroduction of wild-type HADHA in HADHA knockout cells rescues these defects, whereas its dehydrogenase deficiency mutant (E510Q) fails to restore either normal cilia formation or ciliary signaling. Notably, supplementation with sodium acetate, which resupplies intracellular acetyl-CoA, effectively rescues primary cilium in HADHA-deficient cells. Importantly, this acetate-mediated rescue implicates a potential therapeutic strategy for HADHA-related disorders, supporting the translational relevance of modulating acetyl-CoA levels to restore ciliary function. These findings suggest a relevant link between mitochondrial β-oxidation and primary ciliogenesis, highlighting acetyl-CoA as a potential therapeutic target for disorders related to HADHA deficiency.

Keywords:  Acetyl-CoA; Ciliopathy; HADHA; Primary cilia; β-oxidation

DOI:  https://doi.org/10.1038/s41598-025-18451-7
Protein Cell. 2025 Oct 24. pii: pwaf086. [Epub ahead of print]

Tuning the Hsp70 chaperone cycle: emerging roles of GrpE-like NEFs in proteostasis and organelle function.

Marc A Morizono, Tiffany V Safar, Mark A Herzik.

  The heat shock protein 70 (Hsp70) family of molecular chaperones is essential for nearly every cell to support protein homeostasis through folding, signaling, and quality control. Hsp70 functionality critically depends on co-chaperones, including the GrpE-like family of nucleotide exchange factors (NEFs), first identified in Escherichia coli as GrpE. These factors have long been recognized for their ability to catalyze the release of Hsp70 nucleotide and protein substrates, but recent structural and functional studies have revealed that GrpE-like NEFs are more than passive exchange catalysts, instead acting as dynamic regulators that coordinate chaperone activity with cellular stress responses, organelle-specific demands, and allosteric control of substrate binding and release. In this review, we synthesize decades of research on GrpE-like proteins across bacteria and eukaryotes, culminating in high-resolution structures of the human mitochondrial NEF, GrpEL1, in complex with mitochondrial Hsp70. We examine how architectural features of GrpE-like NEFs have evolved to meet specialized demands, such as thermosensing in bacteria, redox-responsive regulation in vertebrates, and coordination of protein import in mitochondria. We further describe how discrete structural domains dynamically control chaperone cycling, including nucleotide and substrate release, and how gene duplication and domain specialization have driven functional diversification in higher eukaryotes. Finally, we highlight emerging evidence linking NEF activity to mitochondrial homeostasis, stress adaptation, and disease, reframing GrpE-like NEFs as tunable regulators rather than static cofactors. This perspective positions them as stress-adaptive control points in proteostasis and offers a conceptual framework for understanding how ancient chaperone systems have evolved to meet the regulatory needs of modern and complex eukaryotic cells.

Keywords:  GrpE; chaperones; heat shock protein 70; nucleotide exchange factor; proteostasis

DOI:  https://doi.org/10.1093/procel/pwaf086
Nat Genet. 2025 Oct 22.

Pathogenic UNC13A variants cause a neurodevelopmental syndrome by impairing synaptic function.

Reza Asadollahi, Aisha Ahmad, Paranchai Boonsawat, Jasmine Shahanoor Hinzen, Mareike Lohse, Boris Bouazza-Arostegui, Siqi Sun, Tillmann Utesch, Jonas D Sommer, Dragana Ilic, Murugesh Padmanarayana, Kati Fischermanns, Mrinalini Ranjan, Moritz Boll, Chandran Ka, Amélie Piton, Francesca Mattioli, Bertrand Isidor, Katrin Õunap, Karit Reinson, Monica H Wojcik, Christian R Marshall, Saadet Mercimek-Andrews, Naomichi Matsumoto, Noriko Miyake, Bruno de Oliveira Stephan, Rachel Sayuri Honjo, Debora R Bertola, Chong Ae Kim, Roman Yusupov, Heather C Mefford, John Christodoulou, Joy Lee, Oliver Heath, Natasha J Brown, Naomi Baker, Zornitza Stark, Martin Delatycki, Nicole J Lake, Shimriet Zeidler, Linda Zuurbier, Saskia M Maas, Chris C de Kruiff, Farrah Rajabi, Lance H Rodan, Stephanie A Coury, Konrad Platzer, Henry Oppermann, Rami Abou Jamra, Skadi Beblo, Caroline Maxton, Robert Śmigiel, Hunter Underhill, Holly Dubbs, Alyssa Rosen, Katherine L Helbig, Ingo Helbig, Sarah McKeown Ruggiero, Mark P Fitzgerald, Dennis Kraemer, Carlos E Prada, Jeffrey Tenney, Parul Jayakar, Sylvia Redon, Jérémie Lefranc, Kevin Uguen, Simone Race, Stephanie Efthymiou, Reza Maroofian, Henry Houlden, Sandra Coppens, Nicolas Deconinck, Balasubramaniem Ashokkumar, Perumal Varalakshmi, Vykunta Raju Gowda K, Fatemeh Eghbal, Ehsan Ghayoor Karimiani, Morteza Heidari, John Neidhardt, Marta Owczarek-Lipska, G Christoph Korenke, Michael J Bamshad, Philippe M Campeau, Anna Lehman, Laura G Hendon, Ingrid M Wentzensen, Kristin G Monaghan, Yanmin Chen, Anna Szuto, Ronald D Cohn, Ping Yee Billie Au, Christoph Hübner, Felix Boschann, Kandamurugu Manickam, Daniel C Koboldt, Aboulfazl Rad, Gabriela Oprea, Kristine K Bachman, Andrea H Seeley, Emanuele Agolini, Alessandra Terracciano, Piscopo Carmelo, Caleb Bupp, Bethany Grysko, Annick Rein-Rothschild, Bruria Ben Zeev, Amy Margolin, Jennifer Morrison, Aditi Dagli, Elliot Stolerman, Raymond J Louie, Camerun Washington, Servi J C Stevens, Malou Heijligers, Fowzan S Alkuraya, Jasmin Lisfeld, Axel Neu, Fabíola Paoli Monteiro, André Luiz Santos Pessoa, Antonio Edvan Camelo-Filho, Fernando Kok, Dwight Koeberl, Kacie Riley, Lydie Burglen, Diane Doummar, Bénédicte Héron, Cyril Mignot, Boris Keren, Perrine Charles, Caroline Nava, Felix P Bernhard, Andrea A Kühn, Sven Thoms, Ryan D Morrie, Shila Mekhoubad, Eric M Green, Sami J Barmada, Aaron D Gitler, Olaf Jahn, Jeong Seop Rhee, Christian Rosenmund, Mišo Mitkovski, Heinrich Sticht, Han Sun, Gerald Le Gac, Holger Taschenberger, Nils Brose, Jeremy S Dittman, Anita Rauch, Noa Lipstein.

