bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2025–05–18
forty-nine papers selected by
Catalina Vasilescu, Helmholz Munich



  1. Mol Syndromol. 2025 Apr 01. 1-7
       Introduction: Mitochondrial DNA depletion syndromes encompass rare genetic disorders stemming from various gene defects, including encephalomyopathic mtDNA depletion syndrome 13 (MTDPS13), an autosomal recessive condition linked to FBXL4 gene variants. Although its prevalence is estimated at 1/100,000-400,000, the mechanism behind MTDPS13 remains incompletely understood. Recent studies suggest FBXL4 variants disrupt mitophagy, contributing to its pathogenesis.
    Case Presentation: A 3-year and 4-month-old male presented with respiratory distress, diarrhea, and unconsciousness. His medical history revealed developmental delay and dysmorphic features. Physical examination unveiled characteristic dysmorphisms, while neurological assessment indicated abnormalities. Laboratory findings exhibited metabolic disturbances consistent with MTDPS13, confirmed by genetic analysis revealing a homozygous c.1555C>T FBXL4 variant.
    Conclusion: FBXL4 defects, found in approximately 0.7% of suspected mitochondrial disease cases, lead to varied phenotypes with nonspecific facial dysmorphisms. The patient's presentation aligned with reported features, including growth delay, hypotonia, and developmental delay. Notably, the diagnosis occurred later than typical onset, highlighting the variability in disease manifestation. Treatment focused on symptom management, with dichloroacetic acid effectively addressing lactic acidosis. This case underscores the importance of considering mitochondrial diseases, particularly FBXL4-related MTDPS13, in patients presenting with metabolic disturbances and dysmorphic features. Early recognition facilitates appropriate management and genetic counseling for affected families.
    Keywords:  Growth retardation; Hyperammonemia; Lactic acidosis; Mitochondrial DNA depletion
    DOI:  https://doi.org/10.1159/000545585
  2. J Cell Sci. 2025 May 01. pii: jcs263639. [Epub ahead of print]138(9):
      Mitochondria undergo constant remodeling via fission, fusion, extension and degradation. Fission, in particular, depends on the accumulation of mitochondrial fission factor (MFF) and subsequent recruitment of the dynamin-related protein DRP1 (also known as DNM1L). We used cryo-scanning transmission electron tomography (cryo-STET) to investigate mitochondrial morphologies in MFF mutant (MFF-/-) mouse embryonic fibroblast (MEF) cells in ATP-depleting conditions that normally induce fission. The capability of cryo-STET to image through the cytoplasmic volume to a depth of 1 µm facilitated visualization of intact mitochondria and their surroundings. We imaged changes in mitochondrial morphology and cristae structure, as well as contacts with the endoplasmic reticulum (ER), degradative organelles and the cytoskeleton at stalled fission sites. We found disruption of the outer mitochondrial membrane at contact sites with the ER and degradative organelles at sites of mitophagy. We identified fission sites where the inner mitochondrial membrane is already separated while the outer membrane is still continuous. Although MFF is a general fission factor, these observations demonstrate that mitochondrial fission can proceed to the final stage in its absence. The use of cryo-STET allays concerns about the loss of structures due to sample thinning required for tomography using cryo-transmission electron microscopy.
    Keywords:  Cryo-ET; Cryo-FM; Cryo-STET; Mitochondrial dynamics; Mitochondrial fission; Mitochondrial fission factor
    DOI:  https://doi.org/10.1242/jcs.263639
  3. Int J Mol Sci. 2025 May 05. pii: 4379. [Epub ahead of print]26(9):
      The mitochondrial phosphate carrier (mPiC), encoded by the nuclear gene SLC25A3, is synthesized with an N-terminus mitochondrial targeting sequence (MTS), enabling its import into the mitochondria. mPiC imports inorganic phosphate (Pi) into the mitochondrial matrix for ATP production and other matrix phosphorylation reactions, as well as regulates mitochondrial Ca2+ uptake and buffering of matrix Ca2+. PiC also imports copper (Cu), crucial to COX subunit holoenzyme assembly. Variants in SLC25A3 exist and lead to mPiC deficiency (MPCD), cause a rare autosomal recessive disease with no current cure; patients with MPCD usually die within the first year of life. We have developed a novel therapeutic approach using TAT-mPiC fusion protein for cellular delivery since the TAT peptide enables delivery of proteins across biological membranes. We designed, produced, and purified the TAT-mPiC fusion protein. The fusion protein is delivered into the mitochondria and localizes within the mIM, its natural cellular location, as a processed protein. Treatment of mPiC-knockdown cells with TAT-mPiC fusion protein increased cell growth and improved bioenergetic capabilities, as measured by oxygen consumption rate (OCR), ATP production, and reduction in lactate secretion. Most importantly, TAT-mPiC restored Pi and Cu delivery into the mitochondrial matrix. TAT-mPiC fusion protein also restored the mitochondrial activity of cells harboring various mitochondrial defects. This study presents the first successful delivery of a mitochondrial transmembrane carrier using the TAT-fusion system, offering a potential early treatment strategy for newborns with mPiC deficiency.
    Keywords:  TAT-mediated therapy; mitochondria; mitochondrial phosphate carrier; mitochondrial phosphate carrier deficiency (MPCD); protein replacement treatment
    DOI:  https://doi.org/10.3390/ijms26094379
  4. J Cereb Blood Flow Metab. 2025 May 14. 271678X251338971
      Extracellular vesicles (EVs) facilitate the transfer of biological materials between cells throughout the body. Mitochondria, membrane-bound organelles present in the cytoplasm of nearly all eukaryotic cells, are vital for energy production and cellular homeostasis. Recent studies highlight the critical role of the transport of diverse mitochondrial content, such as mitochondrial DNA (mt-DNA), mitochondrial RNA (mt-RNA), mitochondrial proteins (mt-Prots), and intact mitochondria by small EVs (<200 nm) and large EVs (>200 nm) to recipient cells, where these cargos contribute to cellular and mitochondrial homeostasis. The interplay between EVs and mitochondrial components has significant implications for health, metabolic regulation, and potential as biomarkers. Despite advancements, the mechanisms governing EV-mitochondria crosstalk and the regulatory effect of mitochondrial EVs remain poorly understood. This review explores the roles of EVs and their mitochondrial cargos in health and disease, examines potential mechanisms underlying their interactions, and emphasizes the therapeutic potential of EVs for neurological and systemic conditions associated with mitochondrial dysfunction.
    Keywords:  Extracellular vesicles; energy metabolism; mitochondria; mitochondrial components
    DOI:  https://doi.org/10.1177/0271678X251338971
  5. Nat Rev Mol Cell Biol. 2025 May 14.
      Mitochondria display intricately shaped deep invaginations of the mitochondrial inner membrane (MIM) termed cristae. This peculiar membrane architecture is essential for diverse mitochondrial functions, such as oxidative phosphorylation or the biosynthesis of cellular building blocks. Conserved protein nano-machineries such as F1Fo-ATP synthase oligomers and the mitochondrial contact site and cristae organizing system (MICOS) act as adaptable protein-lipid scaffolds controlling MIM biogenesis and its dynamic remodelling. Signal-dependent rearrangements of cristae architecture and MIM fusion events are governed by the dynamin-like GTPase optic atrophy 1 (OPA1). Recent groundbreaking structural insights into these nano-machineries have considerably advanced our understanding of the functional architecture of mitochondria. In this Review, we discuss how the MIM-shaping machineries cooperate to control cristae and crista junction dynamics, including MIM fusion, in response to cellular signalling pathways. We also explore how mutations affecting MIM-shaping machineries compromise mitochondrial functions.
