bims-mitdis 2025-05-25 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2025–05–25
forty papers selected by
Catalina Vasilescu, Helmholz Munich

Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases.
How Do Mitochondria Manage Competing Biochemical Metabolic Processes Under Stress?
Mechanistic insights into Bcs1-mediated mitochondrial membrane translocation of the folded Rieske protein.
De novo serine biosynthesis is protective in mitochondrial disease.
Modelling POLG mutations in mice unravels a critical role of POLγΒ in regulating phenotypic severity.
Mitochondrial Bioenergetics in Physiology.
Therapeutic implications of mitochondrial transfer on stem cell fate in regenerative medicine.
SMIM20 promotes complex IV biogenesis and Ca2+ signaling in mice heart.
Silencing mitochondrial gene expression in living cells.
Mitochondrial dysfunction in epilepsy: mechanistic insights and clinical strategies.
Analysis of the Expression and Complexes Assembly of the Mitochondrial Respiratory Chain Proteins in the Fission Yeast Schizosaccharomyces pombe.
Dose-dependent CHCHD10 dysregulation dictates motor neuron disease severity and alters creatine metabolism.
Alpha-synuclein aggregates trigger cardiolipin externalization and mitophagy.
B cell dysfunction in thalamus and brainstem involvement and high lactate caused by novel mutation of EARS2 gene.
Hepatic glutamic-oxaloacetic transaminase (GOT2) promotes mitochondrial respiration energized at complex II and alters whole body metabolism.
In vitro modelling of the neuropathophysiological features of mitochondrial epilepsy.
Overview of methods that determine mitochondrial function in human disease.
A liver-fat crosstalk for iron flux during healthy beiging of adipose tissue.
Hepatic Form of Dihydrolipoamide Dehydrogenase Deficiency (DLDD): Phenotypic Spectrum, Laboratory Findings, and Therapeutic Approaches in 52 Patients.
Identifying Phenotypes for Earlier Diagnosis of Rare Diseases.
Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?
Adaptation of mitochondrial bioenergetics to coenzyme Q deficiency in human endothelial cells after chronic exposure to bisphosphonates.
FOXK2 in skeletal muscle development: a new pathogenic gene for congenital myopathy with ptosis.
AI listens for health conditions.
Caspase-11 drives macrophage hyperinflammation in models of Polg-related mitochondrial disease.
Unravelling cysteine-deficiency-associated rapid weight loss.
I told AI to make me a protein. Here's what it came up with.
Glutamine catabolism supports amino acid biosynthesis and suppresses the integrated stress response to promote photoreceptor survival.
Programmable control of spatial transcriptome in live cells and neurons.
Redox shuttle of cytosolic Thioredoxin to mitochondria protects against hyperoxia-mediated alteration of mitochondrial structure and dysfunction.
Clonal tracing with somatic epimutations reveals dynamics of blood ageing.
Miro1: A potential target for treating neurological disorders.
Human mitochondrial ferritin exhibits highly unusual iron-O2 chemistry distinct from that of cytosolic ferritins.
Inhibition and Rescue of Hyperglycemia-Induced Cellular Senescence by Mitochondrial Transfer from Enucleated Mesenchymal Stem Cell-Derived Microvesicles for Chronic Wound Healing.
Optimized AAV capsids for basal ganglia diseases show robust potency and distribution.
Age-associated nicotinamide adenine dinucleotide decline drives CAR-T cell failure.
The future of gene therapy for Parkinson's disease.
Single cell multiomics and 3D genome architecture reveal novel pathways of human heart failure.
Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.
Gene therapy for Parkinson's disease: trials and technical advances.

Genome Med. 2025 May 22. 17(1): 58

Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases.

MitoMDT Diagnostic Network for Genomics and Omics

   BACKGROUND: Only half of individuals with suspected rare diseases receive a genetic diagnosis following genomic testing. A genetic diagnosis allows access to appropriate care, restores reproductive confidence and reduces the number of potentially unnecessary interventions. A major barrier is the lack of disease agnostic functional tests suitable for implementation in routine diagnostics that can provide evidence supporting pathogenicity of novel variants, especially those refractory to RNA sequencing.
METHODS: Focusing on mitochondrial disease, we describe an untargeted mass-spectrometry based proteomics pipeline that can quantify proteins encoded by > 50% of Mendelian disease genes and > 80% of known mitochondrial disease genes in clinically relevant sample types, including peripheral blood mononuclear cells (PBMCs). In total we profiled > 90 individuals including undiagnosed individuals suspected of mitochondrial disease and a supporting cohort of disease controls harbouring pathogenic variants in nuclear and mitochondrial genes. Proteomics data were benchmarked against pathology accredited respiratory chain enzymology to assess the performance of proteomics as a functional test. Proteomics testing was subsequently applied to individuals with suspected mitochondrial disease, including a critically ill infant with a view toward rapid interpretation of variants identified in ultra-rapid genome sequencing.
RESULTS: Proteomics testing provided evidence to support variant pathogenicity in 83% of individuals in a cohort with confirmed mitochondrial disease, outperforming clinical respiratory chain enzymology. Freely available bioinformatic tools and criteria developed for this study ( https://rdms.app/ ) allow mitochondrial dysfunction to be identified in proteomics data with high confidence. Application of proteomics to undiagnosed individuals led to 6 additional diagnoses, including a mitochondrial phenocopy disorder, highlighting the disease agnostic nature of proteomics. Use of PBMCs as a sample type allowed rapid return of proteomics data supporting pathogenicity of novel variants identified through ultra-rapid genome sequencing in as little as 54 h.
CONCLUSIONS: This study provides a framework to support the integration of a single untargeted proteomics test into routine diagnostic practice for the diagnosis of mitochondrial and potentially other rare genetic disorders in clinically actionable timelines, offering a paradigm shift for the functional validation of genetic variants.

Keywords:  Genetic diagnostics; Mendelian disease; Proteomics; Ultra-rapid genome sequencing; Variant prioritisation

DOI:  https://doi.org/10.1186/s13073-025-01467-z
Curr Protein Pept Sci. 2025 May 16.

How Do Mitochondria Manage Competing Biochemical Metabolic Processes Under Stress?

Drew Hindrer, Tyler Stark, Selman Aydogdu, Cade Ward, Mohamed Eldeeb.



Keywords:  Mitochondrial fission; mitochondrial fusion; mitochondrial quality control.; mitochondrial stress; molecular metabolism; redox reactions

DOI:  https://doi.org/10.2174/0113892037381885250506091434
EMBO J. 2025 May 23.

Mechanistic insights into Bcs1-mediated mitochondrial membrane translocation of the folded Rieske protein.

Cristian Rosales-Hernandez, Matthias Thoms, Otto Berninghausen, Thomas Becker, Roland Beckmann.

  A functional mitochondrial respiratory chain requires coordinated and tightly regulated assembly of mitochondrial- and nuclear-encoded subunits. For bc1 complex (complex III) assembly, the iron-sulfur protein Rip1 must first be imported into the mitochondrial matrix to fold and acquire its 2Fe-2S cluster, then translocated and inserted into the inner mitochondrial membrane (IM). This translocation of folded Rip1 is accomplished by Bcs1, an unusual heptameric AAA ATPase that couples ATP hydrolysis to translocation. However, the molecular and mechanistic details of Bcs1-mediated Rip1 translocation have remained elusive. Here, we provide structural and biochemical evidence on how Bcs1 alternates between conformational states to translocate Rip1 across the IM. Using cryo-electron microscopy (cryo-EM), we identified substrate-bound pre-translocation and pre-release states, revealing how electrostatic interactions promote Rip1 binding to Bcs1. An ATP-induced conformational switch of the Bcs1 heptamer facilitates Rip1 translocation between two distinct aqueous vestibules-one exposed to the matrix, the other to the intermembrane space-in an airlock-like mechanism. This would minimize disruption of the IM permeability barrier, which could otherwise lead to proton leakage and compromised mitochondrial energy conversion.

Keywords:  Bcs1; Cryo-EM; Folded Protein Translocation; Mitochondria; Rieske

DOI:  https://doi.org/10.1038/s44318-025-00459-4
Cell Rep. 2025 May 15. pii: S2211-1247(25)00481-4. [Epub ahead of print]44(5): 115710

De novo serine biosynthesis is protective in mitochondrial disease.

