bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2025–12–21
76 papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Current understanding of mitochondrial DNA genetic diseases and gene therapy.
  2. Transporting the transporter: TIM22 translocates mitoferrins to enable mitochondrial iron-sulfur cluster synthesis.
  3. The TIM22 carrier translocase supports cell proliferation by facilitating mitochondrial iron uptake for Fe-S biogenesis.
  4. Mutant CHCHD10 disrupts cytochrome c oxidation and activates mitochondrial retrograde signaling.
  5. A systematic bi-genomic split-GFP assay illuminates the mitochondrial matrix proteome and protein targeting routes.
  6. Mitochondrial position responds to glucose stimulation in a model of the pancreatic beta cell.
  7. Identification of Intronic Variants in NDUFA3 as a Cause of Leigh Syndrome by Whole Genome Sequencing and RNA Sequencing.
  8. Counseling and Prognostic Challenges in Survivorship and Mortality in Primary Mitochondrial Disease: Reshaping a Once Bleak Landscape.
  9. Partial restoration of mitochondrial dysfunction by AAV-Ant1 protects from dilated cardiomyopathy in Ant1-/- plus mtDNA mutant mice.
  10. Quantifying variability of mitochondrial markers in m3243A > G myopathy.
  11. VPS13B recruits lipid vesicles to promote mitochondrial fission and quality control.
  12. MISO regulates mitochondrial dynamics and mtDNA homeostasis by establishing membrane subdomains.
  13. The microRNA miR-71 suppresses maladaptive UPRmt signaling through both cell-autonomous and cell-non-autonomous mechanisms.
  14. Functional Screening of NDUFAF6 Variants in Knockout Cells and Complementary Computational Analysis.
  15. TMEM65-dependent Ca2+ extrusion safeguards mitochondrial homeostasis.
  16. The cytochrome c oxidase subunit COX6B1 is required for redox-sensitive early assembly and late stabilization of complex IV.
  17. Two genomes, one destiny: Mitophagy at the crossroads of inheritance and disease.
  18. Comprehensive Iranian guidelines for the diagnosis and management of mitochondrial disorders: an evidence- and consensus-based approach.
  19. Mitochondrial Calcium Signaling in Hepatocyte Health and Disease.
  20. RHOA regulates mitochondria-ER contact sites through modulation of the VAPB/PTPIP51 tether.
  21. Unequal mitochondrial segregation promotes asymmetric fates during neurogenesis.
  22. Autophagy-regulated mitochondrial inheritance controls early CD8+ T cell fate commitment.
  23. Arg339Gln Is a Recurrent Variant in Rare Combined Oxidative Phosphorylation Deficiency 4: A New Patient with Biallelic TUFM Gene Variant.
  24. Amino acid supplementation in mitochondrial aminoacyl-tRNA synthetase defects: two case reports of tyrosine supplementation in YARS2-associated disease and a review of the literature.
  25. Phosphorylated Ubiquitin as a Clinical Biomarker for Mitochondrial Damage in Neurodegenerative Diseases.
  26. Glucose-driven mitochondrial transport adds a new dimension to mitochondrial heterogeneity.
  27. Computational prediction of human genetic variants in the mouse genome.
  28. Mitochondrial RNA cytosolic leakage drives the SASP.
  29. Bioenergetic and protein processing imbalances in iPSC-dopamine neurons from individuals with idiopathic Parkinson's disease.
  30. Lactate-induced mitochondrial magnesium uptake and its metabolic implications in the McArdle disease model.
  31. An integrated view of the structure and function of the human 4D nucleome.
  32. Obstetric history of women with m.3243A>G: an observational cohort study.
  33. Combined ketone body and glutamine supplementation restores aerobic energy production in AGC1-deficient neuronal progenitors.
  34. Mitochondrial transfer as a novel therapeutic approach in ischemic stroke treatment: Current challenges and future perspectives.
  35. Mitochondria to the rescue: organelle trafficking in renal health and disease.
  36. Hydrogen Sulfide Signaling in Neurodegenerative Movement Disorders.
  37. Stochasticity contributes to explaining minority and majority MOMP during apoptosis.
  38. The fate of pyruvate dictates cell growth by modulating cellular redox potential.
  39. Mitochondrial membrane chromatography: Discovery of mitochondrial targeting modulators.
  40. Biallelic FOXRED1 mutations cause infantile mitochondrial encephalopathy with complex I disassembly and basal ganglia degeneration.
  41. Endothelial RAB5IF is required for pathological and developmental retinal angiogenesis.
  42. CRISPR/Cpf1-mediated editing of PINK1 in induced pluripotent stem cells.
  43. Rapid whole genome sequencing in newborn screening for metabolic diseases.
  44. Afg3l2 couples mitochondrial vitamin B12 trafficking to amino acid metabolism to safeguard hematopoietic stem cell homeostasis.
  45. Systematic maps reveal how human chromosomes are organized.
  46. Novel Roles for the Ectoenzyme CD38 in the Maintenance of Transcriptional and Metabolic Homeostasis in Astrocytes.
  47. GABAergic neurons are a key cell type in a Drosophila model of PARK14/PLA2G6-associated neurodegeneration.
  48. Modulation of mitochondrial voltage dependent anion channel: studies on bilayer electrophysiology.
  49. Dysregulated hippocampal fatty acid metabolism following intermittent hypoxemia-induced neonatal brain injury is rescued by treatment with acetate.
  50. Defective RNA processing and ELOA-mediated transcriptional elongation in reversible cellular senescence suggest aging by transcription.
  51. Pharmacological Activation of Mitophagy Confers Neuroprotective Benefits for Amyotrophic Lateral Sclerosis.
  52. Short-term high-dose nicotinamide treatment across glaucoma subtypes reveals increased mtDNA content and minimal metabolomic change in blood.
  53. Sodium disrupts mitochondrial energy metabolism to execute NECSO.
  54. Integrating polygenic signals and single-cell multiomics identifies cell-type-specific regulomes critical for immune- and aging-related diseases.
  55. Mass spectrometry protocol for tear fluid proteome profiling and biomarker discovery.
  56. Subcellular In Vivo Cardiac Proteomics Reveals Sarcomere and Ribosome Interactomes and skNAC's Impact on Cardiac Proteostasis.
  57. Ppid is Necessary for Overnutrition-Induced β-cell Loss.
  58. Citrate trafficking supports rewiring of mitochondrial metabolism via RTG signaling in yeast osmoadaptation.
  59. Multilayered regulation of longevity in Caenorhabditis elegans.
  60. The G3BP stress-granule proteins reinforce the integrated stress response translation programme.
  61. SynSeg: A synthetic data-driven approach for robust subcellular structure segmentation.
  62. Mitochondria-Targeted Nanosystems in the Treatment of Central Nervous System Diseases.
  63. Base editing strategies for in vivo correction of two highly recurrent phenylketonuria variants.
  64. Dysregulated lactate metabolism synergizes with ALS genetic risk factors to accelerate motor decline.
  65. Vesicle-coupled mRNA transport and translation govern intracellular organelle networking.
  66. Dual-targeted molybdenum nanomedicine treats acute pancreatitis by blocking mitochondrial DNA-triggered cGAS-STING signaling via ROS modulation.
  67. Targeting PGC-1α axis Rescues Aberrant Development from Thyroid Hormone Defect in Brain Organoids.
  68. Mitochondrial dysfunction in cellular senescence: a bridge to neurodegenerative disease.
  69. Mitochondrial metabolic remodeling and multi-omics profiling identify plasma biomarkers of myocardial infarction.
  70. Comparison of anti-aging effect of PQQ (Pyrroloquinoline Quinone) and NMN/NR (Nicotinamide Mononucleotide /Nicotinamide Riboside) - possible combination use.
  71. Assessing Gastrointestinal Motility in Caenorhabditis elegans RAC1/CED-10 Mutants as a Tool to Study Early Parkinson's Disease.
  72. EVs from Stem Cells Improve Mitochondrial Dysfunction in Neuronal Disorders.
  73. Endothelial mitochondrial-derived vesicles (EMDVs) with retinal targeted homing properties dynamically modulate the eIF2α-ATF4-CHOP signaling pathway and efficiently restore mitochondrial homeostasis in diabetic retina.
  74. An efficient preprocessing workflow tailored for mitochondrial genome assembly from fragmented DNA.
  75. Stem cells strike back: advancements in Alzheimer's and Parkinson's disease treatment and modeling efforts from 2019 to 2024.
  76. A system for high-throughput axonal imaging of induced pluripotent stem cell-derived human i 3 Neurons.
  1. Yi Chuan. 2025 Dec;47(12): 1300-1325
    Current understanding of mitochondrial DNA genetic diseases and gene therapy.
    Cheng Tang, Shun-Qing Xu, Han-Zeng Li.
      Mitochondria, as crucial organelles within eukaryotic cells, have their proteins and RNAs encoded by both the nuclear genome and the mitochondrial genome. They play vital roles in energy regulation, cellular metabolism, signal transduction, and various other physiological activities. Additionally, mitochondria interact with multiple organelles to collectively maintain cellular homeostasis. Mitochondria can also be transferred between cells and tissues through mechanisms such as migrasomes. Mitochondrial DNA (mtDNA) mutations often cause severe inherited rare diseases, characterized by tissue specificity, heterogeneity, multiple mutation sites, and challenges in achieving a complete cure. Gene editing of mtDNA holds promise for fundamentally curing such diseases. Traditional gene-editing nucleases, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nuclease (TALENs), as well as novel gene editors like DddA-derived cytosine base editors (DdCBEs), have been demonstrated to correct certain mtDNA mutations. However, CRISPR-based technologies-despite their superior programmability and efficiency-are currently limited due to the technical bottleneck of inefficient sgRNA delivery into mitochondria. This article systematically reviews the structure and function of mitochondria, related diseases, and the current state of mtDNA gene-editing therapies. Furthermore, it explores future directions for optimizing therapeutic tools to overcome the challenge of sgRNA delivery, thereby addressing the treatment barriers posed by pathogenic mtDNA mutations in inherited rare diseases.
    Keywords:  CRISPR; mitochondria; mtDNA associated rare diseases; mtDNA editing
    DOI:  https://doi.org/10.16288/j.yczz.25-032
  2. Mol Cell. 2025 Dec 18. pii: S1097-2765(25)00943-8. [Epub ahead of print]85(24): 4483-4484
    Transporting the transporter: TIM22 translocates mitoferrins to enable mitochondrial iron-sulfur cluster synthesis.
    Erdem M Terzi, Richard Possemato.
      Iron is a critical nutrient, especially to power mitochondrial iron-sulfur cofactor synthesis. In this issue of Molecular Cell, Liu et al.1 engineer a fluorescent iron sensor, enabling them to define a critical function of the mitochondrial translocase, TIM22, in powering mitochondrial iron use by proper targeting of the mitochondrial iron importers, the mitoferrins.
    DOI:  https://doi.org/10.1016/j.molcel.2025.11.026
  3. Mol Cell. 2025 Dec 18. pii: S1097-2765(25)00939-6. [Epub ahead of print]85(24): 4587-4601.e7
    The TIM22 carrier translocase supports cell proliferation by facilitating mitochondrial iron uptake for Fe-S biogenesis.
    Shuai Liu, Qingyu Li, Mengye Cao, Zefang Bimo Zhao, Cong Liu, Zhuoran Zhen, Jiankun Ren, Chengyang Liu, Danyang Ruan, Luna Zhang, Wenjuan Zhang, Hao Gong, Xiaolong Liu, Xuejie Zhang, Deng Pan, Weijun Pan, Jiajun Zhu.
      Mitochondria host a number of reductive biosynthetic pathways and rely on extensive metabolite exchanges with the cytosol to support cellular anabolic metabolism. Mitochondrial iron-sulfur cluster (Fe-S) biogenesis is essential for multiple cellular functions, and its disruption causes various inborn genetic diseases. How mammalian cells regulate Fe-S biogenesis remains incompletely understood. Here, mitochondria-focused CRISPR screening and DepMap-based gene co-essentiality analysis consistently reveal that components of the carrier translocase of the inner mitochondrial membrane (TIM22) complex, including TIMM29, are selectively required for Fe-S biogenesis. Mechanistically, loss of TIM22 complex function reduced iron transporter presence on mitochondria, thereby impairing iron uptake from the cytosol. Reconstituting mitochondrial iron level was sufficient to restore Fe-S biogenesis and proliferation of TIMM29-deficient cells or rescue the embryonic development of timm29-deficient zebrafish. Thus, a primary function of the TIM22 carrier translocase is to facilitate transporter-mediated iron uptake required for Fe-S biogenesis, underscoring a biosynthetic role of mitochondria in cellular anabolism.
    Keywords:  TIM22 carrier translocase; cellular metabolism; iron-sulfur cluster; mitochondria
    DOI:  https://doi.org/10.1016/j.molcel.2025.11.022
  4. EMBO Mol Med. 2025 Dec 19.
    Mutant CHCHD10 disrupts cytochrome c oxidation and activates mitochondrial retrograde signaling.
    Márcio Augusto Campos-Ribeiro, Erminia Donnarumma, Hendrik Nolte, Paul Cobine, Elodie Vimont, Dusanka Milenkovic, Juan Diego Hernandez-Camacho, Francina Langa-Vives, Etienne Kornobis, Esthel Pénard, Sonny Yde, Thomas Langer, Véronique Paquis-Flucklinger, Timothy Wai.
      Mutations in CHCHD10, a mitochondrial intermembrane space (IMS) protein implicated in proteostasis and cristae maintenance, cause mitochondrial disease. Knock-in mice modeling the human CHCHD10S59L variant associated with ALS-FTD develop a mitochondrial cardiomyopathy driven by CHCHD10 aggregation and activation of the mitochondrial integrated stress response (mtISR). We show that cardiac dysfunction is associated with dual defects originating at the onset of disease: (1) bioenergetic failure linked to impaired mitochondrial copper homeostasis and cytochrome c oxidation, and (2) maladaptive mtISR signaling via the OMA1-DELE1-HRI axis. Using protease-inactive Oma1E324Q/E324Q knock-in mice, we show that blunting mtISR in Chchd10S55L/+ mice delays cardiomyopathy onset without rescuing CHCHD10 insolubility, cristae defects or OXPHOS impairment. Proteomic profiling of insoluble mitochondrial proteins in Chchd10S55L/+ mice reveals widespread disruptions of mitochondrial proteostasis, including IMS proteins involved in cytochrome c biogenesis. Defective respiration in mutant mitochondria is rescued by the addition of cytochrome c, pinpointing IMS proteostasis disruption as a key pathogenic mechanism. Thus, mutant CHCHD10 insolubility compromises metabolic resilience by impairing bioenergetics and stress adaptation, offering new perspectives for the development of therapeutic targets.
    Keywords:  CHCHD10; Cardiomyopathy; Cytochrome c; Mitochondrial Disease; OMA1
    DOI:  https://doi.org/10.1038/s44321-025-00358-5
  5. Elife. 2025 Dec 16. pii: RP98889. [Epub ahead of print]13
    A systematic bi-genomic split-GFP assay illuminates the mitochondrial matrix proteome and protein targeting routes.
    Yury S Bykov, Solene Zuttion, Dunya Edilbi, Marina Polozova, Johanna Arnold, Sergey Malitsky, Maxim Itkin, Bruno Senger, Ofir Klein, Yeynit Asraf, Hadar Meyer, Hubert D Becker, Roza Kucharczyk, Maya Schuldiner.
      The majority of mitochondrial proteins are encoded in the nuclear genome. Many of them lack clear targeting signals. Therefore, what constitutes the entire mitochondrial proteome is still unclear. We here build on our previously developed bi-genomic (BiG) split-GFP assay (Bader et al., 2020) to solidify the list of matrix and inner membrane mitochondrial proteins. The assay relies on one fragment (GFP1-10) encoded in the mitochondrial DNA enabling specific visualization of only the proteins tagged with a smaller fragment, GFP11, and localized to the mitochondrial matrix or the inner membrane. We used the SWAp-Tag (SWAT) strategy to tag every protein with GFP11 and mated them with the BiG GFP strain. Imaging the collection in six different conditions allowed us to visualize almost 400 mitochondrial proteins, 50 of which were never visualized in mitochondria before, and many are poorly studied dually localized proteins. We use structure-function analysis to characterize the dually localized protein Gpp1, revealing an upstream start codon that generates a mitochondrial targeting signal and explore its unique function. We also show how this data can be applied to study mitochondrial inner membrane protein topology and sorting. This work brings us closer to finalizing the mitochondrial proteome and the freely distributed library of GFP11-tagged strains will be a useful resource to study protein localization, biogenesis, and interactions.
    Keywords:  S. cerevisiae; automated microscopy; biochemistry; cell biology; chemical biology; dual localization; mitochondria; mitochondrial proteome; protein targeting; yeast genetics
    DOI:  https://doi.org/10.7554/eLife.98889
  6. Biophys J. 2025 Dec 18. pii: S0006-3495(25)00767-2. [Epub ahead of print]
    Mitochondrial position responds to glucose stimulation in a model of the pancreatic beta cell.