    DOI:  https://doi.org/10.1038/s41580-025-00854-z
  6. J Cell Sci. 2025 May 15. pii: jcs.263850. [Epub ahead of print]
      Mitochondria are dynamic organelles exhibiting diverse shapes. While the variation of shapes, ranging from spheres to elongated tubules, and the transition between them, are clearly seen in many cell types, the molecular mechanisms governing this morphological variability remain poorly understood. Here, we propose a biophysical model for the shape transition between spheres and tubules based on the interplay between the inner and outer mitochondrial membranes. Our model suggests that the difference in surface area, arising from the folding of the inner membrane into cristae, correlates with mitochondrial elongation. Analysis of live cell super-resolution microscopy data supports this correlation, linking elongated shapes to the extent of cristae in the inner membrane. Knocking down cristae shaping proteins further confirms the impact on mitochondrial shape, demonstrating that defects in cristae formation correlate with mitochondrial sphericity. Our results suggest that the dynamics of the inner mitochondrial membrane are important not only for simply creating surface area required for respiratory capacity, but go beyond that to affect the whole organelle morphology. This work explores the biophysical foundations of individual mitochondrial shape, suggesting potential links between mitochondrial structure and function. This should be of profound significance, particularly in the context of disrupted cristae shaping proteins and their implications in mitochondrial diseases.
    Keywords:  Biophysical model; Cristae; Membrane remodeling; Mitochondrial membranes; Mitochondrial shape; Organelle shape
    DOI:  https://doi.org/10.1242/jcs.263850
  7. J Cell Sci. 2025 May 01. pii: jcs263757. [Epub ahead of print]138(9):
      Mitochondria are metabolic hubs that are essential for cellular homeostasis. Most mitochondrial proteins are translated in the cytosol and imported into the organelle. However, import machineries can become overwhelmed or disrupted by physiological demands, mitochondrial damage or diseases, such as metabolic and neurodegenerative disorders. Impaired import affects mitochondrial function and causes un-imported pre-proteins to accumulate not only in the cytosol but also in other compartments, including the endoplasmic reticulum and nucleus. Quality control pathways have evolved to mitigate the accumulation of these mistargeted proteins and prevent proteotoxicity. In this Cell Science at a Glance article and the accompanying poster, we summarize the fate of un-imported mitochondrial proteins and the compartment-specific quality control pathways that regulate them.
    Keywords:  Mitochondrial protein import; Mitochondrial stress; Protein quality control
    DOI:  https://doi.org/10.1242/jcs.263757
  8. Brain Nerve. 2025 May;77(5): 513-525
      Mitochondrial diseases are hereditary disorders caused by abnormalities in nuclear or mitochondrial genes. These diseases primarily lead to a wide range of symptoms due to impaired ATP production. Even with the same genetic mutation, phenotypic variability poses a significant diagnostic challenge. To date, 400 causative genes have been identified, and with ongoing progress in elucidating their pathophysiology, the development of novel therapeutic approaches, including gene therapy, is rapidly advancing.
    DOI:  https://doi.org/10.11477/mf.188160960770050513
  9. J Cereb Blood Flow Metab. 2025 May 14. 271678X251337630
      Mitochondrial metabolism in neurons is necessary for energetically costly processes like synaptic transmission and plasticity. As post-mitotic cells, neurons are therefore faced with the challenge of maintaining healthy functioning mitochondria throughout lifetime. The precise mechanisms of mitochondrial maintenance in neurons, and particularly in morphologically complex dendrites and axons, are not fully understood. Evidence from several biological systems suggests the regulation of cellular metabolism by extracellular vesicles (EVs), secretory lipid-enclosed vesicles that have emerged as important mediators of cell communication. In the nervous system, neuronal and glial EVs were shown to regulate neuronal circuit development and function, at least in part via the transfer of protein and RNA cargo. Interestingly, EVs have been implicated in diseases characterized by altered metabolism, such as cancer and neurodegenerative diseases. Furthermore, nervous system EVs were shown to contain proteins related to metabolic processes, mitochondrial proteins and even intact mitochondria. Here, we present the current knowledge of the mechanisms underlying neuronal mitochondrial maintenance, and highlight recent evidence suggesting the regulation of synaptic mitochondria by neuronal and glial cell EVs. We further discuss the potential implications of EV-mediated regulation of mitochondrial maintenance and function in neuronal circuit development and synaptic plasticity.
    Keywords:  Exosomes; extracellular vesicles; metabolism; mitochondria; synaptic plasticity
    DOI:  https://doi.org/10.1177/0271678X251337630
  10. Cell Rep. 2025 May 14. pii: S2211-1247(25)00475-9. [Epub ahead of print]44(5): 115704
      Excess dietary sugar profoundly impacts organismal metabolism and health, yet it remains unclear how metabolic adaptations in adipose tissue influence other organs, including the brain. Here, we show that a high-sugar diet (HSD) in Drosophila reduces adipocyte glycolysis and mitochondrial pyruvate uptake, shifting metabolism toward fatty acid oxidation and ketogenesis. These metabolic changes trigger mitochondrial oxidation and elevate antioxidant responses. Adipocyte-specific manipulations of glycolysis, lipid metabolism, or mitochondrial dynamics non-autonomously modulate Draper expression in brain ensheathing glia, key cells responsible for neuronal debris clearance. Adipocyte-derived ApoB-containing lipoproteins maintain basal Draper levels in glia via LpR1, critical for effective glial phagocytic activity. Accordingly, reducing ApoB or LpR1 impairs glial clearance of degenerating neuronal debris after injury. Collectively, our findings demonstrate that dietary sugar-induced shifts in adipocyte metabolism substantially influence brain health by modulating glial phagocytosis, identifying adipocyte-derived ApoB lipoproteins as essential systemic mediators linking metabolic state with neuroprotective functions.
    Keywords:  ApoB; CP: Metabolism; CP: Neuroscience; Drosophila; OxPhos; adipokine; glycolysis; high-sugar diet; injury-response; ketogenesis; lipid metabolism; mitochondria; neurodegeneration; pyronic sensor
    DOI:  https://doi.org/10.1016/j.celrep.2025.115704
  11. Trends Cell Biol. 2025 May 13. pii: S0962-8924(25)00105-9. [Epub ahead of print]
      Mitochondria play a vital role in cellular energy metabolism and vascular health, with their function directly influencing endothelial cell (EC) bioenergetics and integrity. Mitochondrial transfer has emerged as a key mechanism of intercellular communication, impacting angiogenesis, tissue repair, and cellular homeostasis. This review highlights recent findings on mitochondrial transfer, including natural mechanisms - such as tunneling nanotubes (TNTs) and extracellular vesicles (EVs) - and artificial approaches like mitochondrial transplantation. These processes enhance EC function and support vascularization under pathological conditions, including ischemia. While early clinical trials demonstrate therapeutic potential, challenges such as mitochondrial instability and scaling host-derived mitochondria persist. Continued research is essential to optimize mitochondrial transfer and advance its application as a therapeutic strategy for restoring vascular health.
    Keywords:  angiogenesis; endothelial cells; mitochondrial transfer; mitochondrial transplantation; vascular regeneration
    DOI:  https://doi.org/10.1016/j.tcb.2025.04.004
  12. Eur J Hum Genet. 2025 May 13.
      Mitochondrial ribosomal protein-small 2 (MRPS2) encodes a vital structural protein essential for assembling mitoribosomal small subunit and thus mitochondrial translation. Any defect in mitochondrial translation impacts OXPHOS activity and cellular respiration. Defects in MRPS2 have been implicated recently in four families with combined oxidative phosphorylation deficiency-36 (MIM# 617950). We herein describe two individuals from two unrelated families with variable phenotypes of acute onset severe metabolic decompensation and symptomatic hypoglycemia. Exome sequencing identified bi-allelic variants in MRPS2 (NM_016034.5) in the affected individuals: P1: c.490 G > A p.(Glu164Lys); and P2: c.413 G > A p.(Arg138His). Further evaluation of the variant c.490 G > A p.(Glu164Lys) in patient-derived skin fibroblasts revealed decreased expression of MRPS2 transcript and protein levels of MRPS2 along with expression of complex I and IV proteins. Proteomics analysis revealed decreased expression of small subunit proteins and increased expression of large subunit proteins. Also, reduced complex I and IV enzyme activities, mitochondrial respiration (OCR), and altered mitochondrial morphology on confocal imaging were observed. Additionally, mrps2 knockout zebrafish larvae demonstrated an abnormal developmental phenotype and reduced Complex IV activity. With these findings, we identify additional families with variants in MRPS2, illustrating the variable clinical spectrum and validate the pathogenicity of defects in MRPS2 through in-vitro and in-vivo assays.
