bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2025–11–30
eighty papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Mitochondrial NAD+ drives liver regeneration.
  2. Drug repurposing screen identifies an HRI activating compound that promotes adaptive mitochondrial remodeling in MFN2-deficient cells.
  3. The Mitochondrial F-box protein 1 and DJ-1 homolog HSP31 support cellular proteostasis during mitochondrial protein import clogging.
  4. The RAB27A effector SYTL5 regulates mitophagy and mitochondrial metabolism.
  5. Mitochondrial Base Editing of the m.8993T>G Mutation Restores Bioenergetics and Neural Differentiation in Patient iPSCs.
  6. MICU2 controls mitochondrial calcium signaling and migration in neurons during development.
  7. Metformin promotes mitochondrial integrity through AMPK-signaling in Leber's hereditary optic neuropathy.
  8. Cell-Intrinsic Vulnerability and Immune Activation Cooperate to Drive Degeneration in a Mitochondrial Complex I Deficiency Model of Optic Neuropathy.
  9. Drosophila HS dendrites are resilient to adult-onset deficits in mitochondrial dynamics.
  10. Neuronal compartmentalization results in "impoverished" axonal mitochondria.
  11. The S-depalmitoylase ABHD10 is essential for sperm mitochondrial sheath formation and male fertility.
  12. Canonical and non-canonical functions of proteins regulating mitochondrial dynamics in mammalian physiology.
  13. Carbohydrate adaptation drives liver-brain axis maturation.
  14. Inhibition of Mitochondrial Complex III Causes Dopaminergic Neurodegeneration by Redox Stress in Caenorhabditis elegans.
  15. Tryptoline Stereoprobe Elaboration Identifies Inhibitors of the GRPEL1-HSPA9 Chaperone Complex.
  16. Intrinsic errors in mitochondrial translation trigger a decline in cell fitness.
  17. Proteome-wide model for human disease genetics.
  18. Electron microscopy visualization of cell-free mitochondrial DNA-containing extracellular vesicles in human plasma, serum, and saliva.
  19. Activity-dependent mitochondrial transport in peri-synaptic glia drives motor function.
  20. Tau-Mitochondria Interactions in Neurodegeneration: Mechanisms and Therapeutic Potential.
  21. Targeting prohibitins activates the ISR through DELE1-HRI by impairing protein import into the mitochondrial matrix.
  22. NAD+ restores proteostasis through splicing-dependent autophagy.
  23. Tank-Binding Kinase 1 protects against MASH progression via mitochondrial quality control.
  24. In vivo mitochondrial base editing restores genotype and visual function in a mouse model of LHON.
  25. Mitochondrial Quality Control and Cell Death.
  26. Autophagy and mitophagy at the synapse and beyond: implications for learning, memory and neurological disorders.
  27. Editorial: Molecular underpinnings of genetic and rare diseases: from diagnostic tools to therapeutic approaches.
  28. Multiple entanglements of different cell death pathways, in which caspase-8 and BID interact with cardiolipin*, have been identified.
  29. The intermediate filament protein GFAP regulates mitochondrial fission in astrocytes.
  30. Drivers of Diagnostic Delay in Mitochondrial Disease: Missed Recognition of Canonical Features.
  31. Expanding the utility of variant effect predictions with phenotype-specific models.
  32. N-terminal α-amino SUMOylation promotes phosphorylation-independent cofilin-1 translocation to the mitochondrial matrix and induces apoptosis.
  33. Ginsenoside Re binds Drp1 Leu94 across species to restore mitochondrial homeostasis via Atg1/ULK1-dependent fission-mitophagy coupling in age-related degeneration.
  34. Kidney transplantation in mitochondrial diseases: a systematic review.
  35. MitoLandscape, a semi-automated pipeline for subcellular localization and quantification of mitochondria.
  36. Targeting TOMM40 and TOMM22 to Rescue Statin-Impaired Mitochondrial Function, Dynamics, and Mitophagy in Skeletal Myotubes.
  37. Loss-of-function variant of SLC27A3 causes mitochondrial dysfunction and a metabolic neurodevelopmental disorder via impaired fatty acid transport.
  38. Transcriptomic analysis of cells following decreased mitochondrial DNA-copy number reveals compensatory mechanisms in mitochondrial DNA replication and cellular energetics.
  39. Inhibition of oligomeric BAX by an anti-apoptotic dimer.
  40. Spatiotemporal control of PIWI compartmentalization by mitochondrial scaffolds defines pachytene piRNA pathway organization.
  41. Visualizing PINK1 Activity Dynamics in Single Cells with a Phase Separation-Based Kinase Activity Reporter.
  42. Cavitating Mitochondrial Leukoencephalopathy: Unmasking SURF-1 Deficiency through Neuroimaging-Genetic Correlation.
  43. Deficient Cardiolipin Remodeling Alters Muscle Fiber Composition and Neuromuscular Connectivity in Barth Syndrome.
  44. Localized Wnt-signaling promotes asymmetric NuMA-dependent oriented divisions and unequal apportioning of mitochondria.
  45. CISD2 ensures adequate ER-mitochondrial coupling, critically supporting mitochondrial function in neurons.
  46. Hypoxia-induced mitoROS triggers M1 linear ubiquitin chains and activates NF-κB signaling.
  47. Mitochondrial movement in pancreatic alpha cells requires Miro2 and is regulated by glucose.
  48. Mitochondrial Nephropathy With m.5538G>A Mutation Within the tRNA-Trp Region Assessed by Mitochondrial Function Analysis: A Case Report.
  49. Mitochondrial Dynamics in Aging Heart.
  50. Gram-scale synthesis of the thiazolidinedione-based mitoNEET ligand NL-1 using a Hantzsch ester reduction.
  51. Drug delivery systems for mitochondrial targeting.
  52. Spectrum and Impact of Mitochondrial DNA Mutations in Ovarian Cancer.
  53. Mechanical confinement induces ferroptosis through mitochondrial dysfunction.
  54. Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like Episodes: A Masquerader of Young-onset Stroke.
  55. The proton motive force maintains mtDNA euploidy by balancing mtDNA replication with cell proliferation.
  56. Cardiac SR-Mitochondria Contacts-Impact on Cardiac Physiology and Mitochondrial Fitness.
  57. Audio long read: Faulty mitochondria cause deadly diseases - fixing them is about to get a lot easier.
  58. Iron Deficiency Impairs Mitochondrial Energetics and Early Axonal Growth and Branching in Developing Hippocampal Neurons.
  59. Double whammy: drugs that inhibit kinase enzymes also speed up their disposal.
  60. APOE4 impairs Nrf2-PINK1/Parkin-dependent mitochondrial clearance through disrupted antioxidant and mitophagy signaling.
  61. Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism.
  62. Engineering a CRISPR-associated IscB system for developing miniature genome-editing tools in human cells and mouse embryos.
  63. Constellation illuminates rare disease genetics.
  64. Supervised machine learning identifies impaired mitochondrial quality control in β cells with development of type 2 diabetes.
  65. Cryo-EM reveals how ASX-173 inhibits human asparagine synthetase to activate the integrated stress response.
  66. NADH dehydrogenase reverses dietary and clock metabolic syndrome.
  67. NNT deficiency alters cardiac structure and function without impairing mitochondrial bioenergetics in aged mice.
  68. Integrated Stress Response Signatures Drive Monocyte Dysfunction in GBA1 - and LRRK2 -Linked Parkinson's Disease.
  69. Visualizing intraorganellar ultrastructures, dynamics, and interactions with open-access background-free Lock-in-SIM.
  70. The histone modification regulator, SIN3, plays a role in the cellular response to changes in glycolytic flux.
  71. Endogenous mitochondrial hydrogen peroxide regulates neurogenesis during cortical development.
  72. MtDNA-depleted neuronal cell transcriptomes reveal Alzheimer's disease-related changes.
  73. Long-read genome sequencing and multi-omics in aging and neurodegeneration.
  74. Cytosolic mtDNA and associated EYA-mediated pro-inflammatory signaling modulate healthspan in Drosophila.
  75. Condensate-Driven Triglyceride Depletion Links α-Synuclein to Mitochondrial Dysfunction.
  76. Imaging Cellular Metabolic Rewiring with SuMMIT-SRS.
  77. NMR assignments of the human homodimeric mitochondrial ATP synthase inhibitor IF1.
  78. The Metabolome Atlas of 22 Tissues in Aging Mice Reveals a Switch in Thermogenesis from Brown Fat to Skeletal Muscle.
  79. Mitochondrial transplantation alleviates acute pancreatitis by suppressing macrophage necroptosis.
  80. Gene therapy strategies in tissue engineering: advances and applications for regenerative therapy.
  1. Nat Metab. 2025 Nov 24.
    Mitochondrial NAD+ drives liver regeneration.
      
    DOI:  https://doi.org/10.1038/s42255-025-01414-7
  2. Proc Natl Acad Sci U S A. 2025 Dec 02. 122(48): e2517552122
    Drug repurposing screen identifies an HRI activating compound that promotes adaptive mitochondrial remodeling in MFN2-deficient cells.
    Prerona Bora, Mashiat Zaman, Samantha Oviedo, Sergei Kutseikin, Nicole Madrazo, Prakhyat Mathur, Meera Pannikkat, Sophia Krasny, Rama Aldakhlallah, Alan Chu, Kristen A Johnson, Danielle A Grotjahn, Timothy E Shutt, R Luke Wiseman.
      Pathogenic variants in the mitochondrial outer membrane GTPase MFN2 cause the peripheral neuropathy Charcot-Marie-Tooth type 2A (CMT2A). These mutations can disrupt MFN2-dependent regulation of diverse aspects of mitochondrial biology including organelle morphology, motility, mitochondrial-endoplasmic reticulum (ER) contacts (MERCs), and respiratory chain activity. However, no therapies currently exist to mitigate the mitochondrial dysfunction linked to genetic deficiencies in MFN2. Herein, we performed a drug repurposing screen to identify compounds that selectively activate the integrated stress response (ISR)-the predominant stress-responsive signaling pathway responsible for regulating mitochondrial morphology and function. This screen identified the compounds parogrelil and MBX-2982 as potent and selective activators of the ISR through the OMA1-DELE1-HRI signaling axis. We show that treatment with these compounds promotes adaptive, ISR-dependent remodeling of mitochondrial morphology and protects mitochondria against genetic and chemical insults. Moreover, we show that pharmacologic ISR activation afforded by parogrelil restores mitochondrial tubular morphology, promotes mitochondrial motility, rescues MERCs, and enhances mitochondrial respiration in MFN2-deficient cells. These results demonstrate the potential for pharmacologic ISR activation through the OMA1-DELE1-HRI signaling pathway as a potential strategy to mitigate mitochondrial dysfunction in CMT2A and other pathologies associated with MFN2 deficiency.
    Keywords:  drug repurposing; integrated stress response; mitochondrial dysfunction
    DOI:  https://doi.org/10.1073/pnas.2517552122
  3. bioRxiv. 2025 Oct 14. pii: 2025.10.13.682092. [Epub ahead of print]
    The Mitochondrial F-box protein 1 and DJ-1 homolog HSP31 support cellular proteostasis during mitochondrial protein import clogging.
    Gargi Mishra, Xiaowen Wang, Eamon Fitzpatrick, Auyon Ghosh, Xin Jie Chen.
      Mitochondrial biogenesis requires the import of ∼1,000-1,500 nuclear-encoded proteins across the Translocase of Outer Membrane (TOM) and the Translocase of Inner Membrane (TIM) 22 or 23 complexes. Protein import defects cannot only impair mitochondrial respiration but also cause mitochondrial Precursor Overaccumulation Stress (mPOS) in the cytosol. Recent studies showed that specific mutations in the nuclear-encoded Adenine Nucleotide Translocase 1 (ANT1) cause musculoskeletal and neurological diseases by clogging TOM and TIM22 and inducing mPOS. Here, we found that overexpression of MFB1 , encoding the mitochondrial F-box protein 1, suppresses cell growth defect caused by a clogger allele of AAC2 , the yeast homolog of Ant1. Disruption of MFB1 synergizes with a clogger allele of aac2 to inhibit cell growth. This is accompanied by increased retention of mitochondrial proteins in the cytosol, suggesting exacerbated defect in mitochondrial protein import. Proximity-dependent biotin identification (BioID) suggested that Mfb1 interacts with several mitochondrial surface proteins including Tom22, a component of the TOM complex. Loss of MFB1 under clogging conditions activates genes encoding cytosolic chaperones including HSP31 . Interestingly, disruption of HSP31 creates a synthetic lethality with protein import clogging under respiring conditions. We propose that Mfb1 functions to maintain mitochondrial protein import competency under clogging conditions, whereas Hsp31 plays an important role in protecting the cytosol against mPOS. Mutations in DJ-1, the human homolog of Hsp31, and mitochondria-associated F-box proteins (eg., Fbxo7) are known to cause early-onset Parkinson's disease. Our work may help to better understand how these mutations affect cellular proteostasis and cause neurodegeneration.
    DOI:  https://doi.org/10.1101/2025.10.13.682092
  4. Elife. 2025 Nov 26. pii: RP105541. [Epub ahead of print]14
    The RAB27A effector SYTL5 regulates mitophagy and mitochondrial metabolism.
    Ana Lapão, Lauren Sophie Johnson, Laura Trachsel-Moncho, Samuel J Rodgers, Sakshi Singh, Matthew Y W Ng, Sigve Nakken, Eeva-Liisa Eskelinen, Anne Simonsen.
      SYTL5 is a member of the Synaptotagmin-Like (SYTL) protein family that differs from the Synaptotagmin family by having a unique N-terminal Synaptotagmin homology domain that directly interacts with the small GTPase RAB27A. Several SYTL protein family members have been implicated in plasma membrane transport and exocytosis, but the specific function of SYTL5 remains unknown. We here show that SYTL5 is a RAB27A effector and that both proteins localise to mitochondria and vesicles containing mitochondrial material. Mitochondrial recruitment of SYTL5 depends on its interaction with functional RAB27A. We demonstrate that SYTL5-RAB27A positive vesicles containing mitochondrial material, autophagy proteins and LAMP1 form during hypoxia and that depletion of SYTL5 and RAB27A reduces mitophagy under hypoxia mimicking conditions, indicating a role for these proteins in mitophagy. Indeed, we find that SYTL5 interacts with proteins involved in vesicle-mediated transport and cellular response to stress and that its depletion compromises mitochondrial respiration and increases glucose uptake. Intriguingly, SYTL5 expression is significantly reduced in tumours of the adrenal gland and correlates positively with survival for patients with adrenocortical carcinoma.
    Keywords:  ACC; Mitochondria; RAB27A; SYTL5; cell biology; hypoxia; mitophagy; none
    DOI:  https://doi.org/10.7554/eLife.105541
  5. Genes (Basel). 2025 Nov 01. pii: 1298. [Epub ahead of print]16(11):
    Mitochondrial Base Editing of the m.8993T>G Mutation Restores Bioenergetics and Neural Differentiation in Patient iPSCs.
    Luke Yin, Angel Yin, Marjorie Jones.
       BACKGROUND: Point mutations in mitochondrial DNA (mtDNA) cause a range of neurometabolic disorders that currently have no curative treatments. The m.8993T>G mutation in the Homo sapiens MT-ATP6 gene leads to neurogenic muscle weakness, ataxia, and retinitis pigmentosa (NARP) when heteroplasmy exceeds approximately 70%.
    METHODS: We engineered a split DddA-derived cytosine base editor (DdCBE), each half fused to programmable TALE DNA-binding domains and a mitochondrial targeting sequence, to correct the m.8993T>G mutation in patient-derived induced pluripotent stem cells (iPSCs). Seven days after plasmid delivery, deep amplicon sequencing showed 35 ± 3% on-target C•G→T•A conversion at position 8993, reducing mutant heteroplasmy from 80 ± 2% to 45 ± 3% with less than 0.5% editing at ten predicted off-target loci.
    RESULTS: Edited cells exhibited a 25% increase in basal oxygen consumption rate, a 50% improvement in ATP-linked respiration, and a 2.3-fold restoration of ATP synthase activity. Directed neural differentiation yielded 85 ± 2% Nestin-positive progenitors compared to 60 ± 2% in unedited controls.
    CONCLUSIONS: Edits remained stable over 30 days in culture. These results establish mitochondrial base editing as a precise and durable strategy to ameliorate biochemical and cellular defects in NARP patient cells.
    Keywords:  DdCBE; MT-ATP6; NARP; base editing; heteroplasmy; iPSCs; m.8993T>G; mitochondrial DNA
    DOI:  https://doi.org/10.3390/genes16111298
  6. Cell Rep. 2025 Nov 20. pii: S2211-1247(25)01355-5. [Epub ahead of print]44(12): 116583
    MICU2 controls mitochondrial calcium signaling and migration in neurons during development.
    Elena Berezhnaya, Benjamín Cartes-Saavedra, Raghavendra Singh, Macarena Rodríguez-Prados, Orly Reiner, Fowzan S Alkuraya, György Hajnóczky.
      Neurological disorders are linked to mitochondrial dysfunction and calcium overload. Mitochondrial calcium uptake is mediated by the mitochondrial calcium uniporter (mtCU), regulated by MICU1, which can be either homodimerized or heterodimerized with MICU2 or MICU3. Though MICU2 is scarce in the adult brain, MICU2 loss in patients leads to a neurodevelopmental disorder. We hypothesized that MICU2 is required for developmental calcium signaling and neuronal migration. MICU2 is present in the developing mouse brain but disappears by maturation, contrasting with other mtCU subunits that increase. MICU2 loss in mice does not affect cytoplasmic calcium but augments the mitochondrial matrix calcium rise in primary cortical neurons, leading to neuronal overmigration in the cortex and behavioral changes at 2 but not 12 months. Consistently, mitochondrial calcium uptake is not significantly affected in the adult animal cortex. MICU2-deficient patient fibroblasts copy the mitochondria-confined calcium alteration in developing neurons. Thus, MICU2 is important during neurodevelopment, likely by regulating the mtCU, and is eliminated by brain maturation.
    Keywords:  CP: cell biology; CP: neuroscience; MCU; MICU2; MICU3; anxiety; brain development; calcium signaling; mitochondria; neurodevelopmental disorders; neurons; radial migration
    DOI:  https://doi.org/10.1016/j.celrep.2025.116583
  7. FEBS Open Bio. 2025 Nov 23.
    Metformin promotes mitochondrial integrity through AMPK-signaling in Leber's hereditary optic neuropathy.