The UNC13A gene encodes a presynaptic protein that is crucial for setting the strength and dynamics of information transfer between neurons. Here we describe a neurodevelopmental syndrome caused by germline coding or splice-site variants in UNC13A. The syndrome presents with variable degrees of developmental delay and intellectual disability, seizures of different types, tremor and dyskinetic movements and, in some cases, death in early childhood. Using assays with expression of UNC13A variants in mouse hippocampal neurons and in Caenorhabditis elegans, we identify three mechanisms of pathogenicity, including reduction in synaptic strength caused by reduced UNC13A protein expression, increased neurotransmission caused by UNC13A gain-of-function and impaired regulation of neurotransmission by second messenger signalling. Based on a strong genotype-phenotype-functional correlation, we classify three UNC13A syndrome subtypes (types A-C). We conclude that the precise regulation of neurotransmitter release by UNC13A is critical for human nervous system function.

DOI: https://doi.org/10.1038/s41588-025-02361-5
Circ Res. 2025 Oct 23.

Increased Intermembrane Space [Ca2+] Drives Mitochondrial Structural Damage in CPVT.

Shanna Hamilton, Radmila Terentyeva, Roland Veress, Fruzsina Perger, Zuzana Nichtova, Mark Bannister, Jinxi Wang, Sage Quiggle, Rachel Battershell, Matthew W Gorr, Sandor Györke, Bum-Rak Choi, Christopher H George, Andriy E Belevych, György Csordás, Dmitry Terentyev.

   BACKGROUND: Mitochondrial dysfunction caused by abnormally high RyR2 (ryanodine receptor) activity is a common finding in cardiovascular diseases. Mechanisms linking RyR2 gain of function with mitochondrial remodeling remain elusive. We hypothesized that RyR2 hyperactivity in cardiac disease increases [Ca2+] in the mitochondrial intermembrane space (IMS) and activates the Ca2+-sensitive protease calpain, driving remodeling of mitochondrial cristae architecture through cleavage of structural protein OPA1 (optic atrophy protein 1).
METHODS: We generated a highly arrhythmogenic rat model of catecholaminergic polymorphic ventricular tachycardia, induced by RyR2 gain-of-function mutation S2236L(±). We created a new biosensor to measure IMS-[Ca2+] in adult cardiomyocytes with intact Ca2+ cycling. We used ex vivo whole heart optical mapping, confocal and electron microscopy, as well as in vivo/in vitro gene editing techniques to test the effects of calpain in the IMS.
RESULTS: We found altered mitochondrial cristae structure, increased IMS-[Ca2+], reduced OPA1 expression, and augmented mito-reactive oxygen species emission in catecholaminergic polymorphic ventricular tachycardia myocytes. We show that calpain-mediated OPA1 cleavage led to disrupted cristae organization and, thereby, decreased electron transport chain supercomplex assembly, resulting in accelerated reactive oxygen species production. Genetic inhibition of calpain activity in IMS reversed mitochondria structural defects in catecholaminergic polymorphic ventricular tachycardia myocytes and reduced arrhythmic burden in ex vivo optically mapped hearts.
CONCLUSIONS: Our data suggest that RyR2 hyperactivity contributes to mitochondrial structural damage by promoting an increase in IMS-[Ca2+], sufficient to activate IMS-residing calpain. Calpain activation leads to proteolysis of OPA1 and cristae widening, thereby decreasing assembly of electron transport chain components into supercomplexes. Consequently, excessive mito-reactive oxygen species release critically contributes to RyR2 hyperactivation and ventricular tachyarrhythmia. Our new findings suggest that targeting IMS calpain may be beneficial in patients at risk for sudden cardiac death.

Keywords:  calcium; cardiovascular diseases; heart failure; mitochondrial proteins; sarcoplasmic reticulum

DOI:  https://doi.org/10.1161/CIRCRESAHA.125.326841
Front Cell Dev Biol. 2025 ;13 1590524

Mitochondrial dysfunction in age-related sarcopenia: mechanistic insights, diagnostic advances, and therapeutic prospects.

Yingtao Huang, Chenchen Wang, Haijian Cui, Guangjiang Sun, Xiaonan Qi, Xiaosheng Yao.

  Sarcopenia is a progressive age-related decline in skeletal muscle mass, strength, and function, representing a significant health burden in older adults. Diagnostic criteria have been established that integrate measures of muscle mass, strength, and physical performance [e.g., European Working Group on Sarcopenia in Older People 2010 (EWGSOP1) and 2019 (EWGSOP2) criteria]. Mechanistically, sarcopenia is driven by hormonal changes, chronic inflammation, cellular senescence, and, importantly, mitochondrial dysfunction. Age-related declines in sex hormones and activation of myostatin impair muscle regeneration and metabolism, while chronic low-grade inflammation disrupts protein synthesis and accelerates proteolysis via the ubiquitin-proteasome system (UPS) and autophagy-lysosome pathway (ALP). The accumulation of senescent cells and their secretory phenotype further exacerbates muscle degeneration and functional decline. Mitochondrial dysfunction plays a central role, characterized by impaired biogenesis, excessive reactive oxygen species (ROS) production, compromised autophagy/mitophagy, and accumulation of mitochondrial DNA (mtDNA) mutations. These defects collectively disrupt muscle energy homeostasis, promoting atrophy. The AMPK/SIRT1/PGC-1α and mTORC1 signaling pathways, along with PINK1/Parkin-mediated and receptor-dependent mitophagy, are essential for regulating mitochondrial biogenesis, protein synthesis, and mitochondrial quality control. Current and emerging therapeutic approaches include resistance and endurance exercise, nutritional and pharmacological agents targeting mitochondrial health, and hormonal modulation. Innovative treatments such as senolytics, exerkines, and gene therapies show promise but require further validation. Future advances in mechanistic understanding, diagnostics, and therapeutic strategies offer hope for mitigating sarcopenia and improving the quality of life in aging populations.

Keywords:  aging; chronic inflammation; mitochondrial dysfunction; muscle atrophy; sarcopenia; therapeutic strategies

DOI:  https://doi.org/10.3389/fcell.2025.1590524
Front Immunol. 2025 ;16 1652516

A crucial role of the malate aspartate shuttle in metabolic reprogramming in TNF-induced SIRS.