Christopher B Jackson, Anastasiia Marmyleva, Geoffray Monteuuis, Ryan Awadhpersad, Takayuki Mito, Nicola Zamboni, Takashi Tatsuta, Amy E Vincent, Liya Wang, Nahid A Khan, Thomas Langer, Christopher J Carroll, Anu Suomalainen.

  The importance of serine as a metabolic regulator is well known for tumors and is also gaining attention in degenerative diseases. Recent data indicate that de novo serine biosynthesis is an integral component of the metabolic response to mitochondrial disease, but the roles of the response have remained unknown. Here, we report that glucose-driven de novo serine biosynthesis maintains metabolic homeostasis in energetic stress. Pharmacological inhibition of the rate-limiting enzyme, phosphoglycerate dehydrogenase (PHGDH), aggravated mitochondrial muscle disease, suppressed oxidative phosphorylation and mitochondrial translation, altered whole-cell lipid profiles, and enhanced the mitochondrial integrated stress response (ISRmt) in vivo in skeletal muscle and in cultured cells. Our evidence indicates that de novo serine biosynthesis is essential to maintain mitochondrial respiration, redox balance, and cellular lipid homeostasis in skeletal muscle with mitochondrial dysfunction. Our evidence implies that interventions activating de novo serine synthesis may protect against mitochondrial failure in skeletal muscle.

Keywords:  CP: Metabolism; de novo serine synthesis; mitochondrial disease; mitochondrial integrated stress response; mitochondrial translation; tissue specificity; treatment

DOI:  https://doi.org/10.1016/j.celrep.2025.115710
Nat Commun. 2025 May 23. 16(1): 4782

Modelling POLG mutations in mice unravels a critical role of POLγΒ in regulating phenotypic severity.

Samantha Corrà, Alessandro Zuppardo, Sebastian Valenzuela, Louise Jenninger, Raffaele Cerutti, Sirelin Sillamaa, Emily Hoberg, Katarina A S Johansson, Urska Rovsnik, Sara Volta, Pedro Silva-Pinheiro, Hannah Davis, Aleksandra Trifunovic, Michal Minczuk, Claes M Gustafsson, Anu Suomalainen, Massimo Zeviani, Bertil Macao, Xuefeng Zhu, Maria Falkenberg, Carlo Viscomi.

DNA polymerase γ (POLγ), responsible for mitochondrial DNA replication, consists of a catalytic POLγA subunit and two accessory POLγB subunits. Mutations in POLG, which encodes POLγA, lead to various mitochondrial diseases. We investigated the most common POLG mutations (A467T, W748S, G848S, Y955C) by characterizing human and mouse POLγ variants. Our data reveal that these mutations significantly impair POLγ activities, with mouse variants exhibiting milder defects. Cryogenic electron microscopy highlighted structural differences between human and mouse POLγ, particularly in the POLγB subunit, which may explain the higher activity of mouse POLγ and the reduced severity of mutations in mice. We further generated a panel of mouse models mirroring common human POLG mutations, providing crucial insights into the pathogenesis of POLG-related disorders and establishing robust models for therapeutic development. Our findings emphasize the importance of POLγB in modulating the severity of POLG mutations.

DOI: https://doi.org/10.1038/s41467-025-60059-y
Acta Physiol (Oxf). 2025 Jun;241(6): e70056

Mitochondrial Bioenergetics in Physiology.

Martin Jastroch, Michaela Keuper.



Keywords:  bioenergetics; brown adipose tissue; disease; ectothermic; endothermic; mitochondria; sarcopenia; ucp1

DOI:  https://doi.org/10.1111/apha.70056
J Transl Med. 2025 May 21. 23(1): 568

Therapeutic implications of mitochondrial transfer on stem cell fate in regenerative medicine.

Ying Liu, Waruna Lakmal Dissanayaka, Cynthia Yiu.

  With the discovery of intercellular mitochondrial transfer, the intricate mitochondrial regulatory networks on stem cell fate have aroused intense academic interest. Apart from capturing freely released mitochondria from donor cells, stem cells are able to receive mitochondria through tunneling nanotubes (TNTs), gap junctional channels (GJCs) and extracellular vesicles (EVs), especially when undergoing stressful conditions such as inflammation, hypoxia, chemotherapy drug exposure, and irradiation. Stem cells that are potentiated by exogenous mitochondria show enhanced potential for proliferation, differentiation, and immunomodulation. The well-tolerated nature of either autogenous or allogenous mitochondria when locally injected in the human ischemic heart has validated the safety and therapeutic potential of mitochondrial transplantation. In children diagnosed with mitochondrial DNA deletion syndrome, functional improvements have been observed when empowering their hematopoietic stem cells with maternally derived mitochondria. Apart from the widely investigated applications of mitochondrial transfer in ischemia-reperfusion injury, neurodegenerative diseases and mitochondrial diseases etc., therapeutic potentials of mitochondrial transfer in tissue repair and regeneration are equally noteworthy, though there has been no systematic summary in this regard.This review analyzed the research and development trends of mitochondrial transfer in stem cells and regenerative medicine over the past decade from a bibliometric perspective, introduced the concept and associated mechanisms of mitochondrial transfer, summarized the regulations of intercellular mitochondrial transfer on stem cell fate. Finally, the therapeutic application of mitochondrial transplantation in diseases and tissue regeneration has been reviewed, including recent clinical studies related to mitochondrial transplantation.Mitochondrial transfer shows promise in modifying and reshaping the cellular properties of stem cells, making them more conducive to regeneration. Mesenchymal stem cells (MSCs)-derived mitochondria have shown multifaceted potential in promoting the revitalization and regeneration of cardiac, cutaneous, muscular, neuronal tissue. This review integrates novel research findings on mitochondrial transfer in stem cell biology and regenerative medicine, emphasizing the crucial translational value of mitochondrial transfer in regeneration. It serves to underscore the significant impact of mitochondrial transfer and provides a valuable reference for further exploration in this field.

Keywords:  Mitochondrial therapeutics; Mitochondrial transfer; Regenerative medicine; Stem cell fate; Tissue repair

DOI:  https://doi.org/10.1186/s12967-025-06472-9
Cell Rep. 2025 May 20. pii: S2211-1247(25)00494-2. [Epub ahead of print]44(6): 115723

SMIM20 promotes complex IV biogenesis and Ca2+ signaling in mice heart.

Angela Boshnakovska, Julius Ryan Pronto, Tanja Gall, Abhishek Aich, Jan Prochazka, Zuzana Nichtova, Radislav Sedlacek, Izzatullo Sobitov, Sofia Ainatzi, Christof Lenz, Dörthe M Katschinski, Henning Urlaub, Niels Voigt, Peter Rehling, Laura S Kremer.

  Mitochondria are key to cellular energetics, metabolism, and signaling. Their dysfunction is linked to devastating diseases, including mitochondrial disorders, diabetes, neurodegenerative diseases, cardiac disorders, and cancer. Here, we present a knockout mouse model lacking the complex IV assembly factor SMIM20/MITRAC7. SMIM20-/- mice display cardiac pathology with reduced heart weight and cardiac output. Heart mitochondria present with reduced levels of complex IV associated with increased complex I activity, have altered fatty acid oxidation, and display elevated levels of ROS production. Interestingly, mutant mouse ventricular myocytes show unphysiological Ca2+ handling, which can be attributed to the increase in mitochondrial ROS production. Our study presents an example of a tissue-specific phenotype in the context of OXPHOS dysfunction. Moreover, our data suggest a link between complex IV dysfunction and Ca2+ handling at the endoplasmic reticulum through ROS signaling.

Keywords:  CP: Cell biology; CP: Molecular biology; OXPHOS; assembly factor; cytochrome c oxidase; mitochondria; mitochondrial disease

DOI:  https://doi.org/10.1016/j.celrep.2025.115723
Science. 2025 May 22. eadr3498

Silencing mitochondrial gene expression in living cells.

