bims-mitdis 2025-03-23 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2025–03–23
37 papers selected by
Catalina Vasilescu, Helmholz Munich

Definition of the human mitochondrial TOM interactome reveals TRABD as new interacting protein.
Mitochondrial fission - changing perspectives for future progress.
Experiences from dual genome next-generation sequencing panel testing for mitochondrial disorders: a comprehensive molecular diagnosis.
Chromogen-based double immunohistochemical detection of mitochondrial respiratory chain deficiencies in human brain tissue.
Acute diacylglycerol production activates critical membrane-shaping proteins leading to mitochondrial tubulation and fission.
Developmental mitochondrial complex I activity determines lifespan.
The Mia40 substrate Mix17 exposes its N-terminus to the cytosolic side of the mitochondrial outer membrane.
Novel biallelic TK2 mutations cause mitochondrial DNA depletion syndrome with infantile early-onset lipid storage myopathy.
TMBIM-2 orchestrates systemic mitochondrial stress response via facilitating Ca2+ oscillations.
In-cell architecture of the mitochondrial respiratory chain.
Natural History of Patients With Mitochondrial ATPase Deficiency Due to Pathogenic Variants of MT-ATP6 and MT-ATP8.
Fibroblasts and hiPS-Derived Astrocytes From CoPAN Patients Showed Different Levels of Iron Overload Correlated With Senescent Phenotype.
Small-molecule hypoxia therapy in mitochondrial disease.
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.
SARM1: The Checkpoint of Axonal Degeneration in the Nervous System Disorders.
Mitochondrial quality control in cardiomyocytes: safeguarding the heart against disease and ageing.
A splendid molecular factory: De- and reconstruction of the mammalian respiratory chain.
Nicotinamide riboside and nicotinamide mononucleotide facilitate NAD+ synthesis via enterohepatic circulation.
Mitochondria: An overview of their origin, genome, architecture, and dynamics.
Optogenetic tools for inducing organelle membrane rupture.
A rare de novo mutation, m.1630A>G, in the mitochondrial tRNAVal (MT-TV) gene in a child with epilepsy: case report and review of the literature.
Advances in mitophagy initiation mechanisms.
DNA damage response regulator ATR licenses PINK1-mediated mitophagy.
Mitochondrial reactive oxygen species regulate acetyl-CoA flux between cytokine production and fatty acid synthesis in effector T cells.
Cryo-EM structure of the brine shrimp mitochondrial ATP synthase suggests an inactivation mechanism for the ATP synthase leak channel.
Organelle-tuning condition robustly fabricates energetic mitochondria for cartilage regeneration.
Long read sequencing enhances pathogenic and novel variation discovery in patients with rare diseases.
β-hydroxybutyrate facilitates mitochondrial-derived vesicle biogenesis and improves mitochondrial functions.
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions.
CLYBL averts vitamin B12 depletion by repairing malyl-CoA.
Mitochondria-Lysosome Contact Sites: Emerging Players in Cellular Homeostasis and Disease.
A novel polyribonucleotide nucleotidyltransferase 1 (PNPT1) gene variant potentially associated with combined oxidative phosphorylation deficiency 13: case report and literature review.
Clinical and molecular spectrum of TK2-deficiency: a large Brazilian cohort.
Baby genomics: newborn sequencing starts to fulfill its promise.
Reply to: An alternative model for maternal mtDNA inheritance.
Axonal RNA localization is essential for long-term memory.
Structures and mechanism of human mitochondrial pyruvate carrier.

J Cell Sci. 2025 Mar 19. pii: jcs.263576. [Epub ahead of print]

Definition of the human mitochondrial TOM interactome reveals TRABD as new interacting protein.

Metin Özdemir, Silke Oeljeklaus, Schendzielorz Alexander, Marcel Morgenstern, Anusha Valpadashi, Roya Yousefi, Bettina Warscheid, Sven Dennerlein.

  The mitochondrial proteome arises from dual genetic origin. Nuclear-encoded proteins need to be transported across or inserted into two distinguished membranes, and the TOM complex represents the main translocase in the outer mitochondrial membrane. Its composition and regulations have been extensively investigated within yeast cells. However, we have little knowledge of the TOM complex composition within human cells. Here, we have defined the TOM interactome in a comprehensive manner using biochemical approaches to isolate the TOM complex in combination with quantitative mass spectrometry analyses. Within these studies, we defined the pleiotropic nature of the human TOM complex, including new interactors, such as TRABD. Our studies provide a framework to understand the various biogenesis pathways that merge at the TOM complex within human cells.

Keywords:  Mitochondria; Mitochondrial Biogenesis; Mitochondrial protein import; Mitochondrial quality control; Protein transport; TOM complex

DOI:  https://doi.org/10.1242/jcs.263576
J Cell Sci. 2025 May 01. pii: jcs263640. [Epub ahead of print]138(9):

Mitochondrial fission - changing perspectives for future progress.

Sukrut C Kamerkar, Ao Liu, Henry N Higgs.

  Mitochondrial fission is important for many aspects of cellular homeostasis, including mitochondrial distribution, stress response, mitophagy, mitochondrially derived vesicle production and metabolic regulation. Several decades of research has revealed much about fission, including identification of a key division protein - the dynamin Drp1 (also known as DNM1L) - receptors for Drp1 on the outer mitochondrial membrane (OMM), including Mff, MiD49 and MiD51 (also known as MIEF2 and MIEF1, respectively) and Fis1, and important Drp1 regulators, including post-translational modifications, actin filaments and the phospholipid cardiolipin. In addition, it is now appreciated that other organelles, including the endoplasmic reticulum, lysosomes and Golgi-derived vesicles, can participate in mitochondrial fission. However, a more holistic understanding of the process is lacking. In this Review, we address three questions that highlight knowledge gaps. First, how do we quantify mitochondrial fission? Second, how does the inner mitochondrial membrane (IMM) divide? Third, how many 'types' of fission exist? We also introduce a model that integrates multiple regulatory factors in mammalian mitochondrial fission. In this model, three possible pathways (cellular stimulation, metabolic switching or mitochondrial dysfunction) independently initiate Drp1 recruitment at the fission site, followed by a shared second step in which Mff mediates subsequent assembly of a contractile Drp1 ring. We conclude by discussing some perplexing issues in fission regulation, including the effects of Drp1 phosphorylation and the multiple Drp1 isoforms.

Keywords:  Drp1 receptors; Dynamin related protein-1; Inner mitochondrial membrane division; Mitochondrial fission

DOI:  https://doi.org/10.1242/jcs.263640
Front Genet. 2025 ;16 1488956

Experiences from dual genome next-generation sequencing panel testing for mitochondrial disorders: a comprehensive molecular diagnosis.

Elizabeth Gorman, Hongzheng Dai, Yanming Feng, William James Craigen, David C Y Chen, Fan Xia, Linyan Meng, Pengfei Liu, Robert Rigobello, Arpita Neogi, Christine M Eng, Yue Wang.

   Introduction: The molecular diagnosis of mitochondrial disorders is complicated by phenotypic variability, genetic heterogeneity, and the complexity of mitochondrial heteroplasmy. Next-generation sequencing (NGS) of the mitochondrial genome in combination with a targeted panel of nuclear genes associated with mitochondrial disease provides the highest likelihood of obtaining a comprehensive molecular diagnosis. To assess the clinical utility of this approach, we describe the results from a retrospective review of patients having dual genome panel testing for mitochondrial disease.
Methods: Dual genome panel testing by NGS was performed on a cohort of 1,509 unrelated affected individuals with suspected mitochondrial disorders. This test included 163 nuclear genes associated with mitochondrial diseases and the entire mitochondrial genome. A retrospective review was performed to evaluate diagnostic yield, disease-gene contributions, and heteroplasmy levels of pathogenic/likely pathogenic (P/LP) mitochondrial DNA (mtDNA) variants.
Results: The overall diagnostic yield was 14.6%, with 7.7% from the nuclear genome and 6.9% from the mtDNA genome. P/LP variants in nuclear genes were enriched in both well-established genes (e.g., POLG) and more recently described genes (e.g., FBXL4), highlighting the importance of keeping the panel design updated.
Conclusion: Variants in nuclear and mitochondrial genomes equally contributed to a 14.6% diagnostic yield in this patient cohort. Dual genome NGS testing provides a comprehensive framework for diagnosing mitochondrial disorders, offering clinical utility that can be considered as first-tier approach compared to single genome testing. Characterizing disease-causing genes, variants, and mtDNA heteroplasmy enhances understanding of mitochondrial disorders. Testing alternative tissues can further increase diagnostic yield.