    Luis Perez, Xue Wen Ng, Michael Mohs, David W Piston, Shankar Mukherji.
      The compartmentalization of eukaryotic cells into membrane-bound organelles with specific subcellular positioning enables precise spatial and temporal control of cellular functions. Although functionally significant mitochondrial localization has been demonstrated in cells such as neurons, it remains unclear how general these cell principles are. Here, we examine the spatial organization of mitochondria within MIN6 pancreatic beta cells under variable glucose conditions. We observe glucose-dependent redistributions of mitochondria, favoring peripheral localization at elevated glucose levels. Our results, formalized into a stochastic model of mitochondrial trafficking, suggest that active mitochondrial transport along microtubules and PKA signaling activity, but not ATP synthesis, are critical regulators of this redistribution. These results suggest that environmentally responsive mitochondrial subcellular positioning may represent a general regulatory mechanism in even nonpolarized cell types.
    DOI:  https://doi.org/10.1016/j.bpj.2025.11.018
  7. Neurol Genet. 2026 Feb;12(1): e200330
    Identification of Intronic Variants in NDUFA3 as a Cause of Leigh Syndrome by Whole Genome Sequencing and RNA Sequencing.
    Kohta Nakamura, Yoshihito Kishita, Ayumu Sugiura, Kokoro Ozaki, Yukiko Yatsuka, Naoyuki Matsumoto, Atsuko Okazaki, Holger Prokisch, Koichi Maruyama, Hiroyasu Iwasa, Kei Murayama, Hiroshi Matsumoto, Akira Ohtake, Yuichi Shiraishi, Yasushi Okazaki.
       Background and Objectives: Leigh syndrome is an important manifestation of childhood-onset primary mitochondrial disease. Panel sequencing and whole exome sequencing are cost-effective for diagnosing mitochondrial diseases; however, more than half of mitochondrial disease cases remain genetically undiagnosed. This study aimed to demonstrate that combining whole genome sequencing (WGS) and RNA sequencing (RNA-seq) analyses can identify disease-causing variants that would otherwise be missed.
    Methods: We performed WGS and RNA-seq on a patient with Leigh syndrome. Chromosomal phasing using Sanger sequencing of parental and patient blood samples was conducted to confirm compound heterozygous variants. RNA-seq data were analyzed for splicing abnormalities. Overexpression studies of wild-type NDUFA3 in patient-derived fibroblasts were performed to assess restoration of mitochondrial function.
    Results: We discovered compound heterozygous intronic variants (c.86-16_86-15del in intron2 and c.164-362G>A in intron3) of the NDUFA3 gene. RNA-seq data analysis revealed intron retention and exonization in NDUFA3. Exonization was related to a variant involving the mobile element Alu that resulted in complex abnormal splicing events. Overexpression of wild-type NDUFA3 restored mitochondrial dysfunction in patient-derived fibroblasts, confirming NDUFA3 as a Leigh syndrome causative gene.
    Discussion: This study highlights the importance of combining WGS and RNA-seq and provides new insights into detecting abnormalities in deep intronic regions, particularly those involving mobile elements, such as Alu. This approach can play a crucial role in identifying genetic variations and elucidating transcriptional control mechanisms that are not readily achieved by conventional methods, especially in the context of mobile element-induced complexities.
    DOI:  https://doi.org/10.1212/NXG.0000000000200330
  8. Pediatr Neurol. 2025 Nov 27. pii: S0887-8994(25)00370-4. [Epub ahead of print]175 223-228
    Counseling and Prognostic Challenges in Survivorship and Mortality in Primary Mitochondrial Disease: Reshaping a Once Bleak Landscape.
    Ibrahim Elsharkawi, Amy Goldstein, Rebecca D Ganetzky, Eva Morava.
      Primary mitochondrial diseases comprise a clinically, genetically, and biochemically heterogenous group of disorders associated with multisystemic involvement and significant morbidity and mortality of various etiologies. To date, no disease modifying therapies have been FDA approved, and treatment is largely symptomatic and supportive. Because of the rarity of mitochondrial specialists, most patients with mitochondrial diseases are cared for by clinicians without mitochondrial-specific expertise. Therefore, these clinicians by necessity rely on existing literature or older prognostic approaches which may be discordant with modern clinical practice and evolving therapeutic strategies and outcomes. Furthermore, existing literature may be skewed to the more severe end of the spectrum as publications may disproportionately focus on the most severe or unusual cases. Prognostic, therapeutic, and palliative discussions should ideally take place in a multidisciplinary setting where shared decision making can take place between the patient, family, and clinician team. Prognosis is increasingly shaped by the unprecedented development of various therapeutic modalities and personalized medicine. We aim to highlight the multipronged challenges and considerations faced in counseling patients and caregivers and draw from our own patient cohorts and observations in contemporary mitochondrial medicine to offer additional insights and future considerations for approaching patient counseling and prognostication.
    Keywords:  Leigh syndrome; MELAS; Mitochondrial disease prognosis; Mitochondrial dysfunction; Primary mitochondrial disease; Survivorship
    DOI:  https://doi.org/10.1016/j.pediatrneurol.2025.11.019
  9. Nat Commun. 2025 Dec 15.
    Partial restoration of mitochondrial dysfunction by AAV-Ant1 protects from dilated cardiomyopathy in Ant1-/- plus mtDNA mutant mice.
    Alessia Angelin, Kierstin Keller, Peiran Lu, Joseph W Guarnieri, Gabrielle A Widjaja, Rasheed Sule, Kevin Janssen, Arnold Olali, Zimu Cen, Valeria Carosi, Maina Beauplan, Deborah G Murdock, Prasanth Potluri, Liming Pei, Douglas C Wallace.
      Primary mitochondrial disease (PMD) patients manifesting cardiomyopathy are twice as likely to die as other PMD patients. One PMD with cardiomyopathy is caused by null mutations in the heart-muscle isoform of the adenine nucleotide translocator (SLC25A4, ANT1) gene, with the severity of cardiomyopathy mediated by mitochondrial DNA. To optimize strategies for addressing mitochondrial cardiomyopathy, we generated an Ant1 null mouse and combined it with the ND6P25L mitochondrial DNA mutation to mimic the hypertrophic versus dilated cardiomyopathies observed in patients. Here, we transduce the neonatal Ant1-/- and Ant1-/-+ND6P25L mouse hearts with an AAV2/9-pDes-Gfp-mAnt1 cDNA vector. We show that restoration of just 10% of Ant1 gene expression was sufficient to ameliorate the cardiomyopathies in these mice. Proteomics and single-nucleus RNA sequencing reveal the reversal of dysregulated mitochondrial metabolic genes, including PGC1α, as well as cardiac contractile and extracellular matrix proteins. Hence, a modest increase in cardiac mitochondrial energetics can have profound benefits on cardiac function and is effective in treating mitochondrial cardiomyopathy.
    DOI:  https://doi.org/10.1038/s41467-025-67134-4
  10. Sci Rep. 2025 Dec 19.
    Quantifying variability of mitochondrial markers in m3243A > G myopathy.
    Tiago M Bernardino Gomes, Jordan B Childs, Valeria Di Leo, Charlotte Warren, Gavin Hudson, Doug M Turnbull, Conor Lawless, Amy E Vincent.
      Myopathy is a prevalent and disabling feature of mitochondrial disease, in which skeletal muscle accumulates fibres with mitochondrial dysfunction in a variable mosaic pattern. This intra-individual spatial heterogeneity, a key consideration in longitudinal assessments, remains largely uncharacterised, hindering mechanistic studies and clinical trials by obscuring or confounding findings. We quantified this variability in m.3243 A > G-related myopathy, a leading cause of adult mitochondrial disease. Post-mortem biopsies from quadriceps femoris and tibialis anterior muscles of four patients were analysed for single-fibre deficiency in oxidative phosphorylation (OXPHOS) complex I and IV, while homogenate mitochondrial DNA (mtDNA) copy number and m.3243 A > G heteroplasmy were respectively determined by quantitative PCR and pyrosequencing. Bootstrapped combinatorial analyses established thresholds for minimum meaningful change above the 97.5th percentile, while accounting for anatomical biopsy distancing. Spatial variability in the proportion of OXPHOS-deficient fibres increased with distancing; within the same muscle, this threshold was 13.8% for NDUFB8 and 9.8% for MT-CO1. Variability in mtDNA copy number modestly increased with distance, while m.3243 A > G heteroplasmy remained largely stable, with within-muscle thresholds of 1,136 copies per nucleus and 8.2%, respectively. These findings provide assay-specific thresholds and offer mechanistic and translational insights for trial design, patient monitoring, and reliable detection of disease progression or therapeutic response.
    Keywords:  Heteroplasmy; M.3243A > G; Mitochondria; Mitochondrial DNA copy number; Myopathy; Oxidative phosphorylation
    DOI:  https://doi.org/10.1038/s41598-025-33106-3
  11. Nat Commun. 2025 Dec 16.
    VPS13B recruits lipid vesicles to promote mitochondrial fission and quality control.
    Soo-Kyeong Lee, Hyun-Ji Ham, Semin Park, Hye Eun Lee, Ji Young Mun, Deok-Jin Jang, Jin-A Lee.
      Mutations in the gene VPS13B, which encodes a Golgi-associated protein, cause the neurodevelopmental disorder Cohen syndrome, but the protein's function is unclear. Here we show that this protein is essential for mitochondrial morphology and quality control. Cells lacking VPS13B, including neurons derived from Cohen syndrome patients, exhibit abnormally elongated and fused mitochondria with reduced membrane potential and impaired mitophagy. Mechanistically, the protein localizes to Mitofusin 2-positive mitochondria via its C-terminal region and recruits phosphatidylinositol-4-phosphate-rich Golgi vesicles to mitochondrial fission sites. Loss of VPS13B or depletion of phosphatidylinositol-4-phosphate results in incomplete mitochondrial fission despite normal recruitment of Dynamin-related protein 1, indicating that lipid transfer by VPS13B is required for membrane fission. VPS13B links Golgi-derived lipid vesicles to the mitochondrial fission machinery, ensuring proper mitochondrial fission and quality control and potentially explaining the mitochondrial defects in Cohen syndrome.
    DOI:  https://doi.org/10.1038/s41467-025-67445-6
  12. Nat Cell Biol. 2025 Dec 15.
    MISO regulates mitochondrial dynamics and mtDNA homeostasis by establishing membrane subdomains.
    Yue Zhang, Yuchen Xia, Xinhui Wang, Yueqin Xia, Shang Wu, Jianshuang Li, Xuan Guo, Qinghua Zhou, Li He.
      Mitochondrial dynamics and mtDNA homeostasis have been linked to specialized mitochondrial subdomains known as small MTFP1-enriched mitochondria (SMEM), though the underlying molecular mechanisms remain unclear. Here we identified MISO (mitochondrial inner membrane subdomain organizer), a conserved protein that regulates both mitochondrial dynamics and SMEM formation in Drosophila and mammalian cells. MISO inhibits fusion by recruiting MTFP1 and promotes fission through FIS1-DRP1. Furthermore, MISO drives SMEM biogenesis and facilitates their peripheral fission that promotes lysosomal degradation of mtDNA. Genetic ablation of MISO abolishes SMEM generation, confirming that MISO is both necessary and sufficient for SMEM formation. Inner mitochondrial membrane stresses, including mtDNA damages, OXPHOS dysfunction and cristae disruption, stabilize the otherwise short-lived MISO protein, thereby triggering SMEM assembly. This process depends on the C-terminal domain of MISO, likely mediated by oligomerization. Together, our findings reveal a molecular pathway through which inner mitochondrial membrane stresses modulate mitochondrial dynamics and mtDNA homeostasis via MISO-orchestrated SMEM organization.
    DOI:  https://doi.org/10.1038/s41556-025-01829-0
  13. Nat Commun. 2025 Dec 14.
    The microRNA miR-71 suppresses maladaptive UPRmt signaling through both cell-autonomous and cell-non-autonomous mechanisms.
    Ina Kirmes, Grace Ching Ching Hung, Anne Hahn, Chuan-Yang Dai, Daniel Campbell, Arnaud Ahier, Rachel Shin Yie Lee, Alexander Palmer, Steven Zuryn.
      Mitochondria play a central role in metabolism and biosynthesis, but function also as platforms that perceive and communicate environmental and physiological stressors to the nucleus and distal tissues. Systemic mitochondrial signaling is thought to synchronize and amplify stress responses throughout the whole body, but during severe or chronic damage, overactivation of mitochondrial stress pathways may be maladaptive and exacerbate aging and metabolic disorders. Here we uncover a protective micro(mi)RNA response to mtDNA damage in Caenorhabditis elegans that prolongs tissue health and function by interfering with mitochondrial stress signaling. Acting within muscle cells, we show that the miRNA miR-71 is induced during severe mitochondrial damage by the combined activities of DAF-16, HIF-1, and ATFS-1, where it restores sarcomere structure and animal locomotion by directly suppressing the inordinate activation of DVE-1, a key regulator of the mitochondrial unfolded protein response (UPRmt). Indirectly, miR-71 also reduces the levels of multiple neuro- and insulin-like peptides and their secretion machinery, resulting in decreased cell-non-autonomous signaling of mitochondrial stress from muscle to glia cells. miR-71 therefore beneficially coordinates the suppression of both local and systemic mitochondrial stress pathways during severe organelle dysfunction. These findings open the possibility that metabolic disorders could be ameliorated by limiting the overactivation of mitochondrial stress responses through targeted small RNAs.
    DOI:  https://doi.org/10.1038/s41467-025-67198-2
  14. J Clin Lab Anal. 2025 Dec 15. e70147
    Functional Screening of NDUFAF6 Variants in Knockout Cells and Complementary Computational Analysis.
    Feng Jiang, Ayumu Sugiura, Yoshihito Kishita, Kohta Nakamura, Xinju Qi, Yuxin Liu, Kei Murayama, Yasushi Okazaki.
       BACKGROUND: NDUFAF6 (NADH:ubiquinone oxidoreductase complex assembly factor 6) is a nuclear-encoded gene essential for the assembly of mitochondrial respiratory chain complex I (NADH:ubiquinone oxidoreductase), the largest and most intricate component of the oxidative phosphorylation system, and its mutations are associated with mitochondrial diseases. However, the functional consequences of many NDUFAF6 variants remain unclear.
    METHODS: We selected 24 NDUFAF6 variants from published studies and our internal sequencing database. Using CRISPR-Cas9, we generated NDUFAF6 knockout HEK293FT cells and transfected them with wild-type or mutant expression vectors. Functional validation was performed using a luminescence-based ATP assay under mitochondrial stress. In silico predictions were conducted using multiple tools, and ColabFold, MitoFates, and ProtScale were used for structural modeling, mitochondrial targeting analysis, and hydrophobicity profiling.
    RESULTS: Six variants (p.Pro26fs, p.Asp69Val, p.Arg113Ter, p.Leu193Ter, p.Arg303Ter, and p.Lys331Arg) failed to restore ATP levels in knockout cells, indicating a significant loss of function. Among these, p.Asp69Val and p.Arg113Ter were consistent with ClinVar classifications. However, other variants such as p.Arg303Ter and p.Lys331Arg also showed functional impairment, highlighting discrepancies between database annotations and experimental results. Most variants retained mitochondrial targeting features, though p.Pro26fs exhibited a shifted MPP cleavage site. Hydrophobicity analysis indicated structural instability in several variants.
    CONCLUSIONS: Our study highlights the importance of experimental validation in improving the classification of NDUFAF6 variants. The ATP-based functional assay provides a useful and quantitative approach for assessing mitochondrial variant effects, which may complement in silico predictions and contribute to future efforts in mitochondrial disease diagnostics.
    Keywords:   NDUFAF6 ; ATP assay; mitochondrial diseases; mitochondrial dysfunction; variants of uncertain significance
    DOI:  https://doi.org/10.1002/jcla.70147
  15. Nat Commun. 2025 Dec 17.
    TMEM65-dependent Ca2+ extrusion safeguards mitochondrial homeostasis.
    Massimo Vetralla, Lena Wischhof, Asrat Kahsay, Vanessa Cadenelli, Enzo Scifo, Beijia Xie, Miriana Sbrissa, Maëlle Sandhira Habert, Dan Ehninger, Rosario Rizzuto, Daniele Bano, Diego De Stefani.
      The bidirectional transport of Ca2+ into and out of mitochondria regulates metabolism, signaling, and cell fate. While influx is mediated by the Mitochondrial Calcium Uniporter (MCU) complex, efflux mechanisms are more diversified, involving Na⁺ or H⁺ exchange pathways. We here demonstrate that TMEM65 is a fundamental component of the Ca2+ efflux machinery of mitochondria. Its overexpression specifically enhances Na⁺- and Li⁺-dependent mitochondrial Ca²⁺ extrusion. This effect is inhibited by CGP-37157 and does not depends on NCLX, currently considered the bona fide mitochondrial Na+/Ca2+ exchanger. Its downregulation chronically elevates basal [Ca²⁺]mt and impairs efflux upon stimulation. In Caenorhabditis elegans, deletion of TMEM65 homologs compromises embryonic development under mild thermal stress, causing necrotic lesions that are suppressed by genetic inhibition of MCU-1. These findings highlight a molecular component that may be relevant in pathological settings in which excessive mitochondrial Ca2+ accumulation critically contribute to degenerative pathways.