    DOI:  https://doi.org/10.1038/s41431-025-01858-1
  13. J Cell Biol. 2025 Jul 07. pii: e202408166. [Epub ahead of print]224(7):
      BNIP3 and NIX are the main receptors for mitophagy, but their mechanisms of action remain elusive. Here, we used correlative light EM (CLEM) and electron tomography to reveal the tight attachment of isolation membranes (IMs) to mitochondrial protrusions, often connected with ER via thin tubular and/or linear structures. In BNIP3/NIX-double knockout (DKO) HeLa cells, the ULK1 complex and nascent IM formed on mitochondria, but the IM did not expand. Artificial tethering of LC3B to mitochondria induced mitophagy that was equally efficient in DKO cells and WT cells. BNIP3 and NIX accumulated at the segregated mitochondrial protrusions via binding with LC3 through their LIR motifs but did not require dimer formation. Finally, the average distance between the IM and the mitochondrial surface in receptor-mediated mitophagy was significantly smaller than that in ubiquitin-mediated mitophagy. Collectively, these results indicate that BNIP3 and NIX are required for the tight attachment and expansion of the IM along the mitochondrial surface during mitophagy.
    DOI:  https://doi.org/10.1083/jcb.202408166
  14. Stem Cell Res. 2025 May 08. pii: S1873-5061(25)00082-0. [Epub ahead of print]86 103732
      iPSC-based models are valuable for studying the mechanisms and potential treatments of mitochondrial disorders. We generated two iPSC lines from fibroblasts of a patient with a novel MT-ATP6/8 mutation (m.8570 T > C). The infant was diagnosed with a mitochondrial disease featuring cardiac hypertrophy, brain atrophy, developmental delay, and metabolic crises with elevated lactate. Mutation heteroplasmy in blood leukocytes was 95 %. Leigh syndrome-like cranial MRI abnormalities were absent at 4 months of age. We introduced reprogramming factors by Sendai virus and assessed the pluripotency of the resulting iPSCs. As control iPSC-line, we characterized the CRMi004-A line from the RUCDR repository.
    DOI:  https://doi.org/10.1016/j.scr.2025.103732
  15. Proc Natl Acad Sci U S A. 2025 May 20. 122(20): e2426179122
      Mitochondrial energy metabolism is vital for muscle function and is tightly controlled at the transcriptional level, both in the basal state and during adaptive muscle remodeling. The importance of the transcription factors estrogen-related receptors (ERRs) in controlling innate mitochondrial energetics has been recently demonstrated. However, whether different ERR isoforms display distinct functions in glycolytic versus oxidative myofibers is largely unknown. Moreover, their roles in regulating exercise-induced adaptive mitochondrial biogenesis remain unclear. Using muscle-specific single and combinatorial knockout mouse models, we have identified both cooperative and distinct roles of the ERR isoforms ERRα and ERRγ in regulating mitochondrial energy metabolism in different muscles. We demonstrate the essential roles of both these ERRs in mediating adaptive mitochondrial biogenesis in response to exercise training. We further show that PGC1α-induced mitochondrial biogenesis is completely abolished in primary myotubes with ERRα deletion but not ERRγ, highlighting distinct roles of these two isoforms in adaptive mitochondrial remodeling. Mechanistically, we find that both ERRs directly bind to the majority of mitochondrial energetic genes and control their expression, largely through collaborative binding to the same genomic loci. Collectively, our findings reveal critical and direct regulatory roles of ERRα and ERRγ in governing both innate and adaptive mitochondrial energetics in skeletal muscle.
    Keywords:  PGC1; energy metabolism; estrogen-related receptor; mitochondria; muscle
    DOI:  https://doi.org/10.1073/pnas.2426179122
  16. Nat Cell Biol. 2025 May;27(5): 847-862
      MPC1 and MPC2 are two well-known components of the mitochondrial pyruvate carrier (MPC) complex maintaining MPC activity to transport pyruvate into mitochondria for tricarboxylic acid (TCA) cycle entry in mammalian cells. It is currently unknown whether there is an additional MPC component crucially maintaining MPC complex activity for pyruvate mitochondrial import. Here we show that ALDH4A1, a proline-metabolizing enzyme localized in mitochondria, serves as a previously unrecognized MPC component maintaining pyruvate mitochondrial import and the TCA cycle independently of its enzymatic activity. Loss of ALDH4A1 in mammalian cells impairs pyruvate entry to mitochondria, resulting in defective TCA cycle entry. ALDH4A1 forms an active trimeric complex with MPC1-MPC2 to maintain the integrity and oligomerization of MPC1-MPC2 and facilitates pyruvate transport in an in vitro system. ALDH4A1 displays tumour suppression by maintaining MPC complex activity. Our study identifies ALDH4A1 as an essential component of MPC for pyruvate mitochondrial import, TCA cycle entry and tumour suppression.
    DOI:  https://doi.org/10.1038/s41556-025-01651-8
  17. Front Immunol. 2025 ;16 1572927
       Introduction: Neutrophils are highly abundant innate immune cells that are constantly produced from myeloid progenitors in the bone marrow. Differentiated neutrophils can perform an arsenal of effector functions critical for host defense. This study aims to quantitatively understand neutrophil mitochondrial metabolism throughout differentiation and activation, and to elucidate the impact of mitochondrial metabolism on neutrophil functions.
    Methods: To study metabolic remodeling throughout neutrophil differentiation, murine ER-Hoxb8 myeloid progenitor-derived neutrophils and human induced pluripotent stem cell-derived neutrophils were assessed as models. To study the metabolic remodeling upon neutrophil activation, differentiated ER-Hoxb8 neutrophils and primary human neutrophils were activated with various stimuli, including ionomycin, monosodium urate crystals, and phorbol 12-myristate 13-acetate. Characterization of cellular metabolism by isotopic tracing, extracellular flux analysis, metabolomics, and fluorescence-lifetime imaging microscopy revealed dynamic changes in mitochondrial metabolism.
    Results: As neutrophils mature, mitochondrial metabolism decreases drastically, energy production is offloaded from oxidative phosphorylation, and glucose oxidation through the TCA cycle is substantially reduced. Nonetheless, mature neutrophils retain the capacity for mitochondrial metabolism. Upon stimulation with certain stimuli, TCA cycle is rapidly activated. Mitochondrial pyruvate carrier inhibitors reduce this re-activation of the TCA cycle and inhibit the release of neutrophil extracellular traps. Treatment with these inhibitors also impacts neutrophil redox status, migration, and apoptosis without significantly changing overall bioenergetics.
    Conclusions: Together, these results demonstrate that mitochondrial metabolism is dynamically remodeled and plays a significant role in neutrophils. Furthermore, these findings point to the therapeutic potential of mitochondrial pyruvate carrier inhibitors in a range of conditions where dysregulated neutrophil response drives inflammation and contributes to pathology.
    Keywords:  TCA cycle; metabolism; mitochondria; neutrophil; neutrophil extracellular traps
    DOI:  https://doi.org/10.3389/fimmu.2025.1572927
  18. BMJ Neurol Open. 2025 ;7(1): e000990
      Genetic myopathies are caused by pathogenic variants in >300 genes across the nuclear and mitochondrial genomes. Although short-read next-generation sequencing (NGS) has revolutionised the diagnosis of genetic disorders, large and/or complex genetic variants, which are over-represented in the genetic myopathies, are not well characterised using this approach. Long-read sequencing (LRS) is a newer genetic testing technology that overcomes many of the limitations of NGS. In particular, LRS provides improved detection of challenging variant types, including short tandem repeat (STR) expansions, copy number variants and structural variants, as well as improved variant phasing and concurrent assessment of epigenetic changes, including DNA methylation. The ability to concurrently detect multiple STR expansions is particularly relevant given the growing number of recently described genetic myopathies associated with STR expansions. LRS will also aid in the identification of new myopathy genes and molecular mechanisms. However, use of LRS technology is currently limited by high cost, low accessibility, the need for specialised DNA extraction procedures, limited availability of LRS bioinformatic tools and pipelines, and the relative lack of healthy control LRS variant databases. Once these barriers are addressed, the implementation of LRS into clinical diagnostic pipelines will undoubtedly streamline the diagnostic algorithm and increase the diagnostic rate for genetic myopathies. In this review, we discuss the utility and critical impact of LRS in this field.