Keywords:  NGS; dual-genome; functional group analysis; heteroplasmy; mitochondria

DOI:  https://doi.org/10.3389/fgene.2025.1488956
Acta Neuropathol Commun. 2025 Mar 20. 13(1): 63

Chromogen-based double immunohistochemical detection of mitochondrial respiratory chain deficiencies in human brain tissue.

Tale L Bjerknes, Anna Rubiolo, Omnia Shadad, Ole-Bjørn Tysnes, Charalampos Tzoulis.

  Studies of the mitochondrial respiratory chain (MRC) have given important insights into the pathology of mitochondrial and neurodegenerative disorders. Immunohistochemical methods for staining MRC complexes are particularly valuable for assessing quantitative changes in situ, especially in complex tissues with cellular heterogeneity, such as the brain. However, traditional approaches have notable limitations. Chromogen-based staining, while preserving tissue morphology, has been restricted to a single antigen per section, preventing co-assessment of MRC complexes and mitochondrial mass on the same section. Immunofluorescence, which allows multiplex staining of multiple targets, partially addresses this limitation but compromises tissue morphology and can be highly variable in postmortem brain samples. To address these challenges, we have established a dual-antigen, chromogen-based immunohistochemical method that allows simultaneous assessment of each MRC complex and the mitochondrial marker voltage-dependent anion channel 1 (VDAC1) on the same section. As proof of concept, we apply this method on brain tissue from patients with neurological disease caused by mutations in the mitochondrial DNA polymerase gamma (POLG). Our findings demonstrate that this approach is both reliable and robust. Moreover, this method enables more precise identification of MRC deficiencies in neurons and significantly reduces the amount of tissue required for analysis, a critical advantage when working with scarce human brain samples.

Keywords:  Human brain; Immunohistochemistry; Mitochondria; Mitochondrial respiratory chain

DOI:  https://doi.org/10.1186/s40478-025-01980-7
Nat Commun. 2025 Mar 19. 16(1): 2685

Acute diacylglycerol production activates critical membrane-shaping proteins leading to mitochondrial tubulation and fission.

Joshua G Pemberton, Krishnendu Roy, Yeun Ju Kim, Tara D Fischer, Vijay Joshi, Elizabeth Ferrer, Richard J Youle, Thomas J Pucadyil, Tamas Balla.

Mitochondrial dynamics are orchestrated by protein assemblies that directly remodel membrane structure, however the influence of specific lipids on these processes remains poorly understood. Here, using an inducible heterodimerization system to selectively modulate the lipid composition of the outer mitochondrial membrane (OMM), we show that local production of diacylglycerol (DAG) directly leads to transient tubulation and rapid fragmentation of the mitochondrial network, which are mediated by isoforms of endophilin B (EndoB) and dynamin-related protein 1 (Drp1), respectively. Reconstitution experiments on cardiolipin-containing membrane templates mimicking the planar and constricted OMM topologies reveal that DAG facilitates the membrane binding and remodeling activities of both EndoB and Drp1, thereby independently potentiating membrane tubulation and fission events. EndoB and Drp1 do not directly interact with each other, suggesting that DAG production activates multiple pathways for membrane remodeling in parallel. Together, our data emphasizes the importance of OMM lipid composition in regulating mitochondrial dynamics.

DOI: https://doi.org/10.1038/s41467-025-57439-9
EMBO Rep. 2025 Mar 17.

Developmental mitochondrial complex I activity determines lifespan.

Rhoda Stefanatos, Fiona Robertson, Beatriz Castejon-Vega, Yizhou Yu, Alejandro Huerta Uribe, Kevin Myers, Tetsushi Kataura, Viktor I Korolchuk, Oliver D K Maddocks, L Miguel Martins, Alberto Sanz.

  Aberrant mitochondrial function has been associated with an increasingly large number of human disease states. Observations from in vivo models where mitochondrial function is altered suggest that maladaptations to mitochondrial dysfunction may underpin disease pathology. We hypothesized that the severity of this maladaptation could be shaped by the plasticity of the system when mitochondrial dysfunction manifests. To investigate this, we have used inducible fly models of mitochondrial complex I (CI) dysfunction to reduce mitochondrial function at two stages of the fly lifecycle, from early development and adult eclosion. Here, we show that in early life (developmental) mitochondrial dysfunction results in severe reductions in survival and stress resistance in adulthood, while flies where mitochondrial function is perturbed from adulthood, are long-lived and stress resistant despite having up to a 75% reduction in CI activity. After excluding developmental defects as a cause, we went on to molecularly characterize these two populations of mitochondrially compromised flies, short- and long-lived. We find that our short-lived flies have unique transcriptomic, proteomic and metabolomic responses, which overlap significantly in discrete models of CI dysfunction. Our data demonstrate that early mitochondrial dysfunction via CI depletion elicits a maladaptive response, which severely reduces survival, while CI depletion from adulthood is insufficient to reduce survival and stress resistance.

Keywords:  Ageing; Complex I; Drosophila; Mitochondria; Mitochondrial Disease

DOI:  https://doi.org/10.1038/s44319-025-00416-6
J Cell Sci. 2025 Mar 17. pii: jcs.263661. [Epub ahead of print]

The Mia40 substrate Mix17 exposes its N-terminus to the cytosolic side of the mitochondrial outer membrane.

Moritz Resch, Johanna S Frickel, Korbinian Dischinger, Rachel Choo Shen Wen, Kai Hell, Max E Harner.

  Mitochondrial architecture and the contacts between the outer and the inner mitochondrial membrane depend on the mitochondrial contact site and cristae organizing system (MICOS) that is highly conserved from yeast to human. Mutations in the mammalian MICOS subunit Mic14/CHCHD10 have been linked to amyotrophic lateral sclerosis and frontotemporal dementia, indicating the importance of this protein. Mic14/CHCHD10 has a yeast ortholog, Mix17, a protein of unknown function, which has not been shown to interact with MICOS so far. As a first step to elucidate the function of Mix17 and its orthologs, we analyzed its interactions, biogenesis and mitochondrial sublocation. We report that Mix17 is no stable MICOS subunit in yeast. Our data suggest that Mix17 is the first Mia40 substrate in the mitochondrial outer membrane. Unlike all other Mia40 substrates, Mix17 spans the outer membrane and exposes its N-terminus to the cytosol. The insertion of Mix17 is likely to be mediated by its interaction with Tom40, the pore of the TOM complex. Moreover, we show that the exposure of Mix17 to the cytosolic side of the membrane depends on its N-terminus.

Keywords:  CHCHD10; Mia40; Mic14; Mix17; Protein import; Tom40

DOI:  https://doi.org/10.1242/jcs.263661
Orphanet J Rare Dis. 2025 Mar 17. 20(1): 130

Novel biallelic TK2 mutations cause mitochondrial DNA depletion syndrome with infantile early-onset lipid storage myopathy.

Duoling Li, Yixin Shi, Hanhan Sun, Chuanzhu Yan, Yan Lin.

   BACKGROUND: Mutations in the TK2 gene are strongly associated with mitochondrial DNA depletion syndrome (MDS), a severe condition with high mortality and poor outcomes. Although many MDS cases are reported, those linked to TK2 mutations with lipid deposition are rare. Large deletions in the TK2 gene are even rarer.
METHODS: We conducted whole-exome sequencing to find the gene linked to MDS, followed by genomic and structural analyses, histopathological, and functional analyses to assess the mutations' pathogenicity. Additionally, a HEK293T cell model with TK2 mutations was created to investigate the impact of large deletions on mitochondrial function.
RESULTS: The patient was found to have a novel compound heterozygous mutation in the TK2 gene, consisting of a large deletion spanning exons 5-10 (E5-E10 del) and a previously reported missense mutation (c.311C > A, p.Arg104His). Analysis of the patient's muscle tissue demonstrated a marked reduction in mtDNA content and a significant impairment in overall mitochondrial function. In the HEK293T cell model, the group with the deletion mutation exhibited a notable reduction in TK2 protein expression and levels of mitochondrial complex subunits when compared to the control group. Furthermore, there was an observed increase in ROS levels, a decrease in ATP production, and compromised mitochondrial respiratory chain function. Moreover, we conducted a comprehensive review of the previously reported genotypic and phenotypic spectrum of TK2 mutations in the literature.
CONCLUSIONS: This case report underscores the detrimental impact of large fragment deletion mutations in the TK2 gene and elucidates their role in the pathogenesis of MDS. It broadens the spectrum of known TK2 mutations and enhances our understanding of the structural and functional consequences of these mutations.

