bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2025–11–02
fifty papers selected by
Catalina Vasilescu, Helmholz Munich



  1. Acta Neurol Belg. 2025 Oct 31.
      Mitochondrial DNA (mtDNA) maintenance defects (specifically mtDNA depletion syndromes, MDS) are autosomal recessive disorders caused by a severe reduction in mtDNA content, leading to impaired oxidative phosphorylation and energy deficiency in affected tissues. The clinical heterogeneity of mtDNA maintenance defects correlates with specific gene mutations, with POLG being one of the most frequently implicated genes in mitochondrial dysfunction. We report a novel case of mtDNA maintenance defects manifesting with progressive ocular symptoms, including blepharoptosis, blurred vision, and diplopia, associated with a rare homozygous POLG mutation (c.924G > T, p.Gln308His), which is the second reported homozygous variant at this nucleotide site. Among five previously reported POLG c.924G > T-associated MDS cases, 4 are heterozygous (compound heterozygous or combined with other mitochondrial gene variants). POLG encodes DNA polymerase γ, essential for mtDNA replication; mutations impair mitochondrial function, reducing respiratory chain activity and ATP production. This case adds to the existing literature on the phenotypic variability of POLG-related disorders and expands the known spectrum of pathogenic POLG variants. Despite the rarity of this mutation, its clinical presentation is consistent with classic progressive external ophthalmoplegia (PEO), underscoring the importance of genetic testing in diagnosing mtDNA maintenance defects. Further studies are needed to clarify genotype-phenotype correlations and develop targeted therapeutic strategies for POLG-associated mitochondrial dysfunction.
    Keywords:  DNA polymerase; Mitochondrial DNA (mtDNA) maintenance defects; Progressive external ophthalmoplegia (PEO); The POLG gene
    DOI:  https://doi.org/10.1007/s13760-025-02922-9
  2. Mitochondrion. 2025 Oct 29. pii: S1567-7249(25)00090-X. [Epub ahead of print] 102093
      The recent development of mitochondrial base editors (mitoBEs) has ushered in a transformational time that has overcome some long-standing limitations in the field of mitochondrial genetics. By closely tracing mitoBE development from the earliest tool mitochondria targeted TALENs to the most recent base editing systems that can precisely convert C•G → T•A and A•T → G•C, we review mitoBEs. We describe the development of recent advancements in mitoBEs including the generation of second generation mitoBEs (mitoBEs v2), which have evidence to identify over 70 mouse mtDNA mutations comparable to human pathogenic variants. Notably, in order to incorporate circular RNA (circRNA) as a delivery vector the editing efficiency has been increased by over 82 %, without experimental evidence of off-target effects. Taking advantage of these gains in technology, these mouse models of mitochondrial diseases, including those associated with Leigh syndrome and LHN, are highly faithful. These models have also confirmed that these specific mtDNA variants have pathological phenotypic evaluations, and have compared to previous editing strategies, mitoBEs v2 have demonstrated improved specificity, stability and safety. We finally discuss the future of mitochondrial base editing and outline the ways it will move forward towards therapeutic potentials in the treatment of the mitochondrial disorders and also in precision medicine.
    Keywords:  ABE; CBE; Mitochondrial diseases; TALED; circRNA; mitoBEs; mtDNA
    DOI:  https://doi.org/10.1016/j.mito.2025.102093
  3. Nat Commun. 2025 Oct 27. 16(1): 9448
      Mitochondria transfer is a spontaneous process that releases functional mitochondria to damaged cells via different mechanisms including extracellular vesicle containing mitochondria (EV-Mito) to restore mitochondrial functions. However, the limited EV-Mito yield makes it challenging to supply a sufficient quantity of functional mitochondria to damaged cells, hindering their application in mitochondrial diseases. Here, we show that the release of EV-Mito from mesenchymal stem cells (MSCs) is regulated by a calcium-dependent mechanism involving CD38 and IP3R signaling (CD38/IP3R/Ca2+ pathway). Activating this pathway through our non-viral gene engineering approach generates super donor MSCs which produce Super-EV-Mito with a threefold increase in yield compared to Ctrl-EV-Mito from normal MSCs. Leber's hereditary optic neuropathy (LHON), a classic mitochondrial disease caused by mtDNA mutations, is used as a proof-of-concept model. Super-EV-Mito rescues mtDNA defects and alleviates LHON-associated symptoms in LHON male mice. This strategy offers a promising avenue for enhancing mitochondria transfer efficiency and advancing its clinical application in mitochondrial disorders.
    DOI:  https://doi.org/10.1038/s41467-025-64486-9
  4. Genes Dev. 2025 Oct 29.
      Mitochondria play a crucial role in cellular energy metabolism and homeostasis and are strongly implicated in aging and age-related diseases. The outer mitochondrial membrane protein voltage-dependent anion channel (VDAC) plays multiple roles in mitochondrial homeostasis, including transport of metabolites, ATP, and Ca2+ Dysregulation of VDAC levels has been associated with cancer, neurodegeneration, metabolic disorders, and aging. Previously, we demonstrated that elevated VDAC-1 levels in Caenorhabditis elegans lead to increased mitochondrial permeability and reduced life span. Here we demonstrate that reduced VDAC-1 function extends life span through the activation of the mitochondrial unfolded protein response (UPRmt), a conserved stress response that maintains mitochondrial proteostasis and is linked to life span extension in multiple species. Leveraging unbiased genomic discovery, we identified genes encoding several proteins in the PeBoW complex as a critical mediator of UPRmt activation following VDAC-1 loss. More broadly, we demonstrated a universal requirement for several PeBoW component genes across diverse mitochondrial stressors in order to fully animate the UPRmt Our findings reveal a heretofore unappreciated role for PeBoW components in UPRmt induction and life span extension in response to mitochondrial stress, highlighting its essential function in mitochondrial quality control and longevity pathways.
    Keywords:  PeBoW; mito-stress; mitoUPR; mitochondria
    DOI:  https://doi.org/10.1101/gad.352979.125
  5. Nat Cell Biol. 2025 Oct 31.
      The mitochondrial proteome is remodelled to meet metabolic demands, but how metabolic cues regulate mitochondrial protein turnover remains unclear. Here we identify a conserved, nutrient-responsive mechanism in which the amino acid leucine suppresses ubiquitin-dependent degradation of outer mitochondrial membrane (OMM) proteins, stabilizing key components of the protein import machinery and expanding the mitochondrial proteome to enhance metabolic respiration. Leucine inhibits the amino acid sensor GCN2, which selectively reduces the E3 ubiquitin ligase cofactor SEL1L at mitochondria. Depletion of SEL1L phenocopies the effect of leucine, elevating OMM protein abundance and mitochondrial respiration. Disease-associated defects in leucine catabolism and OMM protein turnover impair fertility in Caenorhabditis elegans and render human lung cancer cells resistant to inhibition of mitochondrial protein import. These findings define a leucine-GCN2-SEL1L axis that links nutrient sensing to mitochondrial proteostasis, with implications for metabolic disorders and cancer.
    DOI:  https://doi.org/10.1038/s41556-025-01799-3
  6. J Biol Chem. 2025 Oct 27. pii: S0021-9258(25)02712-7. [Epub ahead of print] 110860
      Nuclear-encoded mitochondrial proteins rely on N-terminal targeting sequences (N-MTS) for their import. Most N-MTSs are cleaved in the matrix by the mitochondrial processing peptidase (MPP), a heterodimeric metalloprotease composed of (α) and catalytic (β) subunits, essential for the maturation of imported proteins. Import and processing of PINK1, a kinase implicated in Parkinson's disease, govern its ability to sense mitochondrial damage. The current paradigm suggests PINK1 undergoes two sequential processing steps: first, MPP removes the PINK1 N-MTS in the matrix; second, the inner mitochondrial membrane protease PARL cleaves the PINK1 transmembrane domain, leading to PINK1 degradation. Upon depolarization, PINK1 escapes proteolysis and accumulates on mitochondria to initiate mitophagy. However, the MPP cleavage site on PINK1, the role of MPP in PINK1 signalling, and the mechanisms of substrate recognition by human MPP remain unclear. Here, we define the MPP cleavage site on PINK1 between Ala28-Tyr29 and show it is inefficiently processed compared to canonical N-MTSs. In cells, MPP cleavage is dispensable for both PARL processing and PINK1 function, decoupling PINK1 import and damage sensing from its N-MTS removal. However, in vitro, the PINK1 N-MTS binds potently to MPP, inhibits the cleavage of other substrates, and traps MPP in a slowly processing complex. Exploiting PINK1 as a mechanistic probe, we use hydrogen-deuterium exchange mass spectrometry to map the PINK1 binding site on MPPα. We identify a two-step mechanism involving MPPα lid rearrangement followed by active site engagement, providing key insight into PINK1's unique import pathway and fundamental MPP processing mechanisms.
    Keywords:  PTEN-induced putative kinase 1 (PINK1); Parkinson disease; hydrogen-deuterium exchange; mitochondria; mitochondrial processing peptidase (MPP); protein import; protein processing
    DOI:  https://doi.org/10.1016/j.jbc.2025.110860
  7. Front Cell Dev Biol. 2025 ;13 1677402
       Introduction: Mitochondria are integral components of eukaryotic cells, functioning as energy powerhouses and key mediators of diverse metabolic and signaling cascades. As endosymbiotic remnants, these unique organelles retain and express their own DNA. Mitochondrial DNA (mtDNA) is packaged into DNA-protein complexes called nucleoids, and is also subject to epigenetic modification. We identified a mitochondrial isoform of DNA methyltransferase 1 (mtDNMT1) that binds to mtDNA in critical control regions; however, its enzymatic activity remained unexplored.