Louise Nuyttens, Marah Heyerick, Maxime Roes, Elise Moens, Céline Van Dender, Charlotte Wallaeys, Tino Hochepied, Steven Timmermans, Jolien Vandewalle, Claude Libert.

  Tumor necrosis factor (TNF) causes a lethal systemic inflammatory response syndrome (SIRS) which is characterized by significant metabolic alterations. Based on liver RNA sequencing, we found that TNF impairs the malate-aspartate shuttle (MAS), an essential redox shuttle that transfers reducing equivalents across the inner mitochondrial membrane thereby recycling cytosolic NAD+. This downregulation of MAS genes in TNF-induced SIRS likely results from loss of HNF4α function, which appears to be the key transcription factor involved. Using Slc25a13-/- mice lacking citrin - a crucial MAS component - we demonstrate that MAS dysfunction exacerbates TNF-induced metabolic dysregulations and lethality. Disruptive NAD+ regeneration leads to diminished mitochondrial β-oxidation, leading to elevated levels of circulating free fatty acids (FFAs) and to hepatic lipid accumulation. Simultaneously, MAS dysfunction promotes glycolysis coupled to lactate production and reduces lactate-mediated gluconeogenesis, culminating in severe hyperlactatemia that triggers VEGF-induced vascular leakage. Overall, MAS dysfunction contributes to metabolic failure and lethality in TNF-induced SIRS, highlighting its potential as a promising, therapeutic target.

Keywords:  TNF-induced SIRS; carbohydrate metabolism; citrin; lipid metabolism; malate aspartate shuttle

DOI:  https://doi.org/10.3389/fimmu.2025.1652516
J Inorg Biochem. 2025 Oct 07. pii: S0162-0134(25)00273-9. [Epub ahead of print]275 113093

Progesterone receptor membrane component 1 (PGRMC1) regulates Heme trafficking through mitochondria-ER junctions.

Robert B Piel Iii, Chibuike D Obi, Martonio Ponte Viana, Mathilda M Willoughby, Osiris Martinez-Guzman, Aaliyah Wadley, Yasaman Jami-Alahmadi, James A Wohlschlegel, Kevin G Hicks, Jared Rutter, J Alan Maschek, J Leon Catrow, James Cox, Amit R Reddi, Oleh Khalimonchuk, Amy E Medlock.

  Heme is a cofactor essential for a multitude of biological reactions. The terminal step of heme synthesis occurs in the mitochondrial matrix which means that heme must be trafficked from there to other locales in the cell. Thus, identifying intracellular heme chaperones is crucial to understanding regulation of global cellular metabolism. The heme-binding protein progesterone receptor membrane component 1 (PGRMC1) has been proposed to function as a chaperone for several biologically active molecules including heme, but its cellular role is not fully understood. Here, we investigate the function of PGRMC1 in heme metabolism. By monitoring intracellular heme location and concentrations in Saccharomyces cerevisiae, we show that mutants lacking damage associated protein 1 (Dap1), the yeast ortholog of PGRMC1, have altered nuclear heme trafficking which can be corrected by complementation with DAP1 or PGRMC1. Biochemical analyses reveal that PGRMC1 co-localizes with known mitochondrial-associated membrane (MAM) proteins and proteomic comparison of interaction partners shows enrichment of MAM-associated proteins and pathways. Metabolomics profiling of wild-type and PGRMC1 knockout cells identifies significant changes of several metabolites, including heme, several amino acids, long chain acyl-carnitine, ethanolamine phosphate, and mevalonic acid. Together, these results provide evidence that PGRMC1 is involved in heme trafficking and homeostasis through MAMs.

Keywords:  Ferrochelatase; Heme; MAMs; Mitochondria; PGRMC1

DOI:  https://doi.org/10.1016/j.jinorgbio.2025.113093
J Cardiovasc Pharmacol. 2025 Oct 20.

PHB1 attenuates triptolide-induced cardiotoxicity by regulating mitochondrial dynamics in cultured newborn mice cardiomyocytes.

Wanlin Chen, XinGuo Li.

  Triptolide (TP) is widely used clinically for multiple diseases, but its cardiotoxicity significantly limits its clinical applications. The underlying mechanisms of its cardiotoxicity are still unclear. Mitochondria are crucial for cellular survival and function. Here, we found that TP induced mitochondrial dysfunction and apoptosis of cardiomyocytes, which might be the key process underlying TP-induced cardiotoxicity. Moreover, the expression of prohibitin1 (PHB1) was significantly decreased after TP treatment in a time-dependent manner. Overexpression of PHB1 alleviated mitochondrial dysfunction and inhibited apoptosis of cardiomyocytes after TP treatment. Mechanistically, PHB1 might regulate mitochondrial dynamics, which maintain normal mitochondrial function. Based on the above results, PHB1 might be a potential therapeutic target for TP-induced cardiotoxicity.

Keywords:  PHB1; Triptolide; apoptosis; cardiotoxicity; mitochondrial dynamics

DOI:  https://doi.org/10.1097/FJC.0000000000001766
Cell Death Dis. 2025 Oct 21. 16(1): 741

ZC3H4, a novel regulator of mitochondrial complex I, impacts prostate stromal cell senescence, attachment, adhesion and anoikis resistance.

Teresa T Liu, Mia J Carrarini, Livianna K Myklebust, Kegan O Skalitzky, Nathalie El-Khoury, Ian J Sipula, Alexander Chang, Vishal Soman, Ailing Liu, Nnamdi Ihejirika, Uma R Chandran, Michael J Jurczak, William A Ricke, Donald B DeFranco, Laura E Pascal.

Declining mitochondrial function is an established feature of aging and contributes to most aging-related diseases through its impact on various pathologies such as chronic inflammation, fibrosis and cellular senescence. Our recent work suggests that benign prostatic hyperplasia, which is an aging-related disease frequently associated with inflammation, fibrosis and senescence, is characterized by a decline in mitochondrial function. Here, we utilize glycolytic restriction and pharmacologic inhibition of the mitochondrial electron transfer chain complex I to promote mitochondrial dysfunction and identify the cellular processes impacted by declining mitochondrial function in benign prostate stromal cells. Using this model, we show that mitochondrial dysfunction induced alterations in cell-cell and cell-matrix adhesion, elevated fibronectin expression, resistance to anoikis and stress-induced premature senescence (SIPS). We also showed that ablation of ZC3H4, a transcription termination factor implicated in anoikis-resistance and reduced in BPH relative to normal prostates, phenocopied various phenotypes in the human BHPrS1 prostate stromal cell line that resulted from inhibition of complex I. Furthermore, ZC3H4 ablation resulted in the elevation of mitochondrial superoxide (mtROS) and mitochondrial membrane potential, altered mitochondrial morphology and NAD+/NADH ratio, and reduced CI function in BHPrS1 cells. Thus, ZC3H4 loss promotes mitochondrial dysfunction to drive pathophysiologic changes in the stromal compartment that are features of the aging prostate.