Keywords:  Early-onset; Lipid storage myopathy; MDS; TK2

DOI:  https://doi.org/10.1186/s13023-025-03639-x
J Cell Biol. 2025 May 05. pii: e202408050. [Epub ahead of print]224(5):

TMBIM-2 orchestrates systemic mitochondrial stress response via facilitating Ca2+ oscillations.

Jiasheng Li, Jimeng Cui, Xinyu Li, Di Zhu, Zhenhua Chen, Xiahe Huang, Yingchun Wang, Qingfeng Wu, Ye Tian.

Neuronal mitochondrial function is critical for orchestrating inter-tissue communication essential for overall fitness. Despite its significance, the molecular mechanism underlying the impact of prolonged mitochondrial stresses on neuronal activity and how they orchestrate metabolism and aging remains elusive. Here, we identified the evolutionarily conserved transmembrane protein XBX-6/TMBIM-2 as a key mediator in the neuronal-to-intestinal mitochondrial unfolded protein response (UPRmt). Our investigations reveal that intrinsic neuronal mitochondrial stress triggers spatiotemporal Ca2+ oscillations in a TMBIM-2-dependent manner through the Ca2+ efflux pump MCA-3. Notably, persistent Ca2+ oscillations at synapses of ADF neurons are critical for facilitating serotonin release and the subsequent activation of the neuronal-to-intestinal UPRmt. TMBIM2 expression diminishes with age; however, its overexpression counteracts the age-related decline in aversive learning behavior and extends the lifespan of Caenorhabditis elegans. These findings underscore the intricate integration of chronic neuronal mitochondrial stress into neurotransmission processes via TMBIM-2-dependent Ca2+ equilibrium, driving metabolic adaptation and behavioral changes for the regulation of aging.

DOI: https://doi.org/10.1083/jcb.202408050
Science. 2025 Mar 21. 387(6740): 1296-1301

In-cell architecture of the mitochondrial respiratory chain.

Florent Waltz, Ricardo D Righetto, Lorenz Lamm, Thalia Salinas-Giegé, Ron Kelley, Xianjun Zhang, Martin Obr, Sagar Khavnekar, Abhay Kotecha, Benjamin D Engel.

Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, working in concert to transfer electrons and pump protons. The precise organization of these complexes in native cells is debated. We used in situ cryo-electron tomography to visualize the native structures and organization of several major mitochondrial complexes in Chlamydomonas reinhardtii cells. ATP synthases and respiratory complexes segregate into curved and flat crista membrane domains, respectively. Respiratory complexes I, III, and IV assemble into a respirasome supercomplex, from which we determined a native 5-angstrom (Å) resolution structure showing binding of electron carrier cytochrome c. Combined with single-particle cryo-electron microscopy at 2.4-Å resolution, we model how the respiratory complexes organize inside native mitochondria.

DOI: https://doi.org/10.1126/science.ads8738
Neurology. 2025 Apr;104(7): e213462

Natural History of Patients With Mitochondrial ATPase Deficiency Due to Pathogenic Variants of MT-ATP6 and MT-ATP8.

Sara Carli, Anna Levarlet, Daria Diodato, Enrico Silvio Bertini, Diego Martinelli, Alessandro Malandrini, Diego Lopergolo, Gian Nicola Gallus, Rebecca D Ganetzky, Chiara La Morgia, Valerio Carelli, Guido Primiano, Cristina Domínguez-González, Pablo Serrano-Lorenzo, Miguel A Martín, Anna Ardissone, Costanza Lamperti, Valeria Nicoletta, Thomas Klopstock, Felix Distelmaier, Leopold Zeng, Boriana Büchner, Michelangelo Mancuso, Markus Schuelke, Alessandro Prigione, Caterina Garone.

BACKGROUND AND OBJECTIVES: The mitochondrial DNA (mtDNA) genes MT-ATP6 and MT-ATP8 encode for subunits α and 8 (A6L) of the adenosine triphosphate synthase complex. Pathogenetic variants in MT-ATP6/8 cause incurable mitochondrial syndromes encompassing a wide spectrum of clinical features including ataxia, motor and language developmental delay, deafness, retinitis pigmentosa, and Leigh pattern in brain MRI. Typically, higher levels of mtDNA variants lead to more severe symptomatology although even individuals with similar mtDNA mutational loads exhibit high clinical variability. Hence, the establishment of potential therapeutics is currently challenging. In this article, we present an international multicenter study designed to provide a retrospective natural history of patients with MT-ATP6/8 deficiency and to identify primary and secondary end points for future clinical trials.
METHODS: Clinical, biochemical, and molecular genetics data of patients with genetically confirmed MT-ATP6/8 defects were collected and analyzed from Italian, German, US, and Spain national reference centers through ethical committee-approved mitochondrial patients' national registries or local programs.
RESULTS: A cohort of 111 patients, 98 unreported, were analyzed (55 male, 56 female). Patients had infantile-onset disease (<1 year) in 44% of cases, pediatric-onset (≥1 year and ≤12 years) in 36%, and late-onset (>12 years) in 20%. Kaplan-Meier analysis showed a significant difference (p value = 0.0349) in the survival of infantile and pediatric patients compared with adult patients, although only 8% of patients were not alive at the last follow-up. The CNS was the most frequently affected tissue (93%), followed by the muscle (75%), eye (46%), and heart (18%). Brain MRI showed isolated Leigh-like lesions (58%), Leigh-like lesions and cortical and/or cerebellar atrophy (15%), isolated cerebellar atrophy (10%), and other lesions (21%). At the last follow-up, 11% of patients were wheelchair-bound. Metabolic acidosis or acute deterioration complicated the clinical course in ≅55% of early-onset patients. Molecular genetics studies identified 26 pathogenic variants (6 of them novel). Reduced citrulline levels and increased alanine and lactate levels were reported in 56%, 49%, and 71% of patients, respectively, suggesting their role as potential biomarkers.
DISCUSSION: Our results define a more accurate classification based on the age at onset for MT-ATPase deficiency and provide fundamental clinical and biochemical data for disease management.

DOI: https://doi.org/10.1212/WNL.0000000000213462
Glia. 2025 Mar 19.

Fibroblasts and hiPS-Derived Astrocytes From CoPAN Patients Showed Different Levels of Iron Overload Correlated With Senescent Phenotype.

Anna Cozzi, Paolo Santambrogio, Andrea Stefano Moro, Alessio Pelagatti, Alicia Rubio, Chiara Balestrucci, Ivano Di Meo, Valeria Tiranti, Sonia Levi.

  COASY protein-associated neurodegeneration (CoPAN) is a rare autosomal recessive disorder within the Neurodegeneration with Brain Iron Accumulation spectrum, resulting from mutations in COASY. This gene encodes the bifunctional enzyme essential for the final steps of coenzyme A biosynthesis. To elucidate the pathophysiology and iron dyshomeostasis underlying CoPAN, we analyzed fibroblasts and human induced pluripotent stem (hiPS)-derived astrocytes from two patients carrying distinct COASY mutations. Our findings reveal that CoPAN fibroblasts display altered iron homeostasis, characterized by iron aggregates, elevated cytosolic labile iron pool, and impaired tubulin acetylation. Patients hiPS-derived astrocytes showed mitochondrial morphological abnormalities and compromised vesicular trafficking. Notably, both cell types demonstrated evidence of ferroptosis, but the astrocytes exhibited more pronounced iron accumulation and lipid peroxidation. These results demonstrate that astrocytes may more accurately recapitulate the pathological phenotype of CoPAN compared to fibroblasts. Interestingly, astrocytes exhibited different levels of iron accumulation concomitant with cellular senescence, indicating a possible role of iron-induced cellular senescence. This finding suggests that the accumulation of cytosolic iron, possibly caused by mitochondrial dysfunction, actively promotes senescence. Our data emphasize the potential therapeutic efficacy of drugs that enhance mitochondrial functionality to attenuate the effects of CoPAN.