    Results: Here, we show that endogenously-tagged mtDNMT1 purified from mitochondria exhibits time- and concentration-dependent CpG-specific DNA methyltransferase activity, but it is not working alone: DNMT3b cooperates with mtDNMT1 to methylate mtDNA and regulate mitochondrial transcription. In addition, we detect ten-eleven translocase (TET)-like hydroxymethylase activity in mitochondria, demonstrating that mechanisms for both writing and erasing 5-methylcytosine marks are functional in this organelle. CRISPR/Cas9-mediated inactivation of mtDNMT1 and/or DNMT3b activity resulted in a stepwise decrease in mitochondrial methylation across the heavy and light strand promoters of mtDNA, with a significant reduction in transcription of several mtDNA-encoded OXPHOS genes. Interestingly, the effects of mtDNA methylation on mitochondrial transcription are diametrically opposed to the role of promoter methylation in the nucleus, suggesting a novel mode of gene regulation in mitochondria. Cells lacking mtDNMT1 and/or DNMT3b also exhibited a modest reduction in mtDNA content, suggesting that methylation impacts both mtDNA transcription and replication.
    Discussion: These observations implicate mtDNA methylation in the fine-tuning of mitochondrial function and suggest a role for aberrant mitochondrial methylase activity in disease.
    Keywords:  DNA demethylation; DNA methylation; DNA methyltransferase; DNA replication; epigenetics; mitochondrial DNA (mtDNA); transcription
    DOI:  https://doi.org/10.3389/fcell.2025.1677402
  8. Anal Biochem. 2025 Oct 29. pii: S0003-2697(25)00243-X. [Epub ahead of print] 116004
      We present an optimised luminometric method for measuring muscle mitochondrial ATP production rate (MAPR), adapted to a 96-well microplate format. The enhanced assay enables quantification of ATP production from 12 or more substrate combinations within 15 minutes, using only 10 μL of isolated mitochondria. The method demonstrates high accuracy and precision, with a validated measurement range of 0.3-70 nmol/min/L. To support clinical interpretation, a reference dataset was established from 92 individuals aged seven months to 79 years. All these individuals were referred for muscle biopsy but were subsequently deemed unlikely to have a mitochondrial disorder following comprehensive clinical evaluation. An overview of the current version of our assays for oxidative phosphorylation (OXPHOS) enzymes is also provided. As proof of concept, we present three patients carrying pathogenic variants in mitochondrial DNA (ATP6 and MT-TL1) and the nuclear PDHA1 gene. All exhibited decreased MAPR with one or more substrates, along with additional clinical, biochemical, and morphological features consistent with mitochondrial disease. Furthermore, we illustrate the age-dependent development of MAPR in muscle across the human lifespan, demonstrating a 60-80% higher maximal capacity for oxidative ATP production in adults compared with young children. In contrast, MAPR supported by fatty acid-derived substrates remains unchanged over the same period. In conclusion, the improved MAPR assay offers a robust and efficient tool for assessing mitochondrial function in both clinical diagnostics and research. Its high-throughput format and reliable performance make it particularly well-suited for the investigation of suspected mitochondrial disorders.
    Keywords:  ATP; luciferase; mitochondria; muscle; oxidative phosphorylation; pyruvate
    DOI:  https://doi.org/10.1016/j.ab.2025.116004
  9. Protein Sci. 2025 Nov;34(11): e70357
      Uncoupling Protein 1 (UCP1) is a mitochondrial protein which drives thermogenesis in brown adipose tissue. UCP1 facilitates the dissipation of the proton gradient as heat and plays a critical role in energy expenditure and metabolic regulation. We employ advanced molecular simulations and mutagenesis to reveal the mechanism of UCP1-mediated proton and fatty acid (FA) transport. We demonstrate that FAs bind spontaneously to UCP1's central substrate-binding site. In the binding site, a proton transfer to the FA is facilitated by a key aspartate residue (D28) and a coordinating water molecule. The protonated FA exits UCP1 through a well-defined pathway, and releases its proton into the mitochondrial matrix. UCP1 then facilitates the return of deprotonated FAs to the intermembrane space. Nucleotide binding disrupts this mechanism by inducing conformational changes in the transmembrane helices and obstructing the FA return pathway. Our mechanism explains every step of the transport cycle, is supported by simulation and biochemical data, and explains a diverse set of biochemical data about the transport mechanisms in UCP1 and its analogues: ANT, UCP2, and UCP3.
    Keywords:  UCP1; free energy calculations; mitochondrial energetics; molecular biophysics; molecular dynamics; protein dynamics; protein function; proton transport
    DOI:  https://doi.org/10.1002/pro.70357
  10. Nat Commun. 2025 Oct 31. 16(1): 9623
    Genome Aggregation Database Consortium
      Incomplete penetrance, or absence of disease phenotype in an individual with a disease-associated variant, is a major challenge in variant interpretation. Studying individuals with apparent incomplete penetrance can shed light on underlying drivers of altered phenotype penetrance. Here, we investigate clinically relevant variants from ClinVar in 807,162 individuals from the Genome Aggregation Database (gnomAD), demonstrating improved representation in gnomAD version 4. We then conduct a comprehensive case-by-case assessment of 734 predicted loss of function variants in 77 genes associated with severe, early-onset, highly penetrant haploinsufficient disease. Here, we identify explanations for the presumed lack of disease manifestation in 701 of 734 variants (95%). Individuals with unexplained lack of disease manifestation in this set of disorders are rare, underscoring the need and power of deep case-by-case assessment presented here to minimize false assignments of disease risk, particularly in unaffected individuals with higher rates of secondary properties that result in rescue.
    DOI:  https://doi.org/10.1038/s41467-025-61698-x
  11. Int J Mol Sci. 2025 Oct 18. pii: 10140. [Epub ahead of print]26(20):
      Mitochondrial long-chain fatty acid β-oxidation supplies energy to the heart, liver, and skeletal muscle. Impairment of this process due to a block at the step catalyzed by long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) leads to bioenergetic failure, manifesting as hypoglycemia, recurrent rhabdomyolysis, cardiomyopathy, and hepatic dysfunction. Accumulation of toxic intermediates-long-chain 3-hydroxyacyl-CoAs and the corresponding 3-hydroxyacylcarnitines-contributes to pigmentary retinopathy and peripheral neuropathy. Early diagnosis and careful dietary management can reduce life-threatening decompensation in childhood and improve survival into adulthood. This review examines the genetics of human LCHAD deficiency, describes its multisystem complications, and outlines nutritional strategies used to bypass the enzymatic block. We also explore nutrigenomic signals elicited by dietary treatment in LCHAD deficiency.
    Keywords:  MCT; fatty acid oxidation; human; medium-chain fatty acids; mitochondrial diseases; nutritional regulation; nutritional therapy
    DOI:  https://doi.org/10.3390/ijms262010140
  12. iScience. 2025 Oct 17. 28(10): 113563
      Mitochondria coordinate well-described maintenance functions within neuronal axons and dendrites. However, less is known about how mitochondria are regulated during axon development and maturation. Here, we demonstrate that within the developing visual system, retinal ganglion cell (RGC) axons in the retina and optic nerve exhibit increases in mitochondria size, number, and total area in vivo. Our findings indicate that these developmental changes in mitochondria are driven by neuronal activity associated with eye opening and by brain-derived neurotrophic factor (BDNF). These events occur in concert with downstream gene and protein expression changes consistent with mitochondrial biogenesis and energetics pathways. We further demonstrate that activity- and BDNF-regulated transcripts are localized and translated at mitochondria within RGC axons in vivo, concomitant with the regulation of mitochondrial dynamics. These data highlight the previously undescribed regulation of mitochondrial dynamics in axonal maturation, dependent on mechanisms involving neuronal activity and neurotrophic factor signaling, coordinated with mitochondrial-localized translation.
    Keywords:  Biological sciences; Natural sciences; Neuroscience; Systems neuroscience
    DOI:  https://doi.org/10.1016/j.isci.2025.113563
  13. BBA Adv. 2025 ;8 100171
      Mitochondrial outer membrane protein, voltage-dependent anion channel 1 (VDAC1), is a gatekeeper of transport, metabolism, and cellular apoptosis. Ablation of VDAC1 or treatment with small molecular VDAC1 inhibitors often causes metabolic reprogramming in cells. However, the mechanism of VDAC1-mediated reprogramming of mitochondrial oxidative phosphorylation (OXPHOS) is still unclear. To address this problem, we tested how the high-affinity VDAC1 inhibitor, 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid (DIDS), changes cell viability and mitochondrial functions. The IC50 value of DIDS was found 508 µM and 580 µM after 24 h of treatment on human osteosarcoma U2OS and mouse NIH-3T3 fibroblast cells. Moreover, when we inhibited mitochondrial OXPHOS by oligomycin A, 500 µM DIDS was found to uncouple the respiration like the conventional uncoupler CCCP in both the cells. Additionally, we observed that 50-200 µM DIDS, even after 2 h of treatment, depolarizes mitochondrial membrane potential. Also, brief DIDS treatment leads to an increase in cell population with hyperfused mitochondria and attenuation of DRP1 recruitment to mitochondria in U2OS cells. However, no significant alteration in the steady-state level of mitochondrial respiratory chain complex I and complex V subunits was noticed after DIDS treatment. Similar to cell lines, DIDS treatment also showed significant respiratory uncoupling in isolated mitochondria prepared from the normal muscle, liver, and sarcoma tumor tissues of mice. Finally, in silico modeling using AutoDock Vina and AlphaFold3 identified that DIDS binds inside the beta-barrel structure of VDAC1. Together, our findings directly demonstrate that DIDS binds to the VDAC1 inner pocket, uncouples OXPHOS, and promotes mitochondrial hyperfusion.