Luis Daniel Cruz-Zaragoza, Drishan Dahal, Mats Koschel, Angela Boshnakovska, Aiturgan Zheenbekova, Mehmet Yilmaz, Marcel Morgenstern, Jan-Niklas Dohrke, Julian Bender, Anusha Valpadashi, Kristine A Henningfeld, Silke Oeljeklaus, Laura Sophie Kremer, Mirjam Breuer, Oliver Urbach, Sven Dennerlein, Michael Lidschreiber, Stefan Jakobs, Bettina Warscheid, Peter Rehling.

Mitochondria fulfill central functions in metabolism and energy supply. They express their own genome, which encodes key subunits of the oxidative phosphorylation system. However, central mechanisms underlying mitochondrial gene expression remain enigmatic. A lack of suitable technologies to target mitochondrial protein synthesis in cells has limited experimental access. Here, we silenced the translation of specific mitochondrial mRNAs in living human cells by delivering synthetic peptide-morpholino chimeras. This approach allowed us to perform a comprehensive temporal monitoring of cellular responses. Our study provides insights into mitochondrial translation, its integration into cellular physiology, and provides a strategy to address mitochondrial gene expression in living cells. The approach can potentially be used to analyze mechanisms and pathophysiology of mitochondrial gene expression in a range of cellular model systems.

DOI: https://doi.org/10.1126/science.adr3498
Mol Biol Rep. 2025 May 20. 52(1): 470

Mitochondrial dysfunction in epilepsy: mechanistic insights and clinical strategies.

Xiaolu Zhang, Zhengjuan Wu, Xu Zhou, Hua Tao.

  Epilepsy is a common neurological disorder that is increasingly recognized for its significant association with mitochondrial dysfunction. This review explores the intricate relationship between mitochondrial dysfunction and epilepsy, highlighting the molecular mechanisms, diagnostic strategies, and therapeutic approaches involved. Mitochondrial abnormalities, including defects in the electron transport chain, impaired mitochondrial dynamics, disrupted autophagy, and increased oxidative stress, are implicated in epilepsy pathogenesis. The molecular mechanisms involve respiratory chain impairments, fission-fusion imbalances, inadequate mitophagy, and oxidative stress-induced neuronal excitability. The diagnosis of mitochondrial epilepsy requires a multifaceted approach, combining clinical assessment, biochemical testing, imaging, and genetic analysis, with a particular focus on mtDNA mutations. Therapeutic strategies include antiepileptic drugs with variable mitochondrial effects, the ketogenic diet, and emerging potential approaches such as antioxidants and mitochondrial-targeted therapies. Despite advances in understanding and treatment, challenges persist due to the complexity of mtDNA mutations and treatment resistance. Future directions involve gene-editing technologies, mitochondrial transplantation, and induced pluripotent stem cells, which hold promise for addressing the underlying defects and improving epilepsy management.

Keywords:  Epilepsy; Ketogenic diet; Mitochondria; Mutation; Oxidative stress

DOI:  https://doi.org/10.1007/s11033-025-10577-1
J Vis Exp. 2025 May 02.

Analysis of the Expression and Complexes Assembly of the Mitochondrial Respiratory Chain Proteins in the Fission Yeast Schizosaccharomyces pombe.

Guangchun Lu, Jinjie Shang, Gang Feng.

The mitochondrial respiratory chain is crucial for cellular energy metabolism, serving as the core of oxidative phosphorylation. The mitochondrial respiratory chain comprises five enzyme complexes and their interacting supercomplexes. Analysis of the expression and complexes assembly of these proteins is vital to understanding mitochondrial function. This can be studied by combining biochemical and genetic methods in an excellent model organism fission yeast Schizosaccharomyces pombe (S. pombe), which provides a compensatory system to budding yeast for studies of mitochondrial biology. Here, we present a detailed protocol for the isolation of S. pombe mitochondria and analysis of expression levels and complexes assembly of the mitochondrial respiratory proteins by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and blue native-PAGE (BN-PAGE). Briefly, mitochondria from the wild-type and gene mutants are purified, and then their complexes are solubilized and subjected to SDS-PAGE/BN-PAGE and immunoblotting. This method enables the characterization of a gene's novel function in the mitochondrial respiratory chain.

DOI: https://doi.org/10.3791/68336
Acta Neuropathol Commun. 2025 May 22. 13(1): 111

Dose-dependent CHCHD10 dysregulation dictates motor neuron disease severity and alters creatine metabolism.

Sandra Harjuhaahto, Manu Jokela, Jayasimman Rajendran, Minea Rokka, Bowen Hu, Jouni Kvist, Fuping Zhang, Tomáš Zárybnický, Kimmo Haimilahti, Liliya Euro, Eija Pirinen, Nadine Huber, Sanna-Kaisa Herukka, Annakaisa Haapasalo, Emilia Kuuluvainen, Swetha Gopalakrishnan, Pekka Katajisto, Ville Hietakangas, Thibaut Burg, Ludo Van Den Bosch, Xiaoping Huang, Derek P Narendra, Satu Kuure, Emil Ylikallio, Henna Tyynismaa.

  Dominant defects in CHCHD10, a mitochondrial intermembrane space protein, lead to a range of neurological and muscle disease phenotypes including amyotrophic lateral sclerosis. Many patients present with spinal muscular atrophy Jokela type (SMAJ), which is caused by heterozygous p.G66V variant. While most disease variants lead to aggregation of CHCHD10 and activation of proteotoxic stress responses, the pathogenic mechanisms of the p.G66V variant are less clear. Here we report the first homozygous CHCHD10 patient, and show that the variant dosage dictates the severity of the motor neuron disease in SMAJ. We demonstrate that the amount of the mutant CHCHD10 is reduced, but the disease mechanism of p.G66V is not full haploinsufficiency as residual mutant CHCHD10 protein is present even in a homozygous state. Novel knock-in mouse model recapitulates the dose-dependent reduction of mutant CHCHD10 protein and the slow disease progression of SMAJ. With metabolome analysis of patients' primary fibroblasts and patient-specific motor neurons, we show that CHCHD10 p.G66V dysregulates energy metabolism, leading to altered redox balance and energy buffering by creatine metabolism.

Keywords:  ALS; CHCHD10; CHCHD2; Creatine; Metabolomics; Mitochondria

DOI:  https://doi.org/10.1186/s40478-025-02039-3
Autophagy Rep. 2024 ;3(1): 2314361

Alpha-synuclein aggregates trigger cardiolipin externalization and mitophagy.

Rebeca Martín-Jiménez, Olivier Lurette, Etienne Hebert-Chatelain.

  Accumulation of Lewy bodies in dopaminergic neurons is associated to Parkinson disease (PD). The main component of Lewy bodies appears to be aggregates of alpha-synuclein (α-syn). Several mutations of the gene encoding this protein promote its aggregation. Thus, clustering of α-syn is considered a central event in the onset of PD. An old theory also postulates that mitochondrial dysfunction represents another cause of PD pathogenesis. However, the impact of α-syn aggregates on mitochondria remains poorly understood considering the technical difficulties to discriminate between the different forms of α-syn. In this punctum, we describe our recent work in which we used a newly developed optogenetic tool to control the aggregation of α-syn and examine the impact on mitochondria. This work revealed that α-syn aggregates dynamically interact with mitochondria, triggering their depolarization and leading to cardiolipin translocation to the surface of mitochondria and mitophagy. Abbreviations: α-syn: alpha-synuclein; BNIP3L: BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like; FUNDC1: FUN14 domain-containing protein 1; IMM: inner mitochondrial membrane; LIPA: light-induced protein aggregation; OMM: outer mitochondrial membrane; PD: Parkinson disease; SNc: substantia nigra par compacta.

Keywords:  Lewy bodies; PLSCR3; mitochondrial fission; mitochondrial membrane potential; parkinson disease; selective autophagy; ubiquitin

DOI:  https://doi.org/10.1080/27694127.2024.2314361
Ital J Pediatr. 2025 May 19. 51(1): 143

B cell dysfunction in thalamus and brainstem involvement and high lactate caused by novel mutation of EARS2 gene.

Yu Wen, Yanmei Huang, Wendi Zhang, Ping Chen, Xiufen Hu, Xin Xiong, Li Luo.