Keywords:  CoPAN disease; NBIA disorders; iron metabolism; mitochondrial dysfunction; neurodegenerative diseases

DOI:  https://doi.org/10.1002/glia.70017
Cell. 2025 Mar 20. pii: S0092-8674(25)00207-7. [Epub ahead of print]188(6): 1462-1465

Small-molecule hypoxia therapy in mitochondrial disease.

Marni J Falk.

In this issue of Cell, Blume et al. provide compelling rationale for pursuing pharmacologic optimization of a small-molecule "HypoxyStat," which left-shifts the oxyhemoglobin dissociation curve in red blood cells in an attempt to induce an effective and sustained reduction of chronic tissue hyperoxia in primary mitochondrial disease (PMD) and was well-tolerated and effective for both pre-symptomatic and advanced disease treatment to extend survival and improve neurologic outcomes in a mouse model of Leigh syndrome spectrum.

DOI: https://doi.org/10.1016/j.cell.2025.02.019
Genome Res. 2025 Mar 20.

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.

Undiagnosed Diseases Network

Rare structural variants (SVs)-insertions, deletions, and complex rearrangements-can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore Technologies long-read genomes of 68 individuals from the undiagnosed disease network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4× increase from short reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably, these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that do not incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression toward improving the prioritization of functional SVs and TREs in rare disease patients.

DOI: https://doi.org/10.1101/gr.279323.124
Mol Neurobiol. 2025 Mar 17.

SARM1: The Checkpoint of Axonal Degeneration in the Nervous System Disorders.

Aaditi Karnik, Abhijeet Joshi.

  Axons are metabolically active neuronal segments with well-controlled axonal degeneration and regeneration. External stress or injury displaces this equilibrium toward degeneration leading to axonal dysfunction observed in the pathology of several diseases. The demand and supply matrix of energy at the synapses are maintained by the axonal transport. Nicotinamide adenine dinucleotide (NAD+) is a major energy-driving coenzyme of cells that controls mitochondrial, cytoplasmic, and other organellar energy cycles generating high amounts of adenosine triphosphate (ATP). NAD+ participates in various cellular cycles and is consumed by several enzymes. One of the key enzymes targeting NAD+ is Sterile alpha and TIR motif-containing protein 1 (SARM1) which gets activated in response to external noxious stimuli. SARM1 is an octamer consisting of multiple domains of which the TIR domain governs NAD+ hydrolysis which eventually leads to axonal deficits. Besides its localization in neurons, SARM1 is also present in astrocytes, microglia, and macrophages in which it regulates inflammatory responses associated with disease pathology. SARM1 localization in the outer mitochondrial membrane is responsible for its association with mitochondrial dynamics. SARM1-mediated mitochondrial dysfunction further drives the axonal degeneration associated with peripheral and central nervous system disorders. Several genetic and pharmacological studies highlight the role of SARM1 in axonal degeneration. SARM1 is thus becoming a popular target for preventing axonal degeneration. Several small molecules consisting of isoquinoline, isothiazole, pyridine, and tryptoline acrylamide moieties have been tested for their activity against SARM1 with a promising foundation for drug discovery in targeting SARM1. In our review, we highlight the role of SARM1 in axonal degeneration associated with several disease pathologies focusing on genetic and pharmacological evaluation.

Keywords:  ATP; Axonal degeneration; Cytoskeleton; Mitochondria; Mutations; NAD+ ; SARM1; Wallerian degeneration

DOI:  https://doi.org/10.1007/s12035-025-04835-3
Nat Rev Cardiol. 2025 Mar 20.

Mitochondrial quality control in cardiomyocytes: safeguarding the heart against disease and ageing.

Rishith Ravindran, Åsa B Gustafsson.

Mitochondria are multifunctional organelles that are important for many different cellular processes, including energy production and biosynthesis of fatty acids, haem and iron-sulfur clusters. Mitochondrial dysfunction leads to a disruption in these processes, the generation of excessive reactive oxygen species, and the activation of inflammatory and cell death pathways. The consequences of mitochondrial dysfunction are particularly harmful in energy-demanding organs such as the heart. Loss of terminally differentiated cardiomyocytes leads to cardiac remodelling and a reduced ability to sustain contraction. Therefore, cardiomyocytes rely on multilayered mitochondrial quality control mechanisms to maintain a healthy population of mitochondria. Mitochondrial chaperones protect against protein misfolding and aggregation, and resident proteases eliminate damaged proteins through proteolysis. Irreparably damaged mitochondria can also be degraded through mitochondrial autophagy (mitophagy) or ejected from cells inside vesicles. The accumulation of dysfunctional mitochondria in cardiomyocytes is a hallmark of ageing and cardiovascular disease. This accumulation is driven by impaired mitochondrial quality control mechanisms and contributes to the development of heart failure. Therefore, there is a strong interest in developing therapies that directly target mitochondrial quality control in cardiomyocytes. In this Review, we discuss the current knowledge of the mechanisms involved in regulating mitochondrial quality in cardiomyocytes, how these pathways are altered with age and in disease, and the therapeutic potential of targeting mitochondrial quality control pathways in cardiovascular disease.

DOI: https://doi.org/10.1038/s41569-025-01142-1
Proc Natl Acad Sci U S A. 2025 Mar 25. 122(12): e2416162122

A splendid molecular factory: De- and reconstruction of the mammalian respiratory chain.

Lukas Rimle, Ben P Phillips, Isabela M Codo Costa Barra, Noëlle Arnold, Charlie Hennebert, Thomas Meier, Christoph von Ballmoos.

  Mitochondrial respiratory complexes I to IV and the F1Fo-ATP synthase (complex V) are large protein assemblies producing the universal cellular energy currency adenosine triphosphate (ATP). Individual complexes have been extensively studied in vitro, but functional co-reconstitution of several mammalian complexes into proteoliposomes, in particular, the combination of a primary pump with the ATP synthase, is less well understood. Here, we present a generic and scalable strategy to purify mammalian respiratory complexes I, III and the ATP synthase from enriched mitochondria in enzymatically fully active form, and procedures to reassemble the complexes into liposomes. A robust functionality can be shown by in situ monitoring of ATP synthesis rates and by using selected inhibitors of the respiratory chain complexes. By inclusion of cytochrome c oxidase, our procedures allowed us to reconstruct the entire mitochondrial respiratory chain (complexes I, III, IV, and V) in ubiquinone Q10 containing liposomes, demonstrating oxidative phosphorylation by nicotinamide adenine dinucleotide hydrogen driven ATP synthesis. The system was fully coupled at all levels and was used to probe cardiolipin as an essential component to activate the mammalian respiratory chain. Structural characterization using electron cryomicroscopy allowed us to resolve apo-state complex III and complex V at high and medium resolution, respectively, using in silico particle sorting, confirming the presence of all protein subunits and cofactors in native stoichiometry and conformation. The reported findings will facilitate future endeavors to characterize or modulate these key bioenergetic processes.

Keywords:  artificial ATP production; cryo-EM; mitochondria; oxidative phosphorylation; respiratory chain

DOI:  https://doi.org/10.1073/pnas.2416162122
Sci Adv. 2025 Mar 21. 11(12): eadr1538

Nicotinamide riboside and nicotinamide mononucleotide facilitate NAD+ synthesis via enterohepatic circulation.

Keisuke Yaku, Sailesh Palikhe, Tooba Iqbal, Faisal Hayat, Yoshiyuki Watanabe, Shiho Fujisaka, Hironori Izumi, Tomoyuki Yoshida, Mariam Karim, Hitoshi Uchida, Allah Nawaz, Kazuyuki Tobe, Hisashi Mori, Marie E Migaud, Takashi Nakagawa.