    Keywords:  GENETICS; MUSCLE DISEASE; MUSCULAR DYSTROPHY; MYOPATHY; NEUROGENETICS
    DOI:  https://doi.org/10.1136/bmjno-2024-000990
  19. J Cell Sci. 2025 May 01. pii: jcs263895. [Epub ahead of print]138(9):
      Mitochondrial contact sites are specialized interfaces where mitochondria physically interact with other organelles. Stabilized by molecular tethers and defined by unique proteomic and lipidomic profiles, these sites enable direct interorganellar communication and functional coordination, playing crucial roles in cellular physiology and homeostasis. Recent advances have expanded our knowledge of contact site-resident proteins, illuminated the dynamic and adaptive nature of these interfaces, and clarified their contribution to pathophysiology. In this Cell Science at a Glance article and the accompanying poster, we summarize the mitochondrial contacts that have been characterized in mammals, the molecular mechanisms underlying their formation, and their principal functions.
    Keywords:  Contact sites; Mitochondria; Organelles
    DOI:  https://doi.org/10.1242/jcs.263895
  20. J Cereb Blood Flow Metab. 2025 May 14. 271678X251340232
      Mitochondrial transplantation is an emerging therapeutic approach for ischemia-reperfusion injury, offering the potential to restore cellular function through the engraftment of extracellular mitochondria. The successful clinical application of this strategy depends on the delivery of metabolically active mitochondria, yet the impact of circulating therapeutic agents on mitochondrial viability remains poorly understood. This study evaluates the effects of five clinically relevant agents commonly used during endovascular treatment of ischemic stroke-alteplase, cefazolin, lidocaine, phenylephrine, and heparinized saline-on extracellular mitochondria using an ex vivo model. Mitochondria were isolated from human skeletal muscle and mouse liver and exposed to these agents at clinically relevant and supra-physiological concentrations. Metabolic activity was assessed using a resazurin reduction assay as an indicator of mitochondrial viability. Even at concentrations up to 8-fold above clinical exposure, none of the agents significantly impaired mitochondrial function. These findings provide critical toxicological data demonstrating the compatibility of commonly used therapeutics with mitochondrial transplantation, supporting the development of safer and more optimized clinical protocols.
    Keywords:  Drug toxicity; extracellular mitochondria; ischemia-reperfusion injury; mitochondrial transplantation; mitochondrial viability
    DOI:  https://doi.org/10.1177/0271678X251340232
  21. Pediatr Nephrol. 2025 May 14.
       BACKGROUND: Renal tubular dysgenesis (RTD) is a severe kidney disease characterized by poor development of proximal tubules and persistent fetal anuria leading to oligohydramnios. It can be acquired during fetal life or inherited as an autosomal recessive disease associated with bi-allelic pathogenic variants in one of the genes encoding the renin-angiotensin system (RAS) components, AGT, REN, ACE, or AGTR1. Few cases of RTD remain unsolved despite the lack of fetal cause and comprehensive screening of RAS genes.
    METHODS: We investigated a case of unsolved RTD with low renin expression by whole genome sequencing, and then screened a series of unsolved RTD by sequencing of a targeted gene panel of genes coding mitochondrial proteins. Oxidative phosphorylation complexes were studied by SDS-PAGE and immunoblotting.
    RESULTS: We identified a rare homozygous variant in RMND1, a gene known to be responsible for an autosomal recessive mitochondrial disease, in a case presenting with RTD-like phenotype with low renin expression but without identified RAS disease-causing variant. We demonstrate a severe reduction of combined oxidative phosphorylation complexes I and IV subunits in this case. Next, we identified another RMND1 homozygous variant in another unsolved RTD case belonging to a consanguineous family with recurrent fetal demise.
    CONCLUSIONS: Our study shows that biallelic RMND1 pathogenic variants likely cause severe prenatal kidney disease presenting with RTD-like phenotype, and prompts to screen RMND1 in unelucidated severe fetal nephropathies to provide diagnosis and, ultimately, genetic counselling. In addition, these data confirm a still poorly understood link between RMND1-associated mitochondrial dysfunction and renin expression.
    Keywords:   RMND1 ; Mitochondria; Renal tubular dysgenesis; Renin
    DOI:  https://doi.org/10.1007/s00467-025-06787-1
  22. Aging Cell. 2025 May 12. e70096
      Sex differences in Parkinson's disease (PD) offer insights into mechanisms of dopaminergic cell resilience. Female dopamine (DA) neurons are more resilient via mechanisms that remain unclear. Here, we discovered key sex and regional differences in mitochondrial generation of cytotoxic reactive oxygen species (ROS) and their implications for DA neuron resilience using the Drosophila model. While aging raised mitochondrial ROS in DA neurons of both sexes, we observed a sexually dimorphic response in the paraquat (PQ) PD model. DA neuron knockdown of the Drosophila vesicular glutamate transporter (dVGLUT) increased mitochondrial ROS only in males, leaving females protected. Cell depolarization, a physiological stressor, similarly raised mitochondrial ROS in DA neurons selectively in males following dVGLUT knockdown. We also identified dVGLUT-dependent changes in intracellular ATP in both sexes. Overall, we discovered sexually dimorphic relationships between dVGLUT, ATP synthesis, and ROS generation in DA neurons, providing a mechanistic basis for DA neuron resilience.
    Keywords:   Drosophila ; Parkinson's disease; aging; dVGLUT; dopamine; glutamate; mitochondria; reactive oxygen species
    DOI:  https://doi.org/10.1111/acel.70096
  23. Cells. 2025 Apr 25. pii: 638. [Epub ahead of print]14(9):
      Inherited metabolic disorders (IMDs) are genetic disorders that occur in as many as 1:2500 births worldwide. Nevertheless, they are quite rare individually and even more rare is the co-occurrence of two IMDs in one individual. To better understand the metabolic cross-talk between glycosylation changes and deficient energy metabolism, and its potential effect on outcomes, we evaluated patient fibroblasts with likely pathogenic variants in PGM1 and pathogenic variants in NDUFA13 derived from a patient who passed away at 16 years of age. The patient presented with characteristic of PGM1-CDG including bifid uvula, muscle involvement, abnormal glycosylation in blood, and elevated liver transaminases. In addition, hearing loss, seizures, elevated plasma and CSF lactate and a Leigh-like MRI brain pattern were present, which are commonly associated with Leigh syndrome. PGM1-CDG has been reported in about 70 individuals, while NDUFA13 deficiency has so far only been reported in 13 patients. As abundant energy is essential for glycosylation, and both PGM1 and NDUFA13 are linked to energy metabolism, we sought to better understand the underlying biochemical cause of the patient's clinical presentation. To do so, we performed extensive investigations including tracer metabolomics, lipidomics and enzymatic studies on the patient's fibroblasts. We found a profound depletion of UDP-hexoses, consistent with PGM1-CDG. Complex I enzyme activity and mitochondrial function were also impaired, corroborating complex I deficiency and Leigh syndrome. Further, lipidomics analysis showed similarities with both PGM1-CDG and OXPHOS-deficient patients. Based on our results, the patient was diagnosed with both PGM1-CDG and Leigh syndrome. In summary, we present the first case of combined CDG and Leigh syndrome, caused by (likely) pathogenic variants in PGM1 and NDUFA13, and underline the importance of considering the synergistic effects of multiple disease-causing variants in patients with complex clinical presentation, leading to the patient's early demise.