    Keywords:  DIDS; Mitochondrial dynamics; OXPHOS; Uncoupling; VDAC1; mitochondria
    DOI:  https://doi.org/10.1016/j.bbadva.2025.100171
  14. Curr Med Chem. 2025 Oct 24.
      
    Keywords:  Atherosclerosis; CRISPR-Cas9; cybrid; disease model; drug discovery.; epigenetic regulation; gene editing; gene regulation; mitochondrial DNA mutations; next-generation sequencing
    DOI:  https://doi.org/10.2174/0109298673450033251020095814
  15. Mol Genet Metab Rep. 2025 Dec;45 101266
      The F-box and leucine-rich repeat protein 4 (FBXL4) is a nuclear encoded mitochondrial protein essential for mitochondrial DNA (mtDNA) maintenance. Biallelic variants in FBXL4 cause FBXL4-related mitochondrial DNA depletion syndrome (FBXL4-MTDPS), characterized by lactic acidosis and developmental delay. We report two siblings diagnosed with FBXL4-MTDPS who died of fulminant pneumonia in infancy; autopsy revealed extensive pulmonary inflammation consistent with severe bacterial infection. FBXL4-MTDPS may involve intrinsic defects in pulmonary infection defense, increasing susceptibility to fatal infection such as pneumonia.
    Keywords:  Encephalomyopathic mitochondrial DNA depletion syndrome; F-box and leucine-rich repeat protein 4; Fatal fulminant pneumonia; Lactic acidosis; Mitophagy
    DOI:  https://doi.org/10.1016/j.ymgmr.2025.101266
  16. J Chem Inf Model. 2025 Oct 31.
      Mitochondria rely on the efficient import of proteins to maintain their functions and regenerate. The translocase of the outer mitochondrial membrane (TOM) complex serves as the primary entry point for the import of mitochondrial proteins. Previous studies have established Tom22 as a multifunctional subunit within the complex and reported mechanosensitive gating-like behavior of the TOM complex. In this study, all-atom molecular dynamics simulations of the TOM core complex reveal large motions of the Tom22 helices that are coupled to global structural rearrangements within the complex, particularly with the α2 helix within the Tom40 pore subunit. Microseconds-long simulations with restraints on the Tom22 helices yield an alternative conformation of the α2 helix that is associated with a reduced ion permeability. The outcome corroborates previous experimental results that reported a reduction in calcium ion flux for transiently stalled TOM complexes. These findings provide a molecular view of a mechanism by which Tom22 modulates the pore architecture of Tom40 and regulates permeability, thus linking the receptor dynamics to the functional control of the mitochondrial protein import.
    DOI:  https://doi.org/10.1021/acs.jcim.5c01761
  17. Toxicol Res. 2025 Nov;41(6): 635-647
      Mitochondria are essential for cellular energy production and play a critical role in maintaining overall cellular homeostasis. Mitochondrial dysfunction primarily affects energy-demanding tissues such as heart and skeletal muscle, as well as tissues (e.g., the liver) that are exposed to xenobiotics. In fact, mitochondrial toxicity is recognized as a major contributor to drug-induced liver injury (DILI). However, reliable methods for assessment of mitochondrial toxicity in vitro or in vivo remain lacking. Here, through a series of in vitro and in vivo experiments, we identified amiodarone as a model compound for evaluation of mitochondrial toxicity in hepatocytes and liver tissues. Among five known hepatotoxic agents tested, amiodarone consistently induced characteristic features of mitochondrial toxicity, including reduced mitochondrial membrane potential, elevated mitochondrial reactive oxygen species (ROS), and disrupted mitochondrial dynamics in both primary hepatocytes and surrogate cell lines. Because mitochondrial damage frequently triggers activation of antioxidant defense pathways, we further confirmed increased antioxidant gene expression and serum transaminase level elevation in mice administered with amiodarone. Indeed, the hepatotoxicity induced by amiodarone was significantly enhanced in Nrf2-deficient mice. Our approach, importantly, can be applied to the evaluation of drug-induced mitochondrial damage in the liver.
    Supplementary Information: The online version contains supplementary material available at 10.1007/s43188-025-00310-2.
    Keywords:  Amiodarone; Hepatocytes; Mitochondrial toxicity; Nrf2
    DOI:  https://doi.org/10.1007/s43188-025-00310-2
  18. Nat Commun. 2025 Oct 30. 16(1): 9611
      The proximal tubule of the nephron performs energy-demanding functions such as resorption of water, amino acids and glucose. Formation of the energy-producing machinery is an essential step in proximal tubule epithelial cell differentiation, and this report asks how mitochondria are localized within these cells. We show that mitochondria move from the apical to basolateral side of the proximal tubule cell coincident with the initiation of lumen flow and that proximal tubules deficient in filtration maintain mitochondria in the apical position. Mitochondrial localization depends on the activity of LRRK2 and modeling fluid flow on cultured proximal tubule epithelial cells demonstrates that LRRK2 activity is regulated by fluid shear stress, explaining how onset of flow in the newly differentiated proximal tubule may trigger the apical-to-basolateral dissemination of mitochondria. These findings indicate that mitochondrial redistribution is one component of a cellular program in the nascent proximal tubule that drives function and that this process is triggered by flow.
    DOI:  https://doi.org/10.1038/s41467-025-64598-2
  19. Clin Genet. 2025 Oct 29.
      Mitochondrial DNA depletion syndrome 1 (MTDPS1) is a rare autosomal recessive disorder caused by mutations in the TYMP gene, leading to mitochondrial failure. Hallmark features include gastrointestinal dysmotility, cachexia, peripheral neuropathy, ocular signs, hearing loss, and leukoencephalopathy. We present a 39-year-old woman with premature ovarian insufficiency (POI) as a novel endocrine manifestation of MTDPS1. She had normal pubertal development with menarche at age 10. In her mid-20s, she developed fatigue, nausea, vomiting, abdominal pain, weight loss, and amenorrhoea at age 29. Investigations revealed POI with elevated FSH levels, a normal karyotype, negative autoimmune markers. Imaging showed a thin endometrium, small ovaries, osteoporosis, severe gastroparesis. An incidental renal angiomyolipoma prompted an MRI of the brain, revealing symmetrical abnormal white matter changes, suggestive of leukodystrophy. Given diagnostic uncertainty and a history of consanguinity she was referred to clinical genetics and underwent whole genome sequencing which identified a novel homozygous variant (c.559C > T; p.(Gln 187*)) in the TYMP gene, confirming MTDPS1. Though POI is not a well-established feature of MTDPS1, mutations in other genes linked with mitochondrial function are known to be associated with POI and we postulate that this is an endocrine manifestation of MTDPS1. Genetic assessment should be considered in unexplained POI, particularly if associated with other clinical features/consanguinity.
    Keywords:  TYMP gene mutation; mitochondrial DNA depletion syndrome 1; premature ovarian insufficiency
    DOI:  https://doi.org/10.1111/cge.70100
  20. Mol Cell. 2025 Oct 28. pii: S1097-2765(25)00819-6. [Epub ahead of print]
      The de novo purine synthesis pathway is fundamental for nucleotide production, yet the role of mitochondrial metabolism in modulating this process remains underexplored. Here, we identify that succinate dehydrogenase (SDH) is essential for maintaining de novo purine synthesis. Genetic or pharmacological inhibition of SDH suppresses purine synthesis, contributing to a decrease in cell proliferation. Mechanistically, SDH inhibition elevates succinate, which in turn promotes the succinylation of serine hydroxymethyltransferase 2 (SHMT2) within the mitochondrial tetrahydrofolate (THF) cycle. This post-translational modification lowers formate output, depriving cells of one-carbon units needed for purine assembly. In turn, cancer cells activate the purine salvage pathway, a metabolic compensatory adaptation that represents a therapeutic vulnerability. Notably, co-inhibition of SDH and purine salvage induces pronounced antiproliferative and antitumoral effects in preclinical models. These findings reveal a signaling role for mitochondrial succinate in tuning nucleotide metabolism and highlight a dual-targeted strategy to exploit metabolic dependencies in cancer.