Decreased nicotinamide adenine dinucleotide (oxidized form) (NAD+) levels are reportedly associated with several aging-related disorders. Thus, supplementation with NAD+ precursors, such as nicotinamide mononucleotide (NMN) and nicotinamide riboside (NR), exhibits beneficial effects against these disorders. However, the in vivo metabolic pathways of NMN and NR remain to be elucidated. In this study, we comprehensively analyzed the fate of orally and intravenously administered NMN and NR in mice using NAD+ metabolomics. We found that only a small portion of orally administered NMN and NR was directly absorbed from the small intestine and that most of them underwent gut microbiota-mediated deamidation and conversion to nicotinic acid (NA). Moreover, intravenously administered NMN and NR were rapidly degraded into nicotinamide and secreted to bile followed by deamidation to NA by gut microbiota. Thus, enterohepatic circulated NA is preferentially used in the liver. These findings showed that NMN and NR are indirectly converted to NAD+ via unexpected metabolic pathways.

DOI: https://doi.org/10.1126/sciadv.adr1538
Biochim Biophys Acta Mol Basis Dis. 2025 Mar 19. pii: S0925-4439(25)00148-6. [Epub ahead of print] 167803

Mitochondria: An overview of their origin, genome, architecture, and dynamics.

João P Moura, Paulo J Oliveira, Ana M Urbano.

  Mitochondria are traditionally viewed as the powerhouses of most eukaryotic cells, i.e., the main providers of the metabolic energy required to maintain their viability and function. However, the role of these ubiquitous intracellular organelles far extends energy generation, encompassing a large suite of functions, which they can adjust to changing physiological conditions. These functions rely on a sophisticated membrane system and complex molecular machineries, most of which imported from the cytosol through intricate transport systems. In turn, mitochondrial plasticity is rooted on mitochondrial biogenesis, mitophagy, fusion, fission, and movement. Dealing with all these aspects and terminology can be daunting for newcomers to the field of mitochondria, even for those with a background in biological sciences. The aim of the present educational article, which is part of a special issue entitled "Mitochondria in aging, cancer and cell death", is to present these organelles in a simple and concise way. Complex molecular mechanisms are deliberately omitted, as their inclusion would defeat the stated purpose of the article. Also, considering the wide scope of the article, coverage of each topic is necessarily limited, with the reader directed to excellent reviews, in which the different topics are discussed in greater depth than is possible here. In addition, the multiple cell type-specific genotypic and phenotypic differences between mitochondria are largely ignored, focusing instead on the characteristics shared by most of them, with an emphasis on mitochondria from higher eukaryotes. Also ignored are highly degenerate mitochondrion-related organelles, found in various anaerobic microbial eukaryotes lacking canonical mitochondria.

Keywords:  Educational article; Mitochondrial endosymbiosis; Mitochondrial function; Mitochondrial morphology; Mitochondrial plasticity and dynamics; mtDNA

DOI:  https://doi.org/10.1016/j.bbadis.2025.167803
J Biol Chem. 2025 Mar 18. pii: S0021-9258(25)00270-4. [Epub ahead of print] 108421

Optogenetic tools for inducing organelle membrane rupture.

Yuto Nagashima, Tomoya Eguchi, Ikuko Koyama-Honda, Noboru Mizushima.

  Disintegration of organelle membranes induces various cellular responses and has pathological consequences, including autoinflammatory diseases and neurodegeneration. Establishing methods to induce membrane rupture of specific organelles is essential to analyze the downstream effects of membrane rupture; however, the spatiotemporal induction of organelle membrane rupture remains challenging. Here, we develop a series of optogenetic tools to induce organelle membrane rupture by using engineered Bcl-2-associated X protein (BAX), which primarily functions to form membrane pores in the outer mitochondrial membrane (OMM) during apoptosis. When BAX is forced to target mitochondria, lysosomes, or the endoplasmic reticulum (ER) by replacing its C-terminal transmembrane domain (TMD) with organelle-targeting sequences, the BAX mutants rupture their targeted membranes. To regulate the activity of organelle-targeted BAX, the photosensitive light-oxygen-voltage-sensing 2 (LOV2) domain is fused to the N-terminus of BAX. The resulting LOV2-BAX fusion protein exhibits blue light-dependent membrane-rupture activity on various organelles, including mitochondria, the ER, and lysosomes. Thus, LOV2-BAX enables spatiotemporal induction of membrane rupture across a broad range of organelles, expanding research opportunities on the consequences of organelle membrane disruption.

Keywords:  Bcl-2-associated X protein (BAX); Membrane rupture; light-oxygen-voltage-sensing 2 (LOV2) domain; lysosomal membrane permeabilization (LMP); mitochondrial outer membrane permeabilization (MOMP); optogenetics

DOI:  https://doi.org/10.1016/j.jbc.2025.108421
Transl Pediatr. 2025 Feb 28. 14(2): 367-372

A rare de novo mutation, m.1630A>G, in the mitochondrial tRNAVal (MT-TV) gene in a child with epilepsy: case report and review of the literature.

Qiong Wang, Yan Chen, Jun Li, Baomin Li.

   Background: Mitochondrial diseases represent a diverse group of disorders caused by defects in mitochondrial DNA (mtDNA) or nuclear DNA (nDNA), leading to a wide range of clinical manifestations. These diseases can affect multiple organs, particularly the nervous system, and present with symptoms such as epilepsy, neurodevelopmental delays, and muscular disorders. Over 300 genetic mutations have been linked to these conditions, with clinical heterogeneity being a hallmark of mitochondrial diseases. Early diagnosis and management are crucial, especially in pediatric cases where the disease burden may evolve with age. The aim of this study is to explore the variability in clinical presentation and progression associated with specific genetic mutations, using the case of a rare de novo mutation in the MT-TV gene as an illustrative example, and to discuss the implications for clinical diagnosis.
Case Description: This paper reports on a rare de novo mutation, m.1630A>G, in the MT-TV gene of a 3-year-old boy with epilepsy. In contrast to previously reported cases of the mitochondrial neurogastrointestinal encephalopathy (MNGIE)-like disease/the mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) associated with the m.1630A>G mutation, this patient exhibited an earlier age of onset, simpler clinical manifestations, and lower heterogeneity levels in the blood.
Conclusions: This case offers significant insights into the intricate nature of mitochondrial diseases, especially in pediatric populations. It highlights the critical importance of regular physical examinations and vigilant monitoring for potential multi-system involvement, which are essential for early detection and timely symptomatic intervention to mitigate further damage. Furthermore, this case underscores the necessity to investigate factors influencing clinical penetrance, such as the interplay between mitochondrial and nuclear gene mutations, heterogeneity levels, and age-related accumulation of cellular damage, to better understand disease progression and optimize therapeutic strategies.

Keywords:  MT-TV; Mitochondrial disease; case report; m.1630A>G

DOI:  https://doi.org/10.21037/tp-24-462
Curr Opin Cell Biol. 2025 Mar 20. pii: S0955-0674(25)00031-6. [Epub ahead of print]94 102493

Advances in mitophagy initiation mechanisms.

Catharina Küng, Michael Lazarou, Thanh Ngoc Nguyen.

Mitophagy is an important lysosomal degradative pathway that removes damaged or unwanted mitochondria to maintain cellular and organismal homeostasis. The mechanisms behind how mitophagy is initiated to form autophagosomes around mitochondria have gained a lot of interest since they can be potentially targeted by mitophagy-inducing therapeutics. Mitophagy initiation can be driven by various autophagy receptors or adaptors that respond to different cellular and mitochondrial stimuli, ranging from mitochondrial damage to metabolic rewiring. This review will cover recent advances in our understanding of how mitophagy is initiated, and by doing so reveal the mechanistic plasticity of how autophagosome formation can begin.

DOI: https://doi.org/10.1016/j.ceb.2025.102493
Nucleic Acids Res. 2025 Feb 27. pii: gkaf178. [Epub ahead of print]53(5):

DNA damage response regulator ATR licenses PINK1-mediated mitophagy.