    Keywords:  Leigh syndrome; NDUFA13; PGM1; congenital disorder of glycosylation; inborn errors of metabolism; metabolomics
    DOI:  https://doi.org/10.3390/cells14090638
  24. MedComm (2020). 2025 May;6(5): e70214
      Mitochondrial homeostasis is essential for cell survival and function, necessitating quality control mechanisms to ensure a healthy mitochondrial network. Death-associated protein 3 (DAP3) serves as a subunit of the mitochondrial ribosome, playing a pivotal role in the translation of mitochondrial-encoded proteins. Apart from its involvement in protein synthesis, DAP3 has been implicated in the process of cell death and mitochondrial dynamics. In this study, we demonstrate that DAP3 mediates cell death via intrinsic apoptosis by triggering excessive mitochondrial fragmentation, loss of mitochondrial membrane potential (ΔΨm), ATP decline, and oxidative stress. Notably, DAP3 induces mitochondrial fragmentation through the Mitochondrial Rho GTPase 1 (Miro1), independently of the canonical fusion/fission machinery. Mechanistically, DAP3 promotes mitochondrial calcium accumulation through the MCU complex, leading to decreased cytosolic Ca2+ levels. This reduction in cytosolic Ca2+ is sensed by Miro1, which subsequently drives mitochondrial fragmentation. Depletion of Miro1 or MCU alleviates mitochondrial fragmentation, oxidative stress, and cell death. Collectively, our findings reveal a novel function of the mitoribosomal protein DAP3 in regulating calcium signalling and maintaining mitochondrial homeostasis.
    Keywords:  calcium; cell death; death‐associated protein 3; mitochondrial dynamics; reactive oxygen species
    DOI:  https://doi.org/10.1002/mco2.70214
  25. Front Immunol. 2025 ;16 1542369
      Mitochondria, as the primary energy factories of cells, play a pivotal role in maintaining nervous system function and regulating inflammatory responses. The balance of mitochondrial quality control is critical for neuronal health, and disruptions in this balance are often implicated in the pathogenesis of various neurological disorders. Mitochondrial dysfunction not only exacerbates energy deficits but also triggers neuroinflammation through the release of damage-associated molecular patterns (DAMPs), such as mitochondrial DNA (mtDNA) and reactive oxygen species (ROS). This review examines the mechanisms and recent advancements in mitochondrial quality control in neurological diseases, focusing on processes such as mitochondrial fusion and fission, mitophagy, biogenesis, and protein expression regulation. It further explores the role of mitochondrial dysfunction and subsequent inflammatory cascades in conditions such as ischemic and hemorrhagic stroke, neurodegenerative diseases and brain tumors. Additionally, emerging research highlights the significance of mitochondrial transfer mechanisms, particularly intercellular transfer between neurons and glial cells, as a potential strategy for mitigating inflammation and promoting cellular repair. This review provides insights into the molecular underpinnings of neuroinflammatory pathologies while underscoring the translational potential of targeting mitochondrial quality control for therapeutic development.
    Keywords:  mitochondrial; mitochondrial quality control; mitochondrial transfer; neuroinflammation; neurological disorders
    DOI:  https://doi.org/10.3389/fimmu.2025.1542369
  26. Nat Commun. 2025 May 12. 16(1): 4374
      Alterations in mitochondrial metabolism in obesity may indicate disrupted communication between mitochondria and nucleus, and DNA methylation may influence this interplay. Here, we leverage data from the Finnish Twin Cohort study subcohort (n = 173; 86 full twin pairs, 1 singleton), including comprehensive measurements of obesity-related outcomes, mitochondrial DNA quantity and nuclear DNA methylation levels in adipose and muscle tissue, to identify one CpG at SH3BP4 significantly associated with mitochondrial DNA quantity in adipose tissue (FDR < 0.05). We also show that SH3BP4 methylation correlates with its gene expression. Additionally, we find that 14 out of the 35 obesity-related traits display significant associations with both SH3BP4 methylation and mitochondrial DNA quantity in adipose tissue. We use data from TwinsUK and the Scandinavian T2D-discordant monozygotic twin cohort, to validate the observed associations. Further analysis using ICE FALCON suggests that mitochondrial DNA quantity, insulin sensitivity and certain body fat measures are causal to SH3BP4 methylation. Examining mitochondrial DNA quantity and obesity-related traits suggests causation from mitochondrial DNA quantity to obesity, but unmeasured within-individual confounding cannot be ruled out. Our findings underscore the impact of mitochondrial DNA quantity on DNA methylation and expression of the SH3BP4 gene within adipose tissue, with potential implications for obesity.
    DOI:  https://doi.org/10.1038/s41467-025-59576-7
  27. Front Genet. 2025 ;16 1539288
      F-box and leucine-rich repeat protein 4 (FBXL4) plays a crucial role in mitochondrial bioenergetics, mitochondrial DNA (mtDNA) maintenance, and mitochondrial dynamics. The variations in the FBXL4 gene can give rise to encephalomyopathy mitochondrial DNA depletion syndrome-13 (MTDPS13) characterized by the reduction of mtDNA copy number, leading to deficiencies in mitochondrial functions, which is a serious and rare autosomal recessive genetic disorder. Patients with FBXL4 variations are usually diagnosed due to the emergence of symptoms in the early stages of life. Commonly observed are lactic acidemia, developmental retardation, and hypotonia. A portion of patients may be accompanied by comorbidities such as cardiovascular diseases, epilepsy, ophthalmopathy, hearing impairment, and movement disorders. Currently, there have been no reported cases of prenatal diagnosis for FBXL4 gene variations. Here, we report for the first time the prenatal diagnosis of a fetus with a compound heterozygous mutation in the FBXL4 gene (NM_012160.5: c.1288C>T, p. Arg430* and c.518_523del, p. Glu173_Leu175delinsVal) by trio-WES, the nonsense mutation (c.1288C>T) was reported only once in an unrelated individual and no detailed clinical phenotype; the deletion mutation (c.518_523del) has not been reported yet. Additionally, we monitor prenatal phenotypes of fetus at different stages of pregnancy using ultrasound and magnetic resonance imaging (MRI), present prenatally with nuchal translucency (NT) thickening and progressive brain developmental abnormalities. Our report indicates that the application of trio whole exome sequencing (trio-WES) and imaging monitoring can facilitate prenatal diagnosis of FBXL4 gene-related MTDPS13, and this will modify the decision-making process for couples with FBXL4 variations.
    Keywords:  FBXL4; MTDPS13; NT thickening; prenatal diagnosis; trio-WES
    DOI:  https://doi.org/10.3389/fgene.2025.1539288
  28. Methods Mol Biol. 2025 ;2920 173-202
      Cells require energy in the form of ATP to function. The two main ways in which cells generate energy in mammalian cells is through glycolysis and oxidative phosphorylation (OXPHOS). Glycolysis takes place in the cytosol and involves the breakdown of glucose molecules, generating ATP and pyruvate, while OXPHOS takes place in the mitochondria and is responsible for producing the majority of ATP for the cell. A dysregulation of these cellular processes has been reported in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). In order to understand the mechanisms of the disease, it is imperative to understand how the bioenergetic pathways are altered in ME/CFS. Here we describe a method for measuring mitochondrial function and glycolytic function using the Agilent Seahorse Extracellular Flux Analyzer. We have optimized these assays for use in actively proliferating lymphoblastoid cell lines that are generated from blood cells. This assay measures oxygen consumption rate and extracellular acidification rates providing an overview of mitochondrial function and efficiency and glycolytic rate and capacity, respectively. These assays are performed on live, intact cells, and enable us to view different components and measurements of energy metabolism through the injection of different compounds that stimulate or inhibit various sections of these pathways. The below method details an optimized glycolysis and mitochondrial assay for 96-well plates with modifications noted for use in 24-well plates.