DOI: https://doi.org/10.1038/s41419-025-08027-8
Invest Ophthalmol Vis Sci. 2025 Oct 01. 66(13): 34

Development of Two In Vitro ND1-LHON Models for Evaluating Gene Therapy Efficacy.

Xin Li, Jun Yuan, Zhang Chen, Yue Zhang, Yuefeng Liu, Yong Zhang.

Purpose: The purpose of this study was to address the lack of effective treatments for NADH-ubiquinone oxidoreductase chain 1 (ND1)-related Leber hereditary optic neuropathy (LHON), this study aimed to (1) establish in vitro models mimicking mitochondrial dysfunction in LHON and (2) evaluate the therapeutic potential of recombinant adeno-associated virus (AAV)-mediated ND1 gene therapy (rAAV-ND1).
Methods: Two in vitro models were developed: (1) transmitochondrial cybrid cells carrying the m.3460G>A mutation in the ND1 gene; and (2) patient-derived induced pluripotent stem cells (iPSC)-differentiated retinal ganglion cells (RGCs). Mitochondrial function was assessed via measurements of oxygen consumption and adenosine triphosphate (ATP) production. The efficacy of rAAV-ND1 was tested by infecting both models to rescue mitochondrial deficiency.
Results: Our two LHON models - ND1-mutant cybrid cells and patient-derived iPSC-RGCs - successfully recapitulated characteristic mitochondrial dysfunction, demonstrating impaired oxidative phosphorylation and reduced ATP production. Through qPCR and subcellular fractionation analyses, we confirmed dose-dependent ND1 transgene expression and proper mitochondrial localization. Notably, rAAV2-ND1 treatment effectively restored mitochondrial function in both models: in ND1-cybrids, it recovered spare respiratory capacity to 85% of the control levels, enhanced complex I activity from 65.5% to 90.5%, and increased ATP production from 47.6% to 69.5%; whereas in ND1-RGCs, it also ameliorated bioenergetic deficits, partially reversing SRC reduction, and improving ATP-linked respiration.
Conclusions: The study demonstrates the utility of transmitochondrial cybrids and iPSC-derived RGCs as reliable in vitro models for studying ND1-related LHON. The rAAV-ND1 gene therapy effectively restored mitochondrial function, highlighting its potential as a treatment for LHON caused by ND1 mutations. These findings underscore the value of in vitro systems for evaluating therapies when robust animal models are unavailable.

DOI: https://doi.org/10.1167/iovs.66.13.34
Am J Transl Res. 2025 ;17(9): 6743-6754

Mic60/Mitofilin inhibitor, Miclxin, induces rat H9C2 cardiomyoblast death by inhibiting the removal of damaged mitochondria.

Muhammad S Khan, Somayyeh Nasiripour, Michele Oyarzabal, Swati Banerjee, Kumar Sharma, Manzoor A Bhat, Jean C Bopassa.

  Mitochondrial dysfunction is a hallmark of various pathologic conditions, including ischemia/reperfusion injury, stroke, myocardial infarction, neurodegeneration and metabolic syndrome. As with all biological organelles, the function of mitochondria is tightly linked to their structure. The inner mitochondrial membrane is a highly regulated membrane with a large surface area that hosts the electron transport chain machinery, generates the membrane potential necessary for ATP generation, and forms the signature cristae folds of mitochondria. The mitochondrial inner membrane protein (Mitofilin/Mic60) is part of a large complex that constitutes the mitochondrial inner membrane organizing system, which is critical in maintaining mitochondrial architecture and function. Recent evidence has shown that Mic60/Mitofilin elimination during reperfusion determines the extent of myocardial infarct size after ischemia/reperfusion. Here, we investigated the effects and mechanisms of action of Miclxin, a novel Mic60/Mitofilin inhibitor using H9c2 cardiomyoblasts. Cultured rat H9c2 cardiomyoblasts were incubated with 0, 5, 10, or 20 μM of Miclxin. Cell viability was determined using 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assays, and cell death was determined by flow cytometry using propidium iodide dye. Mitochondrial membrane potential was measured using MitoTracker Red CMXROS assay kits, and mitophagy in mitochondria was detected using Mitophagy Detection Kits. Mitochondrial morphology was assessed using electron microscopy, and proteins were measured by Western blot analyses and immunofluorescence staining. After 24 hours of treatment, Miclxin decreased cell viability in a dose-dependent manner and reduced the number of viable cells measured with MTT assays. This effect was associated with pronounced reduction of Mic60 protein levels measured by Western blots and immunocytochemistry. Miclxin's reduction of cell viability was related to its inhibition of mitochondrial elimination by mitophagy. Our findings suggest that Miclxin decreases levels of Mic60, and thereby reduces cell viability by increasing structural damage and dysfunction in mitochondria via impairment of mitophagy.

Keywords:  H9C2 rat cardiomyomyoblasts; Mic60/Mitofilin protein; Miclxin; cell viability; mitochondria; mitophagy

DOI:  https://doi.org/10.62347/UPML8062
Sci Rep. 2025 Oct 23. 15(1): 37168

High-resolution native electrophoresis in-gel activity assay reveals biological insights of medium-chain fatty acyl-CoA dehydrogenase deficiency.

Sergio Guerrero-Castillo, Alice Grün, Nicole Lewandowski, Polina Gundorova, Lisa Ela Blettenberger, Nora Constanze Laubach, Katrin Küchler, Madalena Barroso, Charlotte Uetrecht, Søren W Gersting.

  Medium-chain specific acyl-CoA dehydrogenase (MCAD) is a mitochondrial homotetrameric flavoprotein that catalyzes the first step in fatty acid beta-oxidation. MCAD deficiency arises from variants that either impair enzymatic activity or destabilize interactions between subunits, leading to protein aggregation. Standard enzymatic assays measure the overall MCAD activity but cannot differentiate between tetramers and other protein forms-critical for understanding the impact of pathogenic variants on structure destabilization. In this study, we adapted a native gel colorimetric assay to quantify the activity of MCAD tetramers separately from other protein forms, providing novel insights into how pathogenic variants affect MCAD structure and function. The assay showed a linear correlation between protein amount and enzymatic activity for octanoyl-CoA, a physiological MCAD substrate. Applying this method to clinically relevant MCAD variants allowed us to distinguish subtle differences in protein shape, enzymatic activity, and FAD content, offering profound implications for understanding the molecular basis of MCADD. This methodology can be extended to analyze variants in other acyl-CoA dehydrogenase family members-such as glutaryl-CoA, isovaleryl-CoA or short-chain fatty acyl-CoA dehydrogenases-that are implicated in disorders of fatty acid and amino acid metabolism.