    DOI:  https://doi.org/10.1038/s41467-025-67647-y
  16. J Biol Chem. 2025 Dec 17. pii: S0021-9258(25)02922-9. [Epub ahead of print] 111070
    The cytochrome c oxidase subunit COX6B1 is required for redox-sensitive early assembly and late stabilization of complex IV.
    Kristýna Čunátová, Marek Vrbacký, Michal Knězů, Alena Pecinová, Lukáš Alán, Josef Houštěk, Erika Fernández-Vizarra, Tomáš Mráček, Petr Pecina.
      COX6B1 is a nuclear-encoded subunit of the human mitochondrial cytochrome c oxidase (cIV) located in its intermembrane space-facing region. The relevance of COX6B1 in mitochondrial physiopathology was highlighted by the missense pathogenic variants associated with cIV deficiency. Despite the assigned COX6B1 role as a late incorporation subunit, the COX6B1 human cell line knock-out (KO) exhibited a total loss of cIV. To get a deeper insight into the mechanisms driving the lack of cIV assembly or destabilization in the absence of COX6B1, we used the COX6B1 KO cell background to express alternative oxidase and COX6B1 pathogenic variants. These analyses uncovered that the COX6B1 subunit is indispensable for redox-sensitive early cIV assembly steps, besides its contribution to the stabilization of cIV in the late assembly stages. In addition, we have evidenced the incorporation of partially assembled cIV modules directly into supercomplex structures, supporting the 'cooperative assembly' model for respiratory chain biogenesis.
    Keywords:  COX; COX6B1; COX6B2; OXPHOS assembly; alternative oxidase; cIV; complex IV; cytochrome c oxidase; mitochondrial deficiency; respiratory chain supercomplexes
    DOI:  https://doi.org/10.1016/j.jbc.2025.111070
  17. Cell Chem Biol. 2025 Dec 18. pii: S2451-9456(25)00390-3. [Epub ahead of print]32(12): 1439-1441
    Two genomes, one destiny: Mitophagy at the crossroads of inheritance and disease.
    Chih-Yao Chung, Kritarth Singh, Brigida R Pinho, Jorge M A Oliveira, Michael R Duchen.
      Mechanisms ensuring mito-nuclear compatibility are poorly understood. In a recent study published in Science,1 Frison et al. found that a mouse mitochondrial DNA (mtDNA) mutation can escape mitochondrial surveillance in embryogenesis by repressing the ubiquitin-proteasome system. Inhibition of USP30 restored ubiquitin-mediated mitophagy and reduced mutant burden, suggesting a potential therapeutic target for mtDNA disorders.
    DOI:  https://doi.org/10.1016/j.chembiol.2025.11.010
  18. Orphanet J Rare Dis. 2025 Dec 19. 20(1): 623
    Comprehensive Iranian guidelines for the diagnosis and management of mitochondrial disorders: an evidence- and consensus-based approach.
    Setila Dalili, Noushin Rostampour, Seyedeh Tahereh Mousavi, Saeid Sadeghi Joni, Nejat Mahdieh, Afagh Hassanzadeh Rad, Seyede Tahoura Hakemzadeh, Sara Nikpour, Ali Talea, Hossein Moravvej.
      Mitochondrial disorders are a heterogeneous group of inherited metabolic diseases resulting from dysfunctions in oxidative phosphorylation. These conditions predominantly affect high-energy-demand organs such as the brain, heart, liver, and muscles, leading to diverse clinical manifestations and diagnostic challenges. This article presents the first comprehensive Iranian guideline for the diagnosis and management of mitochondrial diseases, developed through an evidence-based and consensus-driven methodology. We conducted a structured literature review across major biomedical databases from 2000 to 2023 and engaged a multidisciplinary panel of Iranian experts to establish context-specific recommendations. The guideline covers clinical presentations, laboratory biomarkers, neuroimaging features, genetic diagnostics, and treatment approaches including "cocktail therapy" and acute management protocols. It also integrates a mitochondrial disease scoring system to standardize diagnosis and provides detailed insights into safe anesthesia practices for affected individuals. Special attention is given to practical implementation in resource-limited settings. These guidelines aim to enhance diagnostic accuracy, optimize management strategies, and improve the quality of life for patients with mitochondrial disorders across Iran and similar healthcare systems.
    Keywords:  Diagnosis; Genetic testing; Mitochondrial diseases
    DOI:  https://doi.org/10.1186/s13023-025-04127-y
  19. Cold Spring Harb Perspect Biol. 2025 Dec 19. pii: a041773. [Epub ahead of print]
    Mitochondrial Calcium Signaling in Hepatocyte Health and Disease.
    David R Eberhardt, Dipayan Chaudhuri.
      Calcium (Ca2+) is vital in hepatocyte metabolism and plays a dual role in liver mitochondrial function: Physiological Ca2+ stimulates respiration and mitochondrial dynamics-processes crucial for proper metabolic functioning. However, Ca2+ overload can be catastrophic, leading to mitochondrial dysfunction and the halt of metabolic processes. This dichotomy plays out in liver diseases such as metabolic dysfunction-associated steatohepatitis (MASH) and alcoholic liver disease (ALD), where excess lipid and alcohol, respectively, result in pathological changes in this precarious Ca2+ balance, impairing liver function and contributing to liver failure. In this review, we discuss the complex processes of Ca2+ signaling in hepatic mitochondria and how these processes are altered or fail in liver disease states.
    DOI:  https://doi.org/10.1101/cshperspect.a041773
  20. Nat Commun. 2025 Dec 14. 16(1): 11260
    RHOA regulates mitochondria-ER contact sites through modulation of the VAPB/PTPIP51 tether.
    Zheng Yang, Shintaro Nakajima, Hsiuchen Chen, Yogaditya Chakrabarty, Huibao Feng, David C Chan.
      The mitochondria-endoplasmic reticulum contact site (MERCS) is critical for calcium exchange, phospholipid transfer, and bioenergetics. Impairment of MERCS is implicated in numerous pathological conditions, including cancer and neurodegenerative diseases. Remodeling of MERCS can affect calcium signaling or metabolism, but the mechanisms involved in dynamic MERCS remodeling are unknown. Employing a genome-wide CRISPRi screen, we uncover the ability of the small GTPase RHOA to tune the cellular MERCS level. RHOA knockdown, or increasing its degradation by CUL3 overexpression, reduces the MERCS level; conversely, upregulation of RHOA increases the MERCS level. RHOA binds to the ER protein VAPB and regulates complex formation between VAPB and mitochondrial PTPIP51, which form a tethering complex at the interface between ER and mitochondria. Furthermore, this regulatory mechanism is perturbed by disease alleles of RHOA, CUL3, and VAPB involved in cancer, hyperkalemia, and neurodegeneration, suggesting that MERCS may be affected in a range of pathological conditions. This study identifies RHOA as a regulator of mitochondria-ER communication, providing mechanistic insights into the dynamic remodeling of MERCS and potential therapeutic strategies for diseases linked to MERCS dysfunction.
    DOI:  https://doi.org/10.1038/s41467-025-66138-4
  21. Nat Commun. 2025 Dec 15. 16(1): 11049
    Unequal mitochondrial segregation promotes asymmetric fates during neurogenesis.
    Benjamin Bunel, Rémi Leclercq, Rosette Goïame, Arnaud Gautier, Xavier Morin, Evelyne Fischer.
      Asymmetric cell division plays a critical role during vertebrate neurogenesis by generating neuronal cells while maintaining a pool of progenitors. It relies on unequal distribution of cell fate determinants during progenitor division. Here, we use live imaging in the chick embryonic neuroepithelium to demonstrate that mitochondria behave as asymmetric fate determinants during mitosis. We show that the frequency of unequal distribution of mitochondria increases in parallel with the rate of asymmetric divisions during development. Furthermore, fate tracking experiments reveals that following progenitor division, a cell inheriting fewer mitochondria than its sister consistently differentiates into a neuron. We set up a chemogenetic approach to experimentally displace mitochondria specifically during mitosis to force their unequal inheritance and find that this drives premature neuronal differentiation. In this work, we establish a direct causal relationship between unequal mitochondrial inheritance and the asymmetric fate of sister cells in vivo, revealing a pivotal mechanism for neurogenesis.
    DOI:  https://doi.org/10.1038/s41467-025-66932-0
  22. Nat Cell Biol. 2025 Dec 19.
    Autophagy-regulated mitochondrial inheritance controls early CD8+ T cell fate commitment.
    Mariana Borsa, Ana Victoria Lechuga-Vieco, Amir H Kayvanjoo, Edward Jenkins, Yavuz Yazicioglu, Ewoud B Compeer, Felix C Richter, Simon Rapp, Robert Mitchell, Tom Youdale, Hien Bui, Emilia Kuuluvainen, Michael L Dustin, Linda V Sinclair, Pekka Katajisto, Anna Katharina Simon.
      T cell immunity deteriorates with age, accompanied by a decline in autophagy and asymmetric cell division. Here we show that autophagy regulates mitochondrial inheritance in CD8+ T cells. Using a mouse model that enables sequential tagging of mitochondria in mother and daughter cells, we demonstrate that autophagy-deficient T cells fail to clear premitotic old mitochondria and inherit them symmetrically. By contrast, autophagy-competent cells that partition mitochondria asymmetrically produce daughter cells with distinct fates: those retaining old mitochondria exhibit reduced memory potential, whereas those that have not inherited old mitochondria and exhibit higher mitochondrial turnover are long-lived and expand upon cognate-antigen challenge. Multiomics analyses suggest that early fate divergence is driven by distinct metabolic programmes, with one-carbon metabolism activated in cells retaining premitotic mitochondria. These findings advance our understanding of how T cell diversity is imprinted early during division and support the development of strategies to modulate T cell function.
    DOI:  https://doi.org/10.1038/s41556-025-01835-2
  23. Mol Syndromol. 2025 Nov 17.
    Arg339Gln Is a Recurrent Variant in Rare Combined Oxidative Phosphorylation Deficiency 4: A New Patient with Biallelic TUFM Gene Variant.
    Aysel Tekmenuray-Unal, Muhammet Tas, Murat Kangin, A Ergul Bozaci.
       Introduction: Combined oxidative phosphorylation deficiency 4 (COXPD4, OMIM #610678) is a very rare mitochondrial disorder caused by biallelic variants in TUFM gene. The condition is characterized by microcephaly, severe early-onset lactic acidosis, and progressive, often fatal, infantile encephalopathy. To date, only 8 patients with biallelic TUFM variants have been reported.
    Case Presentation: We present a case of a female infant with microcephaly who died from severe lactic acidosis at 7 months of age. Genetic analysis revealed homozygous c.1016G>A (p.Arg339Gln) variant in the TUFM gene, which has previously been reported in three other COXPD4 cases. This is the fourth publication describing the same variant in this rare disorder, suggesting that it is a recurrent variant in COXPD4 patients.
    Conclusion: Arg339Gln variant was found in all patients from Turkey and is considered a potential founder mutation. This report aims to contribute to the phenotypic spectrum of COXPD4, explore the frequency and clinical presentation of the reported variants, enhance the understanding of genotype-phenotype correlations, and raise awareness of rare mitochondrial disorders.
    Keywords:  Arg339Gln; Combined oxidative phosphorylation deficiency 4; Elongation factor Tu; R339Q; TUFM; c.1016G>A
    DOI:  https://doi.org/10.1159/000549573
  24. Front Pediatr. 2025 ;13 1699348
    Amino acid supplementation in mitochondrial aminoacyl-tRNA synthetase defects: two case reports of tyrosine supplementation in YARS2-associated disease and a review of the literature.
    Giulia Ferrera, Giorgia Segre, Eleonora Lamantea, Daniele Ghezzi, Marta Rivelli, Anna Ardissone.
       Background: Mitochondrial diseases (MDs) caused by pathogenic variants in aminoacyl-tRNA synthetase (ARS) genes, either cytosolic (ARS1) or mitochondrial (ARS2), are rare and clinically diverse. YARS2 deficiency causes myopathy, lactic acidosis, and sideroblastic anemia (MLASA2). No treatments exist, although targeted amino acid (AA) supplementation could function as a possible therapy, as many ARS variants retain partial activity. While benefits have been reported in several ARS1 disorders, evidence in ARS2 diseases, including YARS2 deficiency, remains limited.
    Methods: We report two siblings with genetically confirmed MLASA2 due to homozygous YARS2 variants who received oral tyrosine for 12 months. Clinical, biochemical, cardiac, and thyroid safety assessments were performed at baseline and follow-up. Standardized measures tracked motor function, symptoms, and quality of life. A systematic review of AA supplementation in ARS2 deficiencies was also conducted.
    Results: Tyrosine was well tolerated. The more severely affected sibling showed improvements in motor function, endurance, and quality of life, with modest prolongation of transfusion intervals. The milder sibling reported increased energy and functional gains. Cardiac function remained stable. Literature review revealed only five prior ARS2 cases treated with AA supplementation, with variable outcomes.
    Conclusion: YARS2-related MLASA2 is a severe disorder associated with high morbidity and premature mortality. No spontaneous recovery has been reported, supporting tyrosine as the likely driver of observed improvements. No cardiac or thyroid toxicities were detected during treatment. Prior reports, although limited, support the feasibility of this treatment. Our findings suggest tyrosine is a promising candidate therapy in YARS2 deficiency; larger multicenter studies are needed to validate our data.
    Keywords:  ARS2; MLASA2; YARS2; amino acids; aminoacyl-tRNA synthetase defect; treatment; tyrosine
    DOI:  https://doi.org/10.3389/fped.2025.1699348
  25. Aging Dis. 2025 Dec 05.
    Phosphorylated Ubiquitin as a Clinical Biomarker for Mitochondrial Damage in Neurodegenerative Diseases.
    Fabienne C Fiesel, Jens O Watzlawik, Michael G Heckman, Sophia G Blumenfeld, Michael J Rigby, Mohammed Kehili, Katja Lohmann, Christine Klein, Derek P Narendra, Clemens R Scherzer, Nilufer Ertekin-Taner, Neill R Graff-Radford, Zbigniew K Wszolek, Owen A Ross, Wolfdieter Springer.
      Phosphorylated ubiquitin (pS65-Ub) is generated by the kinase-ligase pair PINK1-Parkin to selectively label damaged mitochondria for degradation via the autophagy-lysosome system (mitophagy). Consistent with increasing mitochondrial and lysosomal dysfunctions, pS65-Ub accumulates with aging in human autopsy brain and in mice. pS65-Ub levels are strongly and independently elevated in brains from subjects with Alzheimer's or Parkinson's disease compared to age-matched, neurologically normal controls. Furthermore, pS65-Ub levels have been used to identify disease risk and potential resilience factors in cells and in human brain. However, it remains unknown whether pS65-Ub measured in biofluids may also be suitable as a clinical biomarker. Here, we used a validated sandwich ELISA based on the Mesoscale discovery platform to assess pS65-Ub levels in over 1500 plasma samples from different cohorts across a spectrum of mild cognitive impairment, Alzheimer's disease, or Parkinson's disease. We further analyzed almost 150 CSF samples from two independent case-control series with Parkinson's disease to determine whether pS65-Ub levels are associated with disease status and other clinical parameters. While pS65-Ub levels are significantly changed with disease compared to controls in certain samples, current measurements in plasma are not sufficiently discriminatory to serve as a robust diagnostic marker. However, in CSF, pS65-Ub levels were decreased in patients with Parkinson's disease compared to controls, and there was better discrimination between these groups. Our data indicate that pS65-Ub shows promise as a biomarker in CSF but will require further replication in larger cohorts and possibly in combination with additional other measures.
    DOI:  https://doi.org/10.14336/AD.2025.1220
  26. Biophys J. 2025 Dec 18. pii: S0006-3495(25)00768-4. [Epub ahead of print]
    Glucose-driven mitochondrial transport adds a new dimension to mitochondrial heterogeneity.
    Abdul Haseeb Khan, Tatsuhisa Tsuboi.
      
    DOI:  https://doi.org/10.1016/j.bpj.2025.11.019
  27. Nat Biotechnol. 2025 Dec 18.
    Computational prediction of human genetic variants in the mouse genome.
    Kexin Dong, Samuel I Gould, Minghang Li, Francisco J Sánchez Rivera.
      The design of genetically engineered mouse models would benefit from a computational pipeline to predict mouse genetic variants that mirror the sequence and functional effects of human disease variants. Here we present H2M (human-to-mouse), which achieves this by integrating mouse-to-human and paralog-to-paralog variant mapping analyses with genome-editing tools. We provide a database containing >3 million human-mouse equivalent mutation pairs and base-editing and prime-editing libraries to engineer 4,944 variant pairs.