    Chatnapa Panusatid, Rapasviranda Soiyangsuk, Maneeluck Tanadjindarat, Chayanon Peerapittayamongkol.
      Leber's hereditary optic neuropathy (LHON) is a maternally inherited disorder caused by mitochondrial DNA mutations in complex I of the respiratory chain, leading to impaired ATP production, mitochondrial fragmentation, and oxidative stress that contribute to vision loss. This study investigated the potential repurposing of metformin, a widely used antidiabetic drug, in fibroblasts from LHON patients carrying the m.11778G>A mutation. Fibroblasts from LHON patients and healthy individuals were treated with metformin, and mitochondrial function was assessed using high-content imaging, biochemical assays, immunoblotting, immunofluorescence, and Seahorse analysis. Metformin reduced mitochondrial fragmentation, increased network length, stabilized mitochondrial membrane potential, enhanced ATP production, and lowered ROS accumulation under oxidative stress. Metformin significantly increased mitophagy and autophagic flux, as shown by LC3B puncta quantification with and without chloroquine, and activated AMPK signaling through increased AMPKα1/2 phosphorylation and AMPKβ1 Ser182 phosphorylation. In addition, metformin promoted PGC-1α nuclear translocation, indicating stimulation of mitochondrial biogenesis, while maintaining mtDNA copy number and supporting oxidative phosphorylation. These findings suggest that metformin, at clinically relevant concentrations, enhances mitochondrial health and function in LHON fibroblasts, supporting its potential as an affordable and safe therapeutic option to mitigate vision loss in LHON.
    Keywords:  AMPK activation; Leber's hereditary optic neuropathy; Metformin; Mitochondrial dynamics; Mitophagy; Primary fibroblasts
    DOI:  https://doi.org/10.1002/2211-5463.70165
  8. bioRxiv. 2025 Oct 09. pii: 2025.10.08.681245. [Epub ahead of print]
    Cell-Intrinsic Vulnerability and Immune Activation Cooperate to Drive Degeneration in a Mitochondrial Complex I Deficiency Model of Optic Neuropathy.
    Daniela Santamaría-Muñoz, Raenier V Reyes, Miranda R Krueger, Andrea García-Llorca, Brennan Marsh-Armstrong, Xin Duan, Yang Hu, Derek S Welsbie, Nicholas Marsh-Armstrong, Elisenda Sanz, Albert Quintana, Sergi Simó, Anna La Torre.
      Mitochondrial dysfunction is a central hallmark of many optic neuropathies, yet the mechanisms linking intrinsic metabolic stress to retinal ganglion cell (RGC) degeneration remain unclear. To bridge this gap, we developed conditional transgenic models targeting the mitochondrial complex I subunit Ndufs4 in the retina. Broad deletion of Ndufs4 in the retina resulted in vision loss, progressive RGC degeneration, and pronounced immune activation before overt RGC death. Strikingly, depletion of myeloid cells significantly preserved RGCs, demonstrating that inflammation is not simply a downstream consequence but a participant in the degeneration process. To further distinguish between intrinsic and extrinsic mechanisms, we generated a mosaic model in which only subsets of retinal cells lacked Ndufs4 . In this paradigm, the degeneration first appeared selectively in mutant regions, suggesting that mitochondrial impairment within RGCs is necessary to initiate vulnerability. At later stages, however, the degeneration extended beyond mutant territories, highly suggestive of a propagation through non-cell autonomous processes. Together, these findings support a model in which mitochondrial dysfunction creates the conditions for neuronal vulnerability, while immune responses govern the timing and extent of cell loss. This framework explains the consistent co-occurrence of metabolic deficits and neuroinflammation in optic neuropathies and highlights the importance of their interactions in disease progression. By clarifying the intersection of intrinsic and extrinsic mechanisms, this work advances our understanding of RGC degeneration and provides a conceptual basis for deciphering pathogenic processes across diverse optic neuropathies.
    DOI:  https://doi.org/10.1101/2025.10.08.681245
  9. bioRxiv. 2025 Nov 09. pii: 2025.11.07.687201. [Epub ahead of print]
    Drosophila HS dendrites are resilient to adult-onset deficits in mitochondrial dynamics.
    Hailey Q Wang, Demetria G Fortson, Eavan D Burton, Hunter S Whitbeck, Briana M Robles, Letitia Bortey, Avi J Adler, Jordan I Kalai, Giovanna Napoleone, Erin L Barnhart.
      Mitochondrial transport, fusion, and fission are necessary for neuronal development, but the role of mitochondrial dynamics in neuronal maintenance remains unclear. In this work, we employed functional in vivo imaging of neurons in the Drosophila visual system, HS ("horizontal system") cells, to determine how adult-onset deficits in mitochondrial dynamics affect mitochondrial localization, local regulation of ATP, and dendrite maintenance. In mature HS neurons, inhibition of mitochondrial transport or fusion depleted mitochondria from the dendrite over time but, surprisingly, had no effect on dendrite morphology. Moreover, adult-restricted mitochondrial mis- localization affected neither visual stimulus-driven dendritic calcium responses nor local, dynamic regulation of ATP levels. In contrast, when induced during development, the same perturbations caused mitochondrial mis-localization, loss of dendrite complexity, abrogation of stimulus-locked calcium responses and ATP fluctuations, and age-dependent dendrite degeneration. Thus, although mitochondrial dynamics are necessary during neuronal development, mature dendrites are capable of maintaining form and function in vivo in the absence of properly-positioned mitochondria.
    DOI:  https://doi.org/10.1101/2025.11.07.687201
  10. bioRxiv. 2025 Oct 29. pii: 2025.10.27.684882. [Epub ahead of print]
    Neuronal compartmentalization results in "impoverished" axonal mitochondria.
    Adrian Marti Pastor, Liam S C Lewis, Stephan Müller, Pedro Guedes-Dias, Lorena Olifiers, Polina Pelkonen, Almudena Del Rio Martin, Caroline Fecher, Nikolai P Skiba, Ying Hao, Antoneta Gavoci, Laura Trovo, Mehmet Akif Aktas, Hariharan M Mahadevan, Angelika B Harbauer, Howard M Bomze, Vadim Y Arshavsky, Monika S Brill, Romain Cartoni, Stefan F Lichtenthaler, Sidney M Gospe, Thomas Misgeld.
      Mitochondria differ depending on their location within a neuron. Morphological heterogeneity between somatic, dendritic, and axonal mitochondria is well established. Emerging evidence suggests that further specialization is needed to meet the unique demands of different neuronal compartments. However, the molecular and functional diversity of mitochondria within a neuron remains poorly understood. Here, we utilized proteomics in MitoTag mice to profile somatodendritic and axonal mitochondria across four distinct neuron types, thereby generating a compendium of intracellular mitochondrial diversity. Combining proteomics, functional, and immunofluorescence analyses, we demonstrated that axonal mitochondria are not defined by the presence of unique proteins, but rather by the selective loss or preservation of specific pathways compared to their somatodendritic counterparts. This results in "impoverished" axonal mitochondria, which are characterized by diminished mtDNA expression and impaired oxidative phosphorylation yet retain other pathways, such as fatty acid metabolism. Bioinformatic analyses of multiomic data identified local translation as one mechanism underlying compartment-specific diversity. Together, these findings provide a comprehensive in vivo framework for understanding mitochondrial specialization across neuronal compartments.
    DOI:  https://doi.org/10.1101/2025.10.27.684882
  11. Nat Commun. 2025 Nov 24. 16(1): 10334
    The S-depalmitoylase ABHD10 is essential for sperm mitochondrial sheath formation and male fertility.
    Shumin Zhou, Hao Zhou, Haoran Xu, Mengneng Xiong, Shiming Gan, Dalin Liu, Yifan Zhao, Ziqi Yu, Chunhai Luo, Yujun Zhang, Beibei Zhang, Fei Sun.
      Palmitoylation is the only fully reversible post-translational lipid modification that impacts 10-20% of the human proteome, but its role during spermatogenesis remains enigmatic. In this study, through generating HA-tagged Abhd10 knock-in mice, Abhd10-null mice, and combining super-resolution fluorescence imaging and electron microscopy, we identify that the S-depalmitoylase ABHD10 (abhydrolase domain containing 10) is a mitochondrial matrix protein, specifically expressed in testis and is essential for male fertility. Abhd10 knockout mice manifest severe sperm motility defects accompanied by malformed mitochondrial sheaths of sperm. Mitochondrial proteomic analysis reveals that ABHD10 deficiency downregulates respiratory chain complex proteins and mitochondrial sheath formation factors SPATA19 and GK2. Using mass spectrometry-based mitochondrial acyl-biotin exchange assays, we systematically identify that loss of ABHD10 leads to the hyper-palmitoylation of multiple functionally critical proteins, including mitochondrial sheath formation factors (SPATA19 and GK2) and aerobic respiration regulators (PDHX, NDUFV1 and SDHB). Co-immunoprecipitation and proximity labeling assays reveal the physical interactions between ABHD10 and its substrates (SPATA19, GK2, PDHX). Collectively, ABHD10 may bind to and mediate the S-depalmitoylation of SPATA19, GK2, and PDHX, thereby regulating the formation of the sperm mitochondrial sheath and mitochondrial function. This work not only identifies S-depalmitoylase ABHD10 as a key determinant of male fertility but also advances our understanding of post-translational regulation during spermatogenesis.
    DOI:  https://doi.org/10.1038/s41467-025-65300-2
  12. J Physiol. 2025 Nov 22.
    Canonical and non-canonical functions of proteins regulating mitochondrial dynamics in mammalian physiology.
    Rémi Chaney, Vincent Marcangeli, Krystel Desjardins, Shima Taherkhani, Gilles Gouspillou.
      Mitochondria are dynamic and multifunctional organelles central to cellular bioenergetics and metabolism and acting as vital signalling hubs. Their morphology is finely regulated by the opposing processes of fusion and fission, predominantly controlled by four key GTPases: mitofusin 1 (MFN1), mitofusin 2 (MFN2), optic atrophy 1 (OPA1) and dynamin-related protein 1 (DRP1). In humans, mutations in their genes are linked to a broad range of pathological disorders. In animal models, both loss- and gain-of-function manipulations of these proteins lead to diverse physiological outcomes. Recent research has uncovered that, beyond their canonical roles in shaping mitochondrial morphology, these GTPases also participate in a variety of non-canonical cellular functions, impacting broader aspects of cell physiology. In this review, we examine the established functions of these GTPases in mitochondrial dynamics alongside their emerging roles beyond shaping mitochondrial morphology. We also provide an in-depth overview of how alterations in their expression or activity influence mammalian health and physiology. By highlighting the multifaceted roles and broad physiological impact of mitochondrial fusion and fission proteins, we aim to underscore their complex biology and promote further investigation into their broader physiological significance.
    Keywords:  GTPases; Mitofusins; dynamin‐related protein 1; mitochondrial dynamics; mitochondrial fission; mitochondrial fusion; mitochondrial quality control; optic atrophy 1
    DOI:  https://doi.org/10.1113/JP287149
  13. bioRxiv. 2025 Nov 06. pii: 2025.11.05.685548. [Epub ahead of print]
    Carbohydrate adaptation drives liver-brain axis maturation.
    Hongmei Cui, Zheng Wu, Yuannyu Zhang, Hieu S Vu, Hongli Chen, Xiaofei Gao, Yan Jin, Donghong Cai, Sarada Achyutuni, Phong Nguyen, Chunxiao Pan, Hui Cao, Camenzind G Robinson, Jeffery D Steinberg, Laura J Janke, Sara M Nowinski, Jian Xu, Ralph J DeBerardinis, Min Ni.
      Mammalian postnatal life requires adaptation to a carbohydrate-rich diet, yet how metabolic programs are coordinated within and across organs is unclear. Using time-resolved transcriptomic and metabolomic analyses from the neonatal period through adulthood, we show that mouse liver rapidly acquires oxidative and detoxification capacity after weaning. This transition enables the brain to establish energy-sufficient, low-toxicity metabolic environment for neuronal function. This maturation process is marked by progressive activation of the hepatic electron transport chain (ETC), with the mitochondrial RNA endoribonuclease LACTB2 acting as a key regulator. LACTB2 prevents the accumulation of mitochondrial RNAs and sustains expression of mtDNA-encoded ETC subunits, thereby preserving mitochondrial competence for oxidative metabolism. LACTB2 is postnatally induced in hepatocytes, and its loss causes defective glucose utilization, systemic metabolic toxicity, and impaired brain metabolism and myelination, leading to prepubertal lethality, particularly in males. Restoring ETC function through liver-targeted expression of yeast NADH dehydrogenase NDI1, inhibiting the integrated stress response or ammonia scavenging improved survival. Our findings identify LACTB2-dependent hepatic mitochondrial maturation as a central mechanism that aligns carbohydrate adaptation with the liver-brain metabolic coordination to support early-life development.
    DOI:  https://doi.org/10.1101/2025.11.05.685548
  14. bioRxiv. 2025 Oct 23. pii: 2025.10.21.683798. [Epub ahead of print]
    Inhibition of Mitochondrial Complex III Causes Dopaminergic Neurodegeneration by Redox Stress in Caenorhabditis elegans.
    Javier Huayta, Joel N Meyer.
      Environmental factors including chemical exposures are important contributors to Parkinson's disease (PD). Nearly all well-validated chemicals involved in PD affect mitochondria, and the great majority of those identified inhibit mitochondrial complex I, causing ATP depletion and oxidative stress. We hypothesized that inhibition of mitochondrial complex III would also cause dopaminergic neurodegeneration. Using Caenorhabditis elegans to evaluate the in vivo effects of the complex III-inhibiting pesticides antimycin A and pyraclostrobin, we found that both caused neurodegeneration. Neurodegeneration was specific to the dopamine neurons, and complex III inhibition caused a more-oxidized cellular environment in those neurons. Pharmacological and genetic antioxidant interventions rescued neurodegeneration, but energetic rescue attempts did not. Finally, optogenetic production of superoxide anion specifically at complex III caused dopaminergic neurodegeneration. Thus, redox stress at complex III is sufficient for dopaminergic neurodegeneration, and redox stress following chemical inhibition is necessary for dopaminergic neurodegeneration in vivo in C. elegans.
    DOI:  https://doi.org/10.1101/2025.10.21.683798
  15. bioRxiv. 2025 Oct 20. pii: 2025.10.20.683548. [Epub ahead of print]
    Tryptoline Stereoprobe Elaboration Identifies Inhibitors of the GRPEL1-HSPA9 Chaperone Complex.
    Rachel E Hayward, Raymond F Berkeley, Zijian Gao, Maximilian Garhammer, Marc A Morizono, Evert Njomen, Haoxin Li, Kristen E DeMeester, Victor Cociorva, Mark A Herzik, F Ulrich Hartl, Bruno Melillo, Benjamin F Cravatt.
      Activity-based protein profiling has identified hundreds of proteins from diverse classes that react at specific cysteine residues with stereochemically defined electrophilic compounds (stereoprobes) in human cells. The structure-activity relationships underlying these stereoprobe-protein interactions, however, remain poorly understood. Here we show that the protein interaction landscape of tryptoline acrylamide stereoprobes can be profoundly altered by structural modifications distal to the acrylamide reactive group. The majority of stereoprobe liganding events occurred at non-orthosteric sites and mostly evaded assignment by the machine learning-based co-folding model Boltz-2, which instead tended to misplace the stereoprobes in orthosteric pockets (an outcome we term "orthostery burnout"). We found that stereoprobes reacting with C124 in the nucleotide exchange factor GRPEL1 disrupt interactions with the mitochondrial HSP70 chaperone HSPA9/mortalin, leading to impairments in mitochondrial protein import and induction of mitophagy. Our results highlight tryptoline acrylamides as a versatile source of covalent ligands targeting non-orthosteric sites on proteins, including tool compounds that perturb the mitochondrial HSP70 chaperone system.
    DOI:  https://doi.org/10.1101/2025.10.20.683548
  16. bioRxiv. 2025 Oct 15. pii: 2025.10.13.682189. [Epub ahead of print]
    Intrinsic errors in mitochondrial translation trigger a decline in cell fitness.
    Güleycan Lutfullahoglu Bal, Kah Ying Ng, Eli Berzell, Ani Akpinar, Alex E Ekvik, Lidiia Koludarova, Seyedehshima Naddafi, Clemens Raths, Tania Vane-Tempest, Jordyn J VanPortfliet, Sarah O'Keefe, Arafath K Najumudeen, Tuula A Nyman, James B Stewart, A Phillip West, Brendan J Battersby.
      Defects in the faithful expression of the human mitochondrial genome underlies disease states, from rare inherited disorders to common pathologies and the aging process itself. The ensuing decrease in the capacity for oxidative phosphorylation alone cannot account for the phenotype complexity associated with disease. Here, we address how aberrations in mitochondrial nascent chain synthesis per se exert a decline in cell fitness using a classic model of mitochondrial induced premature aging. We identify how intrinsic errors during mitochondrial nascent chain synthesis destabilize organelle gene expression, triggering intracellular stress responses that rewire cellular metabolism and cytokine secretion. Further, we show how these mechanisms extend to pathogenic variants associated with inherited human disorders. Together, our findings reveal how aberrations in mitochondrial protein synthesis can sensitize a cell to metabolic challenges associated with disease and pathogen infection independent of oxidative phosphorylation.
    Teaser/One-Sentence Summary: Aberrations in mitochondrial translation elongation trigger activation of intracellular stress responses associated with disease and aging.
    DOI:  https://doi.org/10.1101/2025.10.13.682189
  17. Nat Genet. 2025 Nov 24.
    Proteome-wide model for human disease genetics.
    Rose Orenbuch, Courtney A Shearer, Aaron W Kollasch, Aviv D Spinner, Thomas Hopf, Lood van Niekerk, Dinko Franceschi, Mafalda Dias, Jonathan Frazer, Debora S Marks.