Keywords:  Fatty acid oxidation; Gel electrophoresis; In-gel activity; Medium-chain acyl-CoA dehydrogenase; Native electrophoresis; Oligomer

DOI:  https://doi.org/10.1038/s41598-025-24684-3
Science. 2025 10 23. eadi8577

Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes.

Benjamin DeMeo, Charlotte Nesbitt, Samuel A Miller, Daniel B Burkhardt, Inna Lipchina, Doris Fu, Peter Holderrieth, David Kim, Sergey Kolchenko, Artur Szalata, Ishan Gupta, Christine Kerr, Thomas Pfefer, Raziel Rojas-Rodriguez, Sunil Kuppassani, Laurens Kruidenier, Parul B Doshi, Mahdi Zamanighomi, James J Collins, Alex K Shalek, Fabian J Theis, Mauricio Cortes.

Phenotypic drug screening remains constrained by the vastness of chemical space and technical challenges scaling experimental workflows. To overcome these barriers, computational methods have been developed to prioritize compounds, but they rely on either single-task models lacking generalizability or heuristic-based genomic proxies that resist optimization. We designed an active deep-learning framework that leverages omics to enable scalable, optimizable identification of compounds that induce complex phenotypes. Our generalizable algorithm outperformed state-of-the-art models on classical recall, translating to a 13-17x increase in phenotypic hit-rate across two hematological discovery campaigns. Combining this algorithm with a lab-in-the-loop signature refinement step, we achieved an additional two-fold increase in hit-rate and molecular insights. In sum, our framework enables efficient phenotypic hit identification campaigns, with broad potential to accelerate drug discovery.

DOI: https://doi.org/10.1126/science.adi8577
Mol Ther. 2025 Oct 23. pii: S1525-0016(25)00869-X. [Epub ahead of print]

Development of an AAV-Based Gene Therapy for the Ocular Phenotype of Friedreich's Ataxia.

Heyu Tang, Siddhant Gupte, Emily Xu, Kaitlyn R Calabro, Hannah Friend, Sean M Crosson, Diego Fajardo, Zachary Kostamo, Hangning Zhang, James J Peterson, Fangyu Lin, Zbynek Kozmik, Cathleen M Lutz, Sanford L Boye, Shannon E Boye.

Friedreich's Ataxia (FA) is a leading form of hereditary ataxia caused by autosomal recessive mutations in frataxin (FXN). GAA triplet repeat expansions lead to lower levels of FXN expression, abnormal influx of iron into mitochondria and damage to the nervous system. Patients typically present before the second decade with loss of muscular function, speech impediments, and cardiomyopathy. At later stages, vision loss typically manifests. Work is underway to develop gene therapies that address the cardiac and CNS manifestations, but their routes of administration do not lead to efficient transduction of the retina. The purpose of this study was to develop a more direct approach for treating the ocular phenotype of FA which includes loss of retinal ganglion cells (RGCs), thinning of the retinal nerve fiber layer (RNFL), optic nerve atrophy, and loss of visual field. We generated two novel conditional knock-out (KO) models, mRx-Fxn KO and Pou4f2-Fxn KO mice, wherein Fxn is ablated in all retinal cells or RGCs, respectively and showed that FXN deficiency led to retinal dystrophy in both models. Gene supplementation via intravitreal injection of a novel AAV2-based capsid carrying FXN partially preserved retinal structure and/or function in both models, establishing proof-of-concept for this therapeutic strategy.

DOI: https://doi.org/10.1016/j.ymthe.2025.10.048
Stem Cell Res Ther. 2025 Oct 24. 16(1): 577

Human dental pulp stem cell-derived mitochondria restore mitochondrial function and promote neuroregeneration in a cellular model of Parkinson's disease.

Thanasup Gonmanee, Pijitra Petcharat, Satjapot Manprasong, Sujiwan S Sangkhamanee, Tawepong Arayapisit, Hathaitip Sritanaudomchai, Kawinthra Khwanraj, Permphan Dharmasaroja.

   BACKGROUND: Parkinson's disease (PD) is a neurodegenerative disorder characterized by the loss of dopaminergic neurons, primarily due to mitochondrial dysfunction. Current treatments focus on managing symptoms but are unable to regenerate neurons. Human dental pulp stem cells (hDPSCs) offer a promising source for neurodegenerative therapy due to their accessibility and neuro-supportive properties. However, research on the mitochondrial characteristics of hDPSCs and their therapeutic potential remains limited. This study investigates the capacity of mitochondria isolated from hDPSCs to restore mitochondrial function and promote neuronal recovery and function in a PD cellular model.
METHODS: hDPSCs were isolated and characterized for mesenchymal stem cell properties. Mitochondria were isolated, quantified, and assessed for viability and morphology using MitoTracker staining and transmission electron microscopy. Mitochondrial uptake and functional recovery were evaluated in a PD cellular model using MPP⁺-treated differentiated SH-SY5Y cells. Mitochondrial function was assessed by measuring Complex I activity, ATP production, and reactive oxygen species (ROS) levels. Neuroregeneration and synaptic function were analyzed through neurite length, growth-associated protein 43 (GAP43) and tyrosine hydroxylase (TH), Synaptophysin (SYP), dopamine transporter (DAT), calcium imaging, and mitochondrial dynamics.
RESULTS: Isolated hDPSC-derived mitochondria were mostly viable, spherical, and displayed immature cristae. In MPP⁺-treated SH-SY5Y cells, mitochondrial transfer restored Complex I activity, elevated ATP production, and reduced ROS. Treated cells also showed significantly longer neurites and increased expression of GAP43, TH, SYP, and DAT. Calcium imaging revealed restored intracellular calcium responses upon stimulation. Mitochondria from hDPSCs localized in both cell bodies and neurites and remained distinct from damaged host mitochondria, supporting synaptic function.
CONCLUSIONS: Mitochondria derived from hDPSCs can restore bioenergetic function, reduce oxidative stress, and promote structural and functional recovery in a PD cellular model. These findings highlight the foundational therapeutic potential of hDPSC-derived mitochondria as a regenerative approach for neurodegenerative diseases.