    Keywords:  Agilent seahorse XF analyzer; Glycolysis; Lymphoblastoid cell lines; Mitochondria; Myalgic encephalomyelitis/chronic fatigue syndrome
    DOI:  https://doi.org/10.1007/978-1-0716-4498-0_11
  29. Sci Rep. 2025 May 14. 15(1): 16715
      Mitochondrial heterogeneity drives diverse cellular responses in neurodegenerative diseases, complicating the evaluation of mitochondrial dysfunction. In this study, we describe a high-throughput imaging and analysis approach to investigate cell-to-cell mitochondrial variability. We applied known mitochondrial function inhibitors - rotenone, antimycin, and oligomycin to inhibit complexes I, III, and V (ATP synthase) function in human induced pluripotent stem cell-derived cortical neurons, a model commonly used in neurodegenerative disease research. We captured a large number of cell images and extracted a diverse range of mitochondrial morphological features related to shape, size, texture, and spatial distribution, for an unbiased and comprehensive analysis of mitochondrial morphology. Group-level cell analysis, which examines the collective responses of cells exposed to the same mitochondrial inhibitor, showed that cells treated with rotenone, antimycin, or oligomycin clustered together based on their shared morphological changes. Rotenone and antimycin, both targeting different complexes of the electron transport chain, formed sub-clusters within a larger cluster. In contrast, oligomycin, which inhibits ATP synthase, resulted in a distinct cluster likely due to its differing effect on ATP production. Single-cell analysis using dimensionality reduction techniques revealed distinct subpopulations of cells with varying degrees of sensitivity to each mitochondrial inhibitor, identifying the most affected cells. Mitochondrial feature differential expression analysis showed that neurite-related mitochondrial features, such as intensity and size, were more severely impacted than cell body-related mitochondrial features, particularly with rotenone and antimycin, which target the electron transport chain. In contrast, oligomycin which affects ATP synthesis by directly inhibiting ATP synthase showed relatively less severe alterations in neurite-related mitochondrial features, highlighting a distinct effect of the mode of action between inhibitors. By incorporating the most affected cells into machine learning models, we significantly improved the prediction accuracy of mitochondrial dysfunction outcomes - 81.97% for antimycin, 75.12% for rotenone, and 94.42% for oligomycin. This enhancement underscores the value of targeting highly responsive cell subpopulations, offering a more precise method for evaluating mitochondrial modulators and therapeutic interventions in neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s41598-025-99972-z
  30. J Cereb Blood Flow Metab. 2025 May 15. 271678X251341293
      Neurological disorders, including brain cancer, neurodegenerative diseases and ischemic/reperfusion injury, pose a significant threat to global human health. Due to the high metabolic demands of nerve cells, mitochondrial dysfunction is a critical feature of these disorders. The mitochondrial unfolded protein response (UPRmt) is an evolutionarily conserved mitochondrial response, which is critical for maintaining mitochondrial and energetic homeostasis under stress. Previous studies have found that UPRmt participates in diverse physiological processes especially metabolism and immunity. Currently, increasing evidence suggest that targeted regulation of UPRmt can also effectively delay the progression of neurological diseases and improve patients' prognosis. This review provides a comprehensive overview of UPRmt in the context of neurological diseases, with a particular emphasis on its regulatory functions. Additionally, we summarize the mechanistic insights into UPRmt in neurological disorders as investigated in preclinical studies, as well as its potential as a therapeutic target in the clinical management of neurological tumors. By highlighting the importance of UPRmt in the complex processes underlying neurological disorders, this review aims to bridge current knowledge gaps and inspire novel therapeutic strategies for these conditions.
    Keywords:  Mitochondria; aging; neurological disorders; therapy; unfolded protein response
    DOI:  https://doi.org/10.1177/0271678X251341293
  31. Eur Heart J. 2025 May 13. pii: ehaf319. [Epub ahead of print]
      
    Keywords:  Cardiac magnetic resonance imaging; Heart failure; Hypertrophic cardiomyopathy; Implantable cardioverter defibrillator; Late gadolinium enhancement; Mitochondria; Myocarditis; Sudden cardiac death
    DOI:  https://doi.org/10.1093/eurheartj/ehaf319
  32. Sci Rep. 2025 May 14. 15(1): 16678
      Mitochondrial defects can lead to cardiomyopathies, which can be particularly severe in children. However, many cases of pediatric cardiomyopathy have no known etiology. To address this, we sought to explore if mitochondrial genome defects might be a contributor, as this could offer insights into disease mechanisms and guide targeted interventions. We first sequenced cardiomyopathy-related genes in twenty-seven pediatric patients diagnosed with primary non-syndromic cardiomyopathy and performed whole mtDNA sequencing in both patients and thirty-one healthy controls. The initial sequencing identified pathogenic variants in seven patients but subsequent mtDNA sequencing revealed additional insights. Specifically, a variant in FOXRED1, encoding FAD-dependent oxidoreductase domain-containing protein-1 which functions in mitochondrial complex I stability, and another variant in cytochrome c oxidase-I, MT-CO1, crucial for aerobic metabolism, were identified in two siblings with hypertrophic cardiomyopathy. In another case with hypertrophic cardiomyopathy, a variant in cytochrome b, MT-CYB, is likely a key factor in the abnormal contraction of cardiac muscle contraction. Furthermore, a novel 12 S rRNA variant was found in a patient with left ventricular non-compaction, and this offers a promising explanation for the pathogenesis, given the gene's high expression in the left ventricle. Taken together, mtDNA variants act synergistically with others, potentially disrupting myocardial bioenergetics.
    DOI:  https://doi.org/10.1038/s41598-025-01007-0
  33. Int J Mol Sci. 2025 May 07. pii: 4451. [Epub ahead of print]26(9):
      Mitochondrial dysfunction is a hallmark of Parkinson's disease (PD) pathogenesis, contributing to increased oxidative stress and impaired endo-lysosomal-proteasome system efficiency underlying neuronal injury. Genetic studies have identified 19 monogenic mutations-accounting for ~10% of PD cases-that affect mitochondrial function and are associated with early- or late-onset PD. Early-onset forms typically involve genes encoding proteins essential for mitochondrial quality control, including mitophagy and structural maintenance, while late-onset mutations impair mitochondrial dynamics, bioenergetics, and trafficking. Atypical juvenile genetic syndromes also exhibit mitochondrial abnormalities. In idiopathic PD, environmental neurotoxins such as pesticides and MPTP act as mitochondrial inhibitors, disrupting complex I activity and increasing reactive oxygen species. These converging pathways underscore mitochondria as a central node in PD pathology. This review explores the overlapping and distinct mitochondrial mechanisms in genetic and non-genetic PD, emphasizing their role in neuronal vulnerability. Targeting mitochondrial dysfunction finally offers a promising therapeutic avenue to slow or modify disease progression by intervening at a key point of neurodegenerative convergence.
    Keywords:  Parkinson’s disease; genetic PD; mitochondrial dysfunction; neurotoxins; oxidative stress
    DOI:  https://doi.org/10.3390/ijms26094451
  34. Nat Methods. 2025 May 13.
      The subcellular localization of a protein is important for its function, and its mislocalization is linked to numerous diseases. Existing datasets capture limited pairs of proteins and cell lines, and existing protein localization prediction models either miss cell-type specificity or cannot generalize to unseen proteins. Here we present a method for Prediction of Unseen Proteins' Subcellular localization (PUPS). PUPS combines a protein language model and an image inpainting model to utilize both protein sequence and cellular images. We demonstrate that the protein sequence input enables generalization to unseen proteins, and the cellular image input captures single-cell variability, enabling cell-type-specific predictions. Experimental validation shows that PUPS can predict protein localization in newly performed experiments outside the Human Protein Atlas used for training. Collectively, PUPS provides a framework for predicting differential protein localization across cell lines and single cells within a cell line, including changes in protein localization driven by mutations.
    DOI:  https://doi.org/10.1038/s41592-025-02696-1
  35. BMC Biol. 2025 May 13. 23(1): 129
       BACKGROUND: The information content within nucleic acids extends beyond the primary sequence to include secondary structures with functional roles in transcription regulation. Guanine-rich sequences form structures called guanine quadruplexes that result from non-canonical base pairing between guanine residues. These stable guanine quadruplex structures are prevalent in gene promoters in nuclear DNA and are known to be associated with promoter proximal pausing of some genes. However, the transcriptional impact of guanine quadruplexes that form in nascent RNA is poorly understood.