    Keywords:  TCA cycle; cancer; formate; mitochondrial metabolism; nucleotide metabolism; succinate
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.002
  21. Nat Commun. 2025 Oct 27. 16(1): 9481
      The voltage-dependent anion channel (VDAC) is the main gateway for metabolites across the mitochondrial outer membrane. VDAC oligomers are connected to apoptosis induced by various stimuli. However, the mechanistic and structural basis of apoptosis induction by VDAC remains poorly understood. Here, using cryo-EM and NMR we show that VDAC1 oligomerization or confinement in small lipid nanodiscs triggers the exposure of its N-terminal α-helix (VDAC1-N) which becomes available for partner protein binding. NMR and X-ray crystallography data show that VDAC1-N forms a complex with the BH3 binding groove of the anti-apoptotic Bcl2 protein BclxL. Biochemical assays demonstrate that VDAC1-N exhibits a pro-apoptotic function by promoting pore formation of the executor Bcl2 protein Bak via neutralization of BclxL. This mechanism is reminiscent of BH3-only sensitizer Bcl2 proteins that are efficient inducers of Bax/Bak-mediated mitochondrial outer membrane permeabilization and ultimately apoptosis. The VDAC pathway most likely responds to mitochondrial stress or damage.
    DOI:  https://doi.org/10.1038/s41467-025-65363-1
  22. Brain. 2025 Oct 30. pii: awaf414. [Epub ahead of print]
      The p.D620N mutation in VPS35 causes an autosomal dominant form of Parkinson's disease via mechanisms that are poorly understood. PINK1 and parkin, two proteins whose loss of function underlies autosomal recessive Parkinson's disease, cooperate to mediate mitophagy, a quality control pathway for selective elimination of damaged mitochondria. PINK1/parkin-mediated mitophagy is disrupted by LRRK2 mutations, which are the most prevalent cause of autosomal dominant Parkinson's disease. Here, we investigated whether the p.D620N VPS35 mutation has an effect on PINK1/parkin-mediated mitophagy. We identified a novel family with autosomal dominant Parkinson's disease caused by a p.D620N VPS35 mutation. We cultured skin fibroblasts and iPSC-derived dopaminergic neurons from the proband and from a second, unrelated Parkinson's disease patient with the p.D620N VPS35 mutation, and compared them with isogenic and non-isogenic control cells. PINK1/parkin-mediated mitophagy was severely impaired in VPS35 mutant fibroblasts and neurons, while non-selective, starvation-induced autophagy and lysosomal degradative capacity were preserved. siRNA-mediated VPS35 knockdown rescued the mitophagy defect in VPS35 mutant cells, whereas overexpression of wild-type VPS35 did not, suggesting a gain-of-function mechanism of the mutation. The VPS35 mutation did not interfere with activation of PINK1 or parkin after mitochondrial depolarization, but impaired mitochondrial recruitment of the autophagy receptor optineurin. LRRK2 kinase activity was increased in the VPS35 mutant cells, as shown by enhanced levels of the T73-phosphorylated form of the LRRK2 substrate RAB10. The enhanced level of phosphorylated RAB10 in VPS35 mutant cells was decreased by treatment with LRRK2 kinase inhibitors and by VPS35 knockdown. Importantly, the mitophagy defect of VPS35 mutant fibroblasts and neurons was fully rescued by LRRK2 kinase inhibitors as well as by overexpression of PPM1H, a phosphatase that dephosphorylates multiple RAB substrates of LRRK2. Finally, in situ proximity ligation experiments revealed that endogenous VPS35 and LRRK2 are proximity partners in human dopaminergic neurons and that this proximity relationship is enhanced by the VPS35 mutation. In conclusion, the VPS35 mutation impairs PINK1/parkin-mediated mitophagy via a gain-of-function mechanism that involves stimulation of LRRK2 kinase activity. Thus, a VPS35/LRRK2 axis linked to dominant Parkinson's disease intersects with a pathway mediated by proteins encoded by the recessive Parkinson's disease genes.
    Keywords:  Parkinson’s disease; RAB; autophagy; induced pluripotent stem cell; lysosome; mitochondrion
    DOI:  https://doi.org/10.1093/brain/awaf414
  23. Radiol Case Rep. 2025 Dec;20(12): 5929-5933
      Spinal cord involvement in Leigh syndrome (LS) due to an NDUFV1 variant has rarely been reported. The patient is a 4-month-old girl who developed generalized weakness, decreased vigilance, lethargy, cyanosis and unresponsiveness. Investigation revealed lactic acidosis, mild hyponatremia, normocytic anemia, elevated troponin, elevated pro-brain natriuretic peptide, Mobitz II block, systolic dysfunction, and pulmonary hypertension. Cerebral MRI showed symmetrical T2 hyperintensities in the brainstem and supra-tentorial, suggestive of LS, as well as T2 and STIR hyperintensities of the fasciculus gracilis and posterior and lateral gray matter horns, which were hypointense at T1. Seventeen days later, these lesions were more pronounced on T2 and STIR than before. Genetic testing revealed the compound heterozygous variants c.1162+4A>C and c.1138G>C in NDUFV1. In summary, mutations in NDUFV1 can also manifest phenotypically in the spinal cord and present clinically with sensory disturbances, spasticity and spinal ataxia. In patients with LS due to NDUFV1 variants, not only imaging of the brain but also of the spinal cord should be performed.
    Keywords:  Complex-I deficiency; Leigh syndrome; Mitochondrial DNA; NDUFV1; Respiratory chain
    DOI:  https://doi.org/10.1016/j.radcr.2025.08.031
  24. Int J Biol Macromol. 2025 Oct 28. pii: S0141-8130(25)09166-4. [Epub ahead of print]332(Pt 1): 148609
      Nicotinamide nucleotide transhydrogenase (NNT) is a key mitochondrial enzyme generating NADPH by utilizing the proton gradient produced by oxidative phosphorylation (OXPHOS), thereby linking redox homeostasis to mitochondrial energy metabolism. The commonly used C57BL/6 J mouse strain lacks functional NNT, yet its impact during early development remains unclear. This study aimed to characterize adaptive molecular responses in the gastrocnemius muscle of young mice with NNT deficiency. Congenic Nnt deficient (NntΔ; BL6JRcc.BL6J-NntC57BL/6J/Wuhap) and wild-type (Nntwt; B6JRcc(B6J)-Nnt+/Wuhap) mouse lines were newly created. Transcriptome profiling was performed on gastrocnemius muscles of 24-day-old male mice, followed by validation of key findings. Energy metabolism emerged as the most affected process, and NntΔ mice exhibited significant reduced OXPHOS-related genes, particularly within complex I and complex V showing a downregulation of 42.2 % and 50 % of their subunits, respectively. Additionally, expression of Cpt1b, Cpt2, and Slc25a20, involved in fatty acid transport, was reduced by 33 %, 19 % and 23 %, respectively. These results may explain the trend toward decreased oxygen consumption rates using palmitoylcarnitine (29 %; P-value = 0.068) and octanoylcarnitine (18 %; P-value = 0.081). CHRNA1, a protein critical for neuromuscular junction (NMJ) function, was also downregulated by 31 %. These results suggest that functional loss of NNT impairs mitochondrial energy pathways and β-oxidation, potentially influencing NMJ in the gastrocnemius muscle during development.
    Keywords:  Mitochondria; NNT; OXPHOS
    DOI:  https://doi.org/10.1016/j.ijbiomac.2025.148609
  25. Nat Commun. 2025 Oct 31. 16(1): 9644
      The mitochondrion is a highly dynamic organelle, constantly undergoing fusion and fission, which are critical processes for the health of cells. Fusion of the outer mitochondrial membrane (OMM) is mediated by the mitofusins belonging to the dynamin superfamily of GTPases. Most eukaryotic organisms possess two cooperatively functioning mitofusins, but yeast has only one mitofusin (Fzo1). How Fzo1 solely catalyzes OMM fusion is unclear. Here, we present crystal structures of truncated Fzo1 (Fzo1IM) in different nucleotide-loading states and report a special mechanistic feature of Fzo1 through systematic functional studies. Differing from mammalian mitofusins, Fzo1 contains an extra latch bulge (LB) that is essential for the viability of yeast. Upon GTP loading, Fzo1IM dimerizes via the GTPase domain and prefers the closed conformation. This state is then locked by the subsequent trans interaction mediated by the LB of each protomer, so that Fzo1IM remains dimerized in the closed conformation even after GTP hydrolysis. This special mechanistic feature may be relevant to the previous observation that degradation of Fzo1 by the ubiquitin-proteasome system is required for mitochondrial fusion. Our study reveals how mitochondrial fusion in yeast is efficiently ensured with limited GTP consumption, which broadens current understanding of this fundamental biological process.
    DOI:  https://doi.org/10.1038/s41467-025-64646-x
  26. Cardiovasc Res. 2025 Oct 28. pii: cvaf194. [Epub ahead of print]
       AIMS: Aldehyde dehydrogenase 2 (ALDH2) is a critical mitochondrial enzyme responsible for aldehyde detoxification and maintenance of redox homeostasis. The rs671 variant, a prevalent loss-of-function mutation in East Asian populations (30-50% carrier frequency), diminishes ALDH2 enzymatic activity by 60-90% and is associated with elevated thrombotic risk. Although platelet activation is known to play a central role in thrombosis formation, the specific contribution of ALDH2 to this process has not been fully elucidated. This study was designed to investigate the functional role of ALDH2 in platelet activation and thrombus formation.