      Missense variants remain a challenge in genetic interpretation owing to their subtle and context-dependent effects. Although current prediction models perform well in known disease genes, their scores are not calibrated across the proteome, limiting generalizability. To address this knowledge gap, we developed popEVE, a deep generative model combining evolutionary and human population data to estimate variant deleteriousness on a proteome-wide scale. popEVE achieves state-of-the-art performance without overestimating the burden of deleterious variants and identifies variants in 442 genes in a severe developmental disorder cohort, including 123 novel candidates. These genes are functionally similar to known disease genes, and their variants often localize to critical regions. Remarkably, popEVE can prioritize likely causal variants using only child exomes, enabling diagnosis even without parental sequencing. This work provides a generalizable framework for rare disease variant interpretation, especially in singleton cases, and demonstrates the utility of calibrated, evolution-informed scoring models for clinical genomics.
    DOI:  https://doi.org/10.1038/s41588-025-02400-1
  18. medRxiv. 2025 Oct 17. pii: 2025.10.15.25338094. [Epub ahead of print]
    Electron microscopy visualization of cell-free mitochondrial DNA-containing extracellular vesicles in human plasma, serum, and saliva.
    Alexandra Volos, Soah Grace Franklin, Jeremy Michelson, Shannon Rausser, Jonathan R Brestoff, Martin Picard.
      Human biofluids contain cell-free mitochondrial DNA (cf-mtDNA) and extracellular mitochondria (ex-Mito), creating the challenge of defining their origins, destinations, mechanisms of regulation, and purposes. To expand our understanding of cf-mtDNA biology, we present a descriptive electron microscopy analysis of circulating particles from cf-mtDNA-enriched plasma (citrate, heparin, and EDTA), serum (red and gold top), and saliva collected from ten healthy people (5 females, 5 males, mean age 44.9 years). Ex-mito and extracellular vesicles (EVs) were isolated by centrifugation followed by size-exclusion chromatography, imaged by transmission electron microscopy, and morphometrically analyzed. In parallel, cf-mtDNA was quantified in each biofluid. The resulting catalog of the most common circulating particles in plasma, serum, and saliva show that circulating double-membrane extracellular particles- consistent with mitochondrial ultrastructure-are present across human biofluids, along with EVs and other particle types. Combining imaging with cf-mtDNA quantification, we show that individuals with higher plasma cf-mtDNA concentrations tend to contain more double-membrane, ex-Mito-like particles. These preliminary results challenge the notion that, under normal conditions, the majority of cf-mtDNA exists as naked and potentially pro-inflammatory forms. Instead, these results are consistent with the concept of mitochondria transfer or signaling between cells and tissues. The image inventory provided here expands our knowledge of cell-free mitochondrial biology and provides a resource to inform biofluid selection and technical considerations in future studies quantifying ex-Mito and cf-mtDNA.
    DOI:  https://doi.org/10.1101/2025.10.15.25338094
  19. bioRxiv. 2025 Oct 25. pii: 2021.11.29.470476. [Epub ahead of print]
    Activity-dependent mitochondrial transport in peri-synaptic glia drives motor function.
    Dunham D Clark, Sonja A Zolnoski, Emily L Heckman, Michael R Kann, Sarah D Ackerman.
      Neurons have an outsized metabolic demand, requiring continuous metabolic support from non-neuronal cells called glia. When this support fails, toxic metabolic byproducts accumulate, ultimately leading to excitotoxicity and neurodegeneration. Astrocytes, the primary synapse-associated glial cell type, are known to provide essential metabolites ( e.g. lactate) to sustain neuronal function. Here, we leverage the well-characterized Drosophila motor circuit to investigate another means of astrocyte-to-neuron metabolic support: activity-dependent trafficking of astrocyte mitochondria. Following optogenetic activation, motor neuron mitochondria migrate away from synapses. By contrast, astrocytic mitochondria accumulated peri-synaptically, and at times, were transferred into neighboring neurons. A genetic screen identified the mitochondrial adaptor protein Milton as a key regulator of this process. Astrocyte-specific milton knockdown disrupted regular mitochondrial trafficking, resulting in locomotor deficits, dysfunctional motor activity, and altered synapse number at the neuromuscular junction. These findings suggest that astrocytes dynamically redistribute mitochondria to buffer metabolic demand at synapses, highlighting a potential mechanism by which glia protect neural circuits from metabolic failure and neurodegeneration.
    DOI:  https://doi.org/10.1101/2021.11.29.470476
  20. Cell Mol Neurobiol. 2025 Nov 25.
    Tau-Mitochondria Interactions in Neurodegeneration: Mechanisms and Therapeutic Potential.
    Yaisa Castillo-Casaña, Clorinda Arias, Roberto Coria.
      Tau is a microtubule-associated protein encoded by the MAPT gene and is mainly expressed in neurons. Alternative splicing generates preferentially six isoforms differing in N-terminal inserts (0, 1, or 2N) and microtubule-binding repeats (3R or 4R). Isoform expression varies by cell type, developmental stage, and neuronal maturation. Structurally, 4R isoforms bind and stabilize microtubules more effectively than 3R isoforms, while 3R variants are more prone to oligomerization. Differences among isoforms also affect aggregation and post-translational modification patterns, yet their specific roles in tauopathies remain unclear. Beyond its role in microtubule stabilization, tau is increasingly recognized for its functions in other cellular compartments, particularly mitochondria, where it may contribute to mitochondrial dysfunction in neurodegenerative diseases. Its intrinsically disordered conformation and extensive post-translational modifications enable interactions with multiple mitochondrial components, linking tau biology to broader aspects of neuronal health and pathology. The main focus of this review is to analyze how tau protein interacts with mitochondria and disrupts their function. Literature evidence indicates that tau localizes to the outer mitochondrial membrane, intermembrane space, and matrix, where it interferes with key processes. These include disruption of electron transport chain activity, inhibition of ATP synthase, and reduced ATP production, ultimately compromising neuronal energy supply. In parallel, tau destabilizes microtubule-based trafficking, impairing axonal transport and mitochondrial distribution, while also disrupting fission and fusion dynamics that shape mitochondrial morphology. Quality control pathways are affected as well, with tau altering mitophagy and mitochondria-nucleus signaling. Moreover, tau dysregulates calcium buffering and increases reactive oxygen species production, thereby promoting synaptic dysfunction, oxidative stress, and mitochondrial damage. Collectively, these facts establish tau as a central mediator of mitochondrial impairment and neuronal vulnerability. Elucidating the mechanisms by which tau affects mitochondrial physiology underscores its importance as a therapeutic target, with strategies aimed at preserving mitochondrial integrity offering promising avenues to slow neurodegenerative progression. In the last section, we include examples of clinical applications currently in various phases of testing, some of which show promising potential for implementation.
    Keywords:  Mitochondrial bioenergetics; Mitochondrial dynamics; Mitochondrial dysfunctions; Mitochondrial transport; Mitophagy; Neurodegeneration; Tau protein; Tauopathies
    DOI:  https://doi.org/10.1007/s10571-025-01634-1
  21. Cell Death Differ. 2025 Nov 25.
    Targeting prohibitins activates the ISR through DELE1-HRI by impairing protein import into the mitochondrial matrix.
    Ismael Sánchez-Vera, Ana M Cosialls, Nekane Maritorena-Hualde, Max-Hinderk Schuler, Rodolfo Lavilla, Gabriel Pons, Lucas T Jae, Daniel Iglesias-Serret, Joan Gil.
      Prohibitins (PHBs) are predominantly located at the inner mitochondrial membrane, displaying significant roles in tumor progression, invasion, and apoptotic resistance, often overexpressed in primary tumors. Importantly, we developed a synthetic molecule, fluorizoline, that induces apoptosis by selectively targeting PHBs in various cancer cell lines and primary samples from different hematological neoplasms. Fluorizoline induces apoptosis by activating the pro-apoptotic branch of the integrated stress response (ISR) pathway in HeLa and HAP1 cells, specifically via the ATF4-CHOP-NOXA axis. We identified compensatory mechanisms for four ISR-related kinases, with HRI emerging as the primary kinase responsible for the activation of the ISR and apoptosis induction, implicating mitochondrial stress in ISR activation. Here, we investigate the mitochondrial stress response signaling pathway responsible for activating HRI after targeting PHBs either by fluorizoline treatment or by PHBs downregulation in HeLa and HAP1 cancer cell lines. In this study, we describe how PHBs regulate the localization of the mitochondrial stress sensor DELE1, leading to ISR activation and apoptosis induction in HeLa and HAP1 cells. Our findings demonstrate that DELE1 promotes ISR activation upon fluorizoline treatment and PHBs downregulation. Although fluorizoline treatment activates the cleavage of long DELE1 (L-DELE1) to its cleaved form (S-DELE1), OMA1 was found to be dispensable for activating the ISR upon fluorizoline treatment. Furthermore, our findings indicate a potential impairment of the mitochondrial protein import machinery upon targeting PHBs, as the import of other mitochondrial proteins beyond DELE1 is also disrupted. These findings reveal a previously unknown physiological role of PHBs in preserving the mitochondrial protein import pre-sequence pathway, possibly due to the interaction between PHBs and DNAJC19. This novel insight underscores the potential of targeting PHBs, such as with fluorizoline, to overwhelm mitochondrial stress in cancer.
    DOI:  https://doi.org/10.1038/s41418-025-01618-0
  22. Autophagy. 2025 Nov 28.
    NAD+ restores proteostasis through splicing-dependent autophagy.
    Ruixue Ai, Evandro F Fang.
      Autophagy preserves neuronal integrity by clearing damaged proteins and organelles, but its efficiency declines with aging and neurodegeneration. Depletion of the oxidized form of nicotinamide adenine dinucleotide (NAD+) is a hallmark of this decline, yet how metabolic restoration enhances autophagic control has remained obscure. Meanwhile, alternative RNA splicing errors accumulate in aging brains, compromising proteostasis. Here, we identify a metabolic - transcriptional mechanism linking NAD+ metabolism to autophagic proteostasis through the NAD+ -EVA1C axis. Cross-species analyses in C. elegans, mice, and human samples reveal that NAD+ supplementation corrects hundreds of age- or Alzheimer-associated splicing errors, notably restoring balanced expression of EVA1C isoforms. Loss of EVA1C impairs the memory and proteostatic benefits of NAD+, underscoring its essential role in neuronal resilience. Mechanistically, NAD+ rebalances EVA1C isoforms that interact with chaperones BAG1 and HSPA/HSP70, reinforcing their network to facilitate chaperone-assisted selective autophagy and proteasomal degradation of misfolded proteins such as MAPT/tau. Thus, NAD+ restoration coordinates RNA splicing fidelity with downstream proteostatic systems, establishing a metabolic - transcriptional checkpoint for neuronal quality control. This finding expands the paradigm of autophagy regulation, positioning metabolic splice-switching as a crucial mechanism to maintain proteostasis and suggesting new strategies to combat aging-related neurodegenerative diseases.
    Keywords:  Aging; NAD+ precursors; alzheimer disease; machine learning; rna splicing; tauopathy
    DOI:  https://doi.org/10.1080/15548627.2025.2596679
  23. Res Sq. 2025 Oct 09. pii: rs.3.rs-7476559. [Epub ahead of print]
    Tank-Binding Kinase 1 protects against MASH progression via mitochondrial quality control.
    Jin Young Huh, Sung-Min An, Jun Hee Jang, Jin Hyun Sung, Ji Won Myung, Yong Geun Jeon, Won Taek Lee, Jin Won Jeon, Kyung Min Yim, Jae-Ho Lee, Bichen Zhang, Jong Bae Seo, Seung Soon Im, Jae Bum Kim, Alan Saltiel.
      Mitochondrial dysfunction is a critical driver of metabolic dysfunction-associated steatotic liver disease (MASLD) progression to steatohepatitis (MASH), yet the mechanisms governing mitochondrial quality control in hepatocytes remain poorly defined. Here, we identify TANK-binding kinase 1 (TBK1) as an essential regulator of hepatic mitophagy and lysosomal activity. Using TBK1-deficient hepatocytes and liver-specific TBK1 knockout (LTKO) mice, we show that TBK1 loss leads to the accumulation of depolarized, ROS-producing mitochondria due to impaired mitophagy flux, including defective lysosomal degradation. Mechanistically, TBK1 is required for p62 phosphorylation at Ser403 and partially modulates mTOR signaling to preserve lysosomal acidification. Therapeutic restoration of TBK1 expression via AAV8 delivery enhanced mitophagy, reduced mitochondrial burden, and ameliorated liver fibrosis. Notably, both human samples and murine steatohepatitis models exhibited a significant decline in TBK1 kinase activity. Collectively, these findings establish TBK1 as a critical guardian of mitochondrial and lysosomal homeostasis in MASH.
    DOI:  https://doi.org/10.21203/rs.3.rs-7476559/v1
  24. Nat Commun. 2025 Nov 23.
    In vivo mitochondrial base editing restores genotype and visual function in a mouse model of LHON.
    Sanghun Kim, Jieun Kim, Seongkwang Cha, Sungjin Ju, Chae Jin Lim, Seongho Hong, Jiyoung Bae, Yeji Oh, Sungmo Jung, Sol Pin Kim, Hae-Sol Shin, Jae Hee Yoon, Jeeyoon Park, Seungmin Ryou, Soo-Yeon Lim, Su Bin Lee, Seung Hee Choi, Soo-Ji Park, Chang Geun Choi, Mihyun Choi, Lark Kyun Kim, Jiyoon Park, Seonghyun Lee, Kyoung Yul Seo, Je Kyung Seong, Kyoungmi Kim, Jin-Soo Kim, Hyunji Lee.
      Leber hereditary optic neuropathy (LHON), a maternally inherited mitochondrial disorder, results from point mutations in mitochondrial DNA (mtDNA), primarily affecting the MT-ND4 gene. To date, no animal model harboring authentic LHON mutations has been available, limiting therapeutic development. However, when we attempted to generate such models using mitochondrial base editors, we found that activity-enhanced DddA11-based cytosine base editors (DdCBEs) induce off-target mtDNA mutations and developmental arrest in embryos. Using a high-fidelity DdCBE (Hifi-DdCBE), we successfully generate mice carrying the pathogenic MT-ND4 G11778A mutation, the most common LHON variant. These mice exhibit hallmark phenotypes, including retinal ganglion cell loss and impaired visual function. Intravitreal delivery of adeno-associated virus encoding TALE-linked deaminases (TALEDs) restores both phenotype and genotype in these mice. Furthermore, optimized TALEDs corrects the ND4 mutation with minimal off-target effects in LHON patient-derived cells, highlighting the potential of mitochondrial base editing as a therapeutic strategy for mtDNA-associated diseases.
    DOI:  https://doi.org/10.1038/s41467-025-66600-3
  25. Int J Mol Sci. 2025 Nov 16. pii: 11084. [Epub ahead of print]26(22):
    Mitochondrial Quality Control and Cell Death.
    Zurui Zhang, Mengyuan Zhang, Hongchi Jin, Shuang Lv, Yilei Li, Yanru Li.
      Mitochondrial quality control includes mitochondrial biogenesis, fusion, fission (to maintain mitochondrial function), and mitochondrial autophagy (for removing damaged mitochondria). This is a highly delicate and complex process involving many molecules. Mitochondrial quality control is crucial for maintaining mitochondrial homeostasis and function, preserving energy supply, eliminating damaged mitochondria to prevent cytotoxicity, promoting mitochondrial regeneration and repair, protecting cells from oxidative stress and senescence, and facilitating cellular communication and material exchange. In this review, we introduce the structure and function of mitochondria, the mechanisms of quality control, and the relationship between mitochondrial quality control and cellular processes such as pyroptosis, apoptosis, and ferroptosis. We also summarize the proteins, enzymes, and their molecular mechanisms involved in these processes and propose a "spatiotemporal-threshold" model for the mitochondrial quality control-cell death axis.
    Keywords:  apoptosis; ferroptosis; mitochondrial autophagy; mitochondrial dynamics; mitochondrial fission; mitochondrial fusion; mitochondrial quality control; pyroptosis
    DOI:  https://doi.org/10.3390/ijms262211084
  26. Autophagy. 2025 Nov 23. 1-43
    Autophagy and mitophagy at the synapse and beyond: implications for learning, memory and neurological disorders.
    Jiayi Lu, Damian N Di Florio, Patricia Boya, Sandra Maday, Wolfdieter Springer, Charleen T Chu.
      The human brain is one of the most metabolically active tissues in the body, due in large part to the activity of trillions of synaptic connections. Under normal conditions, macroautophagy/autophagy at the synapse plays a crucial role in synaptic pruning and plasticity, which occurs physiologically in the absence of disease- or aging-related stressors. Disruption of autophagy has profound effects on neuron development, structure, function, and survival. Neurons are dependent upon maintaining high-quality mitochondria, and alterations in selective mitochondrial autophagy (mitophagy) are heavily implicated in both genetic and environmental etiologies of neurodegenerative diseases. The unique spatial and functional demands of neurons result in differences in the regulation of metabolic, autophagic, mitophagic and biosynthetic processes compared to other cell types. Here, we review recent advances in autophagy and mitophagy research with an emphasis on studies involving primary neurons in vitro and in vivo, glial cells, and iPSC-differentiated neurons. The synaptic functions of genes whose mutations implicate autophagic or mitophagic dysfunction in hereditary neurodegenerative and neurodevelopmental diseases are summarized. Finally, we discuss the diagnostic and therapeutic potentials of autophagy-related pathways.Abbreviations: AD: Alzheimer disease; ALS: amyotrophic lateral sclerosis; APP: amyloid beta precursor protein; ASD: autism-spectrum disorder; BDNF: brain-derived neurotrophic factor; BPAN: β-propeller protein associated neurodegeneration; CR: caloric restriction; ΔN111: deleted N-terminal region 111 residues; DLG4/PSD95: discs large MAGUK scaffold protein 4; ER: endoplasmic reticulum; FTD: frontotemporal dementia; HD: Huntington disease; LIR: LC3-interacting region; LRRK2: leucine rich repeat kinase 2; LTD: long-term depression; LTP: long-term potentiation; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; OMM: outer mitochondrial membrane; PD: Parkinson spectrum diseases; PGRN: progranulin; PINK1: PTEN induced kinase 1; PRKA/PKA: protein kinase cAMP-activated; PtdIns3P: phosphatidylinositol-3-phosphate; p-S65-Ub: ubiquitin phosphorylated at serine 65; PTM: post-translational modification; TREM2: triggering receptor expressed on myeloid cells 2.