    RESULTS: We examined mitochondrial RNA polymerase (POLRMT) pausing patterns in primary human skin fibroblast cells using the precision nuclear run-on assay and uncovered over 400 pause sites on the mitochondrial genome. We identified that these pauses frequently occur following guanine-rich sequences where quadruplexes form. Using an in vitro primer extension assay, we show that quadruplexes formed in nascent RNA act as mediators of POLRMT pausing, and in cell-based assays their stabilization disrupts POLRMT transcription. Cells exposed to a guanine-quadruplex stabilizing agent (RHPS4) had diminished mitochondrial gene expression and significantly lowered cellular respiration within 24 h. The resulting ATP stress was sufficient to reduce active transport in renal epithelia.
    CONCLUSIONS: Our findings connect RNA guanine quadruplex-mediated pausing with the regulation of POLRMT transcription and mitochondrial function. We demonstrate that tuning of quadruplex dynamics in nascent RNA, rather than template DNA upstream of the polymerase, is sufficient to regulate mitochondrial gene expression.
    Keywords:  Guanine quadruplex; Mitochondria; Proximal tubule; RNA polymerase pausing; Transcription
    DOI:  https://doi.org/10.1186/s12915-025-02229-4
  36. Int J Biol Macromol. 2025 May 13. pii: S0141-8130(25)04695-1. [Epub ahead of print] 144143
      Mitochondria play a crucial role in cellular energy production, signaling and homeostasis. Respiratory supercomplexes represent evolutionary well-conserved, stable associations between membrane complexes and molecules, including proteins and lipids, within the inner mitochondrial membrane. They dynamically respond to metabolic demands and enhance the electron transfer rate, thereby reducing the production of ROS. Recent research has unveiled cytochrome c, a mobile electron carrier between complexes III and IV, as a potential key player in orchestrating the formation of these supra-associations. This study centers on elucidating the role of cytochrome c in modulating the assembly of supercomplexes, using the Saccharomyces cerevisiae yeast as a model system for mitochondrial metabolism. BN-PAGE and mass spectrometry-based proteomic analysis were employed to examine supercomplex organization in yeast strains expressing different cytochrome c isoforms, grown under fermentative and respiratory conditions. Our results demonstrate that both isoforms of cytochrome c contribute to supercomplex assembly, with isoform-2 significantly improving electron transfer and lowering ROS levels. We propose a model in which cytochrome c acts as a scaffold for the recruitment of assembly factors, facilitating the formation of higher order supercomplexes such as III2IV2. This model highlights cytochrome c's role beyond electron transfer, as it regulates supercomplex assembly and mitochondrial homeostasis.
    Keywords:  Cytochrome c; Electron transport chain; Mitochondria; Respiratory supercomplexes; Saccharomyces cerevisiae
    DOI:  https://doi.org/10.1016/j.ijbiomac.2025.144143
  37. Ann Clin Transl Neurol. 2025 May 14.
       OBJECTIVE: Recently, a mitochondrial encephalopathy due to biallelic HPDL variants was described, associated with a broad range of clinical manifestations ranging from severe, infantile-onset neurodegeneration to adolescence-onset hereditary spastic paraplegia. HPDL converts 4-hydroxyphenylpyruvate acid (4-HPPA) into 4-hydroxymandelate (4-HMA), necessary for the synthesis of the mitochondrial electron transporter CoQ10. This suggests a possible bypass of the metabolic block by 4-HMA treatment; however, genotype-phenotype correlations are lacking.
    METHODS: We established an HPDL Patient Registry to prepare for a future clinical trial. Here we report the clinical features of 13 enrolled participants and compare them with 86 previously reported patients. We establish three major clinical classes: severe, intermediate, and mild, presenting onset in early infancy, childhood, and adolescence, respectively. The biallelic genotypes were classified into truncating/truncating, truncating/missense, and missense/missense variants, mapped onto the predicted 3D protein structure, and correlated with severity.
    RESULTS: Patients with biallelic truncating variants presented with severe phenotypes and earlier ages of onset. Missense variants were often associated with milder phenotypes, except those with variants predominantly located in or near the VOC2 domain containing iron-binding sites or the C-terminus, which had more severe phenotypes. In addition, p.Met1? variants were also correlated with more severe phenotypes.
    INTERPRETATION: This study demonstrates the correlation of age of onset and disease severity with genotype for HPDL-related conditions. Patients with truncating variants and specific missense variants correlated with severe, early-onset features, whereas the presence of at least one missense variant located outside of the iron-binding sites correlated with milder presentations.
    TRIAL REGISTRATION: Clinicaltrials.gov HPDL registry: https://clinicaltrials.gov/study/NCT05848271.
    Keywords:  4‐hydroxyphenylpyruvate dioxygenase‐like protein; HPDL; encephalopathy; hereditary spastic paraplegia; mitochondria
    DOI:  https://doi.org/10.1002/acn3.70047
  38. Front Genet. 2025 ;16 1555563
      Mitochondria are membrane-bound cell organelles that undertake the majority of the energetic and metabolic processes within the cell. They are also responsible for mediating multiple apoptotic pathways, balancing redox charges, and scavenging reactive oxygen species. MicroRNAs, which are short, non-coding RNAs widely known for regulating gene expression at the post-transcriptional level, regulate many of these processes. The specific microRNAs that directly or indirectly control mitochondrial dynamics are called mitochondrial miRNAs (mitomiRs). The broadest classification of this type of ncRNA encompasses nuclear-encoded miRNAs that interact with cytoplasmatic mRNAs associated with mitochondrial activity. At the same time, a more specific subset comprises nuclear-encoded miRNAs that translocate into the mitochondria to interact with mRNAs inside of this organelle. Finally, the smallest group of mitomiRs includes those codified by mtDNA and can regulate endogenous mitochondrial transcripts or be transported into the cytoplasm to modulate circulating mRNAs. Regardless of the origin or action mechanism, mitomiRs have been recently recognized to have a key role in the progression of a variety of chronic disorders, such as neurodegenerative and cardiovascular diseases, diabetes, asthma, depression, and even cancer. All of these progressive pathologies have been tightly linked to mitochondrial dysregulation. They are further associated with an aberrant expression of specific miRNAs that regulate cellular metabolism, positioning mitomiRs as reliable biomarkers for diagnosing several chronic diseases. These molecular indicators have also provided insights into how these conditions progress, allowing for the development of different miRNA-based treatment strategies that target dysregulated mitochondrial-related genes, reestablishing their baseline activity and restricting further disease progression.
    Keywords:  biomarkers; chronic diseases; gene regulation; micrornas; mitochondria; mitomirs; therapeutics
    DOI:  https://doi.org/10.3389/fgene.2025.1555563
  39. Ren Fail. 2025 Dec;47(1): 2501204
      COQ8B nephropathy, a mitochondrial disorder caused by mutations in the COQ8B gene, is a major pediatric genetic focal segmental glomerulosclerosis (GFSGS) etiology and stands out as one of the few treatable forms with good response to coenzyme Q10 (CoQ10) supplementation. As the diagnosis and clinical experience of COQ8B nephropathy were predominantly in the pediatric population, the long-term efficacy of CoQ10 supplementation and its application in the adult-onset patients remains largely unknown. Here, we report three cases of adult-onset FSGS from unrelated families, all carrying the Chinese common COQ8B mutation (c.737G > A; p.Ser246Asn) with divergent trajectories of renal function following CoQ10 supplementation initiated in different stages of renal dysfunction, providing valuable evidence on the implication of early disease diagnosis and prompt CoQ10 supplementation for the prognosis of adult patients affected with COQ8B nephropathy.