    METHODS AND RESULTS: Platelet activation and thrombus formation were assessed in wild-type (WT), systemic Aldh2-knockout (Aldh2-/-), and systemic Aldh2E487K/E487K-knockin mice, as well as patients with coronary artery disease (CAD) and healthy volunteers. Mechanistic studies were performed using immunoprecipitation, mass spectrometry, and RNA sequencing. Nicotinamide adenine dinucleotide (NAD+) supplementation was evaluated for its potential to mitigate the effects of ALDH2 variant. Patients with CAD carrying the ALDH2 rs671 variant exhibited enhanced platelet reactivity to collagen compared with those without the variant. Collagen-induced platelet aggregation, granule release, and integrin αIIbβ3 activation were significantly enhanced in Aldh2-/- mice compared with WT mice. Mechanistically, ALDH2 deficiency disrupted mitochondrial complex I assembly and function. This increased reactive oxygen species (ROS) production via the collagen/glycoprotein VI (GPVI)/NAD phosphate oxidase 1 (NOX1) pathway and enhanced platelet reactivity. Similar results were observed in Aldh2487K/E487K-knockin mice. NAD+ supplementation effectively counteracted ALDH2 variant-induced platelet hyperreactivity and thrombosis in both mice and human subjects.
    CONCLUSIONS: The ALDH2 rs671 variant enhances collagen-induced platelet activation and thrombosis by impairing mitochondrial complex I assembly and function. NAD+ supplementation offers a promising strategy to mitigate thrombotic risk in individuals carrying this variant.
    Keywords:  Aldehyde dehydrogenase 2; Mitochondrial complex I; NAD+; Platelet activation; ROS; Thrombosis
    DOI:  https://doi.org/10.1093/cvr/cvaf194
  27. Curr Biol. 2025 Oct 27. pii: S0960-9822(25)01263-1. [Epub ahead of print]
      The mitochondrial fission-fusion cycle is often disrupted in neurodegenerative diseases, but this important, dynamic process is not well characterized in healthy long-lived neurons of animals. We used an efficient cell-type-specific CRISPR strategy to knock out key fission and fusion genes in specific Drosophila neurons. Neither process is essential for neuronal survival and function, but the fusion knockouts had a larger impact than that of fission, especially in older animals. Mutations in the human mitochondrial inner membrane fusion gene Opa1 often cause the disease optic atrophy. Importantly, knockout of Opa1 in neurons causes a dramatic age-dependent transcriptomic response. This response resembles those of cancer cells and includes the upregulation of glycolytic genes, including Lactate dehydrogenase (Ldh). A novel double knockout strategy indicates that Ldh enhances the reduced ATP levels of the fusion mutants and is essential to prevent age-dependent neurodegeneration. This neuroprotective upregulation of Ldh is largely mediated by the transcription factor ATF4. The identified relationship-dysfunctional mitochondrial fusion alters metabolism-is reminiscent of Warburg's original cancer hypothesis, albeit in neurons. These data underscore the similarity of the two molecular programs, which promote growth in cancer and viability in the case of neurodegeneration.
    Keywords:  ATF4; CRISPR; Drosophila; Warburg effect; mitochondrial dynamics; neurodegeneration
    DOI:  https://doi.org/10.1016/j.cub.2025.09.063
  28. Mol Genet Metab. 2025 Oct 24. pii: S1096-7192(25)00256-2. [Epub ahead of print]146(4): 109264
      
    DOI:  https://doi.org/10.1016/j.ymgme.2025.109264
  29. Cell Rep Methods. 2025 Oct 28. pii: S2667-2375(25)00248-6. [Epub ahead of print] 101212
      Mitochondria are central to cardiomyocyte function, and their spatial organization regulates nuclear signaling and gene transcription, holding potential for novel cardioprotective interventions. We developed a transmission electron microscopy platform optimized for resolving mitochondrial subpopulations and nuclear architecture in adult cardiomyocytes. This approach reliably captures longitudinal sections containing the center of the nucleus and perinuclear regions, enabling consistent imaging of subcellular nanostructures, assessment of pharmacological effects within the same organism, and visualization of extracellular vesicles carrying dysfunctional mitochondria. Integrated with an analysis workflow employing machine learning-based segmentation for annotation, the method allows automated quantification of mitochondrial and nuclear architecture and positioning. Using Drp1-deficient mice with impaired mitochondrial fission, we demonstrate this tool's ability to uncover nanoscale remodeling of mitochondria and nuclei under stress. Our platform overcomes challenges in electron microscopy analysis, providing a powerful resource to interrogate mitochondrial-nuclear dynamics in cardiac (patho)physiology. These insights will inform therapeutic targeting of bioenergetic failure.
    Keywords:  CP: cell biology; CP: imaging; automated image analysis; cardiomyocyte; cristae density; morphometric analysis; nucleus; organelle interactions; perinuclear mitochondria; subcellular imaging; transmission electron microscopy; ultrastructure analysis
    DOI:  https://doi.org/10.1016/j.crmeth.2025.101212
  30. Adv Sci (Weinh). 2025 Oct 27. e10482
      Mitochondrial RNA N1-methyladenosine (m1A) is a prevalent and reversible epitranscriptomic modification. While the biological roles of cytosolic m1A have been increasingly understood, the causal relationship between site-specific mitochondrial m1A and phenotypic outcomes remain elusive, partly due to the lack of precise editing tools. Here, a CRISPR-free mitochondrial RNA m1A demethylation (MRD) editor is reported, which fuses mitochondria-localized engineered PUF RNA-binding protein with the m1A demethylase ALKBH3. Independent cellular assays across multiple sites confirm that MRD editor enables precise demethylation of m1A in mitochondrial mRNAs and tRNAs, leading to correlated changes in mitochondrial protein levels with minimal off-target effects. The MRD editor is further employed to systematically investigate how site-specific mitochondrial m1A alterations regulate cell proliferation, ATP production, mitochondrial membrane potential (MMP), and mitochondrial respiration. Finally, in vivo application of the MRD editor reveals that demethylation of m1A at the A9 position of mitochondrial tRNA-Lys (MT-TK9) induces severe immunodeficiency phenotypes in mice, as evidenced by transcriptomic and histopathological analyses. Collectively, the findings establish MRD as a versatile tool for site-specific mitochondrial RNA m1A editing, offering new insights into the functional dissection of these modifications through chemical biology strategies.
    Keywords:  ALKBH3; Mitochondrial RNA; N1‐methyladenosine; PUF; demethylation editor
    DOI:  https://doi.org/10.1002/advs.202510482
  31. Mol Genet Metab. 2025 Oct 24. pii: S1096-7192(25)00258-6. [Epub ahead of print]146(3): 109266
       BACKGROUND: Biallelic variants in RTN4IP1 (OPA10) are associated with a wide phenotypic spectrum including optic atrophy with or without ataxia, impaired intellectual development and seizures (OMIM 616732). Brain imaging ranges from normal to white matter changes and cerebral atrophy. Earlier literature has reported a combined complex I and IV deficiency in RTN4IP1 cases.
    RESULTS: We report on three siblings, compound heterozygous for novel RTN4IP1 variants who presented with a movement disorder with pronounced dyskinesia along with developmental delay, optic atrophy and ataxia. Furthermore, atypical brain MRI findings with symmetrical bilateral substantia nigra abnormalities were observed in two of them. Blue native polyacrylamide gel electrophoresis performed on fibroblasts of two patients revealed a defect in the complex I assembly process.
    CONCLUSION: Thus, we expand the clinical spectrum of RTN4IP1-associated disease with movement disorder, substantia nigra abnormalities and complex I assembly defects.
    Keywords:  Ataxia; Dyskinesia; Movement disorder; OPA10 syndrome; Optic atrophy; RTN4IP1
    DOI:  https://doi.org/10.1016/j.ymgme.2025.109266
  32. Redox Biol. 2025 Oct 17. pii: S2213-2317(25)00415-X. [Epub ahead of print]88 103902
      Mitochondrial transplantation is an upcoming therapeutic modality where transfer of healthy robust mitochondria bio-enhances metabolically dysfunctional cells or tissues. Though the concept of MT germinated in early 1980s in a bid to develop antibiotic resistance between cells, this innovative treatment has since undergone various breakthroughs in addressing metabolic dysfunction in various systemic diseases. Four decades since its advent, MT is now being applied in the field of Ophthalmology, where metabolic disorders affecting various ocular tissues contribute significantly to disease pathogenesis. Encouraged by the success of MT in other organs such as heart, lung and brain, this therapy has recently been applied to ocular disorders. MT is an emerging ocular therapy, with promising therapeutic outcomes for corneal, optic nerve, and retinal disorders. However, before it can be adopted as a "bench to bedside" therapy for ocular disorders, MT faces several potential bottlenecks. This review provides an overview of mitochondrial biology in eye diseases, summarizes the current state-of-the-art in ocular MT, whilst discussing challenges and future direction of bringing MT into clinical practice.
    Keywords:  Bioenergetic rescue; Clinical translation; Mitochondria transplantation; Mitochondrial biology; Ocular metabolic diseases; Oxidative stress
    DOI:  https://doi.org/10.1016/j.redox.2025.103902
  33. Pathogens. 2025 Oct 16. pii: 1045. [Epub ahead of print]14(10):
      We hypothesize that a unified mitochondrial perspective on aging, HIV, and long COVID reveals shared pathogenic mechanisms and specific therapeutic vulnerabilities that are overlooked when these conditions are treated independently. Mitochondrial dysfunction is increasingly recognized as a common factor driving aging, HIV, and long COVID. Shared mechanisms-including oxidative stress, impaired mitophagy and dynamics, mtDNA damage, and metabolic reprogramming-contribute to ongoing energy failure and chronic inflammation. Recent advancements highlight new therapeutic strategies such as mitochondrial transfer, transplantation, and genome-level correction of mtDNA variants, with early preclinical and clinical studies providing proof-of-concept. This review summarizes current evidence on mitochondrial changes across aging and post-viral syndromes, examines emerging organelle-based therapies, and discusses key challenges related to safety, durability, and translation.