Christian Marx, Xiaobing Qing, Yamin Gong, Joanna Kirkpatrick, Kanstantsin Siniuk, Galina V Beznoussenko, Gururaj Rao Kidiyoor, Murat Kirtay, Katrin Buder, Philipp Koch, Martin Westermann, Christopher Bruhn, Eric J Brown, Xingzhi Xu, Marco Foiani, Zhao-Qi Wang.

Defective DNA damage response (DDR) and mitochondrial dysfunction are a major etiology of tissue impairment and aging. Mitochondrial autophagy (mitophagy) is a mitochondrial quality control (MQC) mechanism to selectively eliminate dysfunctional mitochondria. ATR (ataxia-telangiectasia and Rad3-related) is a key DDR regulator playing a pivotal role in DNA replication stress response and genomic stability. Paradoxically, the human Seckel syndrome caused by ATR mutations exhibits premature aging and neuropathies, suggesting a role of ATR in nonreplicating tissues. Here, we report a previously unknown yet direct role of ATR at mitochondria. We find that ATR and PINK1 (PTEN-induced kinase 1) dock at the mitochondrial translocase TOM/TIM complex, where ATR interacts directly with and thereby stabilizes PINK1. ATR deletion silences mitophagy initiation thereby altering oxidative phosphorylation functionality resulting in reactive oxygen species overproduction that attack cytosolic macromolecules, in both cells and brain tissues, prior to nuclear DNA. This study discloses ATR as an integrated component of the PINK1-mediated MQC program to ensure mitochondrial fitness. Together with its DDR function, ATR safeguards mitochondrial and genomic integrity under physiological and genotoxic conditions.

DOI: https://doi.org/10.1093/nar/gkaf178
Cell Rep. 2025 Mar 13. pii: S2211-1247(25)00201-3. [Epub ahead of print]44(3): 115430

Mitochondrial reactive oxygen species regulate acetyl-CoA flux between cytokine production and fatty acid synthesis in effector T cells.

Beibei Wu, Jin Seok Woo, Spyridon Hasiakos, Calvin Pan, Shawn Cokus, Cristiane Benincá, Linsey Stiles, Zuoming Sun, Matteo Pellegrini, Orian S Shirihai, Aldon J Lusis, Sonal Srikanth, Yousang Gwack.

  Genetic and environmental factors shape an individual's susceptibility to autoimmunity. To identify genetic variations regulating effector T cell functions, we used a forward genetics screen of inbred mouse strains and uncovered genomic loci linked to cytokine expression. Among the candidate genes, we characterized a mitochondrial inner membrane protein, TMEM11, as an important determinant of Th1 responses. Loss of TMEM11 selectively impairs Th1 cell functions, reducing autoimmune symptoms in mice. Mechanistically, Tmem11-/- Th1 cells exhibit altered cristae architecture, impaired respiration, and increased mitochondrial reactive oxygen species (mtROS) production. Elevated mtROS hindered histone acetylation while promoting neutral lipid accumulation. Further experiments using genetic, biochemical, and pharmacological tools revealed that mtROS regulate acetyl-CoA flux between histone acetylation and fatty acid synthesis. Our findings highlight the role of mitochondrial cristae integrity in directing metabolic pathways that influence chromatin modifications and lipid biosynthesis in Th1 cells, providing new insights into immune cell metabolism.

Keywords:  CP: Immunology; CP: Metabolism; EAE; MICOS complex; Th1 cells; cytokine production; histone acetylation; mitochondria; mitochondrial cristae architecture; neutral lipids; reactive oxygen species

DOI:  https://doi.org/10.1016/j.celrep.2025.115430
Cell Death Differ. 2025 Mar 19.

Cryo-EM structure of the brine shrimp mitochondrial ATP synthase suggests an inactivation mechanism for the ATP synthase leak channel.

Amrendra Kumar, Juliana da Fonseca Rezende E Mello, Yangyu Wu, Daniel Morris, Ikram Mezghani, Erin Smith, Stephane Rombauts, Peter Bossier, Juno Krahn, Fred J Sigworth, Nelli Mnatsakanyan.

Mammalian mitochondria undergo Ca2+-induced and cyclosporinA (CsA)-regulated permeability transition (mPT) by activating the mitochondrial permeability transition pore (mPTP) situated in mitochondrial inner membranes. Ca2+-induced prolonged openings of mPTP under certain pathological conditions result in mitochondrial swelling and rupture of the outer membrane, leading to mitochondrial dysfunction and cell death. While the exact molecular composition and structure of mPTP remain unknown, mammalian ATP synthase was reported to form voltage and Ca2+-activated leak channels involved in mPT. Unlike in mammals, mitochondria of the crustacean Artemia franciscana have the ability to accumulate large amounts of Ca2+ without undergoing the mPT. Here, we performed structural and functional analysis of A. franciscana ATP synthase to study the molecular mechanism of mPTP inhibition in this organism. We found that the channel formed by the A. franciscana ATP synthase dwells predominantly in its inactive state and is insensitive to Ca2+, in contrast to porcine heart ATP synthase. Single-particle cryo-electron microscopy (cryo-EM) analysis revealed distinct structural features in A. franciscana ATP synthase compared with mammals. The stronger density of the e-subunit C-terminal region and its enhanced interaction with the c-ring were found in A. franciscana ATP synthase. These data suggest an inactivation mechanism of the ATP synthase leak channel and its possible contribution to the lack of mPT in this organism.

DOI: https://doi.org/10.1038/s41418-025-01476-w
Bone Res. 2025 Mar 17. 13(1): 37

Organelle-tuning condition robustly fabricates energetic mitochondria for cartilage regeneration.

Xuri Chen, Yunting Zhou, Wenyu Yao, Chenlu Gao, Zhuomin Sha, Junzhi Yi, Jiasheng Wang, Xindi Liu, Chenjie Dai, Yi Zhang, Zhonglin Wu, Xudong Yao, Jing Zhou, Hua Liu, Yishan Chen, Hongwei Ouyang.

Mitochondria are vital organelles whose impairment leads to numerous metabolic disorders. Mitochondrial transplantation serves as a promising clinical therapy. However, its widespread application is hindered by the limited availability of healthy mitochondria, with the dose required reaching up to 109 mitochondria per injection/patient. This necessitates sustainable and tractable approaches for producing high-quality human mitochondria. In this study, we demonstrated a highly efficient mitochondria-producing strategy by manipulating mitobiogenesis and tuning organelle balance in human mesenchymal stem cells (MSCs). Utilizing an optimized culture medium (mito-condition) developed from our established formula, we achieved an 854-fold increase in mitochondria production compared to normal MSC culture within 15 days. These mitochondria were not only significantly expanded but also exhibited superior function both before and after isolation, with ATP production levels reaching 5.71 times that of normal mitochondria. Mechanistically, we revealed activation of the AMPK pathway and the establishment of a novel cellular state ideal for mitochondrial fabrication, characterized by enhanced proliferation and mitobiogenesis while suppressing other energy-consuming activities. Furthermore, the in vivo function of these mitochondria was validated in the mitotherapy in a mouse osteoarthritis model, resulting in significant cartilage regeneration over a 12-week period. Overall, this study presented a new strategy for the off-the-shelf fabrication of human mitochondria and provided insights into the molecular mechanisms governing organelle synthesis.

DOI: https://doi.org/10.1038/s41413-025-00411-6
Nat Commun. 2025 Mar 14. 16(1): 2500

Long read sequencing enhances pathogenic and novel variation discovery in patients with rare diseases.

Shruti Sinha, Fatma Rabea, Sathishkumar Ramaswamy, Ikram Chekroun, Maha El Naofal, Ruchi Jain, Roudha Alfalasi, Nour Halabi, Sawsan Yaslam, Massomeh Sheikh Hassani, Shruti Shenbagam, Alan Taylor, Mohammed Uddin, Mohamed A Almarri, Stefan Du Plessis, Alawi Alsheikh-Ali, Ahmad Abou Tayoun.