   PURPOSE: The EARS2 gene, a member of the mt-aaRS family, encodes mitochondrial glutamyl-tRNA synthetase (GluRS), which is involved in the synthesis of mitochondrial proteins. Pathogenic defects in EARS2 may cause mitochondrial OXPHOS deficiency, which is associated with a rare autosomal-recessive mitochondrial disease, leukoencephalopathy with thalamus and brainstem involvement and high lactate (LTBL).
METHODS: In this study, clinical features were obtained, and whole-exome sequencing was conducted on a patient with LTBL. B- and T-cell immunophenotyping and protein expression were analyzed using flow cytometry, and B-cell metabolism was investigated using confocal microscopy.
RESULTS: The patient with LTBL exhibited typical neurological manifestations, recurrent respiratory tract infections, and humoral immune disorders. Molecular analysis revealed a compound heterozygous novel mutation in c.1304T > A (p.L435Q) and a previously reported c.319 C > T (p.R107C) mutation of EARS2. The mutations led to protein structural modifications of EARS2. The patient also exhibited disrupted peripheral B-cell differentiation and B-cell receptor signal transduction. The EARS2 mutation led to decreased expression of CD38 and dysfunction of mitochondrial metabolism, with elevated reactive oxygen species levels in B cells.
CONCLUSION: We identified a novel mutation of the EARS2 gene in a patient with LTBL, expanding the mutation database. The mutation of EARS2 modified protein structure and impaired B-cell function, decreased CD38 expression, and led to dysfunction of mitochondrial metabolism, all of which may account for the recurrent respiratory tract infections and humoral immune disorders observed in LTBL.

Keywords:  B cell; BCR signal; EARS2; Gene mutation; LTBL

DOI:  https://doi.org/10.1186/s13052-025-01999-5
J Biol Chem. 2025 May 21. pii: S0021-9258(25)02111-8. [Epub ahead of print] 110261

Hepatic glutamic-oxaloacetic transaminase (GOT2) promotes mitochondrial respiration energized at complex II and alters whole body metabolism.

Brian D Fink, Ritu Som, Adam J Rauckhorst, Eric B Taylor, Liping Yu, William I Sivitz.

  The mitochondrial enzyme, glutamic-oxaloacetic transaminase (GOT2), catalyzes the reaction between oxaloacetate and glutamate generating aspartate and alpha-ketoglutarate (α-KG). Glutamate can also be directly converted to α-KG by glutamate dehydrogenase. We investigated mitochondrial and systemic effects of an inducible liver specific-mouse GOT2 knockout (KO). We observed no differences in body mass or percent fat mass in KO mice, however, KO mice had lower fasting glucose and liver tissue contained more fat. Respiration by liver mitochondria energized at complex II by succinate + glutamate was decreased in KO compared to wildtype (WT) mice at low inner membrane potential (ΔΨ) as induced by titration with ADP. Metabolite studies by NMR showed that at low versus high ΔΨ, GOT2KO mitochondria energized by succinate + glutamate generated more oxaloacetate (a potent inhibitor of succinate dehydrogenase, SDH) and less aspartate. Respiration and mitochondrial metabolites energized by pyruvate + malate or palmitoyl-carnitine + malate did not differ between KO and WT mice. Respiration by GOT2KO mitochondria energized by glutamate + malate was decreased at all levels of ΔΨ. Pathway analysis of LC-MS profile data in liver tissue of KO versus WT mice revealed differential enrichment of the malate aspartate shuttle, TCA cycle, aspartate metabolism, glutamate metabolism, and gluconeogenesis. In summary, GOT2KO impaired potential-dependent complex II energized O2 flux likely due at least in part to oxaloacetate inhibition of SDH.

Keywords:  Mitochondria; glutamic-oxaloacetic transaminase-2; liver; mitochondrial complex II; mitochondrial inner membrane potential; oxaloacetate; respiration; succinate dehydrogenase

DOI:  https://doi.org/10.1016/j.jbc.2025.110261
Seizure. 2025 May 10. pii: S1059-1311(25)00121-9. [Epub ahead of print]

In vitro modelling of the neuropathophysiological features of mitochondrial epilepsy.

Laura A Smith, Ella B Keane, Kate Connor, Felix Chan, Mark O Cunningham.

  Epilepsy is a common and severe neurological manifestation of primary mitochondrial disease, affecting approximately 60 % of paediatric patients and 20 % of adult patients. Many of the mitochondrial epilepsies, particularly those presenting in childhood, are refractory to anti-epileptic treatment. Moreover, these conditions are typically characterised by severe neurodegeneration and closely associated with neurological decline and premature death. Indeed, there persists an urgent need to delineate the mechanisms underpinning mitochondrial epilepsy in order to develop effective treatments. In this review, we provide an overview of currently available in vitro models of the mitochondrial epilepsies. Such models offer opportunities to characterise early disease pathophysiology and interrogate novel mitochondrial-targeting and anti-epileptic treatments, with an overall aim to modulate seizure associated pathology and activity for the mitochondrial epilepsies. We discuss the use of acute cortical and subcortical brain slice preparations, obtained from both neurosurgical patients and rodents, for modelling the common neuropathophysiological features of mitochondrial epilepsy. We also review the use of induced pluripotent stem cell derived neural and glial culture models, and the development of three-dimensional cerebral organoids, generated from fibroblasts obtained from patients with primary mitochondrial disease. Human-derived, disease-relevant in vitro model systems which recapitulate the complexity and pathological features observed in patient brain tissues are crucial to help bridge the gap between animal models and patients living with mitochondrial epilepsy.

Keywords:  Alpers’ syndrome; MELAS; MERRF; Oxidative phosphorylation (OXPHOS); POLG; mtDNA

DOI:  https://doi.org/10.1016/j.seizure.2025.05.005
Metabolism. 2025 May 17. pii: S0026-0495(25)00169-6. [Epub ahead of print]170 156300

Overview of methods that determine mitochondrial function in human disease.

Eashan Sharma, Leila Fotooh Abadi, John Arnaud Kombe Kombe, Monisha Kandala, Jordan Parker, Nolan Winicki, Theodoros Kelesidis.

  Cellular metabolism has a key role in the pathogenesis of human disease. Mitochondria are the organelles that generate most of the energy needed for a cell to function and drive cellular metabolism. Understanding the link between metabolic and mitochondrial function can be challenging due to the variation in methods used to measure mitochondrial function and heterogeneity in mitochondria, cells, tissues, and end organs. Mitochondrial dysfunction can be determined at both the cellular and tissue levels using several methods, such as assessment of cellular bioenergetics, levels of mitochondrial DNA (mtDNA), mitochondrial membrane potential (MMP), mitochondrial reactive oxygen species (mito-ROS), and levels of mitochondrial enzymes. Recent advances involving novel radiotracers in combination with PET imaging have allowed for the determination of mitochondrial function in vivo with high specificity. Understanding the barriers in existing methodologies used to study mitochondrial function may help further establish the assessment of mitochondrial function as a biologically and clinically relevant biomarker for human disease severity and prognosis. Herein, we critically review the existing literature regarding the strengths and limitations of methods that determine mitochondrial function, and we subsequently discuss how emerging research methods have begun to overcome some of these hurdles. We conclude that a combination of techniques, including respirometry and mitochondrial membrane potential assessment, is necessary to understand the complexity and biological and clinical relevance of mitochondrial function in human disease.

Keywords:  Biomarkers; Human disease; Metabolism; Mitochondria; Mitrochondrial function

DOI:  https://doi.org/10.1016/j.metabol.2025.156300
Autophagy Rep. 2024 ;3(1): 2396696

A liver-fat crosstalk for iron flux during healthy beiging of adipose tissue.

Jinying Yang, Limin Shi, Anna L Cubito, James F Collins, Zhiyong Cheng.