    Keywords:  Biomarkers; Parkinson disease; dementia; dendritic spines; mitochondria; neurodegenerative diseases; neurodevelopmental disorders; synaptic plasticity
    DOI:  https://doi.org/10.1080/15548627.2025.2581217
  27. Front Mol Biosci. 2025 ;12 1722468
    Editorial: Molecular underpinnings of genetic and rare diseases: from diagnostic tools to therapeutic approaches.
    Abhilash Kumar Tripathi.
      
    Keywords:  diagnosis; genetic diseases; genetic variants; precision medicine; rare disease
    DOI:  https://doi.org/10.3389/fmolb.2025.1722468
  28. Front Cell Dev Biol. 2025 ;13 1667611
    Multiple entanglements of different cell death pathways, in which caspase-8 and BID interact with cardiolipin*, have been identified.
    Patrice X Petit.
      Mitochondria play a central role in cellular bioenergetics, being major counterparts in ATP production and thus in the maintenance of cells, but they are also key mediators of different types of cell death (apoptosis, necroptosis, ferroptosis, etc.) and are among the main players in autophagy. With respect to death receptor-mediated apoptosis, activation of the mitochondrial pathway is required for the induction of apoptosis in cells (extrinsic pathway), referred to as "type II" cells. In type I cells, activation of the extrinsic pathway through a large amount of caspase-8 allows direct activation of caspase-3 and is sufficient to induce apoptosis. This small review is dedicated to the often forgoten molecule of the BCL-2 family, BID. Special emphasis will be placed on the importance of the cardiolipin/caspase-8/BID platform located at the outer mitochondrial membrane surface that generates tBID, which is the actor of BAX/BAK delocalization and oligomerization at the mitochondrial surface and then transmits death signals in the apoptotic pathway. New insights into the regulation of caspase-8 and BID have emerged, and their originality in the context of their activation and function will be highlighted. We will focus on results from biophysical studies of artificial membranes, i.e., lipid-supported monolayers or giant unilamellar vesicles containing cardiolipin. The destabilization of mitochondrial bioenergetics by tBID insertion at the mitochondrial contact site is presented. Since it inhibits the electron transfer chain, superoxide anion generation is essential for BAX oligomerization. We will take you on a journey through these new developments that reveal a surprisingly high degree of redundancy and crosstalk between the apoptotic, necroptotic, and pyroptotic cell death pathways. Taken together, the mitochondrial contact site and cristae organization system (MICOS) is a critical determinant of mitochondrial membrane architecture and physiology. Its close crosstalk with many other mitochondrial protein machineries identifies the MICOS as a central hub in an interwoven network that ensures mitochondrial functionality and integration into the cellular context. It is becoming increasingly clear that the activation platform built around caspase-8/cardiolipin and BID is involved in multiple types of cell death, including apoptosis, ferroptosis (oxytosis), necroptosis and autophagic death.
    Keywords:  BID; cardiolipin; cardiolipin peroxidation; cell death; giant unilamellar vesicles; mitochondria; outer mitochondrial membrane; tBID
    DOI:  https://doi.org/10.3389/fcell.2025.1667611
  29. Proc Natl Acad Sci U S A. 2025 Dec 02. 122(48): e2524111122
    The intermediate filament protein GFAP regulates mitochondrial fission in astrocytes.
    Ding Xiong, Ye Sing Tan, Fang Yuan, Yinglu Li, Kay En Low, Isabelle Bonne, Sakthikumar Mathivanan, Phil Jun Kang, Zijun Sun, Xueyan Li, Emily Abella, Albee Messing, Linghai Kong, Su-Chun Zhang.
      Mitochondrial plasticity, coordinated by fission and fusion, is crucial to ensure cellular functions. Mitochondrial fission is mediated by the GTPase Drp1 at the constriction site, which is proposed to be driven by the actin-myosin contractile force. However, the mechanism that propels constriction remains unclear, and the potential involvement of additional mechanisms in this process remains an open question. Here, using structured illumination microscopy, electron microscopy, and correlative light electron microscopy (CLEM), we show that the type III intermediate filament glial fibrillary acidic protein (GFAP) participates in mitochondria constriction and fission by interacting with Drp1. Remarkably, loss of GFAP results in hyperfused mitochondria under physiological and even Ca2+-induced mitochondrial fission conditions. Additionally, mutations in GFAP, the cause of Alexander disease, result in more Drp1 localized to GFAP and lead to significantly increased mitochondrial fissions. Taken together, these findings propose a role of type III intermediate filaments in mitochondrial division.
    Keywords:  GFAP; alexander disease; astrocyte; intermediate filament; mitochondrial fission
    DOI:  https://doi.org/10.1073/pnas.2524111122
  30. medRxiv. 2025 Oct 14. pii: 2025.10.09.25337582. [Epub ahead of print]
    Drivers of Diagnostic Delay in Mitochondrial Disease: Missed Recognition of Canonical Features.
    Rory J Tinker, Neil Jacob, Mohammad Ghouse Syed, Janhawi Kelkar, Colleen Donnelly, Ibrahim Elsharkawi, Jaya Ganesh, Bruce Gelb, Vikas Pejaver, Tamas Kozicz, Eva Morava.
       Background: Diagnostic delay is common in mitochondrial disease, and its drivers remain unclear despite advances in molecular diagnostics.
    Methods: We retospectively analyzed 58 individuals with molecularly confirmed mitochondrial disease at the Mount Sinai Mitochondrial Disease Clinic, diagnosed after 2016. Diagnostic delay was partitioned into intervals from symptom onset to clinical suspicion, and from suspicion to molecular diagnosis. Demographic, phenotypic, and genetic data were abstracted from health records, and Human Phenotype Ontology terms were compared before and after diagnosis using ClinPhen.
    Results: Most delays occurred between symptom onset and clinical suspicion (mean 8.17 years) rather than after suspicion (mean 0.63 years), yielding a mean total delay of 8.8 years (median 3.0). Delay decreased sharply by year of birth (r = -0.99, p < 1.5 × 10^-48) and symptom onset (r = -0.98, p < 1.4 × 10^-36), but showed no meaningful trend with year of diagnosis. Developmental delay predicted shorter diagnostic intervals. Canonical features such as seizures, hypotonia, and stroke were frequently documented years before suspicion, underscoring missed opportunities.
    Conclusions: Diagnostic delay reflects missed recognition rather than testing limitations. Systematic capture of early phenotypes and AI/NLP-based mining of electronic health records could proactively flag patients for reflexive sequencing, shortening diagnostic delay.
    DOI:  https://doi.org/10.1101/2025.10.09.25337582
  31. Nat Commun. 2025 Nov 28.
    Expanding the utility of variant effect predictions with phenotype-specific models.
    David Stein, Meltem Ece Kars, Baptiste Milisavljevic, Matthew Mort, Peter D Stenson, Jean-Laurent Casanova, David N Cooper, Bertrand Boisson, Peng Zhang, Avner Schlessinger, Yuval Itan.
      Current methods for variant effect prediction do not differentiate between pathogenic variants resulting in different disease outcomes and are restricted in application due to a focus on variants with a single molecular consequence. We have developed Variant-to-Phenotype (V2P), a multi-task, multi-output machine learning model to predict variant pathogenicity conditioned on top-level Human Phenotype Ontology disease phenotypes (n = 23) for single nucleotide variants and insertions/deletions throughout the human genome. V2P leverages a unique approach for the modeling of variant effect that incorporates resultant disease phenotypes as output and during training to improve the quality of variant disease phenotype and effect predictions, simultaneously. We describe the architecture, training strategy, and biological features contributing to V2P's output, revealing initial characteristics underlying the relationship between disease genotype and phenotype. Moreover, we demonstrate the benefit of incorporating disease phenotypes for variant effect predictions by comparing V2P with several variant effect predictors across various high-quality evaluation datasets from manually curated databases and functional assays. Finally, we examine how V2P's predictions result in the successful identification of pathogenic variants in real and simulated patient sequencing data, outperforming other tested methods in initial comparisons. V2P offers a complete mapping of human genetic variants to disease-phenotypes, offering a uniquely conditioned set of variant effect characterizations.
    DOI:  https://doi.org/10.1038/s41467-025-66607-w
  32. Nat Commun. 2025 Nov 27.
    N-terminal α-amino SUMOylation promotes phosphorylation-independent cofilin-1 translocation to the mitochondrial matrix and induces apoptosis.
    Qi Deng, Xiaokun Gu, Jiaqian Feng, Jinhua Xiang, Xinyue Li, Weiji Weng, Gerald W Zamponi, Ou Huang, Si-Jian Pan, Yong Li.
      Cofilin is a central regulator of actin filament turnover, traditionally thought to act through phosphorylation-dependent control of filament assembly. However, its mitochondrial functions remain poorly understood. Here we show that N-terminal α-amino SUMOylation, rather than phosphorylation or actin interaction, governs cofilin-1 translocation to mitochondria and activation of the apoptotic pathway. This modification strengthens the association of cofilin-1 with the mitochondrial import receptors Tom20 and Tom70 through the molecular chaperone HSP70, enabling its delivery to the mitochondrial matrix. Once imported, SUMO-modified cofilin-1 binds cytochrome c1, promotes the dissociation of cytochrome c from complex III, and initiates mitochondrial-mediated apoptosis. These findings redefine cofilin-1 as a regulator of mitochondrial integrity independent of its actin-related roles, uncovering a mechanism by which SUMOylation directs protein targeting and apoptotic signaling. This work broadens current understanding of mitochondrial regulation and may inform therapeutic strategies for diseases linked to defective cell death.
    DOI:  https://doi.org/10.1038/s41467-025-66859-6
  33. Pharmacol Res. 2025 Nov 21. pii: S1043-6618(25)00468-2. [Epub ahead of print]222 108043
    Ginsenoside Re binds Drp1 Leu94 across species to restore mitochondrial homeostasis via Atg1/ULK1-dependent fission-mitophagy coupling in age-related degeneration.
    Chenrong Jin, Juhui Qiao, Huilin Gong, Xiaorui Yu, Xinran Wang, Jiao Xi, Runying Mi, Shiting Yu, Daian Pan, Siming Wang, Xiaolin Tong, Daqing Zhao, Meichen Liu.
      Aging profoundly impacts the brain, serving as a primary driver of neurodegenerative diseases through mechanisms closely linked to mitochondrial dysfunction. Despite its clinical significance, the molecular mechanisms remain unclear, and safe, effective therapies are urgently needed. Here, leveraging ginseng's neuroprotective potential, we screened for blood-brain barrier-permeable saponins with optimal neuroprotective efficacy and identified ginsenoside Re (Re) as the predominant mitochondrially targeted neuroprotective saponin. Midlife Reintervention, temporally aligned with the natural window of mitochondrial hyperfusion, rescued age-related degenerative pathology in Drosophila. Re administration ameliorated dopaminergic neuron loss, mitigated muscles pathology, improved cognitive-motor deficits, and extended healthspan. Mechanistic studies revealed that Re directly binds to the Drp1 across multiple species via the highly conserved L94 residue, triggering robust S616 phosphorylation that drives Drp1 translocation to mitochondria, thereby restoring fission-fusion equilibrium. Re further spatiotemporally coupled fission-mitophagy through the Drp1-Atg1/ULK1 axis, enabling autophagosome initiation and ensuring efficient clearance of damaged organelles. This dual regulation enhanced bioenergetic capacity and delayed functional decline. Genetic ablation of Drp1 L94 completely abolished Re's benefits, while translational studies in mice confirmed that healthspan extension required intact Drp1-L94 functionality. Notably, Re demonstrated conserved neuroprotective efficacy in both human induced pluripotent stem cells-derived dopaminergic neurons and Drosophila Parkinson's model, indicating preservation of the Drp1-mitophagy pathway across species. Our findings establish Re as a geroprotector that targets the conserved Drp1-L94 residue to restore mitochondrial homeostasis. By spatiotemporally coupling fission to Atg1-mediated mitophagy during the critical midlife hyperfusion window, Re delays neurodegeneration, thereby establishing a molecular basis for developing therapies against age-related decline.
    Keywords:  Brain aging; Drp1 mutants; Ginsenoside Re; Mitochondrial dynamics; Mitophagy axis
    DOI:  https://doi.org/10.1016/j.phrs.2025.108043
  34. Pediatr Nephrol. 2025 Nov 27.
    Kidney transplantation in mitochondrial diseases: a systematic review.
    Sze Wa Wong, Cheuk Wing Fung, Fred Tomlin, Jelena Stojanovic.
       BACKGROUND: Primary mitochondrial diseases are a group of rare, heterogeneous, multisystem disorders. While renal involvement is increasingly recognised, especially in paediatric patients, data on kidney transplantation outcomes in this population remain limited.
    OBJECTIVES: To evaluate kidney transplantation outcomes in genetically confirmed primary mitochondrial diseases with multi-organ involvement and provide clinical insights from systematic literature review.
    DATA SOURCES: We systematically searched PubMed, MEDLINE, EMBASE and Google Scholar from inception to 10 June 2025 using keywords and MeSH terms related to "mitochondrial disease", "transplantation" and "outcome".
    STUDY ELIGIBILITY CRITERIA: We included studies that reported post-transplant clinical outcomes in patients with genetically confirmed primary mitochondrial diseases. Studies without genetic confirmation or transplant follow-up were excluded. Patients with Co-enzyme Q 10 deficiency were excluded as they mainly manifest as isolated steroid resistant nephrotic syndrome with subtypes that respond well to co-enzyme replacement.
    PARTICIPANTS AND INTERVENTIONS: Participants included paediatric or adult patients diagnosed with genetically confirmed primary mitochondrial diseases who received isolated kidney transplant from living or deceased donor.
    STUDY APPRAISAL AND SYNTHESIS METHODS: Data were extracted on demographics, genotypes, renal and extra-renal features, transplant characteristics, complications and outcomes. Risk of bias was assessed qualitatively by two independent reviewers. Discrepancies were resolved through consensus or discussion with third reviewer. Due to clinical and methodological heterogeneity, a narrative synthesis was performed.
    RESULTS: Forty-six patients (15 paediatric, 31 adult) were included from 18 eligible studies. Ten patients had RMND1-related disease. All harboured either homozygous or compound heterozygous c.713A > G variants in RMND1. Thirty patients carried the m.3243A > G mtDNA point mutation variant in MT-TL1. The remaining six patients harboured an m.3271 T > C variant in MT-TL1, single mtDNA deletions, m.8618dup in MT-ATP6, m.12418delA in MT-ATP6 and m.13513G > A in MT-ND5 respectively. At nephrology referral, chronic kidney disease and kidney failure each was present in 26.1% of patients. Median time from renal presentation to kidney failure was 6 years. Graft and patient survival exceeded 90% across different genetic mutations and age groups. Post-transplant deterioration of neurological or metabolic features was reported predominantly in patients with an m.3243A > G variant.
    LIMITATIONS: The review is limited by small sample size, selection and reporting bias, heterogeneous follow-up durations and outcome measures. Data were derived mainly from case reports and small case series.
    CONCLUSIONS AND IMPLICATIONS OF KEY FINDINGS: Kidney transplantation is a viable option of kidney replacement therapy for patients with mitochondrial diseases. Patients with primary mitochondrial diseases should be considered for kidney transplantation. Further prospective studies are needed to define optimal transplant timing, immunosuppression strategies and long-term systemic outcomes.
    SYSTEMATIC REVIEW REGISTRATION NUMBER: CRD420251086889.
    Keywords:  Kidney failure kidney transplantation; Patient survival; Primary mitochondrial diseases
    DOI:  https://doi.org/10.1007/s00467-025-07034-3
  35. Front Cell Dev Biol. 2025 ;13 1668779
    MitoLandscape, a semi-automated pipeline for subcellular localization and quantification of mitochondria.
    Enrico Negri, Virginia Fernández, Víctor Borrell.
      The precise characterization of mitochondrial morphology and subcellular localization provides crucial insights into cellular metabolic states and developmental fates. However, accurately analyzing mitochondria in cells with complex morphologies remains challenging, particularly within intact tissues where current methodologies lack sufficient resolution and specificity. Here we introduce MitoLandscape, an innovative pipeline tailored for comprehensive mitochondrial analysis at single-cell resolution in the developing nervous system. MitoLandscape integrates Airyscan super-resolution microscopy, semi-automated segmentation (leveraging ImageJ and 3DSlicer), machine-learning-driven pixel classification (ilastik), and a modular custom Python script for robust and versatile analysis. Using graph-based representations derived from manual annotations and binary mitochondrial images, MitoLandscape efficiently extracts detailed morphological parameters from distinct subcellular compartments, applicable from cells with simple morphologies to complex neuronal architectures. Additionally, the pipeline quantifies mitochondrial distribution relative to specific cellular landmarks, such as nucleus or soma. We validated MitoLandscape in vitro and in neural tissue, demonstrating its capability to precisely and reliably map mitochondrial features in diverse biological contexts. MitoLandscape represents a powerful, user-friendly, and highly adaptable solution for investigating mitochondrial biology in cell and developmental research.
    Keywords:  computational biology; machine learning; morphology; neurodevelopment; organelle; super-resolution
    DOI:  https://doi.org/10.3389/fcell.2025.1668779
  36. Int J Mol Sci. 2025 Nov 13. pii: 10977. [Epub ahead of print]26(22):
    Targeting TOMM40 and TOMM22 to Rescue Statin-Impaired Mitochondrial Function, Dynamics, and Mitophagy in Skeletal Myotubes.
    Neil V Yang, Sean Rogers, Rachel Guerra, Justin Y Chao, David J Pagliarini, Elizabeth Theusch, Ronald M Krauss.
      Statins are the drugs most commonly used for lowering plasma low-density lipoprotein (LDL) cholesterol levels and reducing cardiovascular disease risk. Although generally well-tolerated, statins can induce myopathy, a major cause of non-adherence to treatment. Impaired mitochondrial function has been implicated in the development of statin-induced myopathy, but the underlying mechanism remains unclear. We have shown that simvastatin downregulates the transcription of TOMM40 and TOMM22, genes that encode major subunits of the translocase of the outer mitochondrial membrane (TOM) complex. Mitochondrial effects of knockdown of TOMM40 and TOMM22 in mouse C2C12 and primary human skeletal cell myotubes include impaired oxidative function, increased superoxide production, reduced cholesterol and CoQ levels, and disrupted markers of mitochondrial dynamics and morphology as well as increased mitophagy, with similar effects resulting from simvastatin exposure. Overexpression of TOMM40 and TOMM22 in simvastatin-treated mouse and human skeletal muscle cells rescued effects on markers of mitochondrial dynamics and morphology, but not oxidative function or cholesterol and CoQ levels. These results show that TOMM40 and TOMM22 have key roles in maintaining both mitochondrial dynamics and function and indicate that their downregulation by statin treatment results in mitochondrial effects that may contribute to statin-induced myopathy.