With ongoing improvements in the detection of complex genomic and epigenomic variations, long-read sequencing (LRS) technologies could serve as a unified platform for clinical genetic testing, particularly in rare disease settings, where nearly half of patients remain undiagnosed using existing technologies. Here, we report a simplified funnel-down filtration strategy aimed at enhancing the identification of small and large deleterious variants as well as abnormal episignature disease profiles from whole-genome LRS data. This approach detected all pathogenic single nucleotide, structural, and methylation variants in a positive control set (N = 76) including an independent sample set with known methylation profiles (N = 57). When applied to patients who previously had negative short-read testing (N = 51), additional diagnoses were uncovered in 10% of cases, including a methylation profile at the spinal muscular atrophy locus utilized for diagnosing this life-threatening, yet treatable, condition. Our study illustrates the utility of LRS in clinical genetic testing and the discovery of novel disease variation.

DOI: https://doi.org/10.1038/s41467-025-57695-9
Mol Cell. 2025 Mar 14. pii: S1097-2765(25)00183-2. [Epub ahead of print]

β-hydroxybutyrate facilitates mitochondrial-derived vesicle biogenesis and improves mitochondrial functions.

Min Tang, Yingfeng Tu, Yanqiu Gong, Qin Yang, Jinrui Wang, Zhenzhen Zhang, Junhong Qin, Shenghui Niu, Jiamin Yi, Zehua Shang, Hongyu Chen, Yingying Tang, Qian Huang, Yanmei Liu, Daniel D Billadeau, Xingguo Liu, Lunzhi Dai, Da Jia.

  Mitochondrial dynamics and metabolites reciprocally influence each other. Mitochondrial-derived vesicles (MDVs) transport damaged mitochondrial components to lysosomes or the extracellular space. While many metabolites are known to modulate mitochondrial dynamics, it is largely unclear whether they are involved in MDV generation. Here, we discovered that the major component of ketone body, β-hydroxybutyrate (BHB), improved mitochondrial functions by facilitating the biogenesis of MDVs. Mechanistically, BHB drove specific lysine β-hydroxybutyrylation (Kbhb) of sorting nexin-9 (SNX9), a key regulator of MDV biogenesis. Kbhb increased SNX9 interaction with inner mitochondrial membrane (IMM)/matrix proteins and promoted the formation of IMM/matrix MDVs. SNX9 Kbhb was not only critical for maintaining mitochondrial homeostasis in cells but also protected mice from alcohol-induced liver injury. Altogether, our research uncovers the fact that metabolites influence the formation of MDVs by directly engaging in post-translational modifications of key protein machineries and establishes a framework for understanding how metabolites regulate mitochondrial functions.

Keywords:  MDV; PTMs; metabolite; mitochondrial functions

DOI:  https://doi.org/10.1016/j.molcel.2025.02.022
BMC Bioinformatics. 2025 Mar 14. 26(1): 82

A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions.

Rohan Gnanaolivu, Gavin Oliver, Garrett Jenkinson, Emily Blake, Wenan Chen, Nicholas Chia, Eric W Klee, Chen Wang.

   BACKGROUND: Diagnosing Mendelian and rare genetic conditions requires identifying phenotype-associated genetic findings and prioritizing likely disease-causing genes. This task is labor-intensive for molecular and clinical geneticists, who must review extensive literature and databases to link patient phenotypes with causal genotypes. The challenge is further complicated by the large number of genetic variants detected through next-generation sequencing, which impacts both diagnosis timelines and patient care strategies. To address this, in silico methods that prioritize causal genes based on patient-derived phenotypes offer an effective solution, reducing the time involved in diagnostic case reviews and enhancing the efficiency of clinical diagnosis.
RESULTS: We developed the phenotype prioritization and analysis for rare diseases (PPAR) to rank genes based on human phenotype ontology (HPO) terms, with the specific goal of aiding the interpretation of genetic testing for Mendelian and rare diseases. PPAR leverages embeddings from a knowledge graph and incorporates knowledge from connections between genes, HPO terms, and gene ontology annotations. When applied on a clinical rare disease cohort and the publicly available deciphering developmental disorders (DDD) dataset. PPAR ranked the causal gene in the top 10 for 27% of cases in the clinical cohort and for 85% of cases in the DDD dataset, outperforming other established HPO-based methods.
CONCLUSION: Our findings demonstrate that PPAR, a method developed from the clinical knowledge graph, effectively ranks causal genes based on patient-derived HPO terms in rare and Mendelian disease contexts. PPAR has shown superior performance compared to other well-established HPO-only methods and provides an efficient, accessible solution for clinical geneticists. The Python-based tool is publicly available at https://github.com/dimi-lab/PPAR , offering a user-friendly platform for gene prioritization.

Keywords:  Gene prioritization; Human Phenotype Ontology; Knowledge graph; Rare disease

DOI:  https://doi.org/10.1186/s12859-025-06096-2
Nat Chem Biol. 2025 Mar 19.

CLYBL averts vitamin B12 depletion by repairing malyl-CoA.

Corey M Griffith, Jean-François Conrotte, Parisa Paydar, Xinqiang Xie, Ursula Heins-Marroquin, Floriane Gavotto, Christian Jäger, Kenneth W Ellens, Carole L Linster.

Citrate lyase beta-like protein (CLYBL) is a ubiquitously expressed mammalian enzyme known for its role in the degradation of itaconate, a bactericidal immunometabolite produced in activated macrophages. The association of CLYBL loss of function with reduced circulating vitamin B12 levels was proposed to result from inhibition of the B12-dependent enzyme methylmalonyl-CoA mutase by itaconyl-CoA. The discrepancy between the highly inducible and locally confined production of itaconate and the broad expression profile of CLYBL across tissues suggested a role for this enzyme beyond itaconate catabolism. Here we discover that CLYBL additionally functions as a metabolite repair enzyme for malyl-CoA, a side product of promiscuous citric acid cycle enzymes. We found that CLYBL knockout cells, accumulating malyl-CoA but not itaconyl-CoA, show decreased levels of adenosylcobalamin and that malyl-CoA is a more potent inhibitor of methylmalonyl-CoA mutase than itaconyl-CoA. Our work thus suggests that malyl-CoA plays a role in the B12 deficiency observed in individuals with CLYBL loss of function.

DOI: https://doi.org/10.1038/s41589-025-01857-9
Contact (Thousand Oaks). 2025 Jan-Dec;8:8 25152564251329250

Mitochondria-Lysosome Contact Sites: Emerging Players in Cellular Homeostasis and Disease.

Francesca Rizzollo, Patrizia Agostinis.

  Mitochondria and lysosomes regulate a multitude of biological processes that are essential for the maintenance of nutrient and metabolic homeostasis and overall cell viability. Recent evidence reveals that these pivotal organelles, similarly to others previously studied, communicate through specialized membrane contact sites (MCSs), hereafter referred to as mitochondria-lysosome contacts (or MLCs), which promote their dynamic interaction without involving membrane fusion. Signal integration through MLCs is implicated in key processes, including mitochondrial fission and dynamics, and the exchange of calcium, cholesterol, and amino acids. Impairments in the formation and function of MLCs are increasingly associated with age-related diseases, specifically neurodegenerative disorders and lysosomal storage diseases. However, MLCs may play roles in other pathological contexts where lysosomes and mitochondria are crucial. In this review, we introduce the methodologies used to study MLCs and discuss known molecular players and key factors involved in their regulation in mammalian cells. We also argue other potential regulatory mechanisms depending on the acidic lysosomal pH and their impact on MLC's function. Finally, we explore the emerging implications of dysfunctional mitochondria-lysosome interactions in disease, highlighting their potential as therapeutic targets in cancer.

Keywords:  lysosome; membrane contact sites; mitochondria; mitochondria-lysosome contacts

DOI:  https://doi.org/10.1177/25152564251329250
Transl Pediatr. 2025 Feb 28. 14(2): 338-349

A novel polyribonucleotide nucleotidyltransferase 1 (PNPT1) gene variant potentially associated with combined oxidative phosphorylation deficiency 13: case report and literature review.

Yan-Yan Li, Yan Gao, Xiong-Xiong Zhong, Guang-Fu Chen.