    Keywords:  HIV; SARS-CoV-2; mitochondria
    DOI:  https://doi.org/10.3390/pathogens14101045
  34. Elife. 2025 Oct 31. pii: RP100799. [Epub ahead of print]13
      Parkinson's disease (PD) is the second most common neurodegenerative disorder. Mutations in human leucine-rich repeat kinase 2 (LRRK2), a multi-domain protein containing both a kinase and a GTPase, are a leading cause of the familial form of PD. Pathogenic LRRK2 mutations increase LRRK2 kinase activity. While the bulk of LRRK2 is found in the cytosol, the protein associates with membranes where its Rab GTPase substrates are found, and under certain conditions, with microtubules. Integrative structural studies using single-particle cryo-electron microscopy and in situ cryo-electron tomography (cryo-ET) have revealed the architecture of microtubule-associated LRRK2 filaments, and that formation of these filaments requires LRRK2's kinase to be in the active-like conformation. However, whether LRRK2 can interact with and form filaments on microtubules in its autoinhibited state, where the kinase domain is in the inactive conformation and the N-terminal LRR domain covers the kinase active site, was not known. Using cryo-ET, we show that full-length human LRRK2 can oligomerize on microtubules in its autoinhibited state. Both WT-LRRK2 and PD-linked LRRK2 mutants formed filaments on microtubules. While these filaments are stabilized by the same interfaces seen in the active-LRRK2 filaments, we observed a new interface involving the N-terminal repeats that were disordered in the active-LRRK2 filaments. The helical parameters of the autoinhibited-LRRK2 filaments are different from those reported for the active-LRRK2 filaments. Finally, the autoinhibited-LRRK2 filaments are shorter and less regular, suggesting they are less stable.
    Keywords:  LRRK2; human; microtubules; molecular biophysics; neuroscience; parkinson's disease; structural biology
    DOI:  https://doi.org/10.7554/eLife.100799
  35. PLoS Genet. 2025 Oct 27. 21(10): e1011923
      Telomerase Reverse Transcriptase (TERT), in addition to its well-known role in telomere lengthening, also has non-canonical functions, including gene regulation and protection against apoptosis. Beyond its nuclear functions, it is now recognized for its presence inside mitochondria. However, the biological role of TERT in mitochondrial physiological activity, with its specific mechanism of action, still needs to be clarified. This work clearly demonstrates the presence of TERT inside the mitochondrion under physiological conditions, in different cellular contexts, both with endogenous and ectopic TERT expression, and regardless of the presence of telomerase RNA counterpart TERC. TERT was shown to bind mitochondrial DNA, influencing mitochondrial replication and transcription. Furthermore, electron microscopy analysis of morphology revealed TERT-induced fragmentation of the mitochondrial network. Collectively, our findings suggest that TERT may play a role in regulating mitochondrial biogenesis and dynamics, and influencing processes such as fission and mitophagy, essential for maintaining mitochondrial homeostasis and closely connected to cellular states.
    DOI:  https://doi.org/10.1371/journal.pgen.1011923
  36. Acta Neurol Belg. 2025 Oct 31.
       BACKGROUND: The mitochondrial tRNALeu (MT-TL1) m.3243A > G mutation is one of the most frequent pathogenic variants in mtDNA which is associated with various clinical syndromes including Mitochondrial Encephalomyopathy, Lactic Acidosis and Stroke-like episodes (MELAS). The onset of symptoms associated with the MT-TL1 mutation typically occurs in adolescence or early adulthood. Due to the diversity of its clinical presentation, there is a need to report all cases that do not fully meet the criteria of well-established clinical syndromes.
    CASE PRESENTATION: This paper reports a case of a 3-year-old male patient with a complex perinatal history, whose symptoms emerged at 6 months of age and included epileptic seizures, developmental delay, bilateral convergent strabismus, hypertonia, hyperreflexia, and radiological brain abnormalities. The family history is positive for epilepsy and hearing impairment in females on the maternal side. Genetic testing revealed a pathological variant in the MT-TL1 gene m.3243A > G with a high heteroplasmy level of 76.5% in the blood sample.
    CONCLUSION: The case presents an atypical manifestation of the m.3243A > G mutation, highlighting the importance of genetic screening for mitochondrial disorders in patients with a maternal family history.
    Keywords:  Atypical MT-TL1; Lactic acidosis; MELAS; MT-TL1 mutation; Mitochondrial encephalopathy; Mitochondrial mutation; Stroke
    DOI:  https://doi.org/10.1007/s13760-025-02921-w
  37. Nat Biomed Eng. 2025 Oct 28.
      Phenylketonuria (PKU), pseudoxanthoma elasticum (PXE) and hereditary tyrosinemia type 1 (HT1) are autosomal recessive disorders linked to the PAH, ABCC6, and FAH and HPD genes, respectively. Here we evaluate the off-target editing profiles of clinical lead guide RNAs (gRNAs) that, when combined with adenine base editors (ABEs), correct the recurrent PAH P281L variant, PAH R408W variant or ABCC6 R1164X variant, or disrupt either of two sites in the HPD gene (a modifier gene of HT1) in human hepatocytes. To mitigate off-target mutagenesis, we systematically screen hybrid gRNAs with DNA nucleotide substitutions. Comprehensive and variant-aware specificity profiling of these hybrid gRNAs reveals dramatically reduced off-target editing and reduced bystander editing in cells. In humanized PAH P281L and ABCC6 R1164X mouse models of PKU and PXE, we show that when formulated in lipid nanoparticles with ABE messenger RNA, selected hybrid gRNAs revert disease phenotypes, reduce off-target editing, increase on-target editing and reduce bystander editing in vivo. These studies highlight the use of hybrid gRNAs to improve the safety and efficiency of adenine base-editing therapies.
    DOI:  https://doi.org/10.1038/s41551-025-01545-y
  38. Biomolecules. 2025 Sep 28. pii: 1379. [Epub ahead of print]15(10):
      Mitochondria are crucial for a wide range of cellular processes. One of the most important is innate immunity regulation. Apart from functioning as a signaling hub in immune reactions, mitochondrial nucleic acids can themselves act as damage-associated molecular patterns (DAMPs) to participate in immune processes directly. This review synthesizes the current understanding of mitochondrial RNA (mtRNA) biology and its link to immune activation through aberrant accumulation. We focus on its origin through bidirectional mitochondrial transcription and metabolism, encompassing maturation (cleavage, polyadenylation, modification) and degradation. Dysregulation of mtRNA metabolism leads to mt-dsRNA (mitochondrial double-stranded RNA) accumulation, which escapes mitochondria via specific channels into the cytosol and serves as DAMPs to trigger an immune response. We discuss the critical roles of key regulatory factors, including PNPT1 (PNPase, Polyribonucleotide Nucleotidyltrans ferase 1), in controlling mt-dsRNA levels and preventing inappropriate immune activation. Finally, we review the implications of mt-dsRNA-driven inflammation in human diseases, including autoimmune disorders, cellular senescence, and viral infection pathologies, highlighting unresolved questions regarding mt-dsRNA release mechanisms.
    Keywords:  degradation; immune responds; maturation; mitochondrial RNA; transcription
    DOI:  https://doi.org/10.3390/biom15101379
  39. Cell Death Discov. 2025 Oct 27. 11(1): 490
      EZRIN is a key player in assembling and coordinating molecular signaling, acting as a linker between receptors in plasma membrane and the actin cytoskeleton. High EZRIN expression level has been extensively studied and often associated with metastasis and cancer progression. Recent reports independently suggested associations between Ezrin and mitochondrial alterations or apoptotic processes, the mechanism by which Ezrin modulates these events remain largely unclear. Here we report that the lack of EZRIN-mediated EGFR internalization and translocation on mitochondria is critical for mitochondrial metabolism. Ezrin-deficient (Ezrin-/-) cells exhibit marked impairments in mitochondrial respiratory chain (MRC) activity. These cells also show significantly reduced ATP production and elevated mitochondrial ROS levels, revealing cell metabolism deficit. Furthermore, Ezrin loss induces mitochondrial ROS-mediated apoptosis. In vivo, Medaka fish lacking Ezrin display neuronal cell death associated with inflammation, which appear linked to the compromised mitochondrial metabolism and oxidative stress. Our findings reveal a key mechanism within endo-lysosomal signaling that involves Ezrin and the EGFR/TSC complex. both of which are essential for neuronal homeostasis. In conclusion, our data identify a novel molecular pathway in which the Ezrin/EGFR axis regulates mitochondrial metabolism, thereby supporting cellular energy balance and promoting neuronal cell survival.