    DOI:  https://doi.org/10.1038/s41587-025-02925-0
  28. Nat Commun. 2025 Dec 15. 16(1): 10992
    Mitochondrial RNA cytosolic leakage drives the SASP.
    Stella Victorelli, Madeline Eppard, Hélène Martini, Seung-Hwa Woo, Stacia P A Everts, Gung Lee, Nicholas Pirius, Nuan Han, Eugene Y Liang, Ana Catarina Franco, Yeaeun Han, Dominik Saul, Eva Nóvoa, Rubén Nogueiras, Patrick L Splinter, Steven P O'Hara, Olivia Morgenthaler, Lucía Valenzuela-Pérez, Hyun Se Kim Lee, Diana Jurk, Nicholas F LaRusso, Petra Hirsova, João F Passos.
      Senescent cells secrete proinflammatory factors known as the senescence-associated secretory phenotype (SASP), contributing to tissue dysfunction and aging. Mitochondrial dysfunction is a key feature of senescence, influencing SASP via mitochondrial DNA (mtDNA) release and cGAS/STING pathway activation. Here, we demonstrate that mitochondrial RNA (mtRNA) also accumulates in the cytosol of senescent cells, activating RNA sensors RIG-I and MDA5, leading to MAVS aggregation and SASP induction. Inhibition of these RNA sensors significantly reduces SASP factors. Furthermore, BAX and BAK play a key role in mtRNA leakage during senescence, and their deletion diminishes SASP expression in vitro and in a mouse model of Metabolic Dysfunction-Associated Steatohepatitis (MASH). These findings highlight mtRNA's role in SASP regulation and its potential as a therapeutic target for mitigating age-related inflammation.
    DOI:  https://doi.org/10.1038/s41467-025-66159-z
  29. Neurobiol Dis. 2025 Dec 12. pii: S0969-9961(25)00439-5. [Epub ahead of print] 107222
    Bioenergetic and protein processing imbalances in iPSC-dopamine neurons from individuals with idiopathic Parkinson's disease.
    Kelsey Bernard, Mandi J Corenblum, Paola Tonino, Lalitha Madhavan.
      Patient induced pluripotent stem cell (iPSC)-based models represent a powerful human system to gain insights into the etiopathology of Parkinson's disease (PD). Here, we studied several iPSC-derived dopamine neuron (iPSC-DAN) lines, from individuals with idiopathic PD, which is the most common form of PD. Specifically, using iPSC-DAN differentiated for 50-55 days, we performed an in-depth analysis of different bioenergetic pathways and cellular quality control mechanisms in the cells. Our results showed wide ranging impairments in oxidative phosphorylation (OXPHOS), glycolysis and creatine kinase pathways in the PD dopamine (DA) neurons. Specifically, the PD neurons exhibited reduced oxygen consumption rates (OCR) at baseline and after challenges with mitochondrial inhibitors, as well as decreased glycolytic reserves measured via ECAR. This translated to lower OCR:ECAR ratios signifying more reliance on glycolysis vs OXPHOS in the PD cells. Moreover, a mislocalization of creatine kinase B to mitochondria was seen in the PD cells. These energetic changes occurred alongside the enhanced expression of mitochondrial fission proteins, disrupted mitophagy and oxidative stress. Additionally, the PD neurons contained more monomeric, phosphorylated, and aggregated forms of alpha synuclein and displayed reduced viability. Ultrastructural examination through immuno-electron microscopy showed more alpha synuclein gold particles directly associated with mitochondria and packed into autophagic vesicles. In essence, these data capture a web of key changes, associated with neuronal degeneration, in human iPSC-DAN from persons with idiopathic PD.
    Keywords:  Dopamine neurons; Glycolysis; Human induced pluripotent stem cells; Oxidative phosphorylation; Protein quality control, alpha Synuclein; Sporadic Parkinson's disease
    DOI:  https://doi.org/10.1016/j.nbd.2025.107222
  30. Biochim Biophys Acta Mol Basis Dis. 2025 Dec 11. pii: S0925-4439(25)00480-6. [Epub ahead of print]1872(3): 168130
    Lactate-induced mitochondrial magnesium uptake and its metabolic implications in the McArdle disease model.
    Thiruvelselvan Ponnusamy, Jeremy Mehta, Haris Waseem, Marianne Assogba, Asha Parveen Sakkarai Mohamed, Shibani Kudchadkar, Paul Herold, Kalimuthusamy Natarajaseenivasan, Santhanam Shanmughapriya.
      McArdle disease, caused by mutations in the pygm encoding myophosphorylase, impairs muscle glycogenolysis and lactate production during exercise, leading to severe energy deficits. Here, we report that the decreased lactate production in McArdle disease regulates mitochondrial magnesium (mMg2+) uptake, with major metabolic consequences in skeletal muscle. Using a CRISPR/Cas9-generated pygm knockout (KO) rat model, we demonstrate that KO rats fail to elevate lactate during static muscle contraction and exhibit diminished mMg2+ uptake, disrupted ATP synthesis, and impaired mitochondrial respiration. In vitro, caffeine-stimulated KO myotubes showed preserved Ca2+ oscillations but lacked lactate production and mMg2+ uptake. Restoration of lactate levels via glucose supplementation rescued mMg2+ transport and improved metabolic output. These findings underscore the significance of lactate as a crucial regulator of mMg2+ homeostasis and provide valuable mechanistic insights into the metabolic dysfunction observed in McArdle disease.
    Keywords:  Glycogen storage disease type V; Lactate signaling; Lactate-Mg(2+) axis; McArdle disease; Metabolic myopathy; Mitochondrial Mg(2+) mobilization; Myophosphorylase deficiency
    DOI:  https://doi.org/10.1016/j.bbadis.2025.168130
  31. Nature. 2025 Dec 17.
    An integrated view of the structure and function of the human 4D nucleome.
    Job Dekker, Betul Akgol Oksuz, Yang Zhang, Ye Wang, Miriam K Minsk, Shuzhen Kuang, Liyan Yang, Johan H Gibcus, Nils Krietenstein, Oliver J Rando, Jie Xu, Derek H Janssens, Steven Henikoff, Alexander Kukalev, Willemin Andréa, Warren Winick-Ng, Rieke Kempfer, Ana Pombo, Miao Yu, Pradeep Kumar, Liguo Zhang, Andrew S Belmont, Takayo Sasaki, Tom van Schaik, Laura Brueckner, Daan Peric-Hupkes, Bas van Steensel, Ping Wang, Haoxi Chai, Minji Kim, Yijun Ruan, Ran Zhang, Sofia A Quinodoz, Prashant Bhat, Mitchell Guttman, Wenxin Zhao, Shu Chien, Yuan Liu, Sergey V Venev, Dariusz Plewczynski, Ibai Irastorza Azcarate, Dominik Szabó, Christoph J Thieme, Teresa Szczepińska, Mateusz Chiliński, Kaustav Sengupta, Mattia Conte, Andrea Esposito, Alex Abraham, Ruochi Zhang, Yuchuan Wang, Xingzhao Wen, Qiuyang Wu, Yang Yang, Jie Liu, Lorenzo Boninsegna, Asli Yildirim, Yuxiang Zhan, Andrea Maria Chiariello, Simona Bianco, Lindsay Lee, Ming Hu, Yun Li, R Jordan Barnett, Ashley L Cook, Daniel J Emerson, Claire Marchal, Peiyao Zhao, Peter J Park, Burak H Alver, Andrew J Schroeder, Rahi Navelkar, Clara Bakker, William Ronchetti, Shannon Ehmsen, Alexander D Veit, Nils Gehlenborg, Ting Wang, Daofeng Li, Xiaotao Wang, Mario Nicodemi, Bing Ren, Sheng Zhong, Jennifer E Phillips-Cremins, David M Gilbert, Katherine S Pollard, Frank Alber, Jian Ma, William S Noble, Feng Yue.
      The dynamic three-dimensional (3D) organization of the human genome (the 4D nucleome) is linked to genome function. Here we describe efforts by the 4D Nucleome Project1 to map and analyse the 4D nucleome in widely used H1 human embryonic stem cells and immortalized fibroblasts (HFFc6). We produced and integrated diverse genomic datasets of the 4D nucleome, each contributing unique observations, which enabled us to assemble extensive catalogues of more than 140,000 looping interactions per cell type, to generate detailed classifications and annotations of chromosomal domain types and their subnuclear positions, and to obtain single-cell 3D models of the nuclear environment of all genes including their long-range interactions with distal elements. Through extensive benchmarking, we describe the unique strengths of different genomic assays for studying the 4D nucleome, providing guidelines for future studies. Three-dimensional models of population-based and individual cell-to-cell variation in genome structure showed connections between chromosome folding, nuclear organization, chromatin looping, gene transcription and DNA replication. Finally, we demonstrate the use of computational methods to predict genome folding from DNA sequence, which will facilitate the discovery of potential effects of genetic variants, including variants associated with disease, on genome structure and function.
    DOI:  https://doi.org/10.1038/s41586-025-09890-3
  32. J Med Genet. 2025 Dec 18. pii: jmg-2025-110875. [Epub ahead of print]
    Obstetric history of women with m.3243A>G: an observational cohort study.
    Petra Kuikka, Hilkka Nikkinen, Kari Majamaa, Mika Henrik Martikainen.
       BACKGROUND: Mitochondrial diseases are genetic disorders arising from pathogenic variants in nuclear or mitochondrial DNA (mtDNA) characterised by respiratory chain dysfunction. Clinical manifestations are diverse, and treatment is mostly symptomatic. Mitochondria are maternally inherited, but new reproductive technologies may prevent the transmission of pathogenic mtDNA. We decided to investigate the pregnancies of women with the m.3243A>G mtDNA variant.
    METHODS: 16 women with m.3243A>G were included in this retrospective, observational cohort study. Medical records were screened for pregnancies managed at Oulu University Hospital (Oulu, Finland) during the years 1960-2020. Main outcomes were obstetric complications as well as maternal and neonatal morbidity. All eligible pregnancies (n=38) were reviewed for the course of pregnancy and delivery as well as maternal and neonatal health.
    RESULTS: The median of maternal m.3243A>G load in muscle or buccal epithelium was 59% (range 30-76%). There were 30 deliveries and 31 born children. Among singleton pregnancies, gestational diabetes was present in seven (24%), gestational hypertension or pre-eclampsia in three (10%) and preterm delivery in two (7%). Mean birth weight was 3537 g (1020-5310 g), with a z-score of 0.80±1.37 for girls and 0.77±1.05 for boys. Seven newborns (12%) were treated in the neonatal intensive care unit.
    CONCLUSION: Women harbouring m.3243A>G may have an elevated risk for obstetric complications, such as gestational diabetes and gestational hypertension. Their babies may have an elevated risk of preterm birth and need for intensive care. Pregnancies of women with m.3243A>G should be followed carefully.
    Keywords:  Genetic Diseases, Inborn; Neurology; Neuromuscular Diseases; Reproductive Health; Reproductive medicine
    DOI:  https://doi.org/10.1136/jmg-2025-110875
  33. Cell Death Dis. 2025 Dec 15.
    Combined ketone body and glutamine supplementation restores aerobic energy production in AGC1-deficient neuronal progenitors.
    Simona Nicole Barile, Maria Chiara Magnifico, Eleonora Poeta, Felix Distelmaier, Luigi Viggiano, Nicola Balboni, Michele Protti, Sabrina Petralla, Antonella Pignataro, Giacomo Volpe, Monica De Luise, Massimo Bonora, Marica Antonicelli, Giorgia Babini, Francesca Massenzio, Vito Porcelli, Eleonora Lama, Roberto Arrigoni, Isabella Pisano, Veronica Addabbo, Anna Campana, Francesca Begnozzi, Stewart A Anderson, Giuseppe Fiermonte, Federico Manuel Giorgi, Paolo Pinton, Ferdinando Palmieri, Giuseppe Gasparre, Laura Mercolini, Luigi Palmieri, Douglas C Wallace, Julia Hentschel, Barbara Monti, Francesco Massimo Lasorsa.
      AGC1 deficiency is a rare, early-onset encephalopathy caused by mutations in the SLC25A12 gene, encoding the mitochondrial aspartate/glutamate carrier isoform 1 (AGC1). Patients exhibit epileptic encephalopathy, cerebral hypomyelination, severe hypotonia, and global developmental delay. A hallmark biochemical feature of AGC1 deficiency is reduced brain N-acetylaspartate (NAA), a key metabolite involved in myelin lipid synthesis. However, the underlying mechanisms leading to the hypomyelinating phenotype remain unclear. In this study, we generated neuronal progenitors (NPs) derived from human-induced pluripotent stem cells (hiPSCs) of AGC1-deficient patients to investigate the metabolic and bioenergetic consequences of AGC1 loss. We demonstrated that AGC1-deficient NPs exhibit impaired proliferation, increased apoptosis, and a metabolic shift toward a hyperglycolytic phenotype due to defective mitochondrial pyruvate oxidation. RNA sequencing revealed downregulation of mitochondrial pyruvate carrier MPC1/2, limiting pyruvate-driven oxidative phosphorylation (OXPHOS) and reinforcing glycolysis as the primary energy source. Despite this metabolic shift, AGC1-deficient mitochondria retained the potential for OXPHOS when alternative anaplerotic substrates were provided. Notably, the administration of ketone bodies, in combination with glutamine, fully restored mitochondrial respiration, suggesting a mechanistic basis for the clinical improvements observed in AGC1-deficient patients undergoing ketogenic diet therapy. Our study highlights the importance of alternative metabolic pathways in maintaining neuronal energy homeostasis in AGC1 deficiency and offers insights into potential therapeutic strategies aimed at bypassing the mitochondrial pyruvate oxidation defect.
    DOI:  https://doi.org/10.1038/s41419-025-08314-4
  34. Neuroprotection. 2025 Sep;3(3): 253-265
    Mitochondrial transfer as a novel therapeutic approach in ischemic stroke treatment: Current challenges and future perspectives.
    Shuchen Meng, Min Bai, Changsheng Ma, Bo Han, Mengyuan Duan, Liying Zhang, Jinfen Guo, Changku Shi, Ke Li, Maotao He.
      Ischemic stroke, the second leading cause of human mortality, presents a formidable challenge to healthcare. Following ischemic insult, the brain undergoes intricate pathological transformations, prominently marked by mitochondrial damage, including swelling, fission, and mitophagy, collectively termed mitochondrial quality control disorder. Mitochondria, pivotal in energy regulation and oxidative stress modulation, play a critical role in neuronal apoptosis post-stroke. To solve the problems caused by mitochondrial quality control disorders, mitochondrial transfer has become a new therapeutic strategy for central nervous system diseases. Mitochondrial transfer refers to the process by which certain cell types export their mitochondria and pass them on to other cell types, a process also known as intercellular mitochondrial transfer. Mechanistically, mitochondrial transfer occurs via tunneling nanotubes, extracellular vesicles, and free mitochondrial transfer, exerting multifaceted effects such as anti-inflammatory, anti-lipid peroxidation, ferroptosis modulation, and enhancement of mitochondrial metabolism. This review explores the therapeutic efficacy, current obstacles, and future prospects of mitochondrial transfer in ischemic stroke, offering insights to researchers and instilling hope in patients for conquering this debilitating condition.
    Keywords:  ischemic stroke; mitochondrial dysfunction; mitochondrial therapy; mitochondrial transfer
    DOI:  https://doi.org/10.1002/nep3.70004
  35. Nephron. 2025 Dec 19. 1-18
    Mitochondria to the rescue: organelle trafficking in renal health and disease.
    Luca Perico, Giuseppe Remuzzi, Ariela Benigni.
       BACKGROUND: Mitochondria are central regulators of cellular metabolism, redox signaling, and apoptosis. Their dysfunction plays a pivotal role in the pathogenesis of kidney diseases, including acute kidney injury and diabetic nephropathy.
    SUMMARY: Recent advances have unveiled horizontal mitochondrial transfer as a novel intercellular communication by which renal cells exchange mitochondria to promote tissue repair through the modulation of metabolic processes, oxidative stress, apoptosis, and fibrosis.
    KEY FINDINGS: Horizontal mitochondrial transfer, mediated by tunneling nanotubes and extracellular vesicles, has emerged as a potential homotypic rescue mechanism between injured tubular and glomerular cells. In addition, heterotypic mitochondrial transfer from mesenchymal stromal cells to renal cells has been described. These findings open new perspectives for exploring therapeutic mitochondrial transplantation in both acute and chronic kidney diseases. Nonetheless, significant challenges remain, including elucidating the poorly characterized biological mechanisms underlying mitochondrial transfer, optimizing delivery strategies, and defining the long-term safety and efficacy of mitochondrial-based therapies.
    DOI:  https://doi.org/10.1159/000550092
  36. Handb Exp Pharmacol. 2025 Dec 16.
    Hydrogen Sulfide Signaling in Neurodegenerative Movement Disorders.
    Andrew A Pieper, Bindu D Paul.