   Background: Combined oxidative phosphorylation deficiency 13 (COXPD13) results from mutations in the mitochondrial polyribonucleotide nucleotidyltransferase 1 (PNPT1) gene. However, none of COXPD13 is reported in China. This study presents the clinical and molecular genetic features of an infant of Chinese descent identified with a novel PNPT1 mutation, which may be associated with COXPD13.
Case Description: Here, we presented a case of a Chinese boy exhibiting multiple organ damage, white matter changes, epilepsy, abnormalities in muscle tone and strength, global developmental delay, growth retardation, and visual and auditory impairment. The patient also showed elevated lactate levels in the plasma. Furthermore, whole-exome sequencing (WES) revealed a homozygous mutation, c.1033A>G (p.K345E), in the PNPT1 gene. Self-optimized prediction method (SOPMA) and AlphaFold modeling, along with missense 3-dimensional (3D) prediction, indicated that this variant negatively impacted both the secondary and tertiary structures of the PNPT1 protein. The PNPT1 variant may alter the surface electrostatic potential at position 345 from electropositive to electronegative. Additionally, mutant cutoff scanning matrix (mCSM), and daughters, dudes, mothers, and others fighting cancer together (DUET) predicted that the variant disrupted the stability of the protein structure.
Conclusions: The novel PNPT1 gene variant, c.1033A>G (p.K345E), is predicted to disrupt the secondary and tertiary structures of the PNPT1 protein, impairing its normal function. This disruption may lead to mitochondrial RNA processing defects, contributing to the development of COXPD13.

Keywords:  Case report; combined oxidative phosphorylation deficiency 13 (COXPD13); mitochondrial; polyribonucleotide nucleotidyltransferase 1 gene (PNPT1 gene); whole-exome sequencing (WES)

DOI:  https://doi.org/10.21037/tp-24-419
Sci Rep. 2025 Mar 15. 15(1): 9013

Clinical and molecular spectrum of TK2-deficiency: a large Brazilian cohort.

Cristiane Araujo Martins Moreno, Mariana Cunha Artilheiro, Alulin Tacio Quadros Santos Monteiro Fonseca, André Macedo Serafim da Silva, Tatiana Ribeiro Fernandes, Clara Gontijo Camelo, Michelle Abdo Paiva, Filipe Tupinamba di Pace, Andre Luiz Santos Pessoa, Vitor Lucas Lopes Braga, Tamiris Carneiro Mariano, Eduardo de Paula Estephan, Maria da Penha Morita, Anna Paula Paranhos Miranda Covaleski, Vanessa Van der Linden, Pedro José Tomaselli, Giuliano Roberto Scarpellini, Juliana Gurgel-Giannetti, Lívia Maria Ferreira Sobrinho, Thais Martins de Oliveira, Rodrigo Holanda Mendonça, Elizabeth Lemos Silveira Lucas, Marcelo Maroco Cruzeiro, Carlos Wagner Pereira Junior, Wilson Marques Júnior, Claudia Ferreira da Rosa Sobreira, Acary Sousa Bulle Oliveira, Fernando Kok, Michio Hirano, Andres Nascimento-Osorio, David Schlesinger, Edmar Zanoteli.

  Biallelic pathogenic variants at TK2 lead to a severe and progressive myopathy (TK2d). For a disease with unspecific clinical findings, and the possibility of a supplementation therapy that changes the natural history of the disease, highlighting clinical features that increase suspicion and accelerate diagnosis is essential. Clinical and genetic findings of 36 Brazilian patients with TK2d were identified and presented in this work. Genotype-phenotype correlation was performed for recurrent and novel variants. Motor and respiratory assessments were systematically performed in 13 patients, three of them were receiving the nucleosides replacement therapy. Natural history data was gathered from the follow up of five adult patients. Eight patients with the infantile form, 19 with childhood-onset and five with late-onset form were described. Extramuscular features were present in 30% of the cohort. Neuropathy and encephalopathy were the clinically predominant features for some patients. Four variants were recurrent (p.Thr108M, p.His121Asn, p.Arg183Trp and c.536_538 + 8del) allowing genotype-phenotype correlations, and one was novel (G91D). P.Thr108Met patients presented a milder presentation when compared to the p.His121Asn group. P.Arg183Trp was associated with peripheral nerve involvement and c.536_538 + 8del with encephalomyopathy. Long-term follow-up of 5 patients harbouring p.Thr108Met showed decreased motor, bulbar, and respiratory function, compared to a dramatic improvement in the treated patients. TK2d is a very debilitating and progressive disease among all forms including the childhood-onset as we demonstrated. Early diagnosis is essential since a potential treatment can change the natural history of the disease. Extramuscular involvement plays an important role for diagnostic strategies.

Keywords:  Mitochondrial myopathy; MtDNA depletion syndrome; Nucleosides supplementation; TK2-deficiency

DOI:  https://doi.org/10.1038/s41598-024-84373-5
Nat Biotechnol. 2025 Mar;43(3): 290-292

Baby genomics: newborn sequencing starts to fulfill its promise.

Cormac Sheridan.

DOI: https://doi.org/10.1038/s41587-025-02595-y
Nat Genet. 2025 Mar 20.

Reply to: An alternative model for maternal mtDNA inheritance.

William Lee, Angelica Zamudio-Ochoa, Gina Buchel, Petar Podlesniy, Nuria Marti Gutierrez, Aleksei Mikhalchenko, Ramon Trullas, Shoukhrat Mitalipov, Dmitry Temiakov.

DOI: https://doi.org/10.1038/s41588-025-02150-0
Nat Commun. 2025 Mar 15. 16(1): 2560

Axonal RNA localization is essential for long-term memory.

Bruna R de Queiroz, Hiba Laghrissi, Seetha Rajeev, Lauren Blot, Fabienne De Graeve, Marine Dehecq, Martina Hallegger, Ugur Dag, Marion Dunoyer de Segonzac, Mirana Ramialison, Chantal Cazevieille, Krystyna Keleman, Jernej Ule, Arnaud Hubstenberger, Florence Besse.

Localization of mRNAs to neuronal terminals, coupled to local translation, has emerged as a prevalent mechanism controlling the synaptic proteome. However, the physiological regulation and function of this process in the context of mature in vivo memory circuits has remained unclear. Here, we combined synaptosome RNA profiling with whole brain high-resolution imaging to uncover mRNAs with different localization patterns in the axons of Drosophila Mushroom Body memory neurons, some exhibiting regionalized, input-dependent, recruitment along axons. By integrating transcriptome-wide binding approaches and functional assays, we show that the conserved Imp RNA binding protein controls the transport of mRNAs to Mushroom Body axons and characterize a mutant in which this transport is selectively impaired. Using this unique mutant, we demonstrate that axonal mRNA localization is required for long-term, but not short-term, behavioral memory. This work uncovers circuit-dependent mRNA targeting in vivo and demonstrates the importance of local RNA regulation in memory consolidation.

DOI: https://doi.org/10.1038/s41467-025-57651-7
Nature. 2025 Mar 18.

Structures and mechanism of human mitochondrial pyruvate carrier.

Jiaming Liang, Junhui Shi, Ailong Song, Meihua Lu, Kairan Zhang, Meng Xu, Gaoxingyu Huang, Peilong Lu, Xudong Wu, Dan Ma.

Mitochondrial pyruvate carrier (MPC) is a mitochondrial inner membrane protein complex essential for uptake of pyruvate into matrix as the primary carbon source for tricarboxylic acid (TCA) cycle1,2. Here, we report six cryo-EM structures of human MPC in three different states: three structures obtained at different conditions in intermembrane space (IMS)-open state with highest resolution of 3.2 Å, a structure of pyruvate-treated MPC in occluded state at 3.7 Å, and two structures in matrix-facing state bound with the inhibitor UK5099 or an inhibitory nanobody on the matrix side at 3.2 Å and 3.0 Å, respectively. MPC is assigned into a heterodimer consisting of MPC1 and MPC2, with the transmembrane domain adopting pseudo-C2-symmetry. Approximate rigid body movements occur between the IMS-open state and the occluded state, while structural changes primarily on the matrix side facilitate the transition between the occluded state and the matrix-facing state, revealing the alternating access mechanism during pyruvate transport. In the UK5099-bound structure, the inhibitor fits well and interacts extensively with a pocket that opens to the matrix side. Our findings provide important insights into the mechanisms underlying MPC-mediated substrate transport, and the recognition and inhibition by UK5099, which will facilitate future drug development targeting MPC.

DOI: https://doi.org/10.1038/s41586-025-08873-8