    DOI:  https://doi.org/10.1038/s41420-025-02790-5
  40. EMBO Rep. 2025 Oct 30.
      Mitochondrial DNA (mtDNA) serves as a potent activator for cellular innate immune responses. Topoisomerase 3α (TOP3α), a type IA topoisomerase, is canonically localized to mitochondria and nuclei, but its enigmatic cytosolic fraction-observed over two decades ago-has remained functionally undefined. Here, we uncover a critical role for cytosolic TOP3α in amplifying mtDNA-triggered innate immunity. We observe that aberrant TOP3α expression causes mtDNA clustering and release via mPTP-VDAC, stimulating cGAS-mediated inflammatory responses. Cytosolic TOP3α facilitates the sensing of released mtDNA by cGAS and amplifies downstream innate immune signaling. Using an in vitro cell-free system, we reveal that TOP3α directly augments mtDNA interaction with cGAS, which in turn competes with TOP3α for mtDNA binding. A rare mutation of a highly conserved residue (G250D) of TOP3α impairs the assembly of TOP3α polypeptides into protein complexes and its binding to mtDNA. Furthermore, mutant TOP3α hinders cGAS-mtDNA interaction and compromises cGAS-driven immunity. Our findings reveal a function for cytosolic TOP3α as a regulator for cGAS-driven inflammation.
    Keywords:  Cytosolic TOP3α; Inflammation; Mitochondrial DNA; cGAS
    DOI:  https://doi.org/10.1038/s44319-025-00614-2
  41. Curr Opin Neurobiol. 2025 Oct 30. pii: S0959-4388(25)00163-1. [Epub ahead of print]95 103132
      Since their discovery and development, human induced pluripotent stem cells (iPSCs) have brought about notable advances in biomedical science and have become an essential infrastructure for medical research and applications. This review discusses the current status of iPSC-based cell therapies, drug discovery, and therapeutic developments for neurodegenerative diseases with unmet medical needs. It also highlights research approaches employing cohorts of iPSCs derived from sporadic neurodegenerative diseases to advance prevention and diagnostic support. It further considers future directions for the use of iPSCs in the treatment of neurodegenerative disorders.
    DOI:  https://doi.org/10.1016/j.conb.2025.103132
  42. JHEP Rep. 2025 Nov;7(11): 101539
       Background & aims: Mitochondrial (mt-) D-loop and cell-free circulating (ccf-) mtDNA fragments, respectively reflecting mt-mass and tissue damage, are promising metabolic dysfunction-associated steatotic liver disease (MASLD) biomarkers. We previously found that PNPLA3/MBOAT7/TM6SF2 deficiency in HepG2 cells increased mt-mass, D-loop levels, and ccf-COXIII release. We explored mt-biogenesis and mt-biomarkers in patients with MASLD stratified by the number of risk variants (NRV = 3). We exploited GPT-4 to develop and validate new risk scores, predicting MASLD evolution, in two independent cohorts by integrating anthropometric and genetic data with mt-biomarkers.
    Methods: A cohort of 28 patients with MASLD (Discovery cohort) was consecutively enrolled for hepatic mt-dynamics assessment by transmission electron microscopy and immunohistochemistry. Data were confirmed by quantitative real time-PCR in a retrospective cohort (Hepatic Validation, n = 184). D-loop and ccf-COXIII were retrospectively measured in peripheral blood mononuclear cells and serum samples of biopsied outpatients with MASLD (Serum Validation cohort, n = 824) and individuals with non-invasive MASLD diagnosis (n = 386, Non-invasive cohort). Risk scores were developed using random forest algorithms.
    Results: In the Discovery and Hepatic Validation cohorts, the PNPLA3/MBOAT7/TM6SF2 variants altered hepatic mt-dynamics, enhancing mt-content and D-loop levels (p <0.05) through the p38/PGC-1α pathway. Furthermore, NRV = 3 patients showed an increase in mt-fragmentation at transmission electron microscopy (TEM) and ccf-COXIII release (p <0.05). In the Serum Validation cohort, circulating D-loop and ccf-COXIII positively correlated with genetics [β D-loop :0.17 (95% CI: 0.04-0.29), p = 0.01; βccf-COXIII:0.33 (95% CI: 0.19-0.46), p <0.0001] and MASLD severity [OR D-loop :1.31 (95% CI: 1.01-1.71), p = 0.03; ORccf-COXIII:2.41 (95% CI: 1.69-3.44), p <0.0001] at multivariate analysis. Random forest allowed prediction models named Mitochondrial, Anthropometric, and Genetic Integration with Computational intelligence for assessing hepatocellular carcinoma risk (MAGIC-H), considering age, BMI genetics, D-loop, and ccf-COXIII. In both Serum and Non-invasive cohorts, the MAGIC-H score reached AUC >85% in identifying HCC cases regardless of cirrhosis, outperforming existing non-invasive tests.
    Conclusions: Mt-biomarkers have a prognostic significance in genetically-predisposed patients with MASLD.
    Impact and implications: The study highlights that genetic variants in PNPLA3, MBOAT7, and TM6SF2 genes deeply contribute to metabolic dysfunction-associated steatotic liver disease (MASLD) progression by affecting hepatic mitochondrial adaptability. It also identified two novel biomarkers of mitochondrial origin which are strongly linked to disease severity and genetic background of patients with MASLD. The use of generative artificial intelligence tools, such as GPT-4, can enhance the use of biomarkers and polygenic risk scores for clinical risk stratification. We developed a customized version of GPT-4 (rsGPT-4), which identified a machine-learning approach (random forest) as the best method for creating prediction models for metabolic dysfunction-associated steatohepatitis, fibrosis, and hepatocellular carcinoma. The new scores combined the two mitochondrial biomarkers, genetic data, and anthropometric data and outperformed existing non-invasive tests for monitoring patients with MASLD.
    Keywords:  GPT-4; MASLD-HCC; Non-invasive scores; PNPLA3/MBOAT7/TM6SF2; mtDNA
    DOI:  https://doi.org/10.1016/j.jhepr.2025.101539
  43. Sci Adv. 2025 Oct 31. 11(44): eadt3014
      The integrated stress response (ISR) is a eukaryotic stress-responsive signaling pathway that attenuates global protein synthesis while allowing selective translation of specific mRNAs, which together can reestablish homeostasis following acute stress. Diverse pathologic insults activate one or more of the four ISR kinases, which selectively phosphorylate eIF2α to mediate ISR functions. Recent results suggest that enhancing ISR kinase activity could ameliorate pathologies linked to numerous diseases, including many neurodegenerative disorders. However, few pharmacological strategies exist to selectively activate ISR kinases and downstream adaptive signaling. Here, we report that compound A8 can preferentially activate the ISR through the binding of the cytosolic pattern recognition receptor RIG-I, which subsequently activates the heme-regulated inhibitor (HRI) ISR kinase independent of an interferon response. The establishment of A8 and its active metabolite CC81 provides opportunities to probe the biological and therapeutic relationship between innate immune signaling and ISR activation in health and disease.
    DOI:  https://doi.org/10.1126/sciadv.adt3014
  44. Dis Model Mech. 2025 Oct 01. pii: dmm052510. [Epub ahead of print]18(10):
      Huntington's disease (HD) is traditionally viewed as an age-related disorder. Emerging evidence suggests that mutant huntingtin (mHTT) disrupts early neurodevelopment, although the contribution of developmental alterations to the late disease onset remains to be clarified. Leveraging human pluripotent stem cell-derived brain organoids, we and others are exploring how mHTT affects the developing human brain. These models reveal impaired neural progenitor organization and function, accompanied by a mitochondrial stress response, indicating reduced capacity to manage cellular stress. Enhancing mitochondrial health and promoting neural cell resilience may thus represent potential strategies for improving the brain's compensatory mechanisms, thereby prolonging a healthy state. These insights highlight a potential window of opportunity for therapeutic interventions. Targeting mitochondrial fitness and neurodevelopmental pathways at early stages - long before clinical symptoms emerge - could help prevent or delay disease onset and progression in affected individuals.
    DOI:  https://doi.org/10.1242/dmm.052510
  45. Signal Transduct Target Ther. 2025 Oct 30. 10(1): 355
      The mitochondrial proton motive force (pmf) is a critical driver of cellular energy production and influences various cellular processes. Dysregulation of pmf is implicated in a range of diseases, including neurodegenerative diseases, mitochondrial diseases, cancer and aging-related pathologies. Currently, an efficient strategy to rescue ATP production and mitigate reactive oxygen species (ROS) generation under conditions of energy deprivation is lacking. Here, we engineered a light-sensitive, mitochondria-targeting proton-pumping rhodopsin (PPR), mt-EcGAPR, capable of generating an efficient pmf for ATP synthesis while simultaneously mitigating reactive oxygen species (ROS) generation during stress and decreasing DNA double-strand breaks (DSBs). Owing to its transparency to visible light, eye is the ideal candidate for the noninvasive application of mt-EcGAPR in the treatment of mitochondria-related retinal degenerative diseases. Using a silicone oil-induced ocular hypertension glaucoma mouse model, we demonstrate that ambient light activation of mt-EcGAPR significantly increased ATP production, suppressed ROS accumulation, and protected retinal ganglion cells (RGCs) from degeneration. Mechanistically, mt-EcGAPR inhibited endoplasmic reticulum (ER) stress-ATF6-gasdermin D (GSDMD)-mediated pyroptosis, thereby preserving retinal structure and function. This intervention ultimately led to improved visual acuity in glaucomatous eyes of mice. Collectively, our findings establish mt-EcGAPR as a promising therapeutic strategy for glaucoma and potentially other neurodegenerative diseases associated with mitochondrial dysfunction and impaired bioenergetics.