      Hydrogen sulfide (H2S) is a gaseous signaling molecule, also known as a gasotransmitter, present in nearly all mammalian organs. It plays crucial roles in regulating various physiological processes in both the brain and peripheral systems. The body maintains tight control over H2S levels, as both excessive and deficient levels can disrupt normal physiological functions and lead to disease. H2S has a significant impact on cognitive and motor functions, which are often compromised in neurodegenerative disorders. It modulates signaling and metabolism primarily by post-translationally modifying reactive cysteine residues on proteins through sulfhydration, also known as persulfidation. This chapter reviews the signaling mechanisms regulated by H2S in neurodegenerative diseases that significantly affect motor function, specifically focusing on Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS), spinocerebellar ataxia (SCA), and Leigh syndrome (LS), as well as other mitochondrial disorders. While PD, HD, and SCA are linked to decreased levels of H2S, elevated levels of H2S are associated with ALS, DS, and LS. We also explore potential therapeutic applications of modulating H2S levels in the brain.
    Keywords:  Amyotrophic lateral sclerosis; Cysteine; Huntington’s disease; Hydrogen sulfide; Parkinson’s disease; Spinocerebellar ataxia; Sulfhydration/persulfidation
    DOI:  https://doi.org/10.1007/164_2025_757
  37. Cell Death Dis. 2025 Dec 19. 16(1): 893
    Stochasticity contributes to explaining minority and majority MOMP during apoptosis.
    Jenny Geiger, Fabian Klötzer, Nadine Pollak, Gavin Fullstone, Markus Rehm.
      Apoptosis dysfunction is linked to diseases like cancer and neurodegenerative disorders. A key event during apoptosis is mitochondrial outer membrane permeabilization (MOMP), which typically proceeds in a rapid all-or-none fashion. If MOMP occurs only in a subset of mitochondria (minority MOMP), it can be sublethal and contribute to tumorigenesis and cancer progression. Similarly, individual mitochondria escaping widespread MOMP (majority MOMP) can allow cancer cells to recover if apoptosis execution fails. How such heterogeneities in mitochondrial MOMP responsiveness arise within cells is incompletely understood. In particular, whether stochasticity in subcellular protein distributions and interactions across cytosol and mitochondria can realistically contribute to mitochondrial MOMP heterogeneity has not yet been studied. To assess this, we sequentially built and experimentally parameterized a particle-based, cell-sized model including cytosolic and mitochondrial compartments, and that featured a reduced interactome of MCL-1, BAK and tBID. High-performance computing enabled cell-scale simulations of protein distributions and interactions to understand how and under which conditions stochasticity could contribute to heterogeneity in MOMP susceptibility. Our results show that stochastic effects strongly predispose sub-pools of fragmented mitochondria to MOMP under low apoptotic stress. At higher apoptotic stress, fractions of small mitochondria were more likely to escape MOMP than large mitochondria. Retrospective quantification of mitochondrial sizes in experimental scenarios of minority and majority MOMP confirmed these findings. We therefore conclude that stochasticity substantially contributes to enabling small or fragmented mitochondria to undergo MOMP in minority MOMP scenarios and to escape MOMP in majority MOMP scenarios.
    DOI:  https://doi.org/10.1038/s41419-025-08258-9
  38. Elife. 2025 Dec 16. pii: RP103705. [Epub ahead of print]13
    The fate of pyruvate dictates cell growth by modulating cellular redox potential.
    Ashish G Toshniwal, Geanette Lam, Alex J Bott, Ahmad A Cluntun, Rachel Skabelund, Hyuck-Jin Nam, Dona R Wisidagama, Carl S Thummel, Jared Rutter.
      Pyruvate occupies a central node in carbohydrate metabolism such that how it is produced and consumed can optimize a cell for energy production or biosynthetic capacity. This has been primarily studied in proliferating cells, but observations from the post-mitotic Drosophila fat body led us to hypothesize that pyruvate fate might dictate the rapid cell growth observed in this organ during development. Indeed, we demonstrate that augmented mitochondrial pyruvate import prevented cell growth in fat body cells in vivo as well as in cultured mammalian hepatocytes and human hepatocyte-derived cells in vitro. We hypothesize that this effect on cell size was caused by an increase in the NADH/NAD+ ratio, which rewired metabolism toward gluconeogenesis and suppressed the biomass-supporting glycolytic pathway. Amino acid synthesis was decreased, and the resulting loss of protein synthesis prevented cell growth. Surprisingly, this all occurred in the face of activated pro-growth signaling pathways, including mTORC1, Myc, and PI3K/Akt. These observations highlight the evolutionarily conserved role of pyruvate metabolism in setting the balance between energy extraction and biomass production in specialized post-mitotic cells.
    Keywords:  D. melanogaster; cell biology; cell growth; genetics; hepatocytes; human; pyruvate metabolism; redox state; translation
    DOI:  https://doi.org/10.7554/eLife.103705
  39. J Pharm Anal. 2025 Nov;15(11): 101272
    Mitochondrial membrane chromatography: Discovery of mitochondrial targeting modulators.
    Wu Su, Yu Kong, Hua Li, Yongyao Wang, Lizhuo Wang, Le Shi, Huaizhen He, Shengli Han, Hui Guo, Jiankang Liu, Jiangang Long.
      Mitochondria are fundamental organelles that play a crucial role in cellular energy metabolism, substance metabolism, and various essential cellular signaling pathways. The dysfunction of mitochondria is significantly implicated in the onset and progression of aging, neurodegenerative diseases, metabolic disorders, and tumors, thereby rendering mitochondria-targeted regulation, a vital strategy for disease prevention and treatment. The recently developed mitochondrial membrane chromatography (MMC) technique, which immobilizes mitochondrial proteins as a chromatographic separation medium, has shown great potential for efficiently screening mitochondria-targeted modulators from complex compound library. In contrast to traditional screening methods, MMC has no need to purify mitochondrial proteins and can preserve its in situ and physiological conformation. Consequently, it presents broader application prospects for screening mitochondrial modulators as well as investigating receptor-ligand interactions involving any target protein associated with mitochondria. This review aims to elucidate the critical role of mitochondria in the development and progression of major chronic diseases, discuss recent advancements and applications of MMC, and propose future directions for MMC in the identification of novel mitochondrial modulators.
    Keywords:  Major chronic diseases; Mitochondrial membrane chromatography; Mitochondrial modulators; Mitochondrial nutrients; Molecular screening
    DOI:  https://doi.org/10.1016/j.jpha.2025.101272
  40. Mitochondrion. 2025 Dec 16. pii: S1567-7249(25)00107-2. [Epub ahead of print] 102110
    Biallelic FOXRED1 mutations cause infantile mitochondrial encephalopathy with complex I disassembly and basal ganglia degeneration.
    Cunhui Pan, Ruowei Zhu, Xi Huang, Haolin Duan, Tenghui Wu, Xiaole Wang, Ying Ding, Chen Chen, Fang He, Jing Peng, Fei Yin, Xiaoting Lou, Li Yang.
      Developmental and epileptic encephalopathy (DEE) is a severe neurological disorder. Biallelic mutations in the nuclear-encoded mitochondrial chaperone gene FOXRED1, a specific assembly factor for complex I, cause mitochondrial dysfunction; however, their role in DEE pathogenesis remains unexplored. Clinical data and peripheral blood mononuclear cells (PBMCs) were obtained from two patients with compound heterozygous FOXRED1 mutations (c.850 T > C (p.C284R) / c.1054C > T (p.R352W) and c.1054C > T (p.R352W) / c.3dup (p. I2Dfs*35) and age-matched controls. Mitochondrial phenotyping, included complex I activity, mitochondrial respiration stress test, membrane potential, intracellular ROS, and NAD+/NADH ratio, were performed. Both patients exhibited early-onset refractory seizures, basal ganglia lesions, hyperlacticemia, and developmental regression. FOXRED1 mutations resulted in 50 % reduction in complex I activity, dissasembly of complex I, mitochondrial depolarization, oxidative stress, and NAD+/NADH imbalance. Niacin restored the NAD+/NADH ratio in vitro, while clinical supplementation reduced blood lactate levels, suggesting it may be a potential therapeutic option.
    Keywords:  Developmental and epileptic encephalopathy; FOXRED1; Mitochondrial dysfunction; Niacin; Ohtahara Syndrome
    DOI:  https://doi.org/10.1016/j.mito.2025.102110
  41. Nat Commun. 2025 Dec 13.
    Endothelial RAB5IF is required for pathological and developmental retinal angiogenesis.
    Wen Bai, De-Pei Yin, Gang Chen, Yao Lu, Qin Jiang, Ke-Ran Li, Jin Yao, Cong Cao.
      Retinal angiogenesis drives both normal vascular development and sight-threatening retinal vascular diseases. While mitochondria are known to fuel this process, the roles of many specific mitochondrial proteins are poorly understood. Here we show that the mitochondrial protein RAB5 interacting factor (RAB5IF) as a critical pro-angiogenic regulator of physiological retinal vascular development in neonatal mice (sex-balanced) and pathological retinal angiogenesis in two models: oxygen-induced retinopathy mice (sex-balanced) and laser-induced choroidal neovascularization mice (sex-balanced). Proteomic sequencing identified SUMO2 as a critical downstream protein of RAB5IF. RAB5IF silencing impeded mitochondrial respiration and ribosome biogenesis, specifically suppressing SUMO2 mRNA translation initiation and consequently lowering SUMO2 protein levels in retinal microvascular endothelial cells. We also identify that SUMO2-mediated SUMOylation of Gαi1/3 is required for their roles in mediating VEGF signaling. Mutations at the SUMOylation sites of Gαi1/3 hindered VEGF-induced signaling and pro-angiogenic activity. Together, these findings delineate a RAB5IF-SUMO2-Gαi1/3 signaling axis essential for retinal angiogenesis, presenting new therapeutic targets for neovascular eye diseases.
    DOI:  https://doi.org/10.1038/s41467-025-66212-x
  42. Stem Cell Res. 2025 Dec 12. pii: S1873-5061(25)00237-5. [Epub ahead of print]90 103887
    CRISPR/Cpf1-mediated editing of PINK1 in induced pluripotent stem cells.
    Roohallah Ghodrat, Haribaskar Ramachandran, Barbara Hildebrandt, Stephanie Binder, Andrea Rossi, Andreas S Reichert.
      The PTEN induced kinase 1 (PINK1) gene is crucial for mitophagy and mitochondrial quality control. Mutations in the PINK1 gene are associated with several neurological disorders. To decipher the role of PINK1-mediated mitophagy in human induced pluripotent stem cells (hiPSCs) and in their differentiated counterparts, we used CRISPR/Cpf1 and generated a human iPSC line with homozygous out-of-frame deletions by targeting exon 6 of the PINK1 gene. The generated homozygous PINK1 mutant cell line showed normal cell morphology, genomic stability, and expression of classical stem cell markers. Furthermore, the cells can be differentiated efficiently into the three germ layers.
    DOI:  https://doi.org/10.1016/j.scr.2025.103887
  43. Front Pediatr. 2025 ;13 1686738
    Rapid whole genome sequencing in newborn screening for metabolic diseases.
    Jun Zheng, Xin Yang.
       Background and purpose: Metabolic disorders, which are estimated to include approximately 1,500 distinct conditions such as urea cycle disorders, lysosomal storage diseases, and mitochondrial dysfunctions, pose a significant clinical challenge due to their genetic heterogeneity and rapid onset of symptoms in newborns. Delays in diagnosis often lead to irreversible damage or mortality. Rapid whole genome sequencing (rWGS) has emerged as a transformative diagnostic tool, offering comprehensive genetic insights within 24-72 h.
    Materials and methods: This study reviews the application of rWGS in the early detection and management of metabolic diseases, emphasizing its role in overcoming limitations of traditional diagnostic methods.
    Results: The integration of rWGS into clinical workflows offers a high diagnostic yield, exceeding 50% in neonatal intensive care units (NICUs), where timely interventions are critical. Utilizing advanced sequencing platforms, such as Illumina NovaSeq and Oxford Nanopore, coupled with optimized bioinformatics pipelines, rWGS enables precise variant identification and prioritization. Key findings highlight its capacity to accelerate diagnosis, inform therapeutic decisions, and reduce diagnostic odysseys. For instance, identifying pathogenic variants in genes allows early initiation of targeted therapies, significantly improving outcomes.
    Conclusions: Despite its transformative potential, challenges remain, including cost, data interpretation, and equitable access. Addressing these barriers through investments in infrastructure, training, and policy frameworks will be crucial for broader implementation. This review underscores the critical role of rWGS in neonatal care and highlights its promise as a cornerstone of precision medicine, paving the way for improved diagnostic accuracy and patient outcomes in metabolic diseases.
    Keywords:  NICU diagnostics; metabolic diseases; newborn screening; precisionmedicine; rapid whole genome sequencing
    DOI:  https://doi.org/10.3389/fped.2025.1686738
  44. Cell Rep. 2025 Dec 17. pii: S2211-1247(25)01507-4. [Epub ahead of print]45(1): 116735
    Afg3l2 couples mitochondrial vitamin B12 trafficking to amino acid metabolism to safeguard hematopoietic stem cell homeostasis.
    Meng Zhang, Xiashiyao Zhang, Yandan Chen, Mengmeng Li, Qingwei Ding, Liang Zheng, Junke Zheng, Jun Wan, Bin Guo.
      Mitochondrial proteostasis is essential for hematopoietic stem cell (HSC) maintenance, yet how proteolytic regulation coordinates with metabolic pathways remains unclear. Here, we identify Afg3l2 as a key regulator of cobalamin metabolism and amino acid homeostasis in HSCs through its mediation of Mmadhc degradation. Loss of Afg3l2 leads to Mmadhc accumulation, driving excessive mitochondrial cobalamin import and its conversion to adenosylcobalamin. Elevated adenosylcobalamin levels hyperactivate methylmalonyl-CoA mutase, diverting branched-chain amino acid catabolism toward excessive succinyl-CoA production. This overstimulates the tricarboxylic acid cycle and creates a compensatory dependency on anaplerotic amino acid replenishment. Consequently, Afg3l2-deficient HSCs exhibit increased oxidative stress due to mitochondrial hyperactivation and reactive oxygen species accumulation, ultimately impairing their maintenance and engraftment capacity. Remarkably, Mmadhc overexpression phenocopies these defects, whereas Mmadhc knockdown partially restores HSC function in Afg3l2-deficient models. Our work defines a proteostatic-metabolic circuit in which Afg3l2-mediated Mmadhc degradation regulates cobalamin flux to maintain amino acid and energy balance in HSCs.
    Keywords:  CP: Metabolism; CP: Stem cell research; TCA cycle; amino acid metabolism; cobalamin metabolism; hematopoietic stem cell; mitochondrial protease
    DOI:  https://doi.org/10.1016/j.celrep.2025.116735
  45. Nature. 2025 Dec 17.
    Systematic maps reveal how human chromosomes are organized.
    Elzo de Wit.
      
    Keywords:  Cell biology; Computational biology and bioinformatics; Molecular biology
    DOI:  https://doi.org/10.1038/d41586-025-03808-9
  46. Glia. 2026 Feb;74(2): e70112
    Novel Roles for the Ectoenzyme CD38 in the Maintenance of Transcriptional and Metabolic Homeostasis in Astrocytes.
    S Basak, A M Colafrancesco, R D Hernandez, X Wei, L J McMeekin, D Dang, M Simmons, J L Browning, K Noel, F Zhou, F E Lund, J S Saad, S G Watsen, A M Pickrell, R M Cowell, M L Olsen.
      CD38 is an ectoenzyme that converts NAD+ to NAM to help maintain bioenergetic homeostasis. CD38 dysregulation and gene variation is reported in neurodegenerative conditions such as Parkinson's disease (PD) and Alzheimer's disease (AD), highlighting the need to better understand CD38 biology within the brain. Here, we demonstrate enrichment of Cd38 in midbrain astrocytes and describe how CD38 deficiency influences brain metabolism, astrocytic gene expression, and bioenergetics. We demonstrate increased NAD content, decreased NAM content, and increased NAD/NAM in the midbrain and striatum of CD38-deficient (Cd38-/-) mice, indicating the dependence on CD38 for NAD to NAM conversion in the brain. RNA-sequencing of isolated astrocytes revealed numerous differentially expressed genes in Cd38+/- and Cd38-/- mice, with alterations in mitochondrial, metabolic, senescence-related, astrocyte reactivity, and other genes involved in PD and AD etiology. Furthermore, functional metabolic analysis of midbrain revealed changes in pyruvate oxidation, age-dependent increase of citrate synthase (CS) activity, and reduction of cytochrome c oxidase-to-CS ratio in Cd38 deficiency. These findings identify a novel role for astrocytes in the regulation of CD38-dependent NAD/NAM homeostasis in the brain and provide a framework for future studies evaluating the relationship between CD38 dysfunction, aging, and vulnerability of neuronal populations in neurodegenerative disease. Importantly, these studies underscore the necessity to better resolve the impact of CD38 deficiency on brain metabolism, considering ongoing clinical trials and discussions related to the use of CD38 modulators for the treatment of cancers, age-related decline, and neurodegenerative disease.