    Keywords:  mitochondrial dynamics; skeletal muscle; statin; translocase of outer mitochondrial membrane; transmission electron microscopy
    DOI:  https://doi.org/10.3390/ijms262210977
  37. J Hum Genet. 2025 Nov 25.
    Loss-of-function variant of SLC27A3 causes mitochondrial dysfunction and a metabolic neurodevelopmental disorder via impaired fatty acid transport.
    S Rehan Ahmad, Nazim Nasir, Anupriya Kumari, Atiq Ul Hassan.
      Inborn errors of metabolism (IEMs) lead to early-onset neurodegenerative disorders often caused by mitochondrial dysfunction. In this study, we identified a homozygous frameshift mutation (c.283dupG; p.Cys65LeufsTer13) in SLC27A3, identified through exome sequencing in a 2-month-old female proband presenting with developmental regression, hypotonia, seizure, feeding difficulty, and bilateral putaminal lesions on brain magnetic resonance imaging (MRI). The mutation results in a truncated, non-functional protein and complete loss of SLC27A3 expression in proband-derived fibroblasts. Results show the absence of SLC27A3 and aberrant mitochondrial morphology with clumped networks. Metabolic profiling showed elevated acyl-carnitine levels in the cytosol of proband cells, indicative of disrupted fatty acid oxidation. Additionally, mitochondrial respiratory chain activity was significantly reduced, and flow cytometry revealed increased cell death in mutant cells compared to controls. Protein-protein interaction analysis revealed SLC27A3 networks linked to fatty acid metabolism, ER-associated degradation (ERAD), and ion transport. GO enrichment demonstrated strong associations with transporter activity, protein homeostasis, and ER-mitochondrial membrane networks. Regional expression profiling showed high SLC27A3 transcript levels in the basal ganglia, correlating with the observed neuropathology. These findings position SLC27A3 as a critical lipid transporter involved in neuronal energy metabolism and proteostasis, and implicate its loss in mitochondrial encephalopathy. This study expands the genotypic and phenotypic spectrum of metabolic neurodevelopmental disorders and highlights the importance of fatty acid transport proteins in mitochondrial health and brain development. Our findings propose SLC27A3 as a novel candidate gene for early-onset mitochondrial disorders.
    DOI:  https://doi.org/10.1038/s10038-025-01435-w
  38. bioRxiv. 2025 Nov 11. pii: 2025.11.10.687605. [Epub ahead of print]
    Transcriptomic analysis of cells following decreased mitochondrial DNA-copy number reveals compensatory mechanisms in mitochondrial DNA replication and cellular energetics.
    Jiaqi Xie, Phyo W Win, Charles Newcomb, Shaopeng Zeng, Christina A Castellani, Dan E Arking.
      Mitochondrial DNA copy number (mtDNA-CN) is a metric of mitochondrial function that has been associated with a variety of diseases including cardiovascular disease and all-cause mortality. To investigate genes and pathways affected by mtDNA-CN variation, we perturbed HEK 293T cells with ethidium bromide to deplete mtDNA. Using RNASeq and methylation microarrays, we evaluated transcriptomic and methylomic changes in treated cell lines. We observed an 8-fold decrease in mtDNA-CN and compensatory shifts in mitochondrial transcription to support mtDNA replication. Nuclear transcriptomic and methylomic analysis highlighted changes in metabolic pathways, including oxidative phosphorylation and canonical glycolysis. Longitudinal analyses revealed that the identified genes and pathways have different response timing, with nuclear response lagging behind mitochondrial response. These findings further elucidate the mechanisms behind mtDNA maintenance and responses to cellular energetics as well as mitochondrial-nuclear crosstalk dynamics.
    DOI:  https://doi.org/10.1101/2025.11.10.687605
  39. Cell. 2025 Nov 21. pii: S0092-8674(25)01242-5. [Epub ahead of print]
    Inhibition of oligomeric BAX by an anti-apoptotic dimer.
    Catherine E Newman, Micah A Gygi, Haleh Alimohamadi, Thomas M DeAngelo, Christina M Camara, Julian Mintseris, Ezra Yu, Edward P Harvey, Zachary J Hauseman, Lixin Fan, Yun-Xing Wang, Elizabeth W-C Luo, Marina Godes, Jacob Gehtman, Ann M Cathcart, Steven P Gygi, John R Engen, Gregory H Bird, Gerard C L Wong, Thomas E Wales, Loren D Walensky.
      BAX is a pro-apoptotic BCL-2 protein that resides in the cytosol as a monomer until triggered by cellular stress to form an oligomer that permeabilizes mitochondria and induces apoptosis. The paradigm for apoptotic blockade involves heterodimeric interactions between pro- and anti-apoptotic monomers. Here, we find that full-length BCL-w forms a distinctive, symmetric dimer (BCL-wD) that dissociates oligomeric BAX (BAXO), inhibits mitochondrial translocation, promotes retrotranslocation, blocks membrane-porating activity, and influences apoptosis induction of cells. Structure-function analyses revealed discrete conformational changes upon BCL-w dimerization and reciprocal structural impacts upon BCL-wD and BAXO interaction. Small-angle X-ray scattering (SAXS) analysis demonstrated that BAXO disrupts membranes by inducing negative Gaussian curvature, which is reversed by positive Gaussian curvature exerted by BCL-wD. Systematic truncation and mutagenesis dissected the core features of BCL-wD activity-dimerization, BAXO engagement, and membrane interaction. Our studies reveal a downstream layer of apoptotic control mediated by protein and membrane interactions of higher-order BCL-2 family multimers.
    Keywords:  BAX; BCL-2 family proteins; BCL-w; anti-apoptotic; apoptosis; cell death; chemical crosslinking mass spectrometry; dimer; hydrogen deuterium exchange mass spectrometry; membrane curvature; mitochondria; mitochondrial retrotranslocation; mitochondrial translocation; oligomer; pro-apoptotic; small-angle X-ray scattering
    DOI:  https://doi.org/10.1016/j.cell.2025.10.037
  40. bioRxiv. 2025 Nov 04. pii: 2025.11.02.684826. [Epub ahead of print]
    Spatiotemporal control of PIWI compartmentalization by mitochondrial scaffolds defines pachytene piRNA pathway organization.
    Xiaoyuan Yan, Chao Wei, Jeffrey M Mann, Guanyi Shang, Qianyi Wang, Huirong Xie, Elena Y Demireva, Liangliang Sun, Deqiang Ding, Chen Chen.
      Pachytene piRNAs are the least understood class of piRNAs in the mammalian male germ line. During meiosis, their biogenesis occurs near mitochondrial outer membrane in germ granules known as intermitochondrial cement (IMC). However, how mitochondrial factors regulate the trafficking of PIWI proteins into and out of the IMC remain poorly understood. Here we show that the cytoplasmic PIWI proteins MILI and MIWI are recruited for pachytene piRNA biogenesis via distinct mitochondrial membrane proteins. Loss of the mitochondrial scaffold protein ASZ1 during meiosis in mice disrupts multiple downstream biogenesis steps, leading to misregulation of MILI and MIWI, failure of IMC formation, and a near-complete loss of mature pachytene piRNAs. Strikingly, despite the drastic depletion of pachytene piRNAs, LINE1 transposon silencing remains unaffected. We identify three classes of pachytene piRNA pathway components that coordinate piRNA production and compartmentalization. Our findings reveal that chromatoid body precursors serve as a central hub for the accumulation of pachytene PIWI-piRNA complexes, thus establishing a connection between IMC-based biogenesis and downstream piRNA function.
    DOI:  https://doi.org/10.1101/2025.11.02.684826
  41. bioRxiv. 2025 Oct 16. pii: 2025.10.08.681260. [Epub ahead of print]
    Visualizing PINK1 Activity Dynamics in Single Cells with a Phase Separation-Based Kinase Activity Reporter.
    Katie G Vineall, Alexia Andrikopoulos, Michael J Sun, Anna Yan, Ethan R Hartanto, Danielle L Schmitt.
      Phosphatase and tensin homologue-induced kinase 1 (PINK1) is a serine/threonine kinase that plays roles in mitophagy, cell death, and regulation of cellular bioenergetics. Current approaches for studying PINK1 function depend on bulk techniques that can only provide snapshots of activity and could miss the dynamics and cell-to-cell heterogeneity of PINK1 activity. Therefore, we sought to develop a novel PINK1 kinase activity reporter to characterize PINK1 activity. Taking advantage of the separation of phases-based activity reporter of kinase (SPARK) design, we developed a phase separation-based PINK1 biosensor (PINK1-SPARK). With PINK1-SPARK, we observe real-time PINK1 activity in single cells treated with mitochondria depolarizing agents or pharmacological activators. We then developed a Halo Tag-based PINK1-SPARK for multiplexed imaging of PINK1 activity with live-cell markers of mitochondrial damage. Thus, PINK1-SPARK is a new tool that enables temporal measurement of PINK1 activity in single live cells, allowing for further elucidation of the role of PINK1 in mitophagy and cell function.
    DOI:  https://doi.org/10.1101/2025.10.08.681260
  42. Indian J Pediatr. 2025 Nov 27.
    Cavitating Mitochondrial Leukoencephalopathy: Unmasking SURF-1 Deficiency through Neuroimaging-Genetic Correlation.
    Jayaram Saibaba, Santhakumar Senthilvelan, Nivedita Mondal.
      
    DOI:  https://doi.org/10.1007/s12098-025-05843-w
  43. bioRxiv. 2025 Nov 03. pii: 2025.10.31.685856. [Epub ahead of print]
    Deficient Cardiolipin Remodeling Alters Muscle Fiber Composition and Neuromuscular Connectivity in Barth Syndrome.
    Catalina Matias, Paige L Snider, Elizabeth A Sierra Potchanant, Joshua R Huot, Rahul Raghav, Michael T Chin, Simon J Conway, Jeffrey J Brault.
       Background: Barth syndrome (BTHS) is a rare X-linked mitochondrial disorder caused by mutations in the TAFAZZIN gene, which disrupts cardiolipin (CL) remodeling and mitochondrial function. While cardiac manifestations of BTHS are well characterized, the mechanisms underlying skeletal muscle weakness and fatigability are poorly understood.
    Methods: We investigated neuromuscular and mitochondrial alterations in a novel murine model (Taz PM ) carrying a patient-derived D75H point mutation in Tafazzin . This mutation preserves protein abundance but abolishes enzymatic activity. Skeletal muscle function was assessed via weightlifting and hanging tests. Muscle fiber composition and neuromuscular junction (NMJ) integrity were evaluated using immunofluorescence, western blotting, and in vivo electrophysiology. Mitochondrial morphology was examined by transmission electron microscopy, and bioenergetics were quantified using ultra-performance liquid chromatography. Stress signaling was assessed by western blotting.
    Results: Male Taz PM mice exhibited elevated monolysocardiolipin and reduced mature CL levels, confirming deficient transacylase activity. These mice exhibited lower muscle strength and endurance, smaller muscle fibers of all types, and a shift toward fast-twitch type 2B fibers, which are more susceptible to fatigue. Electrophysiological analysis revealed a 60% reduction in motor unit number and an increase in average single motor unit potential, indicating motor neuron remodeling. NMJ protein analysis showed decreased MUSK and DOK7 and increased CHRNA1, suggesting impaired NMJ integrity. Despite mitochondrial structural abnormalities and reduced expression of key mitochondrial proteins (NDUFB8, MCU, TMEM65), resting ATP, phosphocreatine, and adenine nucleotide ratios were unchanged in both glycolytic and oxidative muscles. However, stress signaling pathways were markedly activated, including phosphorylation of eIF2α, increased CHOP, DELE1, p53 expression, and altered Wnt/β-catenin signaling components.
    Conclusions: Deficiency of Tafazzin enzymatic activity in skeletal muscle is sufficient to result in widespread neuromuscular remodeling, including fiber size/type shifts, motor unit loss, NMJ dysregulation, and stress pathway activation, without overt energetic failure at rest. These findings suggest that myopathy in BTHS arises not solely from mitochondrial ATP insufficiency but rather from cumulative structural and signaling disruptions.
    DOI:  https://doi.org/10.1101/2025.10.31.685856
  44. Nat Commun. 2025 Nov 27. 16(1): 10690
    Localized Wnt-signaling promotes asymmetric NuMA-dependent oriented divisions and unequal apportioning of mitochondria.
    Susanna Eli, Greta Rauso, Paola Ghezzi, James L A Szczerkowski, Michela Bruzzi, Francesca Rizzelli, Fabiola Iommazzo, Alessia Loffreda, Francesco Castagna, Federico Donà, Chiara Gaddoni, Ambra Dondi, Mattia Marenda, Simona Rodighiero, Pierre Tournier, Zeno Lavagnino, Dario Parazzoli, Nils C Gauthier, Simone Tamburri, Diego Pasini, Shukry James Habib, Marina Mapelli.
      In multicellular organisms, the execution of developmental and homeostatic programs often relies on asymmetric cell divisions. These divisions require the alignment of the mitotic spindle axis to cortical polarity cues, and the unequal partitioning of cellular components between progeny cells. Asymmetric divisions are orchestrated by signals from the niche frequently presented in a directional manner, such as Wnt signals. Here we employ bioengineered Wnt-niches to demonstrate that in metaphase NuMA/dynein microtubule motors form a complex with activated LRP6 and β-catenin at the cortical sites of Wnt activation to orient cell division perpendicularly. We show that engagement of LRP6 co-receptors by Wnt ligands locally stabilizes actomyosin contractility through the accumulation of myosin1C. Additionally, we describe a proteomic-based approach to identify mitotic protein complexes enriched at the Wnt-contact site, revealing that mitochondria polarize toward localized Wnt3a sources and are asymmetrically apportioned to the Wnt-proximal daughter cell during Wnt-mediated asymmetric cell division of embryonic stem cells. Mechanistically, we show that CENP-F is required for mitochondria polarization towards localized sites of Wnt3a activation, and that deletion of the Wnt-co-receptor LRP6 impairs the asymmetric apportioning of mitochondria. Our findings enhance the understanding of mitotic Wnt-signaling and elucidate fundamental principles underlying Wnt-dependent mitochondrial polarization.
    DOI:  https://doi.org/10.1038/s41467-025-65775-z
  45. Acta Neuropathol Commun. 2025 Nov 26. 13(1): 242
    CISD2 ensures adequate ER-mitochondrial coupling, critically supporting mitochondrial function in neurons.
    Jens Loncke, Ian de Ridder, Rita La Rovere, Annika Vaarmann, Guizhen Fan, Karan Ahuja, Irina Serysheva, Catherine Verfaillie, Martijn Kerkhofs, Jan B Parys, Allen Kaasik, Geert Bultynck, Tim Vervliet.
      Loss of Cisd2, an iron-sulfur cluster transfer protein, results in type 2 Wolfram syndrome (WS2), a disorder associated with severe impacts on pancreatic β cell and neuronal functions. Cisd2 has been implicated in regulating intracellular Ca2+ signaling. However, the molecular basis and cellular consequences remain poorly understood. In this work, we demonstrate that Cisd2 intersects with intracellular Ca2+ dynamics at different levels, by interacting with the inositol-1,4,5-trisphosphate receptors and as a regulator of ER-mitochondria tethering. As such, loss of Cisd2 in HeLa cells results in reduced ER-mitochondrial Ca2+ transfer while only modestly impacting cytosolic Ca2+ signaling. In HeLa cells, Cisd2 deficiency promotes autophagic flux, yet has minimal impact on mitochondrial function. However, studying the impact of Cisd2 deficiency in human induced pluripotent stem cell -derived cortical neurons revealed a severe loss of glutamate-evoked Ca2+ responses in cytosol and associated uptake in mitochondria due to loss of ER-mitochondria contact sites. Correlating with the profound changes in cellular Ca2+ handling, mitochondrial function (oxygen consumption rate, ATP production, mitochondrial potential maintenance) declined severely, while autophagic flux was increased. Overall, these deficiencies further impact the resilience of Cisd2-deficient cortical neurons to cell stress as Cisd2-KO neurons were highly sensitive to staurosporine, an inducer of apoptosis. Overall, this work is one of the first to decipher the impact of Cisd2 on ER-mitochondria Ca2+ handling in a WS2 disease-relevant cell models, thereby revealing a unique dependence of neurons on Cisd2 for their mitochondrial health and cell stress resilience.
    Keywords:  Apoptosis; Ca2+ signaling; Cisd2; ER-mitochondria contact sites; Neurodegeneration; Wolfram syndrome
    DOI:  https://doi.org/10.1186/s40478-025-02132-7
  46. bioRxiv. 2025 Nov 06. pii: 2025.11.06.686916. [Epub ahead of print]
    Hypoxia-induced mitoROS triggers M1 linear ubiquitin chains and activates NF-κB signaling.
    Kiri Tal, Jonathan Ram, Reis Noa, Maniv Inbal, Ordureau Alban, Michael H Glickman, Sulkshane Prasad.
      Mitochondria are essential organelles responsible for cellular energy production and metabolism. Hypoxia, a pathophysiological condition, impairs the electron transport chain, disrupts mitochondrial function, and produces harmful reactive oxygen species (ROS). Ubiquitin signaling regulates mitochondrial health through several mechanisms, including protein degradation and mitophagy. Here, we show that hypoxia-induced mitophagy occurs independently of ubiquitination. However, mitochondria are heavily ubiquitinated under hypoxic stress. A significant portion of these hypoxia-induced ubiquitin chains constitute a specific type: linear head-to-tail fusions (M1), which are known for their role in NF-κB activation during cytokine signaling. We demonstrate that hypoxia-induced mitochondrial ROS leads to the accumulation of these M1 chains, activating NF-κB signaling and increasing the expression of its target genes. These findings reveal a critical internal signal that helps cells adapt to mitochondrial stress and triggers an inflammatory response.