Keywords:  Human dental pulp stem cells; Mitochondria; Neuroregeneration; Parkinson’s disease

DOI:  https://doi.org/10.1186/s13287-025-04702-x
Cell Metab. 2025 Oct 23. pii: S1550-4131(25)00433-4. [Epub ahead of print]

Nuclear hormone-sensitive lipase regulates adipose tissue mass and adipocyte metabolism.

Jérémy Dufau, Emeline Recazens, Laura Bottin, Camille Bergoglio, Aline Mairal, Karima Chaoui, Marie-Adeline Marques, Veronica Jimenez, Miquel García, Tongtong Wang, Henrik Laurell, Jason S Iacovoni, Remy Flores-Flores, Pierre-Damien Denechaud, Khalil Acheikh Ibn Oumar, Ez-Zoubir Amri, Catherine Postic, Jean-Paul Concordet, Pierre Gourdy, Niklas Mejhert, Mikael Rydén, Odile Burlet-Schiltz, Fatima Bosch, Christian Wolfrum, Etienne Mouisel, Genevieve Tavernier, Dominique Langin.

  In adipocytes, hormone-sensitive lipase (HSL) plays a key role in hydrolyzing triacylglycerols that are stored in lipid droplets. Contrary to the expected phenotype, HSL-deficient mice and humans exhibit lipodystrophy. Here, we show that HSL is also present in the adipocyte nucleus. Mouse models with different HSL subcellular localizations reveal that nuclear HSL is essential for the maintenance of adipose tissue. Gene silencing in human adipocytes shows that HSL, independently of its enzymatic activity, exerts opposing effects on mitochondrial oxidative phosphorylation and the extracellular matrix. Mechanistically, we found that HSL accumulates in the nucleus by interacting with the transforming growth factor β (TGF-β) signaling mediator, mothers against decapentaplegic homolog 3 (SMAD3). Conversely, HSL phosphorylation induces nuclear export. In vivo, HSL accumulates in the nucleus of adipocytes during high-fat feeding with the converse effect during fasting. Together, our data show that as both a cytosolic enzyme and a nuclear factor, HSL plays a pivotal role in adipocyte biology and adipose tissue maintenance.

Keywords:  TGF-β signaling; adipocyte; adipose tissue; cell nucleus; extracellular matrix; hormone-sensitive lipase; lipodystrophy; mitochondrial oxidative phosphorylation; obesity; protein-protein interaction

DOI:  https://doi.org/10.1016/j.cmet.2025.09.014
NPJ Parkinsons Dis. 2025 Oct 20. 11(1): 301

The gut microbiome promotes mitochondrial respiration in the brain of a Parkinson's disease mouse model.

Livia H Morais, Linsey Stiles, Milla Freeman, Anastasiya D Oguienko, Jonathan D Hoang, Jenny Ji, Jeff Jones, Baiyi Quan, Jack Devine, Justin S Bois, Tsui-Fen Chou, Joanne Trinh, Martin Picard, Viviana Gradinaru, Sarkis K Mazmanian.

The pathophysiology of Parkinson's disease (PD) involves gene-environment interactions that impair various cellular processes including mitochondrial dysfunction. Mitochondria-associated mutations increase PD risk, respiration is altered in the PD brain, and mitochondria-damaging toxicants cause PD-like motor and gastrointestinal symptoms in animal models. The gut microbiome is altered in PD, representing an environmental risk, however a relationship between mitochondrial function and the microbiome in PD has not been previously established. Herein, we discover that dysregulation of mitochondria-associated genes and hyperactive striatal mitochondria are induced by the microbiome in α-synuclein-overexpressing (Thy1-ASO) mice. Thy1-ASO mice elaborate increased reactive oxygen species in the striatum whereas germ-free counterparts express increased oxygen scavenging proteins. Indeed, treatment with an antioxidant drug improves motor performance in Thy1-ASO mice and blocking oxidant scavenging in germ-free mice enhances motor deficits in an α-synuclein dependent manner. Thus, the gut microbiome promotes motor symptoms in a mouse model of PD via increased mitochondrial respiration and oxidative stress in the brain.

DOI: https://doi.org/10.1038/s41531-025-01142-5
Sci Adv. 2025 Oct 24. 11(43): eadx4289

Label-free robotic mitochondrial biopsy.

Yanmei Ma, Weikang Hu, Muyang Ruan, Feixiang Bao, Xingguo Liu, Dong Sun, Hongri Gu, Chengzhi Hu.

Robotic micromanipulation has advanced cellular probing, yet achieving precise, minimally invasive intracellular operations without fluorescent labeling remains challenging. Fluorescent techniques often cause photodamage and cytotoxicity and interfere with downstream analyses. Here, we introduce an automated, multifunctional nanoprobing platform capable of label-free extraction of mitochondria from living cells with high spatiotemporal resolution. The nanoprobe integrates two individually addressable nanoelectrodes that perform electrochemical detection of reactive oxygen and nitrogen species, produced by mitochondrial metabolism, followed by dielectrophoretic trapping, manipulation, and extraction of mitochondria. We successfully demonstrated the extraction of mitochondria from living cells, which is validated through fluorescence labeling before and after extraction. Subsequent quantitative polymerase chain reaction further confirmed that the extracted sample contained mitochondria. The fusion of the transplanted mitochondria within the recipient cell's mitochondrial network confirms their activity. This automated, label-free, in situ organelle extraction micromanipulation system offers a powerful tool for understanding disease mechanisms linked to dysfunctional organelles and enables single-cell surgeries for organelle transplantation.

DOI: https://doi.org/10.1126/sciadv.adx4289
BMC Biol. 2025 Oct 21. 23(1): 316

TCA-cycle metabolites in the nucleus: drivers of chromatin and epigenetic control.

Serena Ghisletti, Marta Russo.

  Mitochondrial enzymes are increasingly recognized for their ability to translocate to the nucleus, where they generate metabolites essential for epigenetic regulation and gene expression. Yet, whether this phenomenon broadly involves metabolic enzymes or is restricted to specific subunits remains unclear. In this review, we assess current evidence, highlight knowledge gaps, and suggest future directions on the nuclear localization and functions of metabolic enzymes, with a focus on acyl-CoA producers. Emerging studies reveal multiple mechanisms guiding these enzymes to chromatin for localized metabolite synthesis. Key questions concern nuclear import machinery, chromatin interactions, and the regulatory impact of their activity.

Keywords:  Histone modifications; Metabolism; Mitochondrial enzymes; Transcriptional regulation

DOI:  https://doi.org/10.1186/s12915-025-02423-4
Int J Biol Macromol. 2025 Oct 19. pii: S0141-8130(25)08905-6. [Epub ahead of print] 148348

Structural dynamics of the mitochondrial ADP/ATP carrier support an asymmetric transport mechanism.