    Keywords:  COQ8B; Focal segmental glomerulosclerosis; coenzyme Q10; podocyte
    DOI:  https://doi.org/10.1080/0886022X.2025.2501204
  40. mBio. 2025 May 15. e0078325
      The majority of heterotrophic unicellular eukaryotes have evolved mechanisms to survive periods of starvation, allowing them to endure until conditions are favorable for regrowth. The ciliate Tetrahymena exhibits active swimming behavior in water, preying on microorganisms and growing exponentially at a rate of 0.5-0.75 h⁻¹ under optimal conditions. In this organism, numerous mitochondria localize to the cell cortex along the ciliary rows, likely ensuring an efficient ATP supply necessary for vigorous cell movement. Although mitochondrial reduction occurs immediately under starvation, the underlying mechanism remains unknown. Here, we demonstrated that autophagy is responsible for mitochondrial reduction in Tetrahymena thermophila. Among the five T. thermophila ATG8 homologs, TtATG8A and TtATG8B formed granule- and cup-shaped structures in response to starvation. Fluorescent microscopy further showed that TtATG8A and TtATG8B associate with mitochondria. Moreover, correlative light and electron microscopy analysis revealed that mitochondria colocalized with TtATG8A or TtATG8B were engulfed by autophagosomes and displayed abnormal appearances with disrupted cristae structures. Additionally, repression of TtATG8A or TtATG8B expression significantly attenuated starvation-induced mitochondrial reduction. These findings suggest that TtATG8A- and TtATG8B-mediated autophagy is a key mechanism underlying mitochondrial reduction in starved T. thermophila.
    IMPORTANCE: This study is the first comprehensive description of the mitochondrial degradation process under nutrient starvation in the ciliate Tetrahymena. It is well known that the cell surface structure of ciliates consists of an elaborate spatial arrangement of microtubule networks and associated structures and that this surface repetitive pattern is inherited by the next generation of cells like genetic information. Our findings provide a basis for understanding how ciliates maintain an adequate amount of mitochondria on the cell surface in response to nutritional conditions. Furthermore, we have successfully demonstrated the usefulness of Tetrahymena as an experimental system for studying mitochondrial quality control and turnover. Further studies of Tetrahymena will facilitate comparative studies among diverse biological systems on how eukaryotes other than opisthokonta (yeast, cultured cells, etc.) control their mitochondria.
    Keywords:  ATG8; Tetrahymena; autophagy; mitochondria
    DOI:  https://doi.org/10.1128/mbio.00783-25
  41. Nat Commun. 2025 May 14. 16(1): 4411
      FAN1 is a DNA dependent nuclease whose proper function is essential for maintaining human health. For example, a genetic variant in FAN1, Arg507 to His hastens onset of Huntington's disease, a repeat expansion disorder for which there is no cure. How the Arg507His mutation affects FAN1 structure and enzymatic function is unknown. Using cryo-EM and biochemistry, we have discovered that FAN1 arginine 507 is critical for its interaction with PCNA, and mutation of Arg507 to His attenuates assembly of the FAN1-PCNA complex on a disease-relevant extrahelical DNA extrusions formed within DNA repeats. This mutation concomitantly abolishes PCNA-FAN1-dependent cleavage of such extrusions, thus unraveling the molecular basis for a specific mutation in FAN1 that dramatically hastens the onset of Huntington's disease. These results underscore the importance of PCNA to the genome stabilizing function of FAN1.
    DOI:  https://doi.org/10.1038/s41467-025-59323-y
  42. Nat Metab. 2025 May 13.
      Adipose tissue (AT) is a complex connective tissue with a high relative proportion of adipocytes, which are specialized cells with the ability to store lipids in large droplets. AT is found in multiple discrete depots throughout the body, where it serves as the primary repository for excess calories. In addition, AT has an important role in functions as diverse as insulation, immunity and regulation of metabolic homeostasis. The Human Cell Atlas Adipose Bionetwork was established to support the generation of single-cell atlases of human AT as well as the development of unified approaches and consensus for cell annotation. Here, we provide a first roadmap from this bionetwork, including our suggested cell annotations for humans and mice, with the aim of describing the state of the field and providing guidelines for the production, analysis, interpretation and presentation of AT single-cell data.
    DOI:  https://doi.org/10.1038/s42255-025-01296-9
  43. FEBS Open Bio. 2025 May 16.
      The mitochondrial translation system contains two ribosome rescue factors, ICT1 and MTRFR (C12orf65), which hydrolyze peptidyl-tRNA in stalled ribosomes. ICT1 also functions as a ribosomal protein of the mitochondrial large ribosomal subunit (mtLSU) in mice and humans, and its deletion is lethal. In contrast, MTRFR does not share this role. Although loss-of-function mutations in MTRFR have been linked to human mitochondrial diseases, data on this association in other vertebrates are lacking. Here, attempts to generate Mtrfr knockout mice were unsuccessful. However, knockout zebrafish lines were successfully generated for both ict1 and mtrfr (ict1-/- and mtrfr-/-). Both knockout lines appeared healthy and fertile. ict1-/-, mtrfr-/-, and wild-type adult caudal fin cells showed significant differences in mitochondrial morphology. The ict1 deletion affected the network properties more than the number of individuals and networks, whereas the mtrfr deletion exhibited the opposite effect. Additionally, the survival rates of the knockout line larvae were significantly lower than those of the wild-type larvae under starvation conditions. These results suggest that ict1 and mtrfr are required for survival under specific stress conditions, whereas ict1-/- and mtrfr-/- involve different compensatory mechanisms in response to loss of either factor under nonstress conditions. Ict1 proteins from all teleosts, including zebrafish, lack the N-terminal mtLSU-binding motif found in most metazoans, suggesting that Ict1 does not function as a ribosomal protein in teleosts. Thus, Mtrfr may partially compensate for the loss of Ict1. In conclusion, zebrafish appear to exemplify a limited category of vertebrates capable of enduring genetic abnormalities in ict1 or mtrfr.
    Keywords:  COXPD7; mice; mitochondrial morphology; mitochondrial ribosome rescue; the YSLDK motif; zebrafish
    DOI:  https://doi.org/10.1002/2211-5463.70054
  44. N Engl J Med. 2025 May 15.
      Base editors can correct disease-causing genetic variants. After a neonate had received a diagnosis of severe carbamoyl-phosphate synthetase 1 deficiency, a disease with an estimated 50% mortality in early infancy, we immediately began to develop a customized lipid nanoparticle-delivered base-editing therapy. After regulatory approval had been obtained for the therapy, the patient received two infusions at approximately 7 and 8 months of age. In the 7 weeks after the initial infusion, the patient was able to receive an increased amount of dietary protein and a reduced dose of a nitrogen-scavenger medication to half the starting dose, without unacceptable adverse events and despite viral illnesses. No serious adverse events occurred. Longer follow-up is warranted to assess safety and efficacy. (Funded by the National Institutes of Health and others.).
    DOI:  https://doi.org/10.1056/NEJMoa2504747
  45. Nature. 2025 May;641(8063): 809-812
      
    Keywords:  Brain; Developmental biology; Neuroscience; Technology
    DOI:  https://doi.org/10.1038/d41586-025-01468-3
  46. Front Cell Dev Biol. 2025 ;13 1604307
      
    Keywords:  autophagy; metabolism; mitophagy; neurodegenerative diseases; neurons
    DOI:  https://doi.org/10.3389/fcell.2025.1604307
  47. Epigenomics. 2025 May 10. 1-12
      Early and accurate diagnosis significantly improves the chances of disease survival. DNA methylation (5mC), the major DNA modification in the human genome, is now recognized as a biomarker of immense clinical potential. This is due to its ability to delineate precisely cell-type, quantitate both internal and external exposures, as well as tracking chronological and biological components of the aging process. Here, we survey the current state of DNA methylation as a biomarker and predictor of traits and disease. This includes Epigenome-wide association study (EWAS) findings that inform Methylation Risk Scores (MRS), EpiScore long-term estimators of plasma protein levels, and machine learning (ML) derived DNA methylation clocks. These all highlight the significant benefits of accessible peripheral blood DNA methylation as a surrogate measure. However, detailed DNA methylation biopsy analysis in real-time is also empowering pathological diagnosis. Furthermore, moving forward, in this multi-omic and biobank scale era, novel insights will be enabled by the amplified power of increasing sample sizes and data integration.
    Keywords:  DNA methylation; EWAS; Epigenetics; biological ageing; epigenetic clocks; epigenetic estimators; epigenomics; methylation risk scores
    DOI:  https://doi.org/10.1080/17501911.2025.2500907