    DOI:  https://doi.org/10.1101/2025.11.06.686916
  47. J Biol Chem. 2025 Nov 25. pii: S0021-9258(25)02836-4. [Epub ahead of print] 110984
    Mitochondrial movement in pancreatic alpha cells requires Miro2 and is regulated by glucose.
    Maia H Ekstrand, Sameena Nawaz, Anne Clark, Benoit Hastoy, Jakob G Knudsen.
      Under normal physiological conditions, glucagon is released from pancreatic alpha cells to elevate circulating glucose levels in response to hypoglycaemia. In type 2 diabetic patients, glucagon secretion is dysregulated, but the underlying mechanisms remain unclear. Several hypotheses have been suggested to explain the coupling of blood glucose sensing to electrical activity and glucagon secretion from alpha cells. Here, we show that glucose rapidly regulates mitochondrial motility and localisation in alpha cells. Under conditions of low glucose, mitochondria are arrested in positions further from the nucleus, correlating with increased ATP/ADP in the sub-plasma membrane space. We also find that knock down (KD) of Mitochondrial Rho GTPase 2 (Miro2), but not Miro1, reduces mitochondrial motility in alpha cells and impairs glucose-induced inhibition of glucagon secretion without effects on insulin secretion or mitochondrial motility in non-alpha islet cells. These findings highlight the significance of mitochondrial motility for alpha cell function and reveal fundamental differences between alpha and beta cells.
    Keywords:  Glucagon; alpha cells; beta cells; cell metabolism; insulin; mitochondria; mitochondrial transport
    DOI:  https://doi.org/10.1016/j.jbc.2025.110984
  48. Nephrology (Carlton). 2025 Nov;30(11): e70153
    Mitochondrial Nephropathy With m.5538G>A Mutation Within the tRNA-Trp Region Assessed by Mitochondrial Function Analysis: A Case Report.
    Mari Ikeda, Toshiyuki Imasawa, Takafumi Akanuma, Yu-Ichi Goto, Yasushi Okazaki, Kei Murayama, Mamiko Ohara, Tomo Suzuki.
      Mitochondrial nephropathy (MIT-N) presents with urinary protein in more than 90% of cases and reduced kidney function in approximately 70%. Coenzyme Q10 is effective only in a subset of patients. Herein, we report the first case of MIT-N treated with imeglimin, a drug known to improve mitochondrial function. A 25-year-old man had been diagnosed with minor glomerular abnormality at age 15. As his urinary protein increased (urine protein creatinine ratio 2.2 g/gCre) and decreased kidney function (serum creatinine 1.24 mg/dL), a kidney biopsy was performed. Light microscopy revealed focal segmental glomerulosclerosis, and electron microscopy demonstrated numerous abnormal mitochondria in podocytes. Serum and cerebrospinal fluid lactate levels were 27.8 and 35.5 mg/dL, respectively, raising suspicion of mitochondrial disease. Genetic analysis confirmed the m.5538G>A mutation in the tRNA-Trp region in the blood, urine and skin fibroblasts. Additionally, the enzymatic activity of mitochondrial respiratory chain complex (C) I-IV in dermal fibroblasts showed reduced activity of CIII and CIV. The patient was treated with olmesartan, dapagliflozin and imeglimin for chronic kidney disease with persistent urinary protein levels and new-onset diabetes, respectively. Approximately 1 year after starting treatment with imeglimin, the rate of kidney function decline accelerated, although proteinuria decreased. While it is difficult to attribute a renoprotective effect solely to imeglimin, further studies are needed to verify its long-term efficacy in MIT-N.
    Keywords:  imeglimin; m.5538G>A mutation; mitochondrial nephropathy
    DOI:  https://doi.org/10.1111/nep.70153
  49. Biomedicines. 2025 Oct 24. pii: 2603. [Epub ahead of print]13(11):
    Mitochondrial Dynamics in Aging Heart.
    Pankaj Patyal, Gohar Azhar, Ambika Verma, Shakshi Sharma, Jyotsna Shrivastava, Sayed Aliul Hasan Abdi, Xiaomin Zhang, Jeanne Y Wei.
      Aging is a major risk factor for cardiovascular disease, driving progressive structural and functional decline of the myocardium. Mitochondria, the primary source of ATP through oxidative phosphorylation, are essential for cardiac contractility, calcium homeostasis, and redox balance. In the aging heart, mitochondria show morphological alterations including cristae disorganization, swelling, and fragmentation, along with reduced OXPHOS efficiency. These defects increase proton leak, lower ATP production, and elevate reactive oxygen species (ROS), causing oxidative damage. Concurrent disruptions in mitochondrial fusion and fission further impair turnover and quality control, exacerbating mitochondrial dysfunction and cardiac decline. Serum response factor (SRF) signaling, a crucial regulator of cytoskeletal and metabolic gene expression, plays a key role in modulating mitochondrial function during cardiac aging. Dysregulation of SRF impairs mitochondrial adaptability, contributing to dysfunction. Additionally, reduced levels of nicotinamide adenine dinucleotide (NAD+) hinder sirtuin-dependent deacetylation, further compromising mitochondrial efficiency and stress resilience. These cumulative defects activate regulated cell death pathways, leading to cardiomyocyte loss, fibrosis, and impaired diastolic function. Mitochondrial dysfunction therefore serves as both a driver and amplifier of cardiac aging, accelerating the transition toward heart failure. This narrative review aims to provide a comprehensive overview of mitochondrial remodeling in the aging myocardium, examining the mechanistic links between mitochondrial dysfunction and myocardial injury. We also discuss emerging therapeutic strategies targeting mitochondrial bioenergetics and quality control as promising approaches to preserve cardiac function and extend cardiovascular health span in the aging population.
    Keywords:  apoptosis; cardiac aging; interventions; mitochondria; mtDNA; sirtuins
    DOI:  https://doi.org/10.3390/biomedicines13112603
  50. Tetrahedron Lett. 2026 Jan 15. pii: 155863. [Epub ahead of print]174
    Gram-scale synthesis of the thiazolidinedione-based mitoNEET ligand NL-1 using a Hantzsch ester reduction.
    James Mersch, Yehenew Agazie, Michael Menze, Mary Konkle, Jason D Huber, Werner J Geldenhuys.
      MitoNEET (CISD1), an [2Fe-2S] cluster protein located on the outer mitochondrial membrane and known for its role in cellular redox regulation and bioenergetics, has been identified as a novel ferroptosis-related drug target in neurodegeneration and cancer. The mitoNEET ligand NEET ligand-1 (NL-1) was developed as a pharmacological tool to elucidate the biochemistry of the novel protein in a variety of disease states, ranging from oncology to neurodegenerative disorders. Here, we present a scalable gram-level synthesis of the thiazolidinedione (TZD) containing NL-1 from the precursor CI-987 using the Hantzsch ester reduction as an alternative to conventional lithium borohydride or cobalt chloride-based methods. This optimized protocol enables the reliable production of NL-1 in quantities sufficient for preclinical disease modeling.
    Keywords:  ferroptosis; iron-sulfur cluster; mitochondria; mitophagy; reduction
    DOI:  https://doi.org/10.1016/j.tetlet.2025.155863
  51. Nanoscale. 2025 Nov 24.
    Drug delivery systems for mitochondrial targeting.
    Sofia Tagliavini, Mara Filippini, Alessandro Anderlini, Riccardo Caraffi, Cecilia Baraldi, Barbara Ruozi, Giovanni Tosi, Ilaria Ottonelli, Jason T Duskey.
      Mitochondria are essential organelles involved in both physiological and pathological processes. Dysfunctions in their activity, caused by gene mutations in mitochondrial or nuclear DNA or by other factors, can lead to a broad spectrum of primary and secondary mitochondrial diseases, characterized by diverse symptoms and clinical outcomes. Given the crucial role of this organelle in cellular life, the development of mitochondria-targeted delivery systems is essential to restore its function and offers a significant advantage in the treatment of mitochondria-related diseases, such as oxidative stress-induced conditions, and neurological disorders. Mitochondria can also be targeted in anticancer therapies to induce the death of tumor cells. Notwithstanding the variety of strategies linked to a mitochondrial-targeted therapy, reaching this organelle requires overcoming several biological barriers, ultimately mitochondrial membrane. A promising strategy in this regard is to use nanoparticles functionalized with specific ligands to direct the delivery of material to the mitochondrion. This review examines most recent advancements in nanosystem-based approaches for targeted delivery of nucleic acid therapeutics, including DNA and RNA, and small molecule drugs to this organelle. Overall, rationally designed nanomedicines that target mitochondria hold significant promise for precise therapeutic delivery at the subcellular level.
    DOI:  https://doi.org/10.1039/d5nr02199e
  52. Int J Mol Sci. 2025 Nov 19. pii: 11180. [Epub ahead of print]26(22):
    Spectrum and Impact of Mitochondrial DNA Mutations in Ovarian Cancer.
    Samantha Su Ping Low, Laura Greaves, Ryan Silk, Colin A Semple, Charlie Gourley.
      Mitochondrial DNA (mtDNA) mutations are prevalent across cancer genomes, and growing evidence implicates their multifaceted role in energy metabolism with tumorigenesis. Ovarian cancer, in particular, demonstrates high mtDNA copy numbers and increased incidences of truncating and missense mtDNA mutations, with heteroplasmy levels predictive of prognosis. This review provides a comprehensive description of published mtDNA sequencing data in ovarian cancer, the majority being high-grade serous samples, encompassing both coding and non-coding regions. MtDNA mutations within non-coding regions, such as the D-loop control region, can affect mtDNA replication and transcription, hence affecting overall mtDNA copy numbers, while mtDNA mutations within coding regions can directly impact respiratory complex function and downstream metabolic pathways. MtDNA mutations may serve as clinically valuable diagnostic biomarkers for ovarian cancer and predictors for chemoresistance. We also explore ongoing efforts to deepen our understanding of mitochondrial oncogenetics through the creation of novel cancer models enabled by mitochondrial gene editing techniques. Developing robust human ovarian cancer cell models will be critical to elucidate mechanistic and phenotypic consequences of mtDNA mutations, assess drug response and resistance and identify new therapeutic targets to advance precision oncology in this emerging field.
    Keywords:  gene editing; heteroplasmy; mitochondrial DNA; ovarian cancer; somatic mutations
    DOI:  https://doi.org/10.3390/ijms262211180
  53. Nat Commun. 2025 Nov 28.
    Mechanical confinement induces ferroptosis through mitochondrial dysfunction.
    Fang Zhou, Robert J Ju, Chenlu Kang, Jiayi Li, Ao Yang, Alexandre Libert, Yujie Sun, Ling Liang, Youwei Ai, Xiaoqing Hu, Samantha J Stehbens, Congying Wu.
      Cells in highly crowded environments are exposed to fluctuating mechanical forces. While cells can activate the cortical migration machinery to escape from undesirable compressive stress, the consequence to less motile cells and of prolonged extensive confinement is yet to be uncovered. Here, we demonstrate that nuclear deformation generated by axial confinement triggers a specific form of regulated cell death - ferroptosis. We show that axial confinement is sensed by the nucleus and results in Drp1-dependent mitochondrial fragmentation and mitochondrial ROS accumulation. Meanwhile, we detect cPLA2 translocation to mitochondria. These mitochondrial ROS accumulation and arachidonic acid production concertedly lead to lipid peroxidation and evoke ferroptosis. Interestingly, we find in osteoarthritis, a disease intimately associated with mechanical overloading and inflammation, characteristics of confinement-induced ferroptosis including mitochondrial localization of cPLA2 and high ROS. Together, our findings unveil a pivotal role of cell nucleus and mitochondria in linking mechanical confinement with cell death, highlighting the orchestration of Drp1 and cPLA2 in confinement-induced ferroptosis.
    DOI:  https://doi.org/10.1038/s41467-025-66353-z
  54. J Assoc Physicians India. 2025 Nov;73(11S): 24-26
    Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like Episodes: A Masquerader of Young-onset Stroke.
    Kartik Goel, Nitin Sinha, Divyanshu Singh, Sachin A Jambagi, Ravi Bhargav, Harsh Kansagara.
      Mitochondrial encephalopathy with lactic acidosis and stroke-like episodes, also known as MELAS, is an uncommon genetic disorder of mitochondrial inheritance. It presents as variable neurological and systemic manifestations. Here, we present a case of a young male who was a known case of seizure disorder and multiple neurological deficits. His clinical presentation included progressive hearing loss, diminution of vision, and recurrent headaches with vomiting. Neurological examination showed asymmetric limb weakness. Young-onset stroke was evaluated, and a magnetic resonance imaging (MRI) scan showed bilateral parieto-occipital hyperintensities. Serum lactate levels were high, which increased the suspicion of MELAS. m.3243A>G mutation was detected in mitochondrial DNA, confirming the diagnosis. Treatment involved the adjustment of antiepileptic therapy and the initiation of mitochondrial supplements. Our case emphasizes the heterogeneous clinical presentation and diagnostic challenges of MELAS as an important cause of young-onset stroke, highlighting the importance of early suspicion and confirmatory investigations for personalized management strategies to optimize patient outcomes.
    DOI:  https://doi.org/10.59556/japi.73.1235
  55. bioRxiv. 2025 Oct 27. pii: 2025.10.27.684790. [Epub ahead of print]
    The proton motive force maintains mtDNA euploidy by balancing mtDNA replication with cell proliferation.
    Sneha P Rath, Vamsi K Mootha.
      Human mitochondrial DNA (mtDNA) encodes 13 essential components of the electron transport chain (ETC) 1 . A typical cell contains ∼1000s of copies of mtDNA, but how this copy number is stably maintained is unclear. Here, we track mtDNA copy number (mtCN) recovery in K562 cells following transient, chemically induced depletion to uncover principles of mtCN stability. Below a critical mtCN, ETC activity fails to sustain the proton motive force (PMF) and de novo pyrimidine synthesis-both required for mtDNA replication. PMF-dependent processes like Fe-S cluster biogenesis are also disrupted and stress responses are activated that impair cell proliferation and limit further mtCN dilution by cell division. Nonetheless, mtDNA replication and recovery remain possible via mtDNA-independent PMF, generated by complex V reversal, and uridine salvage. Once mtCN is restored, the ETC and forward complex V activity re-engage, stress responses subside, and proliferation recommences. Each cell division then dilutes mtDNA, serving as a built- in brake on mtCN. Our findings suggest that mtCN homeostasis emerges from the balance of two opposing PMF-driven processes - mtDNA replication and cell proliferation - revealing a bioenergetic logic that preserves mtDNA euploidy through repeated cell divisions.
    DOI:  https://doi.org/10.1101/2025.10.27.684790
  56. Cells. 2025 Nov 11. pii: 1762. [Epub ahead of print]14(22):
    Cardiac SR-Mitochondria Contacts-Impact on Cardiac Physiology and Mitochondrial Fitness.
    Celia Fernandez-Sanz, Shey-Shing Sheu, Sergio De la Fuente.
      In adult cardiomyocytes, within the Mitochondrial Associated Membranes (MAMs), the sarcoplasmic reticulum (SR) and mitochondria juxtapose each other, forming a unique and highly repetitive functional structure throughout the cells. These SR-mitochondria contact sites have emerged as critical structures that regulate various physiological processes, including lipid exchange, calcium (Ca2+) communication, control of excitation-contraction bioenergetics coupling, and reactive oxygen species (ROS) production. Over the years, several scientific studies have reported the accumulation of diverse proteins within these SR-mitochondria close contacts. Some proteins strategically accumulate in these areas to enhance their function, such as the mitochondrial Ca2+ uniporter, while others perform non-canonical roles, such as DRP1 acting as a bioenergetics regulator. The purpose of this review is to provide a comprehensive compilation of the proteins that have been reported to be enriched in cardiac MAMs. We aim to show how their positioning is crucial for proper cardiac physiology and fitness, as well as how mispositioning may contribute to cardiac diseases. Additionally, we will discuss the gaps in our understanding and identify the necessary components to fully comprehend physiological communication between the sarcoplasmic SR and mitochondria in cardiac tissue.
    Keywords:  MAMs; SR; bioenergetics; heart; microdomains; mitochondria
    DOI:  https://doi.org/10.3390/cells14221762
  57. Nature. 2025 Nov 28.
    Audio long read: Faulty mitochondria cause deadly diseases - fixing them is about to get a lot easier.
    Gemma Conroy, Benjamin Thompson.
      
    DOI:  https://doi.org/10.1038/d41586-025-03797-9
  58. bioRxiv. 2025 Oct 15. pii: 2025.10.15.682603. [Epub ahead of print]
    Iron Deficiency Impairs Mitochondrial Energetics and Early Axonal Growth and Branching in Developing Hippocampal Neurons.
    Daniel C Mendez, Karishma Devgun, Timothy R Monko, Luke H Carlson, Daniel J Mickelson, Lorene M Lanier, Michael K Georgieff, Thomas W Bastian.
      Each stage of neuronal development (i.e., proliferation, differentiation, migration, neurite outgrowth and synapse formation) requires functional and highly coordinated metabolic activity to ultimately ensure proper sculpting of complex neural networks. Energy deficits underlie many neurodevelopmental, neuropsychiatric and neurodegenerative diseases implicating mitochondria as a potential therapeutic target. Iron is necessary for neuronal energy output through its direct role in mitochondrial oxidative phosphorylation. Iron deficiency (ID) reduces mitochondrial respiratory and energy capacity in developing hippocampal neurons, causing permanently simplified dendritic arbors and impaired learning and memory. However, the effect of ID on early axonogenesis has not been explored. We used an embryonic mixed-sex primary mouse hippocampal neuron culture model of developmental ID to evaluate mitochondrial respiration and dynamics and effects on axonal morphology. At 7 days in vitro (DIV), ID impaired mitochondrial oxidative phosphorylation capacity and stunted growth of both the primary axon and branches, without affecting branch number. Mitochondrial motility was not altered by ID, suggesting that mitochondrial energy production --- not trafficking --- underlie the axon morphological deficits. These findings provide the first link between iron-dependent neuronal energy production and early axon structural development and emphasize the importance of maintaining sufficient iron during gestation to prevent the negative consequences of ID on brain health across the lifespan.