Yunna Li, Qiuzi Yi, Yabing Cai, Yuchen Zhang, Jianchun Kong, Pingping Jiang, Xiaohui Cang.

  The mitochondrial ADP/ATP carrier (AAC) mediates ADP/ATP exchange across inner mitochondrial membrane via alternating between cytosol-open (c-) and matrix-open (m-) states. Despite the determination of crystallized structures for both states, its transport mechanism still remains unclear. One obstacle is that the structures are co-crystallized with bulky and asymmetric inhibitors. Here, we carried out molecular dynamics simulations on the m-state AAC with and without the co-crystallized nanobody and inhibitor BKA. We found that in apo AAC, the matrix side exhibits enhanced asymmetry, suggesting that the asymmetry observed in crystallized structures is not an artifact of inhibitor binding as previously proposed. Comparative analysis of apo AAC trajectories in m- and c-states reveals that transmembrane helix H2 undergoes the most drastic conformational changes, while the H4-H5 bundle shows the least change among neighboring helix pairs. Further analysis indicates that the PG -level 1 in H2 and H6 separates the carrier into two asymmetric motion units, with the smaller unit undergoing more pronounced movement. Mutagenesis experiments validate functional significance of the asymmetric distribution of highly conserved P×[D/E] × ×[K/R] and [D/E]G motifs among three repeat domains. Free energy calculations further confirm the previously reported asymmetric internal interactions in c-state AAC despite its pseudo-symmetric structure. Collectively, these results point to an asymmetric transport mechanism of AAC. Moreover, the work sheds light on the special internal three-repeat topology of the mitochondrial carrier family, and underscores the necessity of incorporating structural dynamics data when deducing transport mechanisms from static experimental structures in the two states.

Keywords:  ADP-ATP carrier; Asymmetry; Conformational change

DOI:  https://doi.org/10.1016/j.ijbiomac.2025.148348
Nature. 2025 Oct 22.

Google AI aims to make best-in-class scientific software even better.

Matthew Hutson.



Keywords:  Computational biology and bioinformatics; Computer science; Machine learning; Technology

DOI:  https://doi.org/10.1038/d41586-025-03289-w
STAR Protoc. 2025 Oct 23. pii: S2666-1667(25)00563-5. [Epub ahead of print]6(4): 104157

Protocol for image-based monitoring of de novo RNA synthesis at DNA double-strand breaks in human cell lines.

Georgios Pappas, Helena Hagner Gram, Jiri Bartek, Panagiotis Galanos.

  DNA double-strand breaks (DSBs) halt canonical transcription and simultaneously trigger local non-canonical RNA synthesis. Despite its significance, existing approaches to monitor this process are limited. Here, we present a protocol to monitor and quantify nascent transcription on DSBs in the nucleus. We describe steps for employing UV-A laser to induce site-specific DSBs. We then detail procedures for supplementation of the ablated cells with 5-bromouridine 5'-triphosphate (BrUTP) to label nascent RNA. For complete details on the use and execution of this protocol, please refer to Pappas et al.1.

Keywords:  Cell Biology; Cell culture; Gene Expression; Microscopy; Molecular Biology

DOI:  https://doi.org/10.1016/j.xpro.2025.104157
Int J Neonatal Screen. 2025 Oct 10. pii: 91. [Epub ahead of print]11(4):

Analytical Validation of a Genomic Newborn Screening Workflow.

Kristine Hovhannesyan, Laura Helou, Benoit Charloteaux, Valerie Jacquemin, Flavia Piazzon, Myriam Mni, Charlotte Flohimont, Corinne Fasquelle, Davood Mashhadizadeh, Tamara Dangouloff, Vincent Bours, Laurent Servais, Leonor Palmeira, François Boemer.

  Newborn screening (NBS) has evolved significantly since its inception, yet many treatable rare diseases remain unscreened due to technical limitations. The BabyDetect study used gene panel sequencing to expand NBS to treatable conditions not covered by conventional biochemical screening. We present here the analytical validation of this workflow, assessing sensitivity, precision, and reproducibility using dried blood spots from newborns. We implemented strict quality control thresholds for sequencing, coverage, and contamination, ensuring high reliability. Longitudinal monitoring confirmed consistent performance across more than 5900 samples. Automation of DNA extraction improved scalability, and a panel redesign enhanced the coverage and selection of targeted regions. By focusing on known pathogenic/likely pathogenic variants, we minimized false positives and maintained clinical actionability. Our findings demonstrate that gene panel sequencing-based NBS is feasible, accurate, and scalable, addressing critical gaps in current screening programs.

Keywords:  BabyDetect; analytical validation; dried blood spot; genomic; newborn screening; next generation sequencing

DOI:  https://doi.org/10.3390/ijns11040091
Biochim Biophys Acta Mol Basis Dis. 2025 Oct 22. pii: S0925-4439(25)00443-0. [Epub ahead of print] 168093

FUNDC1 deficiency aggravates endothelial senescence and retinal dysfunction.

Jingxin Ning, Ze Li, Yuxue Mu, Xia Li, Kaifeng Li, Wenjuan Xing, Haifeng Zhang.

  Natural aging leads to various age-related changes that impair visual function and cause ocular diseases. Endothelial cells, key components of blood vessels, play a crucial role in vascular aging and retinal degeneration. However, the exact mechanisms by which endothelial cell aging promotes retinopathy are not fully understood. Mitochondrial homeostasis is vital for endothelial cell function, with mitophagy being essential for removing damaged mitochondria. FUNDC1, a receptor involved in mitophagy, regulates cellular senescence and inflammation. This study investigates whether retinal function decline is linked to mitochondrial imbalance in retinal vessels endothelial cells due to reduced FUNDC1 expression. In aged mice, FUNDC1 expression and mitophagy were significantly lower in retinal blood vessels. Aging leads to retinal vascular dysfunction characterized by increased vascular permeability assessed by fluorescein fundus angiography. Moreover, electron microscopy images showed mitochondrial swelling in endothelial cells of aging retina, accompanied with tight junction disruption and reduced expression of junctional proteins (VE-cadherin, occludin, and ZO-1). Strikingly, endothelial knockout of FUNDC1 exacerbated the age-related decline in retinal blood vessel function and retinal function. Cell senescence induced by D-galactose exhibited significantly decreased FUNDC1, impaired mitophagy, increased reactive oxygen species (ROS), and markedly increased endothelial permeability assessed by transendothelial electrical resistance assay. Conversely, overexpression of FUNDC1 can reverse the reduction of mitochondrial autophagy, the decrease in intercellular junction protein expression and the increase in endothelial permeability caused by aging. Collectively, these data suggest that FUNDC1 serves as a potential therapeutic target for the prevention and treatment of age-related degeneration of retinal function.