    DOI:  https://doi.org/10.1038/s41392-025-02450-1
  46. Mol Genet Metab Rep. 2025 Dec;45 101260
      Pyridoxine-Dependent Epilepsy (PDE) is an autosomal recessive disorder caused by biallelic variants in ALDH7A1. The most common presentation is intractable seizures in the neonatal/early infantile period, which respond to pyridoxine. Other manifestations include perinatal asphyxia, hypoglycemia, and neuroimaging abnormalities. Despite early treatment, patients often have neurodevelopmental abnormalities. Treatment guidelines recommend triple therapy with pyridoxine, dietary lysine restriction, and arginine supplementation. We report an individual presenting with laboratory abnormalities suggestive of mitochondrial disease. Born full-term, via NSVD, with normal Apgar scores and cord gases. At 30 min, grunting developed, and at 4 h of life, jerky movements with eye deviation were noted. Laboratory results revealed acidosis (pH 7.15) and increased lactate (11.4 mMol/L, rr <2.1). The patient was started on IV fluids, given 1 mEq/kg of sodium bicarbonate, and transferred for higher-level care. Upon arrival, the evaluation was notable for hypotonia, non-rhythmic jerking movements, rapid eye blinking, and a critically low pH (6.92), high lactate (15.3 mMol/L), hyperammonemia (153 μMol/L, rr < 75), and a creatine kinase level of 15,742 U/L (rr 35-230). A single dose of phenobarbital was given, and the baby was intubated and ventilated. Video electroencephalogram (vEEG) showed a discontinuous background with abnormal, sharply contoured bursts alternating with suppression, with no clinical correlation. The patient was treated with continuous sodium bicarbonate drip and IV fluids, restricting glucose. Abnormal movements, lactic acidosis, and hyperammonemia resolved within 24 h. An electroencephalogram (EEG) at 5 days of life (DOL) showed a mildly discontinuous background with no epileptic activity, and MRI showed a thin corpus callosum, cysts, and cerebellar hypoplasia. Creatine kinase peaked at 30,995 U/L and normalized on DOL 8. Organic acids revealed significant increases in lactate, 2-OH-butyrate, pyruvate, 3-OH-butyrate, 2-OH-isovalerate, and a mild increase in Krebs-cycle intermediates. Rapid whole genome sequence (rWGS) was available on DOL 9, disclosing two variants in ALDH7A1: c.1559C > T p.Ser520Phe, previously reported, and c.1540 A > G p.Lys514Glu, considered a VUS. Treatment with pyridoxine started at 30 mg/kg/day. Pre-treatment biomarkers were consistent with the diagnosis of PDE-ALDH7A1: urine Pipecolate 117.8 mMol/mol, RR ≤10, 6-oxo-Pipecolate 8.4 mMol/mol, RR ≤2.0 and plasma alpha-aminoadipic semialdehyde (AASA) 5.2 uMol/L, RR <0.4. Treatment with arginine was added on DOL 10 (200 mg/kg/day) and a lysine-restricted diet on DOL 12, after TPN was discontinued. Clinical exam improved, no seizures were observed, and EEG normalized. PDE biomarkers decreased, and the patient was discharged home on DOL 25. Elevated lactic acid has been reported in up to 70.3 % of PDE-ALDH7A1 patients with neonatal-onset; however, there is limited information about its severity, etiology, or pathophysiologic mechanism. We, therefore, conducted a review of published cases of neonatal-onset PDE-ALDH7A1 whose actual lactic acid values were reported. A total of 12 patients were analyzed and compared to this case. In most instances, a trigger (such as pulmonary hemorrhage, postnatal hypoxia, or status epilepticus) could be identified as the cause of elevated lactic acid; nevertheless, in many individuals, lactic acidosis remained unexplained. This case expands on the biochemical presentation of PDE-ALDH7A1 and highlights the importance of identifying increased lactic acid as another of its manifestations. We also provide evidence to support the reclassification of the c.1540 A > G (p.Lys514Glu) variant as pathogenic.
    Keywords:  ALDH7A1; Mitochondrial disease; PDE; Pyridoxine-dependent epilepsy; Rhabdomyolysis; hyperCKemia
    DOI:  https://doi.org/10.1016/j.ymgmr.2025.101260
  47. J Patient Rep Outcomes. 2025 Oct 27. 9(1): 127
       BACKGROUND AND OBJECTIVES: Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) is a rare genetic syndrome mostly associated with pathogenic variants in mitochondrial DNA. As there is limited research on the life experience of patients with MELAS, this study aimed to develop an understanding of the patient experience of MELAS through qualitative interviews to identify, describe, and substantiate important and relevant signs, symptoms, and health-related quality-of-life (HRQoL) impact (S/S/I) concepts.
    METHODS: Clinician and patient interviews were conducted virtually using semi-structured interview guides. During 60-minute interviews with five experts in the United States, clinicians were asked for their perspective on S/S/I of patients with MELAS, patient experience of fatigue and cognitive impairment, and whether patients would be able to accurately report and rate their symptoms and complete a 90-minute patient experience interview. During a 45-minute interview conducted with 16 adults with confirmed pathogenic variant and clinical diagnosis of MELAS, patients were asked about S/S/I. Interviews were recorded, transcribed, anonymized, coded, and analyzed for saturation and concept frequency and clarification (e.g., severity, frequency, duration).
    RESULTS: Experts reported 44 distinct S/S and 36 HRQoL impact concepts. All five experts confirmed that cognitive impairment would not inhibit a typical patient's ability to report on their own experiences; three reported that patients with MELAS would not be able to complete a 90-minute interview. Sixteen patient interviews (mean age: 42.3 [11.1], n = 10 women) were conducted. Interviews with patients with MELAS achieved saturation of concept and yielded 35 S/S concepts and 68 HRQoL impacts across 15 domains. The most frequently reported S/S concepts were physical fatigue (n = 15, 93.8%), hearing loss (n = 13, 81.3%), mental fatigue (n = 12, 75.0%), and exercise intolerance and memory problems (n = 11, 68.8% each). The most frequently reported impact domains were adaptive behaviors and work impacts (n = 14, 87.5% each) and emotional function (n = 13, 81.3%).
    DISCUSSION: Patients with MELAS can self-report on S/S/I. Results from both patient and clinician interviews demonstrate that symptoms related to fatigue and cognitive impairment are frequent, bothersome, and important to improve. Assessments of fatigue and cognitive function should therefore be considered key outcome measures in clinical trials enrolling patients with MELAS.
    Keywords:  Concept elicitation; MELAS; Mitochondrial disease; Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes; Patient-centered outcomes; Qualitative interviews
    DOI:  https://doi.org/10.1186/s41687-025-00962-6
  48. Nature. 2025 Oct 31.
      
    Keywords:  CRISPR-Cas9 genome editing; Genetics; Medical research; Personalized medicine
    DOI:  https://doi.org/10.1038/d41586-025-03566-8
  49. Cell Mol Biol Lett. 2025 Oct 28. 30(1): 127
       BACKGROUND: Parkinson's disease (PD) lacks disease-modifying therapies. Fibroblast growth factor 21 (FGF21) is implicated in PD, but its neuroprotective mechanisms via fibroblast growth factor receptor 1 (FGFR1)-sirtuin 1 (Sirt1) remain unclear.
    METHODS: Using 1-methyl-4-phenyl-1,2,3,6-te-trahydropyridine (MPTP)-induced PD mice and lipopolysaccharides (LPS)-stimulated BV2 microglia, this study employed recombinant adeno-associated virus (rAAV)-mediated FGF21 overexpression (OE). Multi-dimensional analyses (behavior, immunofluorescence, molecular docking, Western blot, PCR, transmission electron microscopy (TEM)) assessed FGF21's effects and mechanisms.
    RESULTS: FGF21OE significantly improved motor deficits (gait, rotarod) and non-motor symptoms (depression/anxiety) in PD mice. It repaired the blood-brain barrier (BBB) by upregulating tight junction proteins (claudin, zonula occludens (ZO-1), occludin) and reducing astrocyte activation (glail fibrillary acidicprotein, GFAP). Mechanistically, FGF21 binding to FGFR1 activated Sirt1, enhancing mitochondrial fusion (optic atrophy 1 (OPA1), mitofusin 1 (Mfn1)) and inhibiting fission (dynamin-related protein 1 (Drp1), Fission 1 (Fis1)), improving membrane potential and ultrastructure. FGF21 also activated the AMP-activated protein kinase (AMPK)/mammalian target of rapamycin (mTOR) pathway, boosting PINK1/Parkin-mediated mitophagy and inhibiting Casp3/Bax-dependent apoptosis. Furthermore, FGF21 reduced neuroinflammation by suppressing nuclear factor kappa-B (NF-κB)/NOD-like receptor thermal protein domain associated protein 3 (NLRP3) and shifting microglia from pro-inflammatory M1 to anti-inflammatory M2. Molecular docking and co-IP confirmed FGF21 enhances direct FGFR1-Sirt1 interaction, synergistically regulating these pathways.
    CONCLUSION: FGF21 exerts multi-faceted protection in PD via the FGFR1-Sirt1 axis, including BBB repair, mitochondrial homeostasis restoration, microglial polarization towards M2, balancing autophagy and apoptosis, and promoting neuronal survival.
    Keywords:  Blood–brain barrier; FGF21; Microglia; Mitochondrial dysfunction; Parkinson’s disease; Sirt1
    DOI:  https://doi.org/10.1186/s11658-025-00807-6