    Keywords:  RNA‐sequencing; aging; astrocyte; brain metabolism; mitochondria; neurodegeneration
    DOI:  https://doi.org/10.1002/glia.70112
  47. Front Neurosci. 2025 ;19 1534243
    GABAergic neurons are a key cell type in a Drosophila model of PARK14/PLA2G6-associated neurodegeneration.
    Noah S Meimoun, Shimshon Benji, William Z Besharim, Yair Y Cantor, Eitan S Carroll, Benjamin I Coplin, Moshe B Davidovics, Michael Gerber, Philip M Hirschprung, Ephraim I Jacobson, Aryeh L Levenbrown, David T Levitt, Adam Levy, Yehuda Z Mazin, Avishye D Moskowitz, Jeremy I Purow, Amiel Rimberg, Jacob E Rothstein, Eli Yaakov Saks, Rafael Saperstein, Yosef Y Scher, Yisroel D Schwarcz, Matthew Silver, Yitzchak F Stein, Yisrael Y Wiener, Josefa Steinhauer.
      The causes of sporadic Parkinson's Disease (PD) are still unclear, despite its prevalence. By contrast, inherited parkinsonian disorders have a clear genetic basis and have been studied intensively in laboratory organisms, including Drosophila melanogaster. Because inherited parkinsonian disorders clinically resemble sporadic PD, it has been suggested that they may share an underlying etiology. Loss of function mutations in the gene PLA2G6 give rise to inherited neurodegenerative diseases including autosomal recessive early onset parkinsonism (PARK14). Using RNAi to deplete the Drosophila PLA2G6 homolog iPLA2-VIA, we asked whether subsets of neurons, identified by their neurotransmitter usage, were more susceptible to loss of this gene. To model movement disorders connected with PLA2G6-associated neurodegeneration, we used the well-established climbing assay. Our results demonstrated that loss of iPLA2-VIA in GABAergic neurons alone strongly affected locomotor ability in aged flies, similar to pan-neuronal knockdown. Depletion of iPLA2-VIA in both dopaminergic and serotonergic neurons weakly affected locomotor ability as well. Depletion in other neuronal subsets did not disrupt locomotion. Furthermore, reintroducing wild-type iPLA2-VIA into only the dopaminergic neurons of fly knockouts improved climbing performance slightly, while reintroduction into GABAergic neurons rescued climbing performance strikingly, as well as lifespan. Although much research on this gene has focused on the dopaminergic neurons, whose degeneration leads to clinical parkinsonism, our results highlight the importance of GABAergic neurons to PLA2G6-associated neurodegeneration. Because sporadic PD is not thought to impact most GABAergic neurons directly, our data support the idea that sporadic PD and PARK14 have distinct etiologies despite overlapping clinical presentations.
    Keywords:  PARK14; PLA2G6; PLA2G6-associated neurodegeneration; Parkinson’s disease; locomotor decline
    DOI:  https://doi.org/10.3389/fnins.2025.1534243
  48. Front Physiol. 2025 ;16 1666994
    Modulation of mitochondrial voltage dependent anion channel: studies on bilayer electrophysiology.
    Daniel Tuikhang Koren, Chetan Malik, Shumaila Iqbal Siddiqui, Rajan Shrivastava, Subhendu Ghosh.
      The present paper is a review of the mitochondrial Voltage Dependent Anion Channel (VDAC), popularly known as mitochondrial porin, which is a protein that forms a passive diffusion ion channel across the outer membrane of the mitochondrion. VDAC essentially plays an important role in the transport of metabolites like ATP between the intermembrane space of the mitochondrion and the cytoplasm. However, under certain conditions, it can give rise to cellular dysfunction, e.g., apoptosis. Although VDAC is present in all eukaryotic cells, this review has focused mainly on the animal tissues. Interactions of VDAC with various enzymes, proteins, and small molecules or ligands have been reviewed with a perspective of bilayer electrophysiology. Importantly, the biochemical (post-translational) modifications of the channel protein, namely, phosphorylation (by a series of kinases), acetylation, ubiquitination, oxidative modifications (such as glutathionylation and nitrosylation), etc., and their impact on the electrophysiological properties have been discussed. Finally, the consequences of the above-mentioned experimental findings have been discussed with predictions and hypotheses relevant to living systems.
    Keywords:  apoptosis; bilayer electrophysiology; ligand interactions; mitochondrial dysfunction; oxidative stress; post-translational modifications; protein phosphorylation; voltage-dependent anion channel (VDAC)
    DOI:  https://doi.org/10.3389/fphys.2025.1666994
  49. Nat Commun. 2025 Dec 14.
    Dysregulated hippocampal fatty acid metabolism following intermittent hypoxemia-induced neonatal brain injury is rescued by treatment with acetate.
    Regina F Fernandez, Wedad Fallatah, Yuanyuan Ji, Jace W Jones, Cole C Johnson, Caitlin M Tressler, Kristine Glunde, Rida Ali, Ann B Moser, Michael J Wolfgang, Susanna Scafidi, Joseph Scafidi.
      The brain is a lipid-rich organ that experiences rapid growth and development after birth in a period hallmarked by extensive lipid synthesis. We still lack a fundamental understanding of lipid metabolism during this critical time of brain development and how these dynamics occur in infants born extremely preterm (<28 weeks of gestation) suffering from brain injuries. Using an established model of neonatal brain injury due to intermittent hypoxemia, we recapitulate hippocampal-dependent cognitive impairments and examine the extent of changes in the brain's lipid profile. Our results show changes in hippocampal lipid composition and abnormal fatty acid profile. Furthermore, we provide evidence of an increase in mitochondrial fatty acid β-oxidation, a process that is not classically thought of occurring in the developing brain. We find that a specific alternative fuel, acetate, spares fatty acids from mitochondrial β-oxidation. Here, we show that treatment with acetate in vivo in the form of glycerol-triacetate promotes functional recovery and restores hippocampal fatty acid profile after neonatal brain injury.
    DOI:  https://doi.org/10.1038/s41467-025-67542-6
  50. Mol Cell. 2025 Dec 18. pii: S1097-2765(25)00938-4. [Epub ahead of print]85(24): 4545-4561.e8
    Defective RNA processing and ELOA-mediated transcriptional elongation in reversible cellular senescence suggest aging by transcription.
    Saeid Parast, Simai Wang, Marta Iwanaszko, Yue He, Deniz G Olgun, Sarah Gold, Jacob M Zeidner, Yuki Aoi, Benjamin C Howard, William R Thakur, Vijay Ramani, Ali Shilatifard.
      We previously established distinct roles for the transcriptional elongation factors PAF1, negative elongation factor (NELF), SPT4/5, and SPT6 using auxin-inducible degron systems in human cell lines. Here, we integrate long- and short-read RNA-seq data from these degron lines to quantify transcript isoform usage at single-molecule resolution, identifying elongation factor-specific RNA processing regulons, including a cellular senescence-enriched regulon impacted by NELF and SPT6. Long-term NELF or SPT6 depletion causes reversible growth arrest following early upregulation of senescence-associated genes. Our genetic suppressor screens implicate the elongation factor Elongin A (ELOA) in these effects. ELOA knockout suppresses the progression of RNA polymerase II (RNAPII) past transcription end sites (TESs) at NELF depletion-induced genes. Acute depletion of TES-proximal ELOA causes a loss of RNAPII processivity at the 3' end of genes. ELOA loss also confers a growth advantage to aging primary human fibroblasts. These findings establish NELF/ELOA-dependent mechanisms regulating transcriptional elongation and RNA processing and link them to senescence and aging.
    Keywords:  aging; cellular senescence; gene expression; mRNA processing; transcription; transcriptional elongation
    DOI:  https://doi.org/10.1016/j.molcel.2025.11.021
  51. Aging Dis. 2025 Dec 14.
    Pharmacological Activation of Mitophagy Confers Neuroprotective Benefits for Amyotrophic Lateral Sclerosis.
    Sen Huang, Ang Li, Yixia Ling, Xinyu Yang, Jiayu Wang, Jing Yuan, Dajiang Qin, Xiaoli Yao.
      Amyotrophic lateral sclerosis (ALS) is a rare and devastating neurodegenerative disease characterized by the progressive degeneration of motor neurons in the brain and spinal cord, for which no cure currently exists. Previous studies have shown that abnormal mitochondrial homeostasis and defective mitophagy occur in neurodegenerative diseases, including ALS. Here, we provide evidence that PINK1-Parkin-dependent mitophagy is impaired in multiple ALS mouse models, including the SOD1G93A, TDP43A315T, and rNLS8 strains, leading to the accumulation of damaged mitochondria in affected motor neurons. These findings suggest that mitophagy may be a druggable target for ALS treatment. A classical mitophagy agonist, urolithin A (UA) was used in this study. UA-induced mitophagy antagonizes ALS pathologies in the ALS SOD1G93A transgenic C. elegans model in a pink-1 (PTEN-induced kinase 1)- and pdr-1 (Parkinson's disease-related 1)-dependent manner. Furthermore, pharmacological activation of mitophagy by UA improves locomotor behavior, delays motor neuron degeneration and reduces neuroinflammation in ALS SOD1G93A transgenic mice. In conclusion, our results establish impaired mitophagy as a hallmark of ALS motor neuron degeneration and demonstrate that its pharmacological activation offers a neuroprotective strategy with therapeutic potential.
    DOI:  https://doi.org/10.14336/AD.2025.1224
  52. Exp Eye Res. 2025 Dec 16. pii: S0014-4835(25)00580-9. [Epub ahead of print]263 110807
    Short-term high-dose nicotinamide treatment across glaucoma subtypes reveals increased mtDNA content and minimal metabolomic change in blood.
    Antoni Vallbona-Garcia, James R Tribble, Simon T Gustavsson, Birke J Benedikter, Patrick J Lindsey, Carroll Ab Webers, Hubert Jm Smeets, Gauti Jóhannesson, Theo Gmf Gorgels, Pete A Williams.
      In glaucoma, retinal ganglion cell degeneration has been linked to declining mitochondrial metabolic capacity. Nicotinamide (NAM) supplementation has emerged as a potential treatment for this. We assessed the effects of a 2-week NAM supplementation on blood buffy coat mitochondrial content (qPCR to assess mtDNA amount per cell) and the plasma metabolome (small-molecular-weight high-resolution mass spectrometry) in 90 glaucoma subjects from 3 different glaucoma subtypes (high tension glaucoma (HTG), normal tension glaucoma (NTG), and pseudoexfoliative glaucoma (PEXG), n = 30 per group), and 30 healthy controls with similar age and sex distribution. At baseline (pre-NAM), only ethylmalonic acid, a compound related to defects in β-oxidation and mitochondrial dysfunction, was found to be modestly increased in the 3 glaucoma subtypes in comparison to controls. All groups showed a similar metabolome response to treatment with a specific increase in NAM and related species (1-methylnicotinamide, 6-hydroxynicotinamide, N1-methyl-2-pyridone-5-carboxamide), increased 5-methylcytosine, and decreased 4-pyridoxic acid. Between groups, only sarcosine had a different response, with a small reduction in HTG and NTG post-treatment. NAM treatment resulted in a significant but slight within-group increase in blood mtDNA amount in controls and HTG (12 % and 17 %, respectively). This study suggests that NAM treatment leads to similar plasma metabolome changes between glaucoma groups and controls, which predominantly reflect increased NAM metabolites and intermediates, with minimal effects on the wider metabolome, and a modest increase in mtDNA amount in HTG and controls. As this was observed in a short-term accelerated dosing context, long-term and larger studies with additional timepoints and greater adjustment for systemic metabolic factors will be required to provide more information on the long-term effects of oral NAM supplementation.
    Keywords:  Buffy coat; Glaucoma; Metabolism; Mitochondria; Pseudoexfoliation; mtDNA
    DOI:  https://doi.org/10.1016/j.exer.2025.110807
  53. Nat Commun. 2025 Dec 13.
    Sodium disrupts mitochondrial energy metabolism to execute NECSO.
    Yuhui Qiao, Jianghuang Wang, Bohong Wang, Hong Zhou, Qianlin Ni, Wan Fu, Zeping Hu, Qing Zhong.
      Na+ influx is a critical pathological event in various conditions such as ischemia, hyperosmotic stress, and organ failure. Although persistent activation of the transient receptor potential cation channel subfamily M member 4 (TRPM4) by chemical agonist Necrocide 1 (NC1) triggers necrosis by sodium overload (NECSO), the underlying mechanism remains to be elucidated. Here, we demonstrate that Na+ influx promotes necrosis by suppressing mitochondrial energy production. TRPM4-mediated Na⁺ entry elevates mitochondrial Na⁺ and reduces mitochondrial Ca²⁺ via NCLX, inhibiting oxidative phosphorylation and the Trichloroacetic acid (TCA) cycle, leading to severe energy depletion. This results in Na/K-ATPase inactivation, loss of ion gradients, cellular swelling and lysis. Our study reveals how sodium overload in NECSO disrupts mitochondrial metabolism to cause energy failure, potentially underlying diseases with elevated Na⁺.
    DOI:  https://doi.org/10.1038/s41467-025-67181-x
  54. Nat Aging. 2025 Dec 17.
    Integrating polygenic signals and single-cell multiomics identifies cell-type-specific regulomes critical for immune- and aging-related diseases.
    Yunlong Ma, Yinghao Yao, Yijun Zhou, Wei Dai, Jingjing Li, Yuanyuan Gui, Haojun Sun, Zhengbiao Zhu, Dingping Jiang, Cheng Chen, Chunyu Deng, Yizhou Huang, Haijun Han, Jianhong Zhou, Jianzhong Su.
      Single-cell multiomics provides critical insights into how disease-associated variants identified through genome-wide association studies (GWASs) influence transcription factor eRegulons within a specific cellular context; however, the regulatory roles of genetic variants in aging and disease remain unclear. Here, we present scMORE, a method that integrates single-cell transcriptomes and chromatin accessibility with GWAS summary statistics to identify cell-type-specific eRegulons associated with diseases. scMORE effectively captures trait-relevant cellular features and demonstrates robust performance across simulated and real single-cell datasets, and GWASs for 31 immune- and aging-related traits, including Parkinson's disease (PD). In the human midbrain, scMORE identifies 77 aging-relevant eRegulons implicated in PD across seven brain cell types and reveals sex-dependent dysregulation of these eRegulons in PD neurons compared to both young and aged groups. By linking genetic variation to cell type-resolved eRegulon activity, scMORE illuminates how variants shape trait-relevant regulatory networks and provides a practical framework for mechanistic interpretation of GWAS signals.
    DOI:  https://doi.org/10.1038/s43587-025-01027-5
  55. STAR Protoc. 2025 Dec 15. pii: S2666-1667(25)00668-9. [Epub ahead of print]7(1): 104262
    Mass spectrometry protocol for tear fluid proteome profiling and biomarker discovery.
    Kirstine Juul-Elbaek, Maria Peiris-Pagès, Vyacheslav Akimov, Irene Rebollido-Pedrido, Mark Reardon, Blagoy Blagoev, Petra Hamerlik.
      Here, we present a protocol for tear fluid proteomics using Schirmer strips and liquid chromatography-tandem mass spectrometry (LC-MS/MS). It includes tear sampling from human individuals and mice, followed by protein digestion, peptide desalting, and purification via solid-phase extraction. Supporting both data-dependent acquisition (DDA) and data-independent acquisition (DIA), this 5-h workflow maximizes protein recovery, minimizes contaminants, and enables reproducible biomarker discovery for ocular, neurodegenerative, and systemic diseases. Tear fluid's non-invasive collection and rich proteome make it ideal for clinical proteomics and personalized medicine.
    Keywords:  bioinformatics; cancer; proteomics
    DOI:  https://doi.org/10.1016/j.xpro.2025.104262
  56. Circ Res. 2025 Dec 15.
    Subcellular In Vivo Cardiac Proteomics Reveals Sarcomere and Ribosome Interactomes and skNAC's Impact on Cardiac Proteostasis.
    Rami Haddad, Omer Sadeh, Tamar Ziv, Nardeen Shehdeh, Nadav Keren, Izhak Kehat.
       BACKGROUND: Proteostasis and the regulation of protein folding and sorting play a critical role in maintaining cellular homeostasis. The failure of proteostasis contributes to heart failure and aging, but, despite its importance, the mechanisms and factors regulating proteostasis in cardiomyocytes remain poorly characterized.
    METHODS: Subcellular proteomes of cardiomyocytes were analyzed in vivo using biotin proximity labeling in mouse hearts. We employed a novel homology-independent targeting integration strategy for genetic tagging and for substitution of the muscle-specific skNAC (skeletal nascent polypeptide-associated complex alpha isoform) isoform with the ubiquitous short isoform in cardiomyocytes.