    Significance Statement: This study used a primary mouse hippocampal neuron culture model of iron deficiency to address an important gap in knowledge of how disruption of iron-regulated mitochondrial activities affects axonal development. After axon initiation but prior to rapid dendrite outgrowth, iron chelation reduced mitochondrial oxidative phosphorylation capacity and stunted the growth of the primary axon and branches but without affecting branch number. Mitochondrial motility was not altered in iron-deficient axons, indicating that reduced neuronal energetic capacity and not impaired axonal mitochondrial trafficking may underlie these morphological deficits. Both iron and mitochondrial dyshomeostasis underlies many neurodevelopmental, neuropsychiatric, and neurodegenerative disorders, which can have origins during the period of fetal-neonatal development when rapid axon growth/branching occurs. This study highlights the importance of advancing knowledge on the effects of mitochondrial deficits in early life as it pertains to optimizing brain health throughout the lifespan.
    DOI:  https://doi.org/10.1101/2025.10.15.682603
  59. Nature. 2025 Nov 26.
    Double whammy: drugs that inhibit kinase enzymes also speed up their disposal.
      
    Keywords:  Cell biology; Drug discovery
    DOI:  https://doi.org/10.1038/d41586-025-03816-9
  60. Free Radic Biol Med. 2025 Nov 21. pii: S0891-5849(25)01385-1. [Epub ahead of print]243 245-259
    APOE4 impairs Nrf2-PINK1/Parkin-dependent mitochondrial clearance through disrupted antioxidant and mitophagy signaling.
    Firoz Akhter, Asma Akhter, Donghui Zhu.
      APOE4, the strongest genetic risk factor for sporadic Alzheimer's disease (AD), is closely associated with mitochondrial dysfunction, yet the mechanisms remain poorly defined. We identify a previously unrecognized failure of the Nrf2-PINK1/Parkin axis in APOE4 neurons that compromises mitochondrial quality control. Unlike APOE3, APOE4 neurons fail to activate PINK1/Parkin-dependent mitophagy under stress, a defect compounded by impaired Nrf2 signaling and weakened antioxidant defenses. In vivo, APOE4 mice show age-dependent collapse of this pathway, correlating with progressive mitochondrial dysfunction and disrupted mito-nuclear communication. Pharmacological activation of Nrf2 or PINK1 restores mitochondrial clearance, highlighting the axis as a druggable node. These findings provide a mechanistic link between APOE4 and mitochondrial failure, establishing the Nrf2-PINK1/Parkin pathway as a critical driver of neurodegeneration and a promising target for therapeutic intervention in AD.
    Keywords:  APOE4; Alzheimer's disease (AD); Mito-nuclear communication; Mitochondrial stress; Mitophagy; Nrf2-PINK/Parkin
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2025.11.040
  61. Mol Metab. 2025 Nov 24. pii: S2212-8778(25)00195-4. [Epub ahead of print] 102288
    Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism.
    Orion S Willoughby, Anna S Nichenko, Matthew H Brisendine, Niloufar Amiri, Shelby N Henry, Daniel S Braxton, John R Brown, Braeden J Kraft, Kalyn S Jenkins, Adele K Addington, Alexey V Zaitsev, Steven T Burrows, Ryan P McMillan, Haiyan Zhang, Spencer A Tye, Charles P Najt, Siobhan E Craige, Timothy W Rhoads, Junco S Warren, Joshua C Drake.
      Metabolic flexibility, the capacity to adapt fuel utilization in response to nutrient availability, is essential for maintaining energy homeostasis and preventing metabolic disease. Here, we investigate the role of Ulk1 phosphorylation at serine 555 (S555), a site regulated by AMPK, in coordinating metabolic switching following short-term caloric restriction and fasting. Using Ulk1(S555A) global knock-in mice, we show loss of S555 phosphorylation impairs glucose oxidation in skeletal muscle and liver during short-term CR, despite improved glucose tolerance. Metabolomic, transcriptomic, and mitochondrial respiration analyses suggest a compensatory reliance on autophagy-derived amino acids in Ulk1(S555A) mice. These findings suggest Ulk1(S555) phosphorylation as a critical regulatory event linking nutrient stress to substrate switching. This work highlights an underappreciated role of Ulk1 in maintaining metabolic flexibility, with implications for metabolic dysfunction.
    DOI:  https://doi.org/10.1016/j.molmet.2025.102288
  62. Nat Commun. 2025 Nov 27. 16(1): 10693
    Engineering a CRISPR-associated IscB system for developing miniature genome-editing tools in human cells and mouse embryos.
    Fei Zhang, Yuxin Peng, Dongdong Fan, Guoxu Song, Xing Gao, Yong Tian.
      IscB, as the putative ancestor of Cas9, possesses a compact size, making it suitable for in vivo delivery. OgeuIscB is the first IscB protein known to function in eukaryotic cells but requires a complex TAM (NWRRNA). Here, we characterize a CRISPR-associated IscB system, named DelIscB, which recognizes a flexible TAM (NAC). Through systematically engineering its protein and sgRNA, we obtain enDelIscB with an average 48.9-fold increase in activity. By fusing enDelIscB with T5 exonuclease (T5E), we find that enDelIscB-T5E displays robust efficiency comparable to that of enIscB-T5E in human cells. Moreover, by fusing cytosine or adenosine deaminase with enDelIscB nickase, we establish efficient miniature base editors (ICBE and IABE). Finally, we efficiently generate mouse models by microinjecting mRNA/sgRNA of enDelIscB and enDelIscB-T5E into mouse embryos. Collectively, our work presents a set of enDelIscB-based miniature genome-editing tools with great potential for diverse applications in vivo.
    DOI:  https://doi.org/10.1038/s41467-025-65724-w
  63. medRxiv. 2025 Nov 10. pii: 2025.10.15.25337675. [Epub ahead of print]
    Constellation illuminates rare disease genetics.
    Siyuan Cheng, Qing Zhang, Xinchang Zheng, Shalini Jhangiani, Jacqueline C Weir, Jesse R Farek, Heer H Mehta, Ziad M Khan, Yi Han, Huyen H Dinh, Kerstin P Blankenburg, Jennifer E Posey, Richard A Gibbs, Donna M Muzny, Claudia M B Carvalho, Mitchell A Bekritsky, Ali Crawford, Daniel Calame, James Han, Fritz J Sedlazeck.
      Despite significant advances in genomic sequencing, the resolution of many rare disease cases is still hindered by variant detection limitations. Short reads struggle in homologous regions, and long reads remain costly and difficult to scale. Here, we present the first systematic evaluation of Illumina's Constellation sequencing technology for rare disease research. By fragmenting long DNA molecules directly on the flow cell surface, Constellation unlocks proximity information that enables long-range phasing and structural variant detection. Across 21 families, Constellation independently identified all known causative variants and resolved previously unsolved trios. It reliably resolved complex structural and copy number variants (e.g. impacting MECP2 ) and recovered haplotype phasing information across key disease impacting variants, all from low DNA input using existing Illumina infrastructure. These findings establish Constellation as a scalable, cost-efficient advance, closing critical diagnostic gaps and broadening access to long-range variant analysis in rare disease genomics.
    DOI:  https://doi.org/10.1101/2025.10.15.25337675
  64. bioRxiv. 2025 Oct 23. pii: 2025.10.22.683335. [Epub ahead of print]
    Supervised machine learning identifies impaired mitochondrial quality control in β cells with development of type 2 diabetes.
    Mirza Muhammad Fahd Qadir, Charles Dana, Paul Mauvais-Jarvis, Nazmul Haque, Theodore Dos Santos, Patrick E MacDonald, Franck Mauvais-Jarvis.
      In type 2 diabetes (T2D), molecular pathways driving β cell failure are difficult to resolve with standard single cell analysis. Here we developed an interpretable, supervised machine learning framework that couples sparse rule-based classification (SnakeClassifier), pathway constrained modelling (BlackSwanClassifier), and β cell mitochondrial fitness stratification (Kolmogorov-Arnold Neural Networks KANN), linking and integrating them into disease mechanisms in single cell RNA sequencing (scRNA-seq) from 52 human donors. SnakeClassifier trained on 50 genes accurately predicted T2D at single cell resolution, outperforming classical ensemble machine learning classifier models, and yielded donor level diabetes scores that correlated with chronic hyperglycemia. The clustering of β cell populations (β1-4) revealed a resilient non-diabetic (ND) β1 subtype characterized by preserved β cell identity genes and lower disease risk, whereas T2D β2-4 subtypes exhibited upregulation of genes involved in cellular and mitochondrial stress and suppression of genes promoting oxidative phosphorylation and insulin secretion. Mitophagy emerged as the dominant program linked to T2D and a mitophagy focused BlackSwanClassifier nominated PINK1, BNIP3 , and FUNDC1 as key regulators. PINK1 was enriched in ND β1, decreased with T2D disease score and connected sex stratified mitophagy. We generated a KANN derived mitochondrial fitness index (MFI) integrating mitophagy, mitochondrial proteostasis, biogenesis and oxidative phosphorylation into a single interpretable score (R 2 = 0.934 vs module-based mitochondria quality index), which identified mitophagy PINK1, SQSTM1, PRKN and BNIP3 as top contributors to T2D progression. These transparent models unify prediction with T2D disease mechanism and identify the mitophagy receptor PINK1 as a central determinant of β cell metabolic fitness.
    DOI:  https://doi.org/10.1101/2025.10.22.683335
  65. bioRxiv. 2025 Oct 17. pii: 2025.10.16.682859. [Epub ahead of print]
    Cryo-EM reveals how ASX-173 inhibits human asparagine synthetase to activate the integrated stress response.
    Kirk A Staschke, Nicholas T Walda, Lucciano A Pearce, Ronald C Wek, Wen Zhu, Yuichiro Takagi.
      Targeting asparagine metabolism is a promising strategy for treating asparaginase-resistant acute lymphoblastic leukemia (ALL), sarcoma, and potentially other solid tumors. Here, we characterize the molecular mechanism by which a cell-penetrable small molecule, ASX-173, inhibits human asparagine synthetase (ASNS), the enzyme that catalyzes intracellular asparagine biosynthesis. ASX-173 reduces cellular asparagine levels, induces the integrated stress response (ISR), and reduces cell growth in HEK-293A cells. A cryo-EM structure reveals that ASX-173 engages a unique, hydrophobic pocket formed by AMP, Mg 2+ , and pyrophosphate in the C-terminal synthetase domain of ASNS, thereby enabling multivalent, high-affinity binding. Based on in vitro kinetic and thermal shift assays, we find that ASX-173 binds to the ASNS/Mg 2+ /ATP complex and is therefore a rare example of an uncompetitive enzyme inhibitor with potential therapeutic use. These findings provide a structural and mechanistic basis for targeting ASNS with small molecules, which have application in treating cancer and other human diseases.
    DOI:  https://doi.org/10.1101/2025.10.16.682859
  66. bioRxiv. 2025 Oct 23. pii: 2025.10.22.684030. [Epub ahead of print]
    NADH dehydrogenase reverses dietary and clock metabolic syndrome.
    Chelsea Hepler, Nathan J Waldeck, Benjamin J Weidemann, Biliana Marcheva, You-Jia Chen, Jacqueline Hecker, Ziming Zhu, Rino Nozawa, Joseph V Mastroni, Anneke K Thorne, Colleen R Reczek, Jonathan Cedernaes, Kathryn M Ramsey, Clara B Peek, Grant D Barish, Navdeep S Chandel, Joseph Bass.
      Circadian clocks are internal timing systems that enable organisms to anticipate and adapt to daily environmental changes. These rhythms arise from a transcription-translation feedback loop in which CLOCK/BMAL1 regulate the expression of thousands of genes, including their repressors PER/CRY 1 . Disruption of circadian rhythms contributes to obesity, metabolic disease, and cancer 2-4 , yet how the clock maintains metabolic homeostasis remains limited. Here we report that the clock regulates oxidative metabolism through diurnal respiration of mitochondrial respiratory chain complex I. Genetic loss of the clock and high fat diet feeding in male mice led to reduced complex I respiration within adipocytes, leading to suppression of PPAR and insulin signaling pathways. In contrast, preserving complex I function maintained adipogenic and metabolic gene networks and protected against diet- and circadian-induced metabolic dysfunction independently of weight gain. These findings reveal that circadian disruption impairs metabolic health through mitochondrial complex I dysfunction, establishing clock control of complex I as a key regulator of transcriptional and metabolic homeostasis.
    DOI:  https://doi.org/10.1101/2025.10.22.684030
  67. Redox Biol. 2025 Nov 17. pii: S2213-2317(25)00448-3. [Epub ahead of print]88 103935
    NNT deficiency alters cardiac structure and function without impairing mitochondrial bioenergetics in aged mice.
    Ana P Dalla Costa, Claudia D C Navarro, Edilene S Siqueira-Santos, Rafaela Q S Velasco, João V F Rosada, Andréia R Salgado, Daniele M R Demolin, Luiz A C Passos, Anibal E Vercesi, Annelise Francisco, Roger F Castilho.
      Proton-translocating NAD(P)+ transhydrogenase (NNT) is highly expressed in cardiac tissue, where it physiologically supports mitochondrial NADPH production. However, under certain pathological conditions, NNT may shift toward consuming the mitochondrial NADPH pool. Although NNT has been implicated in redox homeostasis, its contribution to cardiac function during aging remains uncertain. In this study, we assessed cardiac morphology and function, as well as mitochondrial bioenergetics and Ca2+ handling, in NNT-deficient (Nnt-/-) mice and congenic wild-type controls (Nnt+/+) at adult (5 months), middle (12 months), and older (23 months) ages. NNT-deficient mice developed age-related cardiac hypertrophy, along with a moderately reduced ejection fraction and fractional shortening at older ages, suggesting left ventricular dysfunction. These changes were associated with increased mitochondrial H2O2 release under specific conditions, whereas mitochondrial bioenergetic parameters and Ca2+ retention capacity remained largely unaffected by the Nnt genotype at all ages. Our findings indicate that NNT plays a protective role in the aging heart by maintaining redox balance and that NNT deficiency may contribute to late-onset cardiac dysfunction without causing overt mitochondrial bioenergetic failure. These results provide insight into the potential cardiac consequences of pathogenic NNT variants in humans.
    Keywords:  Aging; C57BL/6J mouse; Cardiac function; Mitochondrial bioenergetics; Nicotinamide nucleotide transhydrogenase (NNT); Nnt mutation
    DOI:  https://doi.org/10.1016/j.redox.2025.103935
  68. medRxiv. 2025 Oct 13. pii: 2025.10.08.25337448. [Epub ahead of print]
    Integrated Stress Response Signatures Drive Monocyte Dysfunction in GBA1 - and LRRK2 -Linked Parkinson's Disease.
    Daniele Mattei, Erica Brophy, Mikaela Rosen, Oriol Narcis Majos, Aloysius Domingo, Elena Meijia, Beomjin Jang, Tarek Khashan, Mengxi Yang, Deborah Raymond, Casey Young, Jack Humphrey, Elisa Navarro, Amanda Allan, Katherine Leaver, Viktoriya Katsnelson, Alexander Chung, Benjamin Muller, Matthew Swan, Vicki L Shanker, Mariel Pullman, Adina Wise, Roberto Ortega, Kelly Astudillo, Steven Frucht, Susan Bressman, Giulietta Riboldi, Laurie J Ozelius, Rachel Saunders-Pullman, Towfique Raj.
      Monocytes are increasingly implicated in Parkinson's disease (PD) pathogenesis, with idiopathic cases showing mitochondrial and lysosomal dysfunction. However, the impact of PD-associated mutations on monocytes remains unclear. To address this, we investigated transcriptomic and functional disturbances in peripheral monocytes from patients with GBA1 - and LRRK2 -associated PD and idiopathic PD. Transcriptomic data revealed shared and mutation-specific signatures, including those related to immune dysregulation, and consistent defects in lysosomal and mitochondrial pathways. Network and pathway analyses further uncovered downregulation in protein translation and enrichment of integrated stress response (ISR) signatures, alongside aberrant expression of genes linked to ER stress, proteostasis, mitophagy and type-I interferon signaling. These data suggest that monocyte immune dysfunction in PD may be, at least in part, a consequence of impaired proteostasis, organelle stress and maladaptive ISR activation. We further interrogated these signatures in functional assays in patient-derived macrophages, which revealed impaired mitochondrial potential, proteolysosomal dysfunction, and defective phagocytosis. Our findings define convergent molecular and functional abnormalities in genetic PD monocytes, implicating proteostasis failure and maladaptive ISR activation as upstream drivers of immune dysfunction, highlighting novel targetable pathways for therapeutic intervention.
    DOI:  https://doi.org/10.1101/2025.10.08.25337448
  69. Nat Commun. 2025 Nov 28. 16(1): 10765
    Visualizing intraorganellar ultrastructures, dynamics, and interactions with open-access background-free Lock-in-SIM.
    Wenjie Liu, Meng Zhang, Wenbin Zhu, Shunyu Xie, Jinfeng Zhang, Shuhao Qian, Zhiyi Liu, Xiu Zheng, Qiuyuan Fang, Wei Yang, Yi Wang, Dazhao Zhu, Jianjie Dong, Xu Liu, Youhua Chen, Cuifang Kuang, Yu-Hui Zhang, Lothar Schermelleh.
      Structured illumination microscopy (SIM) is a powerful method for fast and gentle live-cell super-resolution imaging. However, its susceptibility to reconstruction artifacts from out-of-focus blur and background imposes substantial barriers to analyze the dynamics of densely packed volumetric intraorganellar ultrastructures that are typically in a size range of SIM's spatial resolution. To address this limitation, we have developed Lock-in-SIM, an open-access two-dimensional SIM framework that eliminates background and maximizes the recovery of sub-diffraction information with the highest possible frequency extraction. By leveraging the intrinsic modulation differences of volumetric sample structures, Lock-in-SIM enables efficient optical sectioning, extends imaging depth, and improves data fidelity and quantifiability. We demonstrate the superiority of Lock-in-SIM by visualizing various challenging intraorganellar ultrastructures in live cells. Our investigations uncover mechanisms of mitochondrial fission and endoplasmic reticulum-lysosome interactions and provide insights into the intricate yet highly regulated structural remodeling of organelles.
    DOI:  https://doi.org/10.1038/s41467-025-65805-w
  70. PLoS One. 2025 ;20(11): e0335411
    The histone modification regulator, SIN3, plays a role in the cellular response to changes in glycolytic flux.