  Beiging of adipocytes is characteristic of a higher number of mitochondria, the central hub of metabolism in the cell. However, studies show that beiging can improve metabolic health or cause metabolic disorders. Here we discuss a liver-fat crosstalk for iron flux associated with healthy beiging of adipocytes. Deletion of the transcription factor FoxO1 in adipocytes (adO1KO mice) induces a higher iron flux from the liver to white adipose tissue, concurrent with augmented mitochondrial biogenesis that increases iron demands. In addition, adO1KO mice adopt an alternate mechanism to sustain mitophagy, which enhances mitochondrial quality control, thereby improving mitochondrial respiratory capacity and metabolic health. However, the liver-fat crosstalk is not detectable in adipose Atg7 knockout (ad7KO) mice, which undergo beiging of adipocytes but have metabolic dysregulation. Autophagic clearance of mitochondria is blocked in ad7KO mice, which accumulates dysfunctional mitochondria and elevates mitochondrial content but lowers mitochondrial respiratory capacity. Mitochondrial biogenesis is comparable in the control and ad7KO mice, and the iron influx into adipocytes and iron efflux from the liver remain unchanged. Therefore, activation of the liver-fat crosstalk is critical for mitochondrial quality control that underlies healthy beiging of adipocytes.

Keywords:  Adipose beiging; Atg7; FoxO1; iron flux; liver-fat crosstalk

DOI:  https://doi.org/10.1080/27694127.2024.2396696
J Inherit Metab Dis. 2025 May;48(3): e70035

Hepatic Form of Dihydrolipoamide Dehydrogenase Deficiency (DLDD): Phenotypic Spectrum, Laboratory Findings, and Therapeutic Approaches in 52 Patients.

Nicole Hammann, Christian Staufner, Lea Dewi Schlieben, Antal Dezsőfi-Gottl, René G Feichtinger, Johannes Häberle, Norman Junge, Vassiliki Konstantopoulou, Robert Kopajtich, Valérie McLin, Daisy Rymen, Christoph Slavetinsky, Ekkehard Sturm, Johannes A Mayr, Matias Wagner, Stefan Kölker, Holger Prokisch, Georg F Hoffmann, Dominic Lenz.

  Dihydrolipoamide dehydrogenase deficiency (MIM 246900/DLDD) is an autosomal recessive mitochondrial disease with three clinical subgroups. The hepatic form leads to recurrent metabolic decompensations often accompanied by elevated levels of liver transaminases (ELT) in blood, sometimes progressing to acute liver failure (ALF). Genetically, it is linked to the p.G229C variant in the DLD gene, which has been reported in the Ashkenazi Jewish and Arabic population. In this study, we analyzed phenotypic diversity, therapeutic management, and outcome in novel symptomatic individuals with hepatic DLDD identified by whole exome sequencing (n = 7) in Central Europe as well as in previously reported cases (n = 45). Fifty-one of 52 DLDD patients carried the p.G229C variant (39 in a homozygous state). During decompensations, precipitated by febrile infectious disease or fasting, affected individuals presented with nausea, vomiting, abdominal pain, hepatomegaly, hypoglycemia, and lactic acidosis. In individuals homozygous for the p.G229C variant, neurologic manifestations were rare, whereas mild neurologic symptoms were found in individuals (n = 8) carrying a different DLD variant in trans. During decompensation, levels of specific plasma amino acids like citrulline or branched-chain amino acids, and urinary organic acids, like 2-oxoglutaric acid, were frequently elevated. However, known biomarkers-with the exception of lactate-were not consistently elevated during these episodes and typically normal in the interval, highlighting the usefulness of early genetic testing in all children with unexplained ELT or ALF to reduce the time to diagnosis. While there exists consensus for rescue therapy with intravenous glucose during decompensations and maintenance therapy with riboflavin, therapies with thiamine and antioxidants (e.g., N-acetylcysteine) were reported to be useful in single individuals with recurrent decompensations.

Keywords:  DLD; E3; hepatic mitochondriopathy; mitochondrial disease; pediatric acute liver failure

DOI:  https://doi.org/10.1002/jimd.70035
Stud Health Technol Inform. 2025 May 15. 327 123-127

Identifying Phenotypes for Earlier Diagnosis of Rare Diseases.

Casey N Ta, Cong Liu, Chunhua Weng.

  Rare diseases, while individually rare, cumulatively affect a large population, and patients often undergo long and arduous diagnostic odysseys. Toward the goal of supporting earlier diagnosis of rare diseases, we developed generalizable methods of extracting rare diseases and phenotypes from structured electronic health records and clinical notes. We analyzed the distributions of the age of onset of phenotypes per disease to identify disease-phenotype associations, producing a dataset with over 500 thousand associations covering 2300 rare diseases. Disease-phenotype associations are characterized by disease prevalence and mean age of onset of the phenotype to aid phenotype selection according to the priorities of the clinical decision support task.

Keywords:  Clinical Notes; Electronic Health Records; Phenotypes; Rare Diseases

DOI:  https://doi.org/10.3233/SHTI250286
Cell. 2025 May 15. pii: S0092-8674(25)00296-X. [Epub ahead of print]188(10): 2561-2566

Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?

Mohamed S Sarhan, Giacomo Antonello, Hansi Weissensteiner, Claudia Mengoni, Deborah Mascalzoni, Levi Waldron, Nicola Segata, Christian Fuchsberger.

Human DNA is unavoidably present in metagenomic analyses of human microbiomes. While current protocols remove human DNA before submission to public repositories, mitochondrial DNA (mtDNA) has been overlooked and frequently persists. We discuss the privacy risks and research opportunities associated with mtDNA, urging consideration by the scientific, ethics, and legal communities.

DOI: https://doi.org/10.1016/j.cell.2025.03.023
Sci Rep. 2025 May 22. 15(1): 17734

Adaptation of mitochondrial bioenergetics to coenzyme Q deficiency in human endothelial cells after chronic exposure to bisphosphonates.

Adrianna Budzinska, Lukasz Galganski, Krzysztof Wojcicki, Wieslawa Jarmuszkiewicz.

  Nitrogen-containing bisphosphonates (N-BPs), widely used in bone disease therapy, inhibit the mevalonate pathway, which affects coenzyme Q (CoQ) biosynthesis and may compromise mitochondrial function, particularly in endothelial cells where oxidative stress and mitochondrial dysfunction contribute to cardiovascular disease. This study examined the effects of chronic six-day exposure of human endothelial cells to N-BPs on mitochondrial bioenergetic functions, focusing on drug-induced mitochondrial CoQ (mtCoQ) deficiency. Compared with the mitochondria of control cells, those of endothelial cells treated with 5 µM alendronate or 1 µM zoledronate presented a significant 45-50% decrease in total mtCoQ pool, loss of reduced (mtCoQH2) antioxidant mtCoQ pool, and elevated mitochondrial antioxidant protein superoxide dismutase 2 (SOD2) and uncoupling protein 2 (UCP2) levels. Exposing endothelial cells to N-BPs also led to an overall reduction in mitochondrial substrate oxidation, except for increased fatty acid oxidation. Additionally, the mitochondria of N-BP-treated endothelial cells presented decreased respiratory rates, membrane potential, and ATP synthesis efficiency, and increased H2O2 production resulting from increased mtCoQ reduction during the oxidation of complex I (CI) and CII substrates. N-BP-induced mtCoQ deficiency also resulted in rearranged respiratory chain supercomplexes, particularly downregulation of the III2 + IV supercomplex, and decreased CII, CIII, and CV protein levels and activities. Despite the N-BP-induced decrease in a-heme levels, maximal CIV activity remained unaffected in endothelial mitochondria. These findings highlight the role of N-BPs in disrupting mtCoQ redox homeostasis and associated bioenergetic functions in endothelial mitochondria.

Keywords:  Alendronate; Bisphosphonates; Coenzyme Q; Endothelial cells; Mitochondrial respiration; Zoledronate

DOI:  https://doi.org/10.1038/s41598-025-02710-8
EMBO Mol Med. 2025 May 23.

FOXK2 in skeletal muscle development: a new pathogenic gene for congenital myopathy with ptosis.

Peixuan Wu, Nan Song, Yang Xiang, Zhe Tao, Bing Mao, Ruochen Guo, Xin Wang, Dan Wu, Zhenzhen Zhang, Xin Chen, Duan Ma, Tianyu Zhang, Bingtao Hao, Jing Ma.