    RESULTS: We identified hundreds of proteins localized to the Z- and M-lines of sarcomeres, the ribosomes, and the desmosomes, including multiple chaperones. A universal homology-independent targeted integration strategy allowed us to genetically tag endogenous genes in the mouse heart and confirm protein localization. We identified the large muscle-specific isoform of the nascent polypeptide-associated complex protein skNAC as a Z-line and ribosome-associated protein. Replacement of skNAC with a ubiquitous isoform induced dilated cardiomyopathy, accompanied by altered ribosome positioning and markedly reduced mitochondrial protein levels.
    CONCLUSIONS: We unraveled the cardiomyocyte subcellular proteome and show that skNAC, an isoform downregulated in disease, is a key ribosome and Z-line-associated protein responsible for cardiomyocyte proteostasis.
    Keywords:  biotin; desmosomes; heart failure; mitochondria; proteostasis
    DOI:  https://doi.org/10.1161/CIRCRESAHA.125.326929
  57. Am J Physiol Endocrinol Metab. 2025 Dec 15.
    Ppid is Necessary for Overnutrition-Induced β-cell Loss.
    Brittney A Covington, Zihan Tang, Lisette A Maddison, Bingyuan Yang, Wenbiao Chen.
      Type 2 diabetes (T2D) involves progressive loss of functional β-cell mass. In a zebrafish insulin-resistant model (zMIR), overnutrition triggers islet inflammation and nocturnal β-cell death. The cell death is prevented by the cyclophilin D (Ppid) inhibitor, cyclosporin A (CsA). Reducing mitochondrial ROS with mito-TEMPO or mitochondrial calcium with Ru360 protects β cells, further implicating the mitochondrial permeability transition pore (mPTP) in β-cell loss. The timing of β-cell death coincides with lower mitochondrial antioxidant gene expression, indicating diurnal mitochondrial vulnerability. Global ppid-/- preserves β-cell mass without altering islet inflammation or macrophage recruitment. Conversely, β-cell-specific PPID re-expression restores-and exacerbates-β-cell loss, which remains CsA-sensitive. These findings identify Ppid as a β-cell-intrinsic mediator of overnutrition-induced β-cell loss.
    Keywords:  PPID; Zebrafish; beta cell death; diabetes; inflammation
    DOI:  https://doi.org/10.1152/ajpendo.00342.2025
  58. Biochem J. 2025 Dec 16. pii: BCJ20253414. [Epub ahead of print]482(24):
    Citrate trafficking supports rewiring of mitochondrial metabolism via RTG signaling in yeast osmoadaptation.
    Angela Primavera, Luna Laera, Alessandra Castegna, Pasquale Scarcia, Luigi Palmieri, Maria Antonietta Di Noia, Nicoletta Guaragnella.
      Inter-organellar cross-talk is an important component of cellular stress response enabling adaptation and survival. We have demonstrated the activation of RTG retrograde signaling to sustain the peroxisomesmitochondria- nucleus axis in a model of osmostressed Saccharomyces cerevisiae yeast cells. In this work, we aimed to gain insight into the molecular mechanisms regulating the communication between these organelles upon NaCl treatment. A metabolomic analysis revealed that the homeostasis of citrate is a pivotal factor in the osmoadaptive response. Gene expression analysis and citrate synthase activity showed that the synthesis of citrate mainly derives from peroxisomes, as indicated by the up-regulation of CIT2, and not CIT1 and CIT3, under the control of the RTG pathway. Furthermore, the involvement of the mitochondrial citrate transporter, encoded by YHM2, in the osmoadaptive response, as judged by gene and protein expression analysis together with growth assay, is demonstrated. In the absence of YHM2, alternative pathways relying on ODC2 and ACO1 are activated, indicating possible compensatory mechanisms for osmoadaptation. We propose a model in which peroxisome-derived citrate is converted to cytosolic 2-oxoglutarate to replenish TCA cycle and promote its rewiring. This work reveals a new layer of metabolic co-ordination among organelles and identifies citrate shuttling as a crucial adaptive mechanism to osmotic stress.
    Keywords:   YHM2 ; RTG pathway; citrate; mitochondrial carriers; osmoadaptation; yeast
    DOI:  https://doi.org/10.1042/BCJ20253414
  59. Mol Cells. 2025 Dec 11. pii: S1016-8478(25)00132-3. [Epub ahead of print] 100308
    Multilayered regulation of longevity in Caenorhabditis elegans.
    Dajeong Bong, Hyunwoo C Kwon, Seung-Jae V Lee.
      Aging in Caenorhabditis elegans is regulated by evolutionarily conserved pathways that coordinate cellular maintenance and systemic homeostasis. Here, we review recent advances on four major longevity regimens including reduced insulin/insulin-like growth factor 1 signaling (IIS), dietary restriction (DR), mild inhibition of mitochondrial respiration, and germline deficiency. Each longevity-promoting regimen enhances protein and RNA quality control, metabolic remodeling, and stress resistance to delay functional declines with age. Reduced IIS strengthens proteostasis and RNA surveillance. DR remodels metabolism and activates autophagy. Mild mitochondrial inhibition elicits adaptive redox signaling and quality control responses. Germline deficiency links reproductive cues to somatic maintenance. We highlight that longevity arises from integrated regulation of transcriptional, metabolic and inter-tissue signaling networks. Our review will provide valuable insights obtained from C. elegans into the conserved mechanisms of aging, facilitating the development of interventions that promote healthy longevity in humans.
    Keywords:  Caenorhabditis elegans; dietary restriction; germline deficiency; insulin/IGF-1 signaling; longevity; mild mitochondrial inhibition
    DOI:  https://doi.org/10.1016/j.mocell.2025.100308
  60. Nat Cell Biol. 2025 Dec 19.
    The G3BP stress-granule proteins reinforce the integrated stress response translation programme.
    Jarrett Smith, David P Bartel.
      When mammalian cells are exposed to stress, they co-ordinate the condensation of stress granules (SGs) through the action of proteins G3BP1 and G3BP2 (G3BPs) and, simultaneously, undergo a massive reduction in translation. Although SGs and G3BPs have been linked to this translation response, their overall impact has been unclear. Here we investigate the question of how, and indeed whether, G3BPs and SGs shape the stress translation response. We find that SGs are enriched for mRNAs that are resistant to the stress-induced translation shutdown. Although the accurate recruitment of these stress-resistant mRNAs does require the context of stress, a combination of optogenetic tools and spike-normalized ribosome profiling demonstrates that G3BPs and SGs are necessary and sufficient to both help prioritize the translation of their enriched mRNAs and help suppress cytosolic translation. Together, these results support a model in which G3BPs and SGs reinforce the stress translation programme by prioritizing the translation of their resident mRNAs.
    DOI:  https://doi.org/10.1038/s41556-025-01834-3
  61. J Cell Biol. 2026 Mar 02. pii: e202506096. [Epub ahead of print]225(3):
    SynSeg: A synthetic data-driven approach for robust subcellular structure segmentation.
    Zhengyang Guo, Zi Wang, Zihan Chen, Kaiming Xu, Yongping Chai, Jingyi Ke, Jingwen Huang, Yuqi Ye, Hui Wang, Jinxiang Zhang, Guangshuo Ou.
      Accurate subcellular segmentation is crucial for understanding cellular processes, but traditional methods struggle with noise and complex structures. Convolutional neural networks improve accuracy but require large, time-consuming, and biased manually annotated datasets. We developed SynSeg, a pipeline generating synthetic training data for a U-Net model to segment subcellular structures, eliminating manual annotation. SynSeg leverages synthetic datasets with varied intensity, morphology, and signal distribution, delivering context-aware segmentations, even in challenging conditions. We demonstrate SynSeg's superior performance in segmenting vesicles and cytoskeletal filaments from cells and live Caenorhabditis elegans, outperforming traditional methods like Otsu's, ILEE, and FilamentSensor 2.0 and a recent deep learning method. Additionally, SynSeg effectively quantified disease-associated microtubule morphology in live cells, uncovering structural defects caused by mutant Tau proteins linked to neurodegeneration. Furthermore, SynSeg enables high-throughput, automated analysis, revealing that BSCL2 disease mutations increase lipid droplet size and showing its broad generalizability for quantitative cell biology. These results highlight the potential of synthetic data to advance biological segmentation.
    DOI:  https://doi.org/10.1083/jcb.202506096
  62. Int J Nanomedicine. 2025 ;20 14667-14694
    Mitochondria-Targeted Nanosystems in the Treatment of Central Nervous System Diseases.
    Xiaolan Zhang, Jiahui Chen, Bingjie Wan, Yanrong Zheng, Xiaojie Chen.
      Mitochondrial dysfunction represents a pivotal pathological mechanism underlying diverse diseases, particularly those affecting the central nervous system (CNS). Consequently, therapeutic strategies capable of effectively restoring mitochondrial function hold significant promise for treating CNS disorders. Nanotechnology has emerged as a powerful platform in this endeavor, leveraging the modifiability, controllability, and targeting capabilities of nanosystems to intervene at the mitochondrial level. This review delineates the critical role of mitochondrial integrity in CNS pathophysiology and summarizes key mitochondria-targeting strategies, including small-molecule ligands, mitochondrial-penetrating peptides, mitochondrial membrane-derived vesicles, and biomimetic membrane coatings. We also discuss the efficacy of mitochondria-targeted nanosystems in rescuing mitochondrial dysfunction across major CNS conditions, exemplified by neurodegenerative diseases, brain tumors, ischemic stroke, and traumatic brain injury. Ultimately, this review also points out current translational challenges and future research directions pivotal for advancing mitochondrial nanomedicine. Collectively, this work synthesizes progress in mitochondrial nanotherapeutics, highlighting their transformative potential while outlining critical barriers and opportunities for clinical translation in CNS disorders.
    Keywords:  Drug delivery; Mitochondria-targeted therapy; Mitochondrial dysfunction; Nanosystems
    DOI:  https://doi.org/10.2147/IJN.S562666
  63. Mol Ther Nucleic Acids. 2025 Dec 09. 36(4): 102770
    Base editing strategies for in vivo correction of two highly recurrent phenylketonuria variants.
    Aidan Quigley, Ishaan Jindal, Thomas Campion, Delaney Rutherford, Yongseok Han, Walsh Quigley, Ping Qu, Kiran Musunuru, Rebecca Ahrens-Nicklas, Xinying Hong, Xiao Wang.
      Phenylketonuria (PKU) is an autosomal recessive disorder caused by mutations in the phenylalanine hydroxylase (PAH) gene. Previously, we have shown correction of the most recurrent PKU variant using both base editing and prime editing. In this work, we set out to screen base editors and single guide RNAs (sgRNAs) in vitro to identify sgRNA-editor combinations that would provide sufficient correction for phenotypic rescue of the next four most recurrent PKU variants. For three candidates, we established efficient corrective editing in vitro. We then assessed the off-target editing profile of each sgRNA-editor combination. For two of these variants, we demonstrated efficient corrective editing in the livers of humanized mouse models via adeno-associated viral (AAV) delivery. This work identifies base editing strategies for in vivo correction of the second and third most common pathogenic variants of PKU.
    Keywords:  AAV; CRISPR; MT: RNA/DNA Editing; base editing; liver; phenylketonuria
    DOI:  https://doi.org/10.1016/j.omtn.2025.102770
  64. bioRxiv. 2025 Nov 25. pii: 2025.11.24.690227. [Epub ahead of print]
    Dysregulated lactate metabolism synergizes with ALS genetic risk factors to accelerate motor decline.
    Shweta Tendulkar, Tong Wu, Amy Strickland, Amber R Hackett, Yurie Sato-Yamada, Xianrong Mao, Yo Sasaki, Jeffrey Milbrandt, Joseph Bloom, Aaron DiAntonio.
      Neurons rely on glial lactate shuttling for metabolic support, which declines with aging and in neurodegenerative disease. Full disruption of lactate shuttling in peripheral nerves causes progressive axon degeneration, but we were interested to understand how partial disruption, a scenario more relevant to aging and disease, contributes to neurodegeneration risk. Pyruvate and lactate are interconverted by lactate dehydrogenases (LDHA and LDHB) in both lactate producing and consuming cells. We therefore began by investigating Ldhb knockout mice (loss of LDHA, the dominant LDH in liver and muscle, caused embryonic lethality), and discovered that they develop progressive neuromuscular junction atrophy and functional decline without axon degeneration. Because even Ldhb+/- heterozygosity significantly affects motor behavior, we also wondered about a potential link to congenital disease and pursued this by identifying rare loss-of-function LDHB variants among ALS patients. Next, to better understand how LDHB loss leads to motor decline, we selectively deleted it in defined cell types. SC-specific deletion caused robust motor defects, whereas motor neuron-specific deletion has little effect. Reasoning that neuronal LDHB deficiency could model age-associated decline in lactate metabolism, we asked whether it would interact with ALS genetic risk. Indeed, motor-neuron LDHB deficiency synergizes with relatively mild ALS risk variants, TDP43-Q331K and Sod1-D83G knock-in alleles, to produce early motor neuropathy, indicating that LDHB loss enhances disease risk. These findings establish lactate metabolism as a modifier of motor system vulnerability and highlight it as a therapeutic target in peripheral as well as central neurodegeneration.
    DOI:  https://doi.org/10.1101/2025.11.24.690227
  65. EMBO Rep. 2025 Dec 15.
    Vesicle-coupled mRNA transport and translation govern intracellular organelle networking.
    Melissa Vázquez-Carrada, Sainath Shanmugasundaram, Sander H J Smits, Lasse van Wijlick, Michael Feldbrügge.
      Eukaryotic cells are highly compartmentalized, enabling sophisticated division of labour. For example, genetic information is stored in the nucleus while energy is produced in mitochondria. Despite this clear specialisation, compartments depend on intensive communication, including the exchange of metabolites and macromolecules. This is achieved through intracellular trafficking with membranous carriers such as endosomes, which constitute versatile transport vehicles. Key cargos include mRNAs and ribosomes that hitchhike on endosomes, linking RNA and membrane biology. In this review, we summarize recent advances showing how mRNAs are mechanistically attached to membranes of endosomes and lysosomal vesicles and how cargos are identified for transport. The encoded proteins illuminate the biological processes that rely on such spatiotemporal control. This is particularly true for the regulation of subcellular mitochondrial homeostasis, disclosing intensive multi-organelle networking. As a general concept, the underlying protein/protein and protein/RNA interactions exhibit significant redundancy yet are organized in a strict hierarchy with distinct core and accessory functions. This ensures both the robustness and specificity of mRNA hitchhiking.
    Keywords:  Endosomes; Local Translation; Mitochondria; RNA Transport, SLiMs
    DOI:  https://doi.org/10.1038/s44319-025-00666-4
  66. J Control Release. 2025 Dec 15. pii: S0168-3659(25)01163-0. [Epub ahead of print] 114549
    Dual-targeted molybdenum nanomedicine treats acute pancreatitis by blocking mitochondrial DNA-triggered cGAS-STING signaling via ROS modulation.
    Jinjin Liu, Dan Wang, Shuya Wang, Xiaojing Shi, Tingli Xiong, Yebin Lu, Jianbo Yang, Wei Wei, Xuejun Gong, Qiong Huang, Liandong Ji, Kelong Ai.
      Acute pancreatitis (AP), a potentially fatal disorder driven by macrophage-associated inflammation, involves mitochondrial reactive oxygen species (ROS) overproduction with pancreatic acinar cells (PACs). This ROS surge damages mitochondria, causing mitochondrial DNA (mt-DNA) leakage and PACs apoptosis. Released mt-DNA then activates the pro-inflammatory cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway in macrophages, exacerbating disease progression. Critically, while scavenging mitochondrial ROS can halt this cycle, existing mitochondria-targeted drugs fail to penetrate the damaged blood-pancreas barrier (BPB). To overcome this limitation, we developed MTP, a novel dual-targeting nanomedicine synthesized from tannic acid, dopamine, and molybdenum oxides. MTP uniquely achieves dual targeting: actively homing to injured BPB and specifically accumulating within PACs mitochondria. This enables robust mitochondrial ROS scavenging, which protects mitochondrial integrity, reduces mt-DNA release, inhibits PACs apoptosis, and crucially blocks mt-DNA-induced cGAS-STING activation in macrophages, thereby suppressing their pro-inflammatory M1 polarization. By simultaneously interrupting both ROS-mediated PACs damage and macrophage-driven inflammation via this dual-targeting strategy, MTP effectively mitigates AP progression, establishing a breakthrough therapeutic approach.
    Keywords:  Acute pancreatitis; Blood-pancreas barrier; Macrophage-associated inflammation; Mitochondrial targeting; ROS
    DOI:  https://doi.org/10.1016/j.jconrel.2025.114549
  67. Pharmacol Res. 2025 Dec 17. pii: S1043-6618(25)00496-7. [Epub ahead of print] 108071
    Targeting PGC-1α axis Rescues Aberrant Development from Thyroid Hormone Defect in Brain Organoids.
    Emanuela Bottani, Francesca Ciarpella, Benedetta Lucidi, Giulia Pedrotti, Chiara Santanatoglia, Eros Rossi, Enrica Cappellozza, Elisa De Tomi, Sissi Dolci, Giovanni Malerba, Giorgio Malpeli, Ilaria Decimo.