    Imad Soukar, Anindita Mitra, Linh Vo, Melanie Rofoo, Miriam L Greenberg, Lori A Pile.
      Epigenetic regulation and metabolism are connected. Epigenetic regulators, like the SIN3 complex, affect the expression of a wide range of genes, including those encoding metabolic enzymes essential for central carbon metabolism. The idea that epigenetic modifiers can sense and respond to metabolic flux by regulating gene expression has long been proposed. In support of this cross-talk, we provide data linking SIN3 regulatory action on a subset of metabolic genes with the cellular response to changes in metabolic flux. Furthermore, we show that loss of SIN3 is linked to decreases in mitochondrial respiration and the cellular response to mitochondrial and glycolytic stress. Data presented here provide evidence that SIN3 is important for the cellular response to metabolic flux change.
    DOI:  https://doi.org/10.1371/journal.pone.0335411
  71. Redox Biol. 2025 Nov 19. pii: S2213-2317(25)00453-7. [Epub ahead of print]88 103940
    Endogenous mitochondrial hydrogen peroxide regulates neurogenesis during cortical development.
    Regina Mengual, Verónica Bobo-Jiménez, Cristina Rodríguez, Rebeca Lapresa, Darío García-Rodríguez, Daniel Jiménez-Blasco, Elisa Cabiscol, Joaquim Ros, María Delgado-Esteban, Juan P Bolaños, Ángeles Almeida.
      Reactive oxygen species (ROS), particularly superoxide anion (O2•-) and hydrogen peroxide (H2O2), originating from mitochondria, are increasingly recognized as critical mediators of physiological signaling and cellular function. While in the adult brain, mitochondrial ROS, specifically mitochondrial H2O2, modulate metabolism and sustains cognitive processes, their role in the developing cerebral cortex remains undefined. Here, we leverage a knock-in mouse model constitutively expressing mitochondrially targeted catalase (mCAT) to attenuate mitochondrial H2O2 levels and investigate their impact during cortical development. In neurosphere cultures derived from embryonic day 14.5 (E14.5) mCAT mice, reduced mitochondrial H2O2 altered glutathione redox homeostasis and glucose metabolism leading to suppressed progenitor cell proliferation, without compromising viability. In vivo, neural progenitor cell (NPC) proliferation, neuronal differentiation and cortical layering were disrupted starting at gestational day E15. Together, these data uncover a physiological role for mitochondrial hydrogen peroxide in orchestrating neural precursor proliferation and differentiation, ultimately influencing mammalian cerebral cortex formation.
    Keywords:  Cortex development; Hydrogen peroxide; Mitochondria; Neural precursor cells; Neurogenesis
    DOI:  https://doi.org/10.1016/j.redox.2025.103940
  72. Alzheimers Dement. 2025 Nov;21(11): e70929
    MtDNA-depleted neuronal cell transcriptomes reveal Alzheimer's disease-related changes.
    Blaise W Menta, Emily Schueddig, Amol Ranjan, Yanming Li, Shea J Andrews, Heather M Wilkins, Dong Pei, Russell H Swerdlow.
       INTRODUCTION: We determined whether mitochondrial DNA (mtDNA) depletion induced Alzheimer's disease (AD)-relevant transcription changes.
    METHODS: Following RNA sequencing (RNA-seq), we identified differentially expressed genes (DEGs) between SH-SY5Y or NT2 mtDNA-depleted (ρ0) and intact (ρ+) cell lines and quantified concordant DEG changes. Gene set enrichment analysis and over-representation analysis were used to determine the impact on the Kyoto Encyclopedia of Genes and Genomes (KEGG) AD and other neurodegenerative disease pathways, ascertain pathway and term enrichment in the Reactome and Gene Ontology databases, and generate Ingenuity Pathway Analysis z-scores.
    RESULTS: Relative to their ρ+ comparators, ρ0 lines differentially expressed >75% of their genes. The KEGG AD pathway was significantly enriched, and equivalently altered genes ranked the AD, Parkinson's disease, ALS, and Huntington's disease KEGG pathways among the most enriched gene sets. AD-related enriched pathways and terms reflected lipid, insulin signaling, synapse, inflammation/immune response, endosome/endocytosis, RNA, and proteostasis biology.
    CONCLUSION: MtDNA depletion alters gene expression in ways that recapitulate or predictably promote AD molecular phenomena.
    HIGHLIGHTS: MtDNA-depleted neuronal cell lines reshuffle nuclear gene expression. The KEGG AD pathway is enriched with DEGs. Transcription-defined pathways and terms relating to AD biology broadly change.
    Keywords:  Alzheimer's disease; RNA sequencing; mitochondria; mitochondrial DNA; transcriptome
    DOI:  https://doi.org/10.1002/alz.70929
  73. medRxiv. 2025 Oct 29. pii: 2025.10.10.25337775. [Epub ahead of print]
    Long-read genome sequencing and multi-omics in aging and neurodegeneration.
    Tanner D Jensen, Yann Le Guen, Lia Talozzi, Sherry Yang, John E Gorzynski, Andres Pena-Tauber, Ilaria F Stewart, Alexis Ferasse, Daniel Nachun, Taylor M Arriaga, Justin Lee, Rafael Catoia Pulgrossi, Junyoung Park, Jingyu Zhang, Anthony D Wagner, Elizabeth C Mormino, Kathleen L Poston, Victor W Henderson, Zihuai He, Tony Wyss-Coray, Stephen B Montgomery, Euan A Ashley, Michael D Greicius.
      Structural variants (SVs) are a major source of genetic variation yet remain underexplored in healthy aging and neurodegenerative diseases. We performed nanopore long-read genome sequencing (lrGS) on 551 deeply-phenotyped individuals from Stanfords Aging and Memory Study and Alzheimers Disease Research Center, generating a comprehensive SV map integrated with matched methylation, transcriptomic, and proteomic data. Over 60% of SVs identified by lrGS were not detected with short-read WGS, including many poorly tagged by single-nucleotide variants (SNVs). We discovered >60,000 SV-QTLs across molecular traits and showed that SVs were more likely than SNVs to be fine-mapped as causal. Colocalization with Alzheimers and Parkinsons disease GWAS implicated SVs at multiple loci, including TMEM106B, BIN3, and NBEAL1. Multi-omic outlier enrichment and Bayesian modeling prioritized rare functional SVs near known risk genes. Combined, these data reveal widespread regulatory SVs in healthy aging and neurodegeneration, underscoring the importance of lrGS in deciphering complex genetic architecture.
    DOI:  https://doi.org/10.1101/2025.10.10.25337775
  74. Res Sq. 2025 Oct 13. pii: rs.3.rs-7634140. [Epub ahead of print]
    Cytosolic mtDNA and associated EYA-mediated pro-inflammatory signaling modulate healthspan in Drosophila.
    David Walker, Ricardo Aparicio, Roberta Alessi, Agathe Solans, Matin Mojdeh, Vartika Sharma, Paul Oh, Matea Zelich, Toby Frank, Jae Hur.
      Mitochondrial dysfunction and pro-inflammatory signaling are each key drivers of aging. However, a clear understanding of the connections between mitochondrial homeostasis, inflammation and lifespan determination remains elusive. Upon mitochondrial stress or damage, mtDNA can be released into the cytosol thus encountering cytosolic DNA sensors and activating pro-inflammatory responses. Here, we report a striking age-related increase in cytosolic mtDNA, which can be counteracted by mitophagy, in Drosophila brain and muscle tissue. We find that upregulation of DNase II, an acid DNase which digests DNA in the autophagy-lysosome system, reduces cytosolic mtDNA levels in aged flies and prolongs healthspan. Reducing the abundance of cytosolic DNA in aged flies also dampens Rel/NF-κB pro-inflammatory signaling. Furthermore, we show that inhibition of EYA, a Rel/NF-κB-binding protein involved in immune sensing of DNA, in aging neurons counteracts brain aging and prolongs healthspan. Our findings identify DNase II and EYA as therapeutic targets to prolong healthspan.
    DOI:  https://doi.org/10.21203/rs.3.rs-7634140/v1
  75. bioRxiv. 2025 Nov 18. pii: 2025.10.22.682553. [Epub ahead of print]
    Condensate-Driven Triglyceride Depletion Links α-Synuclein to Mitochondrial Dysfunction.
    Tao Zhang, María Eugenia Goya, Alejandro Herron-Bedoya, Jorien C van der Weerd, Dikaia Tsagkari, Suzanne Couzijn, Lale Güngördü, Renée I Seinstra, M Rebecca Heiner Fokkema, Ming Chang, Nektarios Tavernarakis, Folkert Kuipers, Ellen A A Nollen.
      Inclusions of α-Synuclein (αSyn) characterize multiple age-related neurodegenerative diseases, including Parkinson's disease (PD) and Multiple System Atrophy (MSA). While interactions between αSyn and lipids are known to contribute to αSyn pathobiology, the precise cellular mechanisms that link lipids to αSyn toxicity have yet to be elucidated. Through lipidomic profiling of Caenorhabditis elegans, we found that αSyn progressively alters lipid metabolism in aging worms. αSyn strongly reduces overall content of triacylglycerols (TAG) and disrupts the structure of lipid droplets (LD). These pathological changes depend on αSyn's properties to condensate and form inclusions. Apart from lowering TAG levels, αSyn also increases the proportion of long-chain unsaturated fatty acids (LCUFAs). Consequently, genetic inhibition of LCUFA biosynthesis alleviates αSyn-induced loss of C. elegans motility. Strikingly, bypassing lipid metabolic defects by supplementing Medium Chain Fatty Acids (MCFAs) restores the αSyn-impaired mitochondrial response and rescues motility. These results link αSyn condensation to impaired TAG metabolism, which reduces mitochondrial function and enhances overall toxicity. Together with the finding that plasma TAGs are lowered in Parkinson patient cohorts, these results suggest that restoring TAG metabolism could alleviate αSyn-induced toxicity in Parkinson's and other age-related synucleinopathies.
    Keywords:  C. elegans; Dementia with Lewy Bodies (DLB); Multiple System Atrophy (MSA); Parkinson’s Disease; condensates; lipid droplets; mitochondrial respiration; synucleinopathies; triacylglycerols; α-synuclein
    DOI:  https://doi.org/10.1101/2025.10.22.682553
  76. bioRxiv. 2025 Oct 13. pii: 2025.10.10.681769. [Epub ahead of print]
    Imaging Cellular Metabolic Rewiring with SuMMIT-SRS.
    Yajuan Li, Zhi Li, Yuhan Li, Kevin Rhine, Sural Ranamukhaarachchi, Shuo Qin, Hongje Jang, Jorge Villazon, Zhiliang Bai, Stephanie I Fraley, Gene W Yeo, Rong Fan, Lingyan Shi.
      Cells dynamically rewire their metabolic pathways in response to physiological and pathological cues. Such plasticity is particularly critical in neurons, stem cells, cancer cells, and immune cells, where biosynthetic demands can shift rapidly. However, current metabolic imaging techniques using isotope labeling typically track only one metabolite at a time, limiting their ability to capture the rapid dynamics of complex metabolic networks including coordinated precursor utilization, crosstalk, and turnover. Here, we present Subcellular Multiplexed Metabolic Isotope Tracing Stimulated Raman Scattering microscopy (SuMMIT-SRS), a platform that enables simultaneous visualization of multiple metabolic dynamics at subcellular resolution. By exploiting the distinct vibrational signatures of carbon-deuterium bonds derived from multiple deuterated amino acids, lipids, and monosaccharide tracers, SuMMIT-SRS maps co-regulated DNA, RNA, protein, and lipid synthesis at the same time and resolves various individual amino acid-mediated metabolic pathways within intact cells and tissues. We demonstrate SuMMIT's broad utility across Drosophila fat body tissue and developing brain, tumor organoids, aged human neurons, and mouse liver, capturing cell type-specific metabolic rewiring under genetic and pathological perturbations. This approach extends SRS to multiplexed isotope tracing, offering a powerful tool to uncover dynamic and complex biosynthesis programs in development, health, and disease.
    Keywords:  Metabolic rewiring; SRS; lipid; metabolism; multiplex; optical imaging; protein
    DOI:  https://doi.org/10.1101/2025.10.10.681769
  77. Biomol NMR Assign. 2025 Nov 27. 20(1): 6
    NMR assignments of the human homodimeric mitochondrial ATP synthase inhibitor IF1.
    Julia Jerolamon, Nathan N Alder, Andrei T Alexandrescu.
      ATPase inhibitory factor 1 (IF1) is the only known endogenous, proteinaceous inhibitor of mitochondrial ATP synthase in mammals. The inhibitor forms an antiparallel coiled-coil, which binds ATP synthase through an N-terminal α-helix extension that is disordered in the free protein. Because the IF1 dimer affects mitochondrial bioenergetics through its modulation of ATP synthase, it is a therapeutic target for cancer and cardiac disease. Here, we report 1H, 13C and 15N NMR assignments for the mature dimeric form of human IF1. Secondary structure analyses based on chemical shifts and short-range NOE patterns indicate the N-terminal half of the 81-residue IF1 is intrinsically disordered, while the C-terminal half adopts a continuous α-helix. The chemical shift assignments for human IF1 provide a foundation for future mechanistic structure-function studies and NMR-based drug screening.
    Keywords:  ATP synthase; ATPase inhibitor; Coiled-coil dimer; Mitochondria; PH-dependent oligomer
    DOI:  https://doi.org/10.1007/s12104-025-10257-y
  78. Res Sq. 2025 Oct 29. pii: rs.3.rs-7811947. [Epub ahead of print]
    The Metabolome Atlas of 22 Tissues in Aging Mice Reveals a Switch in Thermogenesis from Brown Fat to Skeletal Muscle.
    Oliver Fiehn, Min Liu, Jian Ji, Anthony David, Huaxu Yu, Tong Shen, Yuanyue Li, Lydia Yang.
      Aging impairs thermoregulatory capacity, yet the metabolic mechanisms remain unclear. We report an organ-resolved metabolome atlas of 2,875 structurally annotated metabolites of old (90-96 weeks) versus young mice (16 weeks) across 22 tissues and four biological matrices. For thermoregulation, aging induces widespread remodeling of mitochondrial cardiolipins, with severe depletion of nascent species in brown adipose tissue (BAT) and a compensatory shift in thermogenic workload from BAT to muscle, evidenced by higher levels of long-chain fatty acids, acylcarnitines, and ω-oxidation markers in quadriceps. BAT showed reduced lipolysis and lower levels of the thermogenic lipokine 12,13-DiHOME, whereas muscle exhibited increased 12,13-DiHOME, lipid uptake, β-oxidation, and stress-associated metabolites including oxidized/reduced glutathione ratio. Hence, thermogenic adaptation comes at a cost: aged muscles exhibited signs of proteostatic stress, energetic strain, and oxidative damage, suggesting compensation contributes to sarcopenia. The atlas is publicly available at GitHub https://github.com/minliuUCDavis/AgingMiceAtlas and serves as a cornerstone resource for aging biology.
    DOI:  https://doi.org/10.21203/rs.3.rs-7811947/v1
  79. Biochem Biophys Res Commun. 2025 Nov 24. pii: S0006-291X(25)01760-7. [Epub ahead of print]794 153044
    Mitochondrial transplantation alleviates acute pancreatitis by suppressing macrophage necroptosis.
    Cai Sun, Liang Pan, Chengsi Tang, Yiyuan Liu, Sha Ran, Ying Li, Yan Shen.
      Acute pancreatitis (AP) is a multifactorial disease in which mitochondrial dysfunction plays a key role by triggering inflammatory cascades and necrotic cell death. Mitochondrial transplantation has been reported to alleviate AP, however its underlying mechanisms remain unclear. To investigate the effect of mitochondrial transplantation on macrophage during AP, we stimulated macrophages with supernatant of damaged pancreatic acinar cells to mimic the inflammatory microenvironment. Upon stimulation, macrophages exhibited an enhanced capacity to internalize exogenous mitochondria. These exogenous mitochondria restored mitochondrial function in damaged macrophages by maintaining mitochondrial membrane potential, suppressing excessive reactive oxygen species production, and restoring ATP levels. Furthermore, mitochondria transplantation significantly inhibited macrophages necroptosis, as evidenced by the decreased protein expression and phosphorylation levels of the necroptosis markers RIPK1 and MLKL in macrophages and pancreatic tissue, and decreased cell necrosis. In terms of inflammation, exogenous mitochondria suppressed macrophage polarization toward the pro-inflammatory M1 phenotype and reduced the expression of pro-inflammatory cytokines. Collectively, these findings demonstrate that macrophage-centered inflammatory regulation constitutes a central mechanism underlying the therapeutic effects of mitochondrial transplantation in AP, providing a theoretical foundation for developing mitochondria-based therapeutic strategies.
    Keywords:  Acute pancreatitis; Macrophage; Mitochondrial transplantation; Necroptosis
    DOI:  https://doi.org/10.1016/j.bbrc.2025.153044
  80. Trends Biotechnol. 2025 Nov 27. pii: S0167-7799(25)00453-6. [Epub ahead of print]
    Gene therapy strategies in tissue engineering: advances and applications for regenerative therapy.
    Hasan Akbaba, Lucy Homer, Thi Bao Tram Tran, Nitu Bhaskar, Nidhi Sharma, Gulsah Erel-Akbaba, Suman Pahal, Thanh Duc Nguyen.
      Gene therapy has emerged as a promising strategy for tissue regeneration, offering the potential to address the limitations of conventional treatments. In this review we present an overview of applications of gene therapy in tissue regeneration, emphasizing recent advancements and future directions. Our work addresses gaps in the current literature by examining developments in molecular biology and genetics, such as clustered regularly interspaced short palindromic repeats (CRISPR) gene editing, advances in 3D bioprinting, and progress in gene delivery for tissue engineering. We describe case studies and clinical trials that demonstrate the potential of gene therapy applications in tissue engineering. We conclude by highlighting challenges and future directions, including emerging technologies and personalized gene-based approaches for tissue engineering research.
    Keywords:  gene delivery; gene editing; gene therapy; regenerative medicine; stem cell; tissue engineering
    DOI:  https://doi.org/10.1016/j.tibtech.2025.10.025
This page is being maintained by Thomas Krichel. It was last updated on 2025‒11‒30 at 12:19.