  Congenital ptosis, a genetic disorder involving levator palpebrae muscle dysfunction, is often associated with congenital myopathy. The genetic causes of this condition remain poorly understood. In this study, we identified FOXK2 mutations in five pedigrees with congenital myopathy and ptosis through whole exome sequencing and Sanger sequencing. Zebrafish with foxk2 deficiency exhibited underdeveloped skeletal muscles and reduced mobility, while mice with Foxk2 deletion in skeletal muscle stem cells (MuSCs) showed generalized skeletal muscle abnormalities. Further analysis revealed that FOXK2 deficiency impaired myogenic differentiation in C2C12 cells and disrupted mitochondrial homeostasis in both mouse MuSCs and C2C12 cells. Rescue experiments confirmed the loss-of-function effects of FOXK2 mutation. Coenzyme Q10 treatment improved mitochondrial function and alleviated skeletal muscle development defects in Foxk2-deficient mice. Preliminary omics analysis suggested FOXK2 directly regulates the expression of mitochondrial function-related genes by modulating chromatin accessibility at its binding sites. Our study identifies FOXK2 as a novel pathogenic gene for congenital myopathy with ptosis and highlights its essential role in skeletal muscle development and mitochondrial homeostasis, offering insights for potential diagnostics and therapies.

Keywords:  Coenzyme Q10; FOXK2; Mitochondrial Homeostasis; Ptosis; Skeletal Muscle Development

DOI:  https://doi.org/10.1038/s44321-025-00247-x
Nature. 2025 May 22.

AI listens for health conditions.

Neil Savage.



Keywords:  Diabetes; Diseases; Health care; Machine learning; Medical research

DOI:  https://doi.org/10.1038/d41586-025-01598-8
Nat Commun. 2025 May 20. 16(1): 4640

Caspase-11 drives macrophage hyperinflammation in models of Polg-related mitochondrial disease.

Jordyn J VanPortfliet, Yuanjiu Lei, Muthumeena Ramanathan, Camila Guerra Martinez, Jessica Wong, Tim J Stodola, Brian R Hoffmann, Kathryn Pflug, Raquel Sitcheran, Stephen C Kneeland, Stephen A Murray, Peter J McGuire, Carolyn L Cannon, A Phillip West.

Mitochondrial diseases (MtD) represent a significant public health challenge due to their heterogenous clinical presentation, often severe and progressive symptoms, and lack of effective therapies. Environmental exposures, such bacterial and viral infection, can further compromise mitochondrial function and exacerbate the progression of MtD. However, the underlying immune alterations that enhance immunopathology in MtD remain unclear. Here we employ in vitro and in vivo approaches to clarify the molecular and cellular basis for innate immune hyperactivity in models of polymerase gamma (Polg)-related MtD. We reveal that type I interferon (IFN-I)-mediated upregulation of caspase-11 and guanylate-binding proteins (GBP) increase macrophage sensing of the opportunistic microbe Pseudomonas aeruginosa (PA) in Polg mutant mice. Furthermore, we show that excessive cytokine secretion and activation of pyroptotic cell death pathways contribute to lung inflammation and morbidity after infection with PA. Our work provides a mechanistic framework for understanding innate immune dysregulation in MtD and reveals potential targets for limiting infection- and inflammation-related complications in Polg-related MtD.

DOI: https://doi.org/10.1038/s41467-025-59907-8
Nature. 2025 May 21.

Unravelling cysteine-deficiency-associated rapid weight loss.

Alan Varghese, Ivan Gusarov, Begoña Gamallo-Lana, Daria Dolgonos, Yatin Mankan, Ilya Shamovsky, Mydia Phan, Rebecca Jones, Maria Gomez-Jenkins, Eileen White, Rui Wang, Drew R Jones, Thales Papagiannakopoulos, Michael E Pacold, Adam C Mar, Dan R Littman, Evgeny Nudler.

Around 40% of the US population and 1 in 6 individuals worldwide have obesity, with the incidence surging globally1,2. Various dietary interventions, including carbohydrate, fat and, more recently, amino acid restriction, have been explored to combat this epidemic3-6. Here we investigated the impact of removing individual amino acids on the weight profiles of mice. We show that conditional cysteine restriction resulted in the most substantial weight loss when compared to essential amino acid restriction, amounting to 30% within 1 week, which was readily reversed. We found that cysteine deficiency activated the integrated stress response and oxidative stress response, which amplify each other, leading to the induction of GDF15 and FGF21, partly explaining the phenotype7-9. Notably, we observed lower levels of tissue coenzyme A (CoA), which has been considered to be extremely stable10, resulting in reduced mitochondrial functionality and metabolic rewiring. This results in energetically inefficient anaerobic glycolysis and defective tricarboxylic acid cycle, with sustained urinary excretion of pyruvate, orotate, citrate, α-ketoglutarate, nitrogen-rich compounds and amino acids. In summary, our investigation reveals that cysteine restriction, by depleting GSH and CoA, exerts a maximal impact on weight loss, metabolism and stress signalling compared with other amino acid restrictions. These findings suggest strategies for addressing a range of metabolic diseases and the growing obesity crisis.

DOI: https://doi.org/10.1038/s41586-025-08996-y
Nature. 2025 May;641(8065): 1079-1080

I told AI to make me a protein. Here's what it came up with.

Ewen Callaway.



Keywords:  Machine learning; Structural biology

DOI:  https://doi.org/10.1038/d41586-025-01586-y
Elife. 2025 May 21. pii: RP100747. [Epub ahead of print]13

Glutamine catabolism supports amino acid biosynthesis and suppresses the integrated stress response to promote photoreceptor survival.

Moloy T Goswami, Eric Weh, Shubha Subramanya, Katherine M Weh, Hima Bindu Durumutla, Heather Hager, Nicholas Miller, Sraboni Chaudhury, Anthony Andren, Peter Sajjakulnukit, Li Zhang, Cagri Besirli, Costas A Lyssiotis, Thomas J Wubben.

  Photoreceptor loss results in vision loss in many blinding diseases, and metabolic dysfunction underlies photoreceptor degeneration. So, exploiting photoreceptor metabolism is an attractive strategy to prevent vision loss. Yet, the metabolic pathways that maintain photoreceptor health remain largely unknown. Here, we investigated the dependence of photoreceptors on glutamine (Gln) catabolism. Gln is converted to glutamate via glutaminase (GLS), so mice lacking GLS in rod photoreceptors were generated to inhibit Gln catabolism. Loss of GLS produced rapid rod photoreceptor degeneration. In vivo metabolomic methodologies and metabolic supplementation identified Gln catabolism as critical for glutamate and aspartate biosynthesis. Concordant with this amino acid deprivation, the integrated stress response (ISR) was activated with protein synthesis attenuation, and inhibiting the ISR delayed photoreceptor loss. Furthermore, supplementing asparagine, which is synthesized from aspartate, delayed photoreceptor degeneration. Hence, Gln catabolism is integral to photoreceptor health, and these data reveal a novel metabolic axis in these metabolically demanding neurons.

Keywords:  cell biology; glutaminase; metabolism; mouse; neurodegeneration; neuroscience; photoreceptor

DOI:  https://doi.org/10.7554/eLife.100747
Nature. 2025 May 21.

Programmable control of spatial transcriptome in live cells and neurons.

Mengting Han, Maylin L Fu, Yanyu Zhu, Alexander A Choi, Emmy Li, Jon Bezney, Sa Cai, Leann Miles, Yitong Ma, Lei S Qi.

Spatial RNA organization has a pivotal role in diverse cellular processes and diseases1-4. However, functional implications of the spatial transcriptome remain largely unexplored due to limited technologies for perturbing endogenous RNA within specific subcellular regions1,5. Here we present CRISPR-mediated transcriptome organization (CRISPR-TO), a system that harnesses RNA-guided, nuclease-dead dCas13 for programmable control of endogenous RNA localization in live cells. CRISPR-TO enables targeted localization of endogenous RNAs to diverse subcellular compartments, including the outer mitochondrial membrane, p-bodies, stress granules, telomeres and nuclear stress bodies, across various cell types. It allows for inducible and reversible bidirectional RNA transport along microtubules via motor proteins, facilitating real-time manipulation and monitoring of RNA localization dynamics in living cells. In primary cortical neurons, we demonstrate that repositioned mRNAs undergo local translation along neurites and at neurite tips, and co-transport with ribosomes, with β-actin mRNA localization enhancing the formation of dynamic filopodial protrusions and inhibiting axonal regeneration. CRISPR-TO-enabled screening in primary neurons identifies Stmn2 mRNA localization as a driver of neurite outgrowth. By enabling large-scale perturbation of the spatial transcriptome, CRISPR-TO bridges a critical gap left by sequencing and imaging technologies, offering a versatile platform for high-throughput functional interrogation of RNA localization in living cells and organisms.