      Thyroid hormone (T3) deficiency during central nervous system development leads to severe and often incurable human pathologies, including intellectual disability and motor dysfunction. Using murine dorsal forebrain organoids, we showed that T3 is required to activate mitochondrial β-oxidation and OXPHOS biogenesis to sustain neuronal development, while its absence caused profound neurodevelopmental defects such as defective maturation, astrogliosis, and reduced spontaneous activity. Mechanistically, we identified the transcriptional coactivator PGC-1α as a central mediator of the T3 effect. Pharmacological inhibition of β-oxidation in T3-supplemented organoids recapitulated the T3-deficient phenotype, whereas Ppargc1a gene augmentation rescued neuronal development under T3-deprived conditions. Most importantly, pharmacological stimulation of the PGC-1α axis with Nicotinamide Riboside or Bezafibrate rescues mitochondrial bioenergetics and neuronal development, effectively correcting aberrant brain organoid maturation despite T3 deficiency. These findings reveal for the first time the role of T3 in supporting neurodevelopment via activation of mitochondrial β-oxidation and OXPHOS biogenesis, and identify the PGC-1α axis as a promising therapeutic avenue for otherwise intractable disorders linked to thyroid hormone deficiency.
    Keywords:  brain organoids; fatty acid oxidation; mitochondria; neurodevelopment; thyroid hormone
    DOI:  https://doi.org/10.1016/j.phrs.2025.108071
  68. NPJ Aging. 2025 Dec 16. 11(1): 99
    Mitochondrial dysfunction in cellular senescence: a bridge to neurodegenerative disease.
    Adam J Hruby, Ryo Higuchi-Sanabria.
      Senescent cells, characterized by a state of irreversible proliferative arrest and inflammatory profile, have emerged as drivers of age-related decline. Growing evidence suggests that alterations in mitochondrial function and morphology play a key role in the induction and maintenance of senescence, as well as in promotion of the proinflammatory senescence-associated secretory phenotype (SASP). In this review, we seek to survey the relationship between mitochondrial dysfunction and senescence, focusing on the consequences of changes in oxidative phosphorylation efficiency, calcium handling, mitochondrial metabolites, mitochondrial dynamics and quality control, and release of damage-associated molecular patterns. We first describe these changes before illustrating the pathways and mechanisms through which mitochondrial dysfunction results in cell cycle arrest and the SASP. Lastly, we showcase evidence relating cellular senescence to neurodegenerative disease and propose that mitochondrial dysfunction may act as a bridge between the two.
    DOI:  https://doi.org/10.1038/s41514-025-00291-4
  69. J Mol Cell Cardiol Plus. 2025 Dec;14 100827
    Mitochondrial metabolic remodeling and multi-omics profiling identify plasma biomarkers of myocardial infarction.
    Selvam Paramasivan, Mitchell C Lock, Roberto A Barrero, Paul C Mills, Janna L Morrison, Pawel Sadowski.
      Mitochondrial dysfunction is a hallmark of myocardial infarction (MI), yet the molecular mechanisms linking metabolic reprogramming in the ischemic myocardium to systemic biomarker signatures remain incompletely understood. In this study, we employed a data-independent acquisition mass spectrometry (SWATH-MS) strategy integrating multi-omics analysis with upstream regulatory network analysis to investigate mitochondrial energy pathway alterations in a preclinical ovine model of MI. Proteomic profiling of infarcted myocardium revealed a pronounced shift from oxidative phosphorylation to glycolysis, accompanied by coordinated suppression of mitochondrial fatty acid β-oxidation enzymes. This metabolic reprogramming was strongly associated with four upstream master regulators, most notably predicted inhibition and significant transcriptional downregulation of PPARGC1A, a key coactivator of mitochondrial biogenesis and oxidative metabolism, indicating disrupted mitochondrial energy homeostasis and impaired adaptive responses in ischemic cardiomyocytes. Parallel plasma proteomic analysis identified a distinct panel of differentially expressed proteins enriched in pathways related to carbon metabolism, amino acid biosynthesis, and cardiac muscle contraction. Notably, mitochondrial metabolic enzymes such as SUCLG1, MDH2, HADHA, and HADHB were significantly downregulated at both the transcript and protein levels in cardiac tissue, while their protein abundance was markedly increased in plasma post-MI, highlighting their potential as circulating biomarkers of mitochondrial dysfunction. These findings provide mechanistic insight into the energy metabolic remodeling that occurs during myocardial ischemic injury and establish a systems-level framework for linking tissue-specific mitochondrial alterations with accessible plasma biomarkers. This study supports the translational potential of targeting mitochondrial pathways for diagnostic and therapeutic strategies in ischemic heart disease.
    Keywords:  Mitochondria; Multi-omics; Myocardial infarct; Plasma biomarkers; Proteomics; Upstream regulators
    DOI:  https://doi.org/10.1016/j.jmccpl.2025.100827
  70. Ageing Res Rev. 2025 Dec 11. pii: S1568-1637(25)00338-1. [Epub ahead of print] 102992
    Comparison of anti-aging effect of PQQ (Pyrroloquinoline Quinone) and NMN/NR (Nicotinamide Mononucleotide /Nicotinamide Riboside) - possible combination use.
    Savani Ulpathakumbura, Sicong Kenric Lu, Rasika Gunarathne, John Zhiyong Yang, Johnson Liu, Xiaodong Jin, Qiang Zhou, Jun Lu.
      Aging is a complex biological process characterized by the gradual deterioration of cellular functions, leading to an increased susceptibility to chronic diseases. In the search for interventions to promote healthy aging and extend lifespan, Pyrroloquinoline Quinone (PQQ) and Nicotinamide Mononucleotide/Nicotinamide Riboside (NMN/NR) have emerged as promising anti-aging agents. PQQ exerts its anti-aging effect primarily through enhancing mitochondrial biogenesis, exerting antioxidant activity, and modulating inflammatory pathways. On the other hand, NMN/NR act as key precursors in the biosynthesis of nicotinamide adenine dinucleotide (NAD+), a crucial coenzyme involved in energy metabolism, cellular homeostasis, and DNA repair, thereby promoting longevity. This review systematically compares the mechanisms of action and efficacy of those compounds in mitigating age-related complications. Furthermore, this emphasizes the potent synergistic effect when PQQ and NMN/NR are used in combined formulations, highlighting their complementary pathways to support healthy aging. Despite supporting preliminary data and patented formulations, strong scientific evidence encouraging the synergistic anti-aging potential of PQQ and NMN/NR remains limited, highlighting the need for robust studies. Collectively, PQQ and NMN/NR offer distinct complementary strategies to promote healthy aging and prevent age-related diseases; their combination could offer a more effective approach to enhance healthy aging and longevity.
    Keywords:  NMN; NR; PQQ; anti-aging
    DOI:  https://doi.org/10.1016/j.arr.2025.102992
  71. J Vis Exp. 2025 Nov 28.
    Assessing Gastrointestinal Motility in Caenorhabditis elegans RAC1/CED-10 Mutants as a Tool to Study Early Parkinson's Disease.
    Amanda Muñoz-Juan, Anna Laromaine, Víctor J Yuste, Esther Dalfó.
      Parkinson's disease (PD) is among the most prevalent neurodegenerative disorders and is diagnosed based on motor symptoms that emerge after significant dopaminergic neuron loss. Non-motor symptoms, such as constipation, are the most common and often appear earlier, indicating the onset of the disease. Many animal models are used to study neurodegenerative diseases, yet most focus on the later stages. Because it is difficult to determine the exact start of neurodegeneration, no single model fully represents the entire disease progression. Mammalian models are especially time-consuming and expensive due to their long-life cycles. In contrast, Caenorhabditis elegans (C. elegans), a transparent 1 mm nematode with a short life and reproductive cycle (~3 weeks and 3 days), enables faster, cost-effective experiments thanks to its rapid generation turnover. The defecation motor program in C. elegans consists of rhythmic cycles regulated by a complex genetic network in which Rho/rac GTPases participate, and RAC1 (CED-10 in C. elegans) is among them. We have shown that RAC1/CED-10 mutants exhibit compromised GABAergic morphology and function, which results in disrupted defecation cycles. Here, we present the experimental protocol for measuring constipation in RAC1/CED-10 C. elegans at early stages. In addition to serving as a predictive tool to investigate early PD symptoms prior to neurodegeneration, this protocol could also be employed as an early endpoint to assess the efficacy of pharmacological intervention. Because these changes are not disease-specific, we believe this model provides a valuable tool for investigating alterations that arise early in other illnesses.
    DOI:  https://doi.org/10.3791/69278
  72. Mol Neurobiol. 2025 Dec 19. 63(1): 313
    EVs from Stem Cells Improve Mitochondrial Dysfunction in Neuronal Disorders.
    Sadaf Jahan, Dipak Kumar, Shaheen Ali, Arif Jamal Siddiqui, Mohammed Alaidarous, Johra Khan, Andleeb Khan.
      Mitochondrial dysfunction is a critical pathological trait of numerous neurodegenerative and inflammatory central nervous system (CNS) disorders, including Alzheimer's disease (AD), Parkinson's disease (PD), and multiple sclerosis (MS). Cellular stressors can directly modulate mitochondrial metabolism and increase the production of reactive oxygen species (ROS), thereby triggering mitochondrial retrograde signaling that alters nuclear gene expression and promotes the release of deleterious signal components into the cytoplasm. These processes contribute to neuronal injury and the progression of disease pathology. Emerging evidence underlines the therapeutic potential of extracellular vesicles (EVs) derived from stem cells such as mesenchymal stem cells (MSCs), neuronal stem cells (NSCs), and induced pluripotent stem cells (iPSCs) in reversing mitochondrial dysfunction. These nanoscale vesicles, which encapsulate transcription factors, nucleic acids, proteins, lipids, and even mitochondria, facilitate intercellular communication and influence the biological behaviour of recipient cells. Notably, stem cell-derived EVs have been shown to enhance mitochondrial function by improving the maximal oxygen consumption rate and spare respiratory capacity in injured neuronal cells. The molecular cargo within EVs, including miR-21, miR-29, and antioxidant enzymes, has been implicated in regulating mitochondrial biogenesis, reducing oxidative stress, and modulating pathways associated with apoptosis, mitophagy, and energy metabolism. Importantly, EVs can cross the blood-brain barrier (BBB), offering a minimally invasive strategy for targeted CNS delivery. In conclusion, stem cell-derived EVs represent a promising, cell-free therapeutic approach to restoring mitochondrial homeostasis and preventing neuronal disorders.
    Keywords:  Extracellular vesicles; Mitochondrial dysfunction; Neurodegeneration; Neuronal disorders; Oxidative stress; Stem cells
    DOI:  https://doi.org/10.1007/s12035-025-05623-9
  73. J Nanobiotechnology. 2025 Dec 14.
    Endothelial mitochondrial-derived vesicles (EMDVs) with retinal targeted homing properties dynamically modulate the eIF2α-ATF4-CHOP signaling pathway and efficiently restore mitochondrial homeostasis in diabetic retina.
    Siyu Gui, Jie Gao, Tianchang Tao, Peng Wang, Yueyang Xu, Zhihao Huang, Yuyang She, Jiajie Li, Jingwan Su, Zhe Lu, Jianchao Qiao, Song Wang, Xiaodong Sun, Mohan Li.
      
    Keywords:  Blood-retinal barrier; Diabetic retinopathy; Drug delivery; Endothelial mitochondria-derived vesicles; Integrated stress response; Mitochondrial quality control
    DOI:  https://doi.org/10.1186/s12951-025-03929-3
  74. Forensic Sci Int. 2025 Dec 12. pii: S0379-0738(25)00414-1. [Epub ahead of print]379 112770
    An efficient preprocessing workflow tailored for mitochondrial genome assembly from fragmented DNA.
    Yongheng Zhou, Peng Gao, Shuhui Yang, Yanchun Xu.
      Mitochondrial DNA (mtDNA), characterised by its high copy number, structural stability, and maternal inheritance, is a critical genetic marker in forensic genetics, species identification, and conservation studies. Accurate mtDNA genome assembly is essential for these applications. However, DNA from typical wildlife and historical sources - such as museum specimens, keratinised tissues, environmental samples, and ancient remains - is often highly fragmented and damaged, limiting assembly efficiency and accuracy. Here, we developed a preprocessing workflow (MTAK) specifically designed to improve mtDNA assembly from degraded DNA. MTAK integrates two core steps: (1) extraction of homologous reads via reference-sequence alignment and (2) targeted processing of severely damaged 5' and 3' terminal bases. The workflow was evaluated on 24 degraded samples of varying quality. MTAK substantially enhanced assembly completeness and accuracy, particularly in samples with extensive DNA damage, while reducing computational time by over tenfold and minimising resource consumption. An interaction model was implemented to guide optimal sequencing depth for efficient assembly. This approach is compatible with most existing assembly tools and significantly improves mtDNA recovery from challenging historical and wildlife samples.
    Keywords:  DNA damage; Fragmented DNA; Mitochondrial assembly; Pre-processing workflow
    DOI:  https://doi.org/10.1016/j.forsciint.2025.112770
  75. J Mol Med (Berl). 2025 Dec 13. 104(1): 2
    Stem cells strike back: advancements in Alzheimer's and Parkinson's disease treatment and modeling efforts from 2019 to 2024.
    Jasmina Isaković, Anna Athanassiadis, Marian Khubeis.
      This review critically evaluates the current state of stem cell therapy (SCT) for treating and modeling of Alzheimer's (AD) and Parkinson's disease (PD). It includes an in-depth analysis of both preclinical and clinical studies, with a particular focus on clinical trials conducted between 2019 and 2024, reflecting recent advancements in the field. Preclinical studies were examined to elucidate the molecular mechanisms underlying SCT and identify developments that could be translated into clinical practice. Within these studies, stem cells, including embryonic stem cells (ESCs), mesenchymal stem cells (MSCs), neural stem cells (NSCs), and induced pluripotent stem cells (iPSCs), have shown high differentiation and proliferation abilities. These properties, along with their capacity to inhibit inflammation, prevent apoptosis, and stimulate angiogenesis, make them promising candidates for treating AD and PD. Over the past 15 years, 76 SCT-based trials have been conducted-27 for AD and 48 for PD-with more than half occurring in the past 5 years. Despite the promise of SCT, the field faces challenges such as ethical concerns regarding the use of ESCs, heterogeneity of isolated cultures, and inconsistent results across preclinical trials. Novel materials and electromagnetic fields (EMFs) offer potential solutions to these issues. While bioengineering approaches can enhance the successful engraftment of transplanted stem cells, EMFs can direct the cells' migration and differentiation. In conclusion, although significant progress has been made in SCT, ongoing efforts are needed to address existing challenges. Nevertheless, SCT holds considerable promise for the future, offering potential breakthroughs in the treatment of neurodegenerative diseases.
    Keywords:  Alzheimer’s disease; Clinical trials; Neurodegeneration; Parkinson’s disease; Stem cell therapy; Stem cells
    DOI:  https://doi.org/10.1007/s00109-025-02613-1
  76. bioRxiv. 2025 Nov 25. pii: 2025.11.22.689945. [Epub ahead of print]
    A system for high-throughput axonal imaging of induced pluripotent stem cell-derived human i 3 Neurons.
    Stella A C Whittaker, Elizabeth D McKenna, Stephanie L Sarbanes, Michael S Fernandopulle, Michael E Ward, Antonina Roll-Mecak.
      Neurons have long, thin axons and branched dendritic processes which rely on an extensive microtubule network that functions as a cellular scaffold and substrate for cargo transport. Microtubule defects are a defining pathological feature of neurological disorders. The highly arborized, long, polarized neuronal processes pose challenges for imaging-based assays. Available methods use either dispersed cultures, which are inefficient for compartment-specific analyses, or microfluidic chambers, which allow clear separation of somatodendritic and axonal compartments but are expensive and difficult to maintain. Here, we introduce an "i 3 Neurosphere" culture model of induced pluripotent stem cell (iPSC)-derived human cortical i 3 Neurons that enables high-throughput imaging of hundreds of axons without specialized equipment. We characterize neurite outgrowth, polarization, microtubule dynamics, and motility of diverse cargo, providing a reference for future work on microtubule processes in this system. The high-throughput compartment-specific imaging we present, combined with facile genetic engineering in i 3 Neurons provides a powerful tool to study human neurons.
    SIGNIFICANCE STATEMENT: Human neurons are difficult to study due to limited access to tissue and technical challenges in existing in vitro models of axonal transport. We developed i 3 Neurospheres , a simple and scalable 3D culture system of human iPSC-derived neurons that enables high-throughput imaging of axonal outgrowth, microtubule dynamics, and intracellular transport. This platform provides an accessible, reproducible method for investigating neuronal function and disease mechanisms, offering broad utility for neuroscience research and preclinical drug screening.
    DOI:  https://doi.org/10.1101/2025.11.22.689945
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