Keywords:  Endothelial senescence; FUNDC1; Mitophagy; ROS; Retinal vessels

DOI:  https://doi.org/10.1016/j.bbadis.2025.168093
Circulation. 2025 Oct 20.

Hypercontractility and Oxidative Stress Drive Creatine Kinase Dysfunction in Hypertrophic Cardiomyopathy.

Anton Xu, David Weissman, Katharina J Ermer, Edoardo Bertero, Jan M Federspiel, Felix Stadler, Elisa Grünler, Melina Tangos, Sevasti Zervou, Mark T Waddingham, James T Pearson, Jan-Christian Reil, Smita Scholtz, Jan Dudek, Michael Kohlhaas, Alexander G Nickel, Lucie Carrier, Thomas Eschenhagen, Michelle Michels, Cris Dos Remedios, Sean Lal, Leticia Prates Roma, Nazha Hamdani, Diederik Kuster, Inês Falcão-Pires, Christopher N Johnson, Craig A Lygate, Jolanda van der Velden, Christoph Maack, Vasco Sequeira.

   BACKGROUND: Hypertrophic cardiomyopathy (HCM) is a prevalent inherited cardiac disorder marked by left ventricular hypertrophy and hypercontractility. This excessive mechanical workload creates an energetic mismatch in which consumption exceeds production, leading to myocardial energy depletion. Although CK (creatine kinase) plays a key role in cardiac energy homeostasis, its involvement in HCM remains unclear. This study investigates how hypercontractility-driven mitochondrial stress and the resulting increase in mitochondrial H2O2 disrupt CK function in HCM.
METHODS: CK function was analyzed using myocardial left ventricular tissue from 92 patients with HCM (with and without pathogenic sarcomere variants) and 30 non-failing human controls. Myofilament and mitochondrial CK isoforms were measured using mRNA analysis, protein immunoblotting, enzyme activity assays, mass spectrometry, and redox-sensitive proteomics. To explore links between hypercontractility, mitochondrial reactive oxygen species, and CK dysfunction, we used isolated cardiomyocytes from wild-type, mitochondrion-targeted catalase-overexpressing, CK knockout (myofilament and mitochondrial CK deletion), HCM-associated Mybpc3 knockin, and mito-roGFP2-Orp1 mouse models. We also tested the effects of the Ca2+ sensitizer EMD-57033, the CK inhibitor 1-fluoro-2,4-dinitrobenzene, and the myosin inhibitor MYK-581, a mavacamten derivative.
RESULTS: Our analysis revealed significant reductions in myofilament and mitochondrial CK protein levels, as well as CK activity, in myocardium of patients with HCM, primarily because of oxidative modifications of CK. In isolated mouse cardiomyocytes from wild-type and CK knockouts, hypercontractility induced by EMD-57033 elevated mitochondrial H2O2, causing cellular arrhythmias and CK inactivation. Hypercontractility-induced oxidative stress, arrhythmias, and CK dysfunction were also observed in Mybpc3 knockin cardiomyocytes. Mitochondrion-targeted catalase-overexpressing mice with enhanced H2O2 scavenging were protected against H2O2-induced (EMD-57033-mediated) arrhythmias and CK dysfunction. MYK-581 treatment in Mybpc3 knockin cardiomyocytes reduced hypercontractility, lowered H2O2 production and arrhythmias, and preserved CK function. CK inhibition using 1-fluoro-2,4-dinitrobenzene in wild-type cardiomyocytes elevated mitochondrial H2O2 levels and triggered cellular arrhythmias. This mitochondrial oxidation was independently confirmed in mito-roGFP2-Orp1 cardiomyocytes exposed to 1-fluoro-2,4-dinitrobenzene. Mitochondrion-targeted catalase-overexpressing mice were protected from 1-fluoro-2,4-dinitrobenzene -induced oxidative stress and arrhythmogenic events.
CONCLUSIONS: This study reveals a mechanistic link between hypercontractility, mitochondrial reactive oxygen species, and CK dysfunction in HCM, perpetuating a cycle of energetic dysfunction. Targeting hypercontractility and oxidative stress through myosin inhibition offers a strategy to restore energy balance and reduce arrhythmic risk in HCM.

Keywords:  arrhythmias; creatine kinase; hypercontractility; hypertrophic cardiomyopathy; myocardial energetics; oxidative stress

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.125.074120
Heart. 2025 Oct 20. pii: heartjnl-2024-325280. [Epub ahead of print]

Ribonucleic acid and gene therapies in cardiovascular disease: clinical applications, delivery challenges and emerging precision tools.

Alex J Jordan, Craig Balmforth, Neil Craig, Neeraj Dhaun, Andrew Baker, Marc Richard Dweck, David E Newby.

  Cardiovascular diseases remain a leading cause of global mortality despite advancements in pharmacotherapies, with current treatments facing challenges related to efficacy, tolerability and patient adherence. In response, advanced therapies, such as RNA and gene therapies, have emerged as a promising alternative for addressing both acquired and monogenic cardiovascular conditions. This review explores the current landscape of RNA and gene therapies for cardiovascular disease, focusing on RNA-based therapeutics such as small-interfering RNAs (siRNAs), antisense oligonucleotides and clustered regularly interspaced short palindromic repeats and associated Cas9 endonuclease (CRISPR-Cas9)-based gene editing systems. Recent European Medicines Agency and Food and Drug Administration-approved RNA therapies, including patisiran, vutrisiran and inclisiran, which employ lipid nanoparticle delivery systems, highlight the clinical potential of siRNAs for targeting hepatic molecular pathways. Emerging CRISPR-Cas9 technologies are poised to address genetic mutations at their source, offering permanent correction of pathogenic variants and the potential to treat a broad range of hereditary cardiovascular conditions. Together, these therapies represent a major leap forward in precision medicine, offering long-lasting therapeutic effects and improved patient care and adherence. However, many challenges remain, particularly in targeting such therapies to cardiac tissues and optimising delivery systems. This review discusses the current state of the art in cardiovascular RNA and gene therapies, including current evidence, delivery challenges and the current landscape of gene and RNA therapies in phase I clinical trials and beyond.

Keywords:  Cardiomyopathies; Cardiovascular Diseases; Genetics

DOI:  https://doi.org/10.1136/heartjnl-2024-325280