DOI: https://doi.org/10.1038/s41586-025-09020-z
Redox Biol. 2025 May 13. pii: S2213-2317(25)00191-0. [Epub ahead of print]84 103678

Redox shuttle of cytosolic Thioredoxin to mitochondria protects against hyperoxia-mediated alteration of mitochondrial structure and dysfunction.

Venkatesh Kundumani-Sridharan, Somasundaram Raghavan, Sudhir Kumar, Kumuda C Das.

Cytosolic thioredoxin (Trx) is a critical redox protein that converts protein disulfides to thiols via catalytic activity of thioredoxin reductase-1 (TrxR1) and NADPH. Thioredoxin-2 (Trx2) is a mitochondria-localized isoform. It is generally believed that Trx and Trx2 perform similar functions within the cytosol and mitochondria respectively. Here, we demonstrate that cytosolic Trx shuttles into mitochondria in the presence of normal levels of Trx2 in physiological state and higher levels of Trx translocate to mitochondria in oxidative stress conditions such as exposure to high concentrations of oxygen. This shuttle is required to maintain mitochondrial structure and function during physiological and oxidative stress conditions. Further, reduced Trx (Trx-SH) shuttle into mitochondria to protect against the downregulation of several mitochondrially coded genes and proteins of respiratory chain complexes in oxidative stress. Translocation of Trx occurs only in the reduced state as oxidized or cysteine mutant Trx is unable to translocate to the mitochondria. Accumulation of mitochondrial DNA damage product 8-Oxo-dG in hyperoxia is decreased in the presence of higher levels of cytosolic Trx within the mitochondrion. Collectively, our data demonstrate that shuttling of reduced cytosolic Trx into mitochondria protects against mitochondrial DNA damage, decreased gene and protein expression of respiratory chain complexes and mitochondrial dysfunction resulting in restoration of their native function and cell survival in physiological and oxidative stress conditions.

DOI: https://doi.org/10.1016/j.redox.2025.103678
Nature. 2025 May 21.

Clonal tracing with somatic epimutations reveals dynamics of blood ageing.

Michael Scherer, Indranil Singh, Martina Maria Braun, Chelsea Szu-Tu, Pedro Sanchez Sanchez, Dominik Lindenhofer, Niels Asger Jakobsen, Verena Körber, Michael Kardorff, Lena Nitsch, Pauline Kautz, Julia Rühle, Agostina Bianchi, Luca Cozzuto, Robert Frömel, Sergi Beneyto-Calabuig, Caleb Lareau, Ansuman T Satpathy, Renée Beekman, Lars M Steinmetz, Simon Raffel, Leif S Ludwig, Paresh Vyas, Alejo Rodriguez-Fraticelli, Lars Velten.

Current approaches used to track stem cell clones through differentiation require genetic engineering1,2 or rely on sparse somatic DNA variants3,4, which limits their wide application. Here we discover that DNA methylation of a subset of CpG sites reflects cellular differentiation, whereas another subset undergoes stochastic epimutations and can serve as digital barcodes of clonal identity. We demonstrate that targeted single-cell profiling of DNA methylation5 at single-CpG resolution can accurately extract both layers of information. To that end, we develop EPI-Clone, a method for transgene-free lineage tracing at scale. Applied to mouse and human haematopoiesis, we capture hundreds of clonal differentiation trajectories across tens of individuals and 230,358 single cells. In mouse ageing, we demonstrate that myeloid bias and low output of old haematopoietic stem cells6 are restricted to a small number of expanded clones, whereas many functionally young-like clones persist in old age. In human ageing, clones with and without known driver mutations of clonal haematopoieis7 are part of a spectrum of age-related clonal expansions that display similar lineage biases. EPI-Clone enables accurate and transgene-free single-cell lineage tracing on hematopoietic cell state landscapes at scale.

DOI: https://doi.org/10.1038/s41586-025-09041-8
Neuroscience. 2025 May 20. pii: S0306-4522(25)00371-9. [Epub ahead of print]577 228-239

Miro1: A potential target for treating neurological disorders.

Linghua Zeng, Juan Yang, Conghui Zhang, Junjie Zhu, Saichun Zhong, Xing Liu, Haiyu Xie, Lifeng Wang, Li Chen, Maolin Zhong, Fuzhou Hua, Weidong Liang.

  The Miro1 protein is a member of the mitochondrial Rho GTPase (Miro) protein family and plays a crucial role in regulating the dynamic processes of mitochondria and participating in cellular movement and mitochondrial transport. In the nervous system, it ensures adequate energy supply for normal neuronal function and synaptic transmission. Additionally, Miro1 actively participates in the regulation of mitochondrial quality control and stress responses within neurons. Its primary function is to sense intracellular stress signals to regulate mitochondrial movement and metabolism, thereby adapting to environmental changes. Multiple studies have indicated that the Miro1 protein is associated with the pathogenesis of various neurological disorders, such as Alzheimer's Disease(AD), Parkinson's Disease(PD), and Amyotrophic Lateral Sclerosis(ALS). This article reviews the mechanistic role of Miro1 in these diseases and summarizes the latest research on its involvement in neurological disorders. These efforts aim to provide unified treatment strategies for certain neurological disorders and explore the potential for treating complex neurological diseases.

Keywords:  AD; ALS; Miro1; Mitochondria; Neurological disorders; PD

DOI:  https://doi.org/10.1016/j.neuroscience.2025.05.019
Nat Commun. 2025 May 20. 16(1): 4695

Human mitochondrial ferritin exhibits highly unusual iron-O2 chemistry distinct from that of cytosolic ferritins.

Justin M Bradley, Zinnia Bugg, Jacob Pullin, Geoffrey R Moore, Dimitri A Svistunenko, Nick E Le Brun.

Ferritins are ubiquitous proteins that function in iron storage/detoxification by catalyzing the oxidation of Fe2+ ions and solubilizing the resulting Fe3+-oxo mineral. Mammalian tissues that are metabolically highly active contain, in addition to the widespread cytosolic ferritin, a ferritin that is localized to mitochondria. Mitochondrial ferritin (FtMt) protects against oxidative stress and is found at higher levels in diseases associated with abnormal iron accumulation, including Alzheimer's and Parkinson's. Here we demonstrate that, despite 80% sequence identity with cytosolic human H-chain ferritin, Fe2+ oxidation at the catalytic diiron ferroxidase center of FtMt proceeds via a distinct mechanism. This involves a mixed-valent ferroxidase center (MVFC) that is readily detected under the O2-limiting conditions typical of mitochondria, and formation of a radical on a strictly conserved Tyr residue (Tyr34) that is key for the activation of O2 and stability of the MVFC. The possible origin of the mechanistic differences exhibited by the highly-related human mitochondrial and cytosolic H-chain ferritins is explored.

DOI: https://doi.org/10.1038/s41467-025-59463-1
Adv Sci (Weinh). 2025 May 23. e01612

Inhibition and Rescue of Hyperglycemia-Induced Cellular Senescence by Mitochondrial Transfer from Enucleated Mesenchymal Stem Cell-Derived Microvesicles for Chronic Wound Healing.

Zixuan Dong, Xiaobing Liu, Shichun Li, Xiaoling Fu.

  The aberrant cellular senescence in chronic wounds presents a significant barrier to healing. Mitochondrial dysfunction is critical in initiating and maintaining cellular senescence, underscoring therapeutic potential in restoring mitochondrial function by delivering healthy mitochondria to wound cells. However, approaches for delivering mitochondria to achieve optimized wound repair remain lacking. Herein, enucleated MSCs-derived microvesicles containing functional mitochondria (Mito@euMVs) via simple extrusion are developed. By controlling the size of microvesicles within a small micron-scale range, the mitochondrial encapsulation efficiency is optimized. Mito@euMVs effectively delivered mitochondria into fibroblasts and HUVECs, inhibiting and rejuvenating hyperglycemia-induced cellular senescence. To enhance the clinical applicability, soluble PVA microneedle patches for the transdermal Mito@euMVs delivery are utilized. In diabetic rats with pressure sores, the senescence-inhibiting and -rescuing properties of Mito@euMVs are further validated, along with their therapeutic efficacy, demonstrating their potential for chronic wound repair. Moreover, as a versatile delivery vehicle for mitochondria, Mito@euMVs hold promising for treating mitochondrial dysfunction and aging-related conditions.

Keywords:  cellular senescence; diabetic pressure sore; enucleated mesenchymal stem cells; mitochondrial transfer

DOI:  https://doi.org/10.1002/advs.202501612
Nat Commun. 2025 May 19. 16(1): 4653

Optimized AAV capsids for basal ganglia diseases show robust potency and distribution.

D E Leib, Y H Chen, L Tecedor, P T Ranum, M S Keiser, B C Lewandowski, E M Carrell, S Arora, I Huerta-Ocampo, D Lai, C M Fluta, C Cheng, X Liu, B L Davidson.

Huntington's disease and other disorders of the basal ganglia create challenges for biomolecule-based medicines given the poor accessibility of these deep brain structures following intracerebral or intravascular delivery. Here, we found that low dose, low volume delivery of unbiased AAV libraries into the globus pallidus allowed recovery of novel capsids capable of broad access to key deep brain and cortical structures relevant for human therapies. One such capsid, AAV-DB-3, provided transduction of up to 45% of medium spiny neurons in the adult NHP striatum, along with substantial transduction of relevant deep layer neurons in the cortex. Notably, AAV-DB-3 behaved similarly in mice as in NHPs and potently transduced human neurons derived from induced pluripotent stem cells. Thus, AAV-DB-3 provides a unique AAV for network level brain gene therapies that translates up and down the evolutionary scale for preclinical studies and eventual clinical use.

DOI: https://doi.org/10.1038/s41467-025-60000-3
Nat Cancer. 2025 May 20.

Age-associated nicotinamide adenine dinucleotide decline drives CAR-T cell failure.

Helen Carrasco Hope, Jana de Sostoa, Pierpaolo Ginefra, Massimo Andreatta, Yi-Hsuan Chiang, Catherine Ronet, Christine Pich-Bavastro, Jesús Corria Osorio, François Kuonen, Johan Auwerx, Patrizia D'Amelio, Ping-Chih Ho, Santiago J Carmona, George Coukos, Denis Migliorini, Nicola Vannini.

Chimeric antigen receptor (CAR) T cell therapy is one of the most promising cancer treatments. However, different hurdles are limiting its application and efficacy. In this context, how aging influences CAR-T cell outcomes is largely unknown. Here we show that CAR-T cells generated from aged female mice present a mitochondrial dysfunction derived from nicotinamide adenine dinucleotide (NAD) depletion that leads to poor stem-like properties and limited functionality in vivo. Moreover, human data analysis revealed that both age and NAD metabolism determine the responsiveness to CAR-T cell therapy. Targeting NAD pathways, we were able to recover the mitochondrial fitness and functionality of CAR-T cells derived from older adults. Altogether, our study demonstrates that aging is a limiting factor to successful CAR-T cell responses. Repairing metabolic and functional obstacles derived from age, such as NAD decline, is a promising strategy to improve current and future CAR-T cell therapies.

DOI: https://doi.org/10.1038/s43018-025-00982-7
Lancet Neurol. 2025 Jun;pii: S1474-4422(25)00163-2. [Epub ahead of print]24(6): 476-477

The future of gene therapy for Parkinson's disease.

Roger A Barker, Philip C Buttery.

DOI: https://doi.org/10.1016/S1474-4422(25)00163-2
medRxiv. 2025 May 09. pii: 2025.05.08.25327176. [Epub ahead of print]

Single cell multiomics and 3D genome architecture reveal novel pathways of human heart failure.

Yang Xie, Luca Tucciarone, Elie N Farah, Lei Chang, Qian Yang, Thirupura S Shankar, Weston Elison, Shaina Tran, Jovina Djulamsah, Audrey Lie, Timothy Loe, Alyssa R Holman, Sierra Corban, Justin Buchanan, Sainath Mamde, Haowen Zhou, Ruth M Elgamal, Eleni Tseliou, Vincent Huang, Zhaoning Wang, Jeffery Chiu, Rebecca Melton, Emily Griffin, Qingquan Zhang, Jacinta Lucero, Sutip Navankasattusas, Daofeng Li, Chanrung Seng, Eugin Destici, Craig H Selzman, Agnieszka D'Antonio-Chronowska, Ting Wang, Allen Wang, Stavros G Drakos, Kyle J Gaulton, Bing Ren, Neil C Chi.

Heart failure is a leading cause of morbidity and mortality; yet gene regulatory mechanisms driving cell type-specific pathologic responses remain undefined. Here, we present the cell type-resolved transcriptomes, chromatin accessibility, histone modifications and chromatin organization of 36 non-failing and failing human hearts profiled from 776,479 cells spanning all cardiac chambers. Integrative analyses revealed dynamic changes in cell type composition, gene regulatory programs and chromatin organization, which expanded the annotation of cardiac cis-regulatory sequences by ten-fold and mapped cell type-specific enhancer-gene interactions. Cardiomyocytes and fibroblasts particularly exhibited complex disease-associated cellular states, gene regulatory programs and global chromatin reorganization. Mapping genetic association data onto cell type-specific regulatory programs revealed likely causal genetic contributors to heart failure. Together, these findings provide comprehensive, multimodal gene regulatory maps of the human heart in health and disease, offering a valuable framework for designing precise cell type-targeted therapies for treating heart failure.

DOI: https://doi.org/10.1101/2025.05.08.25327176
Nat Commun. 2025 May 16. 16(1): 4507

Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

Zachery Wolfe, David Liska, Adam Norris.

Profiling alternative splicing in single neurons using RNA-seq is challenging due to low capture efficiency and sensitivity. We therefore know much less about splicing patterns and regulation across neurons than we do about gene expression. Here we leverage unique attributes of C. elegans to investigate deep neuron-specific transcriptomes with biological replicates generated by the CeNGEN consortium, enabling high-confidence assessment of splicing across neuron types even for lowly-expressed genes. Global splicing maps reveal several striking observations, including pan-neuronal genes harboring cell-specific splice variants, and abundant differential intron retention across neuron types. We develop an algorithm to identify unique cell-specific expression patterns, which reveals both cell-specific isoforms and potential regulatory factors establishing these isoforms. Genetic interrogation of these factors in vivo identifies three distinct splicing factors employed to control splicing in a single neuron. Finally, we develop a user-friendly platform for spatial transcriptomic visualization of these splicing patterns with single-neuron resolution.

DOI: https://doi.org/10.1038/s41467-025-58296-2
Lancet Neurol. 2025 Jun;pii: S1474-4422(25)00125-5. [Epub ahead of print]24(6): 548-556

Gene therapy for Parkinson's disease: trials and technical advances.

Graham Winston, Natasha Kharas, Per Svenningsson, Ashwani Jha, Michael G Kaplitt.

Gene therapy has long held promise as a method for targeted alteration of neuronal function in Parkinson's disease. Different gene-therapy approaches aim to correct dysfunctional circuits or have attempted to protect vulnerable neurons to slow disease progression. Clinical trials have used viral vectors to deliver genes either directly into brain regions through stereotaxic injection or globally through infusion into the CSF of the cisterna magna. Bilateral delivery of GAD into the subthalamic nucleus has resulted in some clinical improvements, and the delivery into the putamen of genes that codify for enzymes involved in dopamine synthesis has resulted also in some improvements. Growth factor gene therapy has been the focus of several studies, with both imaging and neuropathological evidence of gene expression and possible neuroprotection. An ongoing trial of gene therapy to correct mutated GBA in patients with Parkinson's disease and GBA mutations is the first to use gene therapy to try to correct a genetic cause of Parkinson's disease in human beings. Technical advancements in vector delivery, such as novel capsids and the disruption of the blood-brain barrier by use of focused ultrasound, will help advance gene therapy in Parkinson's disease.

DOI: https://doi.org/10.1016/S1474-4422(